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Writing index file api.idx
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[]    \OT1/cmtt/m/n/10 * MeanSquareDisplacement                   : sets up a M
ean-Square-Displacement analysis.[] 
 []


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[]    \OT1/cmtt/m/n/10 * RootMeanSquareDeviation                  : sets up a R
oot Mean-Square-Deviation analysis.[] 
 []


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[]    \OT1/cmtt/m/n/10 * CartesianVelocityAutoCorrelationFunction : sets up a C
artesian Velocity AutoCorrelation analysis.[] 
 []


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[]    \OT1/cmtt/m/n/10 * GlobalMotionTrajectoryFilter             : sets up a G
lobal Motion Trajectory Filter.[] 
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[]    \OT1/cmtt/m/n/10 * AngularVelocityAutoCorrelationFunction   : sets up an 
Angular Velocity AutoCorrelation Function.[] 
 []


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[] 
 []


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[]    \OT1/cmtt/m/n/10 - \OMS/cmtt/m/n/10 j\OT1/cmtt/m/n/10 parameters\OMS/cmtt
/m/n/10 j \OT1/cmtt/m/n/10 -- a dictionnary of the input parameters, or 'None' 
to set up the analysis without parameters.[] 
 []


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[]        \OT1/cmtt/m/n/10 * trajectory  -- a trajectory file name or an instan
ce of MMTK.Trajectory.Trajectory class.[] 
 []


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[]        \OT1/cmtt/m/n/10 * timeinfo    -- a string of the form 'first:last:st
ep' where 'first' is an integer specifying the first frame[] 
 []


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[]                         \OT1/cmtt/m/n/10 number to consider, 'last' is an in
teger specifying the last frame number to consider and[] 
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[]                         \OT1/cmtt/m/n/10 'step' is an integer specifying the
 step number between two frames.[] 
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[]        \OT1/cmtt/m/n/10 * projection  -- a string of the form 'vx,vy,vz' spe
cifying the vector along which the analysis[] 
 []


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[]                         \OT1/cmtt/m/n/10 will be computed. 'vx', 'vy', and '
vz' are floats specifying respectively the x, y and z value[] 
 []


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[]        \OT1/cmtt/m/n/10 * subset      -- a selection string specifying the a
toms to consider for the analysis.[] 
 []


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[]        \OT1/cmtt/m/n/10 * deuteration -- a selection string specifying the h
ydrogen atoms whose atomic parameters will be those of the deuterium.[] 
 []


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[]        \OT1/cmtt/m/n/10 * weights     -- a string equal to 'equal', 'mass', 
'coherent' , 'incoherent' or 'atomicNumber' that specifies the weighting[] 
 []


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[]        \OT1/cmtt/m/n/10 * msd         -- the output NetCDF file name. A CDL 
version of this file will also be generated with the '.cdl' extension[] 
 []


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[]        \OT1/cmtt/m/n/10 * pyroserver  -- a string specifying if Pyro will be
 used and how to run the analysis.[] 
 []

[25


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[]    \OT1/cmtt/m/n/10 - To save the analysis to 'file' file name do: a.saveAna
lysis(file) where a is the analysis object.[] 
 []

[26]
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\OT1/cmr/m/n/12 y-sis(), set-Input-Pa-ram-e-ters(), sub-set-S-e-lec-tion(), up-
date-JobProgress(), weight-ingScheme() 
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[] 
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[]    \OT1/cmtt/m/n/12 - \OMS/cmtt/m/n/12 j\OT1/cmtt/m/n/12 parameters\OMS/cmtt
/m/n/12 j \OT1/cmtt/m/n/12 -- a dictionnary of the input parameters, or 'None' 
to set up the analysis without parameters.[] 
 []


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[]        \OT1/cmtt/m/n/12 * trajectory     -- a trajectory file name or an ins
tance of MMTK.Trajectory.Trajectory class.[] 
 []


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[]        \OT1/cmtt/m/n/12 * timeinfo       -- a string of the form 'first:last
:step' where 'first' is an integer specifying the first frame[] 
 []

[27]
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[]                            \OT1/cmtt/m/n/12 number to consider, 'last' is an
 integer specifying the last frame number to consider and[] 
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[]                            \OT1/cmtt/m/n/12 'step' is an integer specifying 
the step number between two frames.[] 
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[]        \OT1/cmtt/m/n/12 * referenceframe -- an integer in [1,len(trajectory)
] specifying which frame should be the reference.[] 
 []


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[]        \OT1/cmtt/m/n/12 * subset         -- a selection string specifying th
e atoms to consider for the analysis.[] 
 []


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[]        \OT1/cmtt/m/n/12 * deuteration    -- a selection string specifying th
e hydrogen atoms whose atomic parameters will be those of the deuterium.[] 
 []


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[]        \OT1/cmtt/m/n/12 * weights        -- a string equal to 'equal', 'mass
', 'coherent' , 'incoherent' or 'atomicNumber' that specifies the weighting[] 
 []


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[]        \OT1/cmtt/m/n/12 * rmsd           -- the output NetCDF file name. A C
DL version of this file will also be generated with the '.cdl' extension[] 
 []


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[]        \OT1/cmtt/m/n/12 * pyroserver     -- a string specifying if Pyro will
 be used and how to run the analysis.[] 
 []


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[]    \OT1/cmtt/m/n/12 - To run the analysis do: a.runAnalysis() where a is the
 analysis object.[] 
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[]    \OT1/cmtt/m/n/12 - To estimate the analysis do: a.estimateAnalysis() wher
e a is the analysis object.[] 
 []


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[]    \OT1/cmtt/m/n/12 - To save the analysis to 'file' file name do: a.saveAna
lysis(file) where a is the analysis object.[] 
 []

[28]
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\OT1/cmr/m/n/12 y-sis(), set-Input-Pa-ram-e-ters(), sub-set-S-e-lec-tion(), up-
date-JobProgress(), weight-ingScheme() 
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[] 
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[29]
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[]    \OT1/cmtt/m/n/12 - \OMS/cmtt/m/n/12 j\OT1/cmtt/m/n/12 parameters\OMS/cmtt
/m/n/12 j \OT1/cmtt/m/n/12 -- a dictionnary of the input parameters, or 'None' 
to set up the analysis without parameters.[] 
 []


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[]        \OT1/cmtt/m/n/12 * trajectory      -- a trajectory file name or an in
stance of MMTK.Trajectory.Trajectory class.[] 
 []


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[]        \OT1/cmtt/m/n/12 * timeinfo        -- a string of the form 'first:las
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[]                             \OT1/cmtt/m/n/12 number to consider, 'last' is a
n integer specifying the last frame number to consider and[] 
 []


Overfull \hbox (123.04527pt too wide) in paragraph at lines 568--568
[]                             \OT1/cmtt/m/n/12 'step' is an integer specifying
 the step number between two frames.[] 
 []


Overfull \hbox (265.07034pt too wide) in paragraph at lines 569--569
[]        \OT1/cmtt/m/n/12 * differentiation -- an integer in [0,5] specifying 
the order of the differentiation used to get the velocities[] 
 []


Overfull \hbox (302.12036pt too wide) in paragraph at lines 570--570
[]                             \OT1/cmtt/m/n/12 out of the coordinates. 0 means
 that the velocities are already present in the trajectory loaded[] 
 []


Overfull \hbox (190.9703pt too wide) in paragraph at lines 572--572
[]        \OT1/cmtt/m/n/12 * projection      -- a string of the form 'vx,vy,vz'
 specifying the vector along which the analysis[] 
 []


Overfull \hbox (289.77036pt too wide) in paragraph at lines 573--573
[]                             \OT1/cmtt/m/n/12 will be computed. 'vx', 'vy', a
nd 'vz' are floats specifying respectively the x, y and z value[] 
 []


Overfull \hbox (283.59535pt too wide) in paragraph at lines 575--575
[]        \OT1/cmtt/m/n/12 * normalize       -- a string being one of 'Yes' or 
'No' specifying whether the analysis should be normalized to 1[] 
 []


Overfull \hbox (135.39528pt too wide) in paragraph at lines 577--577
[]        \OT1/cmtt/m/n/12 * subset          -- a selection string specifying t
he atoms to consider for the analysis.[] 
 []


Overfull \hbox (351.52039pt too wide) in paragraph at lines 578--578
[]        \OT1/cmtt/m/n/12 * deuteration     -- a selection string specifying t
he hydrogen atoms whose atomic parameters will be those of the deuterium.[] 
 []


Overfull \hbox (370.0454pt too wide) in paragraph at lines 579--579
[]        \OT1/cmtt/m/n/12 * weights         -- a string equal to 'equal', 'mas
s', 'coherent' , 'incoherent' or 'atomicNumber' that specifies the weighting[] 

 []


Overfull \hbox (351.52039pt too wide) in paragraph at lines 581--581
[]        \OT1/cmtt/m/n/12 * vacf            -- the output NetCDF file name. A 
CDL version of this file will also be generated with the '.cdl' extension[] 
 []


Overfull \hbox (135.39528pt too wide) in paragraph at lines 583--583
[]        \OT1/cmtt/m/n/12 * pyroserver      -- a string specifying if Pyro wil
l be used and how to run the analysis.[] 
 []


Overfull \hbox (5.72021pt too wide) in paragraph at lines 587--587
[]    \OT1/cmtt/m/n/12 - To run the analysis do: a.runAnalysis() where a is the
 analysis object.[] 
 []


Overfull \hbox (67.47025pt too wide) in paragraph at lines 588--588
[]    \OT1/cmtt/m/n/12 - To estimate the analysis do: a.estimateAnalysis() wher
e a is the analysis object.[] 
 []


Overfull \hbox (166.2703pt too wide) in paragraph at lines 589--589
[]    \OT1/cmtt/m/n/12 - To save the analysis to 'file' file name do: a.saveAna
lysis(file) where a is the analysis object.[] 
 []

[30]
Overfull \hbox (32.37648pt too wide) in paragraph at lines 731--732
\OT1/cmr/m/n/12 y-sis(), set-Input-Pa-ram-e-ters(), sub-set-S-e-lec-tion(), up-
date-JobProgress(), weight-ingScheme() 
 []

[31]
Overfull \hbox (105.38887pt too wide) in paragraph at lines 767--777
[] 
 []


Overfull \hbox (222.337pt too wide) in paragraph at lines 787--787
[]    \OT1/cmtt/m/n/12 - \OMS/cmtt/m/n/12 j\OT1/cmtt/m/n/12 parameters\OMS/cmtt
/m/n/12 j \OT1/cmtt/m/n/12 -- a dictionnary of the input parameters, or 'None' 
to set up the analysis without parameters.[] 
 []


Overfull \hbox (166.2703pt too wide) in paragraph at lines 788--788
[]        \OT1/cmtt/m/n/12 * trajectory      -- a trajectory file name or an in
stance of MMTK.Trajectory.Trajectory class.[] 
 []


Overfull \hbox (283.59535pt too wide) in paragraph at lines 789--789
[]        \OT1/cmtt/m/n/12 * timeinfo        -- a string of the form 'first:las
t:step' where 'first' is an integer specifying the first frame[] 
 []


Overfull \hbox (258.89534pt too wide) in paragraph at lines 790--790
[]                             \OT1/cmtt/m/n/12 number to consider, 'last' is a
n integer specifying the last frame number to consider and[] 
 []


Overfull \hbox (123.04527pt too wide) in paragraph at lines 791--791
[]                             \OT1/cmtt/m/n/12 'step' is an integer specifying
 the step number between two frames.[] 
 []


Overfull \hbox (265.07034pt too wide) in paragraph at lines 792--792
[]        \OT1/cmtt/m/n/12 * differentiation -- an integer in [0,5] specifying 
the order of the differentiation used to get the velocities[] 
 []


Overfull \hbox (302.12036pt too wide) in paragraph at lines 793--793
[]                             \OT1/cmtt/m/n/12 out of the coordinates. 0 means
 that the velocities are already present in the trajectory loaded[] 
 []


Overfull \hbox (190.9703pt too wide) in paragraph at lines 795--795
[]        \OT1/cmtt/m/n/12 * projection      -- a string of the form 'vx,vy,vz'
 specifying the vector along which the analysis[] 
 []


Overfull \hbox (289.77036pt too wide) in paragraph at lines 796--796
[]                             \OT1/cmtt/m/n/12 will be computed. 'vx', 'vy', a
nd 'vz' are floats specifying respectively the x, y and z value[] 
 []


Overfull \hbox (320.64537pt too wide) in paragraph at lines 798--798
[]        \OT1/cmtt/m/n/12 * fftwindow       -- a float in ]0.0,100.0[ specifyi
ng the width of the gaussian, in percentage of the trajectory length[] 
 []


Overfull \hbox (135.39528pt too wide) in paragraph at lines 800--800
[]        \OT1/cmtt/m/n/12 * subset          -- a selection string specifying t
he atoms to consider for the analysis.[] 
 []


Overfull \hbox (351.52039pt too wide) in paragraph at lines 801--801
[]        \OT1/cmtt/m/n/12 * deuteration     -- a selection string specifying t
he hydrogen atoms whose atomic parameters will be those of the deuterium.[] 
 []


Overfull \hbox (370.0454pt too wide) in paragraph at lines 802--802
[]        \OT1/cmtt/m/n/12 * weights         -- a string equal to 'equal', 'mas
s', 'coherent' , 'incoherent' or 'atomicNumber' that specifies the weighting[] 

 []


Overfull \hbox (351.52039pt too wide) in paragraph at lines 804--804
[]        \OT1/cmtt/m/n/12 * dos             -- the output NetCDF file name. A 
CDL version of this file will also be generated with the '.cdl' extension[] 
 []


Overfull \hbox (135.39528pt too wide) in paragraph at lines 806--806
[]        \OT1/cmtt/m/n/12 * pyroserver      -- a string specifying if Pyro wil
l be used and how to run the analysis.[] 
 []


Overfull \hbox (5.72021pt too wide) in paragraph at lines 810--810
[]    \OT1/cmtt/m/n/12 - To run the analysis do: a.runAnalysis() where a is the
 analysis object.[] 
 []

[32]
Overfull \hbox (67.47025pt too wide) in paragraph at lines 811--811
[]    \OT1/cmtt/m/n/12 - To estimate the analysis do: a.estimateAnalysis() wher
e a is the analysis object.[] 
 []


Overfull \hbox (166.2703pt too wide) in paragraph at lines 812--812
[]    \OT1/cmtt/m/n/12 - To save the analysis to 'file' file name do: a.saveAna
lysis(file) where a is the analysis object.[] 
 []


Overfull \hbox (32.37648pt too wide) in paragraph at lines 954--955
\OT1/cmr/m/n/12 y-sis(), set-Input-Pa-ram-e-ters(), sub-set-S-e-lec-tion(), up-
date-JobProgress(), weight-ingScheme() 
 []

[33]
Overfull \hbox (94.81113pt too wide) in paragraph at lines 990--1000
[] 
 []


Overfull \hbox (222.337pt too wide) in paragraph at lines 1010--1010
[]    \OT1/cmtt/m/n/12 - \OMS/cmtt/m/n/12 j\OT1/cmtt/m/n/12 parameters\OMS/cmtt
/m/n/12 j \OT1/cmtt/m/n/12 -- a dictionnary of the input parameters, or 'None' 
to set up the analysis without parameters.[] 
 []


Overfull \hbox (166.2703pt too wide) in paragraph at lines 1011--1011
[]        \OT1/cmtt/m/n/12 * trajectory      -- a trajectory file name or an in
stance of MMTK.Trajectory.Trajectory class.[] 
 []


Overfull \hbox (283.59535pt too wide) in paragraph at lines 1012--1012
[]        \OT1/cmtt/m/n/12 * timeinfo        -- a string of the form 'first:las
t:step' where 'first' is an integer specifying the first frame[] 
 []


Overfull \hbox (258.89534pt too wide) in paragraph at lines 1013--1013
[]                             \OT1/cmtt/m/n/12 number to consider, 'last' is a
n integer specifying the last frame number to consider and[] 
 []


Overfull \hbox (123.04527pt too wide) in paragraph at lines 1014--1014
[]                             \OT1/cmtt/m/n/12 'step' is an integer specifying
 the step number between two frames.[] 
 []


Overfull \hbox (265.07034pt too wide) in paragraph at lines 1015--1015
[]        \OT1/cmtt/m/n/12 * differentiation -- an integer in [0,5] specifying 
the order of the differentiation used to get the velocities[] 
 []


Overfull \hbox (302.12036pt too wide) in paragraph at lines 1016--1016
[]                             \OT1/cmtt/m/n/12 out of the coordinates. 0 means
 that the velocities are already present in the trajectory loaded[] 
 []


Overfull \hbox (190.9703pt too wide) in paragraph at lines 1018--1018
[]        \OT1/cmtt/m/n/12 * projection      -- a string of the form 'vx,vy,vz'
 specifying the vector along which the analysis[] 
 []


Overfull \hbox (289.77036pt too wide) in paragraph at lines 1019--1019
[]                             \OT1/cmtt/m/n/12 will be computed. 'vx', 'vy', a
nd 'vz' are floats specifying respectively the x, y and z value[] 
 []


Overfull \hbox (129.22028pt too wide) in paragraph at lines 1021--1021
[]        \OT1/cmtt/m/n/12 * armodelorder    -- an integer in [1, len(trajector
y)[ specifying the order of the model[] 
 []


Overfull \hbox (135.39528pt too wide) in paragraph at lines 1022--1022
[]        \OT1/cmtt/m/n/12 * subset          -- a selection string specifying t
he atoms to consider for the analysis.[] 
 []


Overfull \hbox (351.52039pt too wide) in paragraph at lines 1023--1023
[]        \OT1/cmtt/m/n/12 * deuteration     -- a selection string specifying t
he hydrogen atoms whose atomic parameters will be those of the deuterium.[] 
 []


Overfull \hbox (370.0454pt too wide) in paragraph at lines 1024--1024
[]        \OT1/cmtt/m/n/12 * weights         -- a string equal to 'equal', 'mas
s', 'coherent' , 'incoherent' or 'atomicNumber' that specifies the weighting[] 

 []


Overfull \hbox (351.52039pt too wide) in paragraph at lines 1026--1026
[]        \OT1/cmtt/m/n/12 * ara             -- the output NetCDF file name. A 
CDL version of this file will also be generated with the '.cdl' extension[] 
 []


Overfull \hbox (135.39528pt too wide) in paragraph at lines 1028--1028
[]        \OT1/cmtt/m/n/12 * pyroserver      -- a string specifying if Pyro wil
l be used and how to run the analysis.[] 
 []

[34]
Overfull \hbox (5.72021pt too wide) in paragraph at lines 1032--1032
[]    \OT1/cmtt/m/n/12 - To run the analysis do: a.runAnalysis() where a is the
 analysis object.[] 
 []


Overfull \hbox (67.47025pt too wide) in paragraph at lines 1033--1033
[]    \OT1/cmtt/m/n/12 - To estimate the analysis do: a.estimateAnalysis() wher
e a is the analysis object.[] 
 []


Overfull \hbox (166.2703pt too wide) in paragraph at lines 1034--1034
[]    \OT1/cmtt/m/n/12 - To save the analysis to 'file' file name do: a.saveAna
lysis(file) where a is the analysis object.[] 
 []

[35]
Overfull \hbox (32.37648pt too wide) in paragraph at lines 1176--1177
\OT1/cmr/m/n/12 y-sis(), set-Input-Pa-ram-e-ters(), sub-set-S-e-lec-tion(), up-
date-JobProgress(), weight-ingScheme() 
 []


Overfull \hbox (119.6125pt too wide) in paragraph at lines 1212--1222
[] 
 []


Overfull \hbox (222.337pt too wide) in paragraph at lines 1232--1232
[]    \OT1/cmtt/m/n/12 - \OMS/cmtt/m/n/12 j\OT1/cmtt/m/n/12 parameters\OMS/cmtt
/m/n/12 j \OT1/cmtt/m/n/12 -- a dictionnary of the input parameters, or 'None' 
to set up the analysis without parameters.[] 
 []


Overfull \hbox (135.39528pt too wide) in paragraph at lines 1233--1233
[]        \OT1/cmtt/m/n/12 * trajectory -- a trajectory file name or an instanc
e of MMTK.Trajectory.Trajectory class.[] 
 []


Overfull \hbox (252.72034pt too wide) in paragraph at lines 1234--1234
[]        \OT1/cmtt/m/n/12 * timeinfo   -- a string of the form 'first:last:ste
p' where 'first' is an integer specifying the first frame[] 
 []


Overfull \hbox (228.02032pt too wide) in paragraph at lines 1235--1235
[]                        \OT1/cmtt/m/n/12 number to consider, 'last' is an int
eger specifying the last frame number to consider and[] 
 []


Overfull \hbox (92.17026pt too wide) in paragraph at lines 1236--1236
[]                        \OT1/cmtt/m/n/12 'step' is an integer specifying the 
step number between two frames.[] 
 []


Overfull \hbox (228.02032pt too wide) in paragraph at lines 1237--1237
[]        \OT1/cmtt/m/n/12 * filter     -- a string of the form 'low:high' wher
e 'low' and 'high' are floats specifying respectively[] 
 []


Overfull \hbox (18.07022pt too wide) in paragraph at lines 1238--1238
[]                        \OT1/cmtt/m/n/12 the lower and the upper bounds of th
e pass-band filter.[] 
 []


Overfull \hbox (104.52026pt too wide) in paragraph at lines 1239--1239
[]        \OT1/cmtt/m/n/12 * subset     -- a selection string specifying the at
oms to consider for the analysis.[] 
 []


Overfull \hbox (104.52026pt too wide) in paragraph at lines 1241--1241
[]        \OT1/cmtt/m/n/12 * pyroserver -- a string specifying if Pyro will be 
used and how to run the analysis.[] 
 []

[36]
Overfull \hbox (5.72021pt too wide) in paragraph at lines 1245--1245
[]    \OT1/cmtt/m/n/12 - To run the analysis do: a.runAnalysis() where a is the
 analysis object.[] 
 []


Overfull \hbox (67.47025pt too wide) in paragraph at lines 1246--1246
[]    \OT1/cmtt/m/n/12 - To estimate the analysis do: a.estimateAnalysis() wher
e a is the analysis object.[] 
 []


Overfull \hbox (166.2703pt too wide) in paragraph at lines 1247--1247
[]    \OT1/cmtt/m/n/12 - To save the analysis to 'file' file name do: a.saveAna
lysis(file) where a is the analysis object.[] 
 []

[37]
Overfull \hbox (32.37648pt too wide) in paragraph at lines 1389--1390
\OT1/cmr/m/n/12 y-sis(), set-Input-Pa-ram-e-ters(), sub-set-S-e-lec-tion(), up-
date-JobProgress(), weight-ingScheme() 
 []


Overfull \hbox (61.65553pt too wide) in paragraph at lines 1425--1435
[] 
 []


Overfull \hbox (222.337pt too wide) in paragraph at lines 1445--1445
[]    \OT1/cmtt/m/n/12 - \OMS/cmtt/m/n/12 j\OT1/cmtt/m/n/12 parameters\OMS/cmtt
/m/n/12 j \OT1/cmtt/m/n/12 -- a dictionnary of the input parameters, or 'None' 
to set up the analysis without parameters.[] 
 []


Overfull \hbox (160.09529pt too wide) in paragraph at lines 1446--1446
[]        \OT1/cmtt/m/n/12 * trajectory     -- a trajectory file name or an ins
tance of MMTK.Trajectory.Trajectory class.[] 
 []


Overfull \hbox (277.42035pt too wide) in paragraph at lines 1447--1447
[]        \OT1/cmtt/m/n/12 * timeinfo       -- a string of the form 'first:last
:step' where 'first' is an integer specifying the first frame[] 
 []


Overfull \hbox (252.72034pt too wide) in paragraph at lines 1448--1448
[]                            \OT1/cmtt/m/n/12 number to consider, 'last' is an
 integer specifying the last frame number to consider and[] 
 []


Overfull \hbox (116.87027pt too wide) in paragraph at lines 1449--1449
[]                            \OT1/cmtt/m/n/12 'step' is an integer specifying 
the step number between two frames.[] 
 []


Overfull \hbox (129.22028pt too wide) in paragraph at lines 1450--1450
[]        \OT1/cmtt/m/n/12 * subset         -- a selection string specifying th
e atoms to consider for the analysis.[] 
 []


Overfull \hbox (345.34538pt too wide) in paragraph at lines 1451--1451
[]        \OT1/cmtt/m/n/12 * rog            -- the output NetCDF file name. A C
DL version of this file will also be generated with the '.cdl' extension[] 
 []


Overfull \hbox (129.22028pt too wide) in paragraph at lines 1453--1453
[]        \OT1/cmtt/m/n/12 * pyroserver     -- a string specifying if Pyro will
 be used and how to run the analysis.[] 
 []


Overfull \hbox (5.72021pt too wide) in paragraph at lines 1457--1457
[]    \OT1/cmtt/m/n/12 - To run the analysis do: a.runAnalysis() where a is the
 analysis object.[] 
 []


Overfull \hbox (67.47025pt too wide) in paragraph at lines 1458--1458
[]    \OT1/cmtt/m/n/12 - To estimate the analysis do: a.estimateAnalysis() wher
e a is the analysis object.[] 
 []


Overfull \hbox (166.2703pt too wide) in paragraph at lines 1459--1459
[]    \OT1/cmtt/m/n/12 - To save the analysis to 'file' file name do: a.saveAna
lysis(file) where a is the analysis object.[] 
 []

[38]
Overfull \hbox (32.37648pt too wide) in paragraph at lines 1601--1602
\OT1/cmr/m/n/12 y-sis(), set-Input-Pa-ram-e-ters(), sub-set-S-e-lec-tion(), up-
date-JobProgress(), weight-ingScheme() 
 []

[39]
Overfull \hbox (144.1222pt too wide) in paragraph at lines 1637--1647
[] 
 []


Overfull \hbox (222.337pt too wide) in paragraph at lines 1657--1657
[]    \OT1/cmtt/m/n/12 - \OMS/cmtt/m/n/12 j\OT1/cmtt/m/n/12 parameters\OMS/cmtt
/m/n/12 j \OT1/cmtt/m/n/12 -- a dictionnary of the input parameters, or 'None' 
to set up the analysis without parameters.[] 
 []


Overfull \hbox (135.39528pt too wide) in paragraph at lines 1658--1658
[]        \OT1/cmtt/m/n/12 * trajectory -- a trajectory file name or an instanc
e of MMTK.Trajectory.Trajectory class.[] 
 []


Overfull \hbox (252.72034pt too wide) in paragraph at lines 1659--1659
[]        \OT1/cmtt/m/n/12 * timeinfo   -- a string of the form 'first:last:ste
p' where 'first' is an integer specifying the first frame[] 
 []


Overfull \hbox (228.02032pt too wide) in paragraph at lines 1660--1660
[]                        \OT1/cmtt/m/n/12 number to consider, 'last' is an int
eger specifying the last frame number to consider and[] 
 []


Overfull \hbox (92.17026pt too wide) in paragraph at lines 1661--1661
[]                        \OT1/cmtt/m/n/12 'step' is an integer specifying the 
step number between two frames.[] 
 []


Overfull \hbox (104.52026pt too wide) in paragraph at lines 1662--1662
[]        \OT1/cmtt/m/n/12 * subset     -- a selection string specifying the at
oms to consider for the analysis.[] 
 []


Overfull \hbox (104.52026pt too wide) in paragraph at lines 1664--1664
[]        \OT1/cmtt/m/n/12 * pyroserver -- a string specifying if Pyro will be 
used and how to run the analysis.[] 
 []


Overfull \hbox (5.72021pt too wide) in paragraph at lines 1668--1668
[]    \OT1/cmtt/m/n/12 - To run the analysis do: a.runAnalysis() where a is the
 analysis object.[] 
 []


Overfull \hbox (67.47025pt too wide) in paragraph at lines 1669--1669
[]    \OT1/cmtt/m/n/12 - To estimate the analysis do: a.estimateAnalysis() wher
e a is the analysis object.[] 
 []


Overfull \hbox (166.2703pt too wide) in paragraph at lines 1670--1670
[]    \OT1/cmtt/m/n/12 - To save the analysis to 'file' file name do: a.saveAna
lysis(file) where a is the analysis object.[] 
 []

[40]
LaTeX Font Info:    Font shape `OMS/cmr/m/n' in size <12> not available
(Font)              Font shape `OMS/cmsy/m/n' tried instead on input line 1760.


Overfull \hbox (32.37648pt too wide) in paragraph at lines 1813--1814
\OT1/cmr/m/n/12 y-sis(), set-Input-Pa-ram-e-ters(), sub-set-S-e-lec-tion(), up-
date-JobProgress(), weight-ingScheme() 
 []

[41]
Overfull \hbox (100.06387pt too wide) in paragraph at lines 1849--1859
[] 
 []


Overfull \hbox (222.337pt too wide) in paragraph at lines 1869--1869
[]    \OT1/cmtt/m/n/12 - \OMS/cmsy/m/n/12 j\OT1/cmtt/m/n/12 parameters\OMS/cmsy
/m/n/12 j \OT1/cmtt/m/n/12 -- a dictionnary of the input parameters, or 'None' 
to set up the analysis without parameters.[] 
 []


Overfull \hbox (135.39528pt too wide) in paragraph at lines 1870--1870
[]        \OT1/cmtt/m/n/12 * trajectory -- a trajectory file name or an instanc
e of MMTK.Trajectory.Trajectory class.[] 
 []


Overfull \hbox (252.72034pt too wide) in paragraph at lines 1871--1871
[]        \OT1/cmtt/m/n/12 * timeinfo   -- a string of the form 'first:last:ste
p' where 'first' is an integer specifying the first frame[] 
 []


Overfull \hbox (228.02032pt too wide) in paragraph at lines 1872--1872
[]                        \OT1/cmtt/m/n/12 number to consider, 'last' is an int
eger specifying the last frame number to consider and[] 
 []


Overfull \hbox (92.17026pt too wide) in paragraph at lines 1873--1873
[]                        \OT1/cmtt/m/n/12 'step' is an integer specifying the 
step number between two frames.[] 
 []


Overfull \hbox (252.72034pt too wide) in paragraph at lines 1874--1874
[]        \OT1/cmtt/m/n/12 * group      -- a selection string specifying the gr
oups of atoms on which the center of mass will be defined[] 
 []


Overfull \hbox (104.52026pt too wide) in paragraph at lines 1877--1877
[]        \OT1/cmtt/m/n/12 * pyroserver -- a string specifying if Pyro will be 
used and how to run the analysis.[] 
 []


Overfull \hbox (5.72021pt too wide) in paragraph at lines 1881--1881
[]    \OT1/cmtt/m/n/12 - To run the analysis do: a.runAnalysis() where a is the
 analysis object.[] 
 []


Overfull \hbox (67.47025pt too wide) in paragraph at lines 1882--1882
[]    \OT1/cmtt/m/n/12 - To estimate the analysis do: a.estimateAnalysis() wher
e a is the analysis object.[] 
 []


Overfull \hbox (166.2703pt too wide) in paragraph at lines 1883--1883
[]    \OT1/cmtt/m/n/12 - To save the analysis to 'file' file name do: a.saveAna
lysis(file) where a is the analysis object.[] 
 []

[42]
Overfull \hbox (32.37648pt too wide) in paragraph at lines 2026--2027
\OT1/cmr/m/n/12 y-sis(), set-Input-Pa-ram-e-ters(), sub-set-S-e-lec-tion(), up-
date-JobProgress(), weight-ingScheme() 
 []

[43]
Overfull \hbox (94.31252pt too wide) in paragraph at lines 2062--2072
[] 
 []


Overfull \hbox (222.337pt too wide) in paragraph at lines 2082--2082
[]    \OT1/cmtt/m/n/12 - \OMS/cmsy/m/n/12 j\OT1/cmtt/m/n/12 parameters\OMS/cmsy
/m/n/12 j \OT1/cmtt/m/n/12 -- a dictionnary of the input parameters, or 'None' 
to set up the analysis without parameters.[] 
 []


Overfull \hbox (141.57028pt too wide) in paragraph at lines 2083--2083
[]        \OT1/cmtt/m/n/12 * trajectory  -- a trajectory file name or an instan
ce of MMTK.Trajectory.Trajectory class.[] 
 []


Overfull \hbox (258.89534pt too wide) in paragraph at lines 2084--2084
[]        \OT1/cmtt/m/n/12 * timeinfo    -- a string of the form 'first:last:st
ep' where 'first' is an integer specifying the first frame[] 
 []


Overfull \hbox (234.19533pt too wide) in paragraph at lines 2085--2085
[]                         \OT1/cmtt/m/n/12 number to consider, 'last' is an in
teger specifying the last frame number to consider and[] 
 []


Overfull \hbox (98.34526pt too wide) in paragraph at lines 2086--2086
[]                         \OT1/cmtt/m/n/12 'step' is an integer specifying the
 step number between two frames.[] 
 []


Overfull \hbox (110.69527pt too wide) in paragraph at lines 2088--2088
[]        \OT1/cmtt/m/n/12 * subset      -- a selection string specifying the a
toms to consider for the analysis.[] 
 []


Overfull \hbox (5.72021pt too wide) in paragraph at lines 2093--2093
[]    \OT1/cmtt/m/n/12 - To run the analysis do: a.runAnalysis() where a is the
 analysis object.[] 
 []


Overfull \hbox (67.47025pt too wide) in paragraph at lines 2094--2094
[]    \OT1/cmtt/m/n/12 - To estimate the analysis do: a.estimateAnalysis() wher
e a is the analysis object.[] 
 []


Overfull \hbox (166.2703pt too wide) in paragraph at lines 2095--2095
[]    \OT1/cmtt/m/n/12 - To save the analysis to 'file' file name do: a.saveAna
lysis(file) where a is the analysis object.[] 
 []


Overfull \hbox (228.02032pt too wide) in paragraph at lines 2099--2099
[]    \OT1/cmtt/m/n/12 - This analysis is used to get effective modes of vibrat
ion from fluctuations calculated by an MD simulation.[] 
 []


Overfull \hbox (246.54533pt too wide) in paragraph at lines 2100--2100
[]      \OT1/cmtt/m/n/12 The results of such an analysis can be seen by generat
ing pseudo-trajectories reproducing the vibrations along[] 
 []

[44]
Overfull \hbox (32.37648pt too wide) in paragraph at lines 2190--2191
\OT1/cmr/m/n/12 y-sis(), set-Input-Pa-ram-e-ters(), sub-set-S-e-lec-tion(), up-
date-JobProgress(), weight-ingScheme() 
 []


Overfull \hbox (68.64305pt too wide) in paragraph at lines 2226--2236
[] 
 []

[45]
Overfull \hbox (222.337pt too wide) in paragraph at lines 2246--2246
[]    \OT1/cmtt/m/n/12 - \OMS/cmsy/m/n/12 j\OT1/cmtt/m/n/12 parameters\OMS/cmsy
/m/n/12 j \OT1/cmtt/m/n/12 -- a dictionnary of the input parameters, or 'None' 
to set up the analysis without parameters.[] 
 []


Overfull \hbox (166.2703pt too wide) in paragraph at lines 2247--2247
[]        \OT1/cmtt/m/n/12 * trajectory      -- a trajectory file name or an in
stance of MMTK.Trajectory.Trajectory class.[] 
 []


Overfull \hbox (283.59535pt too wide) in paragraph at lines 2248--2248
[]        \OT1/cmtt/m/n/12 * timeinfo        -- a string of the form 'first:las
t:step' where 'first' is an integer specifying the first frame[] 
 []


Overfull \hbox (258.89534pt too wide) in paragraph at lines 2249--2249
[]                             \OT1/cmtt/m/n/12 number to consider, 'last' is a
n integer specifying the last frame number to consider and[] 
 []


Overfull \hbox (123.04527pt too wide) in paragraph at lines 2250--2250
[]                             \OT1/cmtt/m/n/12 'step' is an integer specifying
 the step number between two frames.[] 
 []


Overfull \hbox (234.19533pt too wide) in paragraph at lines 2251--2251
[]        \OT1/cmtt/m/n/12 * triplet         -- a selection string specifying t
he groups of three atoms that will define the plane on[] 
 []


Overfull \hbox (197.14531pt too wide) in paragraph at lines 2253--2253
[]        \OT1/cmtt/m/n/12 * atomorder       -- a string of the form 'atom1,ato
m2,atom3' where 'atom1', 'atom2' and 'atom3' are[] 
 []


Overfull \hbox (203.32031pt too wide) in paragraph at lines 2254--2254
[]                             \OT1/cmtt/m/n/12 respectively the MMTK atom name
s of the atoms in the way they should be ordered.[] 
 []


Overfull \hbox (351.52039pt too wide) in paragraph at lines 2255--2255
[]        \OT1/cmtt/m/n/12 * ac              -- the output NetCDF file name. A 
CDL version of this file will also be generated with the '.cdl' extension[] 
 []


Overfull \hbox (135.39528pt too wide) in paragraph at lines 2257--2257
[]        \OT1/cmtt/m/n/12 * pyroserver      -- a string specifying if Pyro wil
l be used and how to run the analysis.[] 
 []


Overfull \hbox (5.72021pt too wide) in paragraph at lines 2261--2261
[]    \OT1/cmtt/m/n/12 - To run the analysis do: a.runAnalysis() where a is the
 analysis object.[] 
 []


Overfull \hbox (67.47025pt too wide) in paragraph at lines 2262--2262
[]    \OT1/cmtt/m/n/12 - To estimate the analysis do: a.estimateAnalysis() wher
e a is the analysis object.[] 
 []


Overfull \hbox (166.2703pt too wide) in paragraph at lines 2263--2263
[]    \OT1/cmtt/m/n/12 - To save the analysis to 'file' file name do: a.saveAna
lysis(file) where a is the analysis object.[] 
 []

[46]
Overfull \hbox (32.37648pt too wide) in paragraph at lines 2406--2407
\OT1/cmr/m/n/12 y-sis(), set-Input-Pa-ram-e-ters(), sub-set-S-e-lec-tion(), up-
date-JobProgress(), weight-ingScheme() 
 []


Overfull \hbox (78.99026pt too wide) in paragraph at lines 2442--2452
[] 
 []

[47]
Overfull \hbox (222.337pt too wide) in paragraph at lines 2462--2462
[]    \OT1/cmtt/m/n/12 - \OMS/cmsy/m/n/12 j\OT1/cmtt/m/n/12 parameters\OMS/cmsy
/m/n/12 j \OT1/cmtt/m/n/12 -- a dictionnary of the input parameters, or 'None' 
to set up the analysis without parameters.[] 
 []


Overfull \hbox (160.09529pt too wide) in paragraph at lines 2463--2463
[]        \OT1/cmtt/m/n/12 * trajectory     -- a trajectory file name or an ins
tance of MMTK.Trajectory.Trajectory class.[] 
 []


Overfull \hbox (277.42035pt too wide) in paragraph at lines 2464--2464
[]        \OT1/cmtt/m/n/12 * timeinfo       -- a string of the form 'first:last
:step' where 'first' is an integer specifying the first frame[] 
 []


Overfull \hbox (252.72034pt too wide) in paragraph at lines 2465--2465
[]                            \OT1/cmtt/m/n/12 number to consider, 'last' is an
 integer specifying the last frame number to consider and[] 
 []


Overfull \hbox (116.87027pt too wide) in paragraph at lines 2466--2466
[]                            \OT1/cmtt/m/n/12 'step' is an integer specifying 
the step number between two frames.[] 
 []


Overfull \hbox (203.32031pt too wide) in paragraph at lines 2467--2467
[]        \OT1/cmtt/m/n/12 * referenceframe -- an integer in [1,len(trajectory)
] specifying which frame should be the reference.[] 
 []


Overfull \hbox (295.94536pt too wide) in paragraph at lines 2468--2468
[]        \OT1/cmtt/m/n/12 * stepwiserbt    -- a string being one of 'Yes' or '
No' specifying whether the reference frame for frame i should be[] 
 []


Overfull \hbox (240.86201pt too wide) in paragraph at lines 2469--2469
[]                            \OT1/cmtt/m/n/12 the frame i - 1 ('Yes') or shoul
d be a fixed frame defined with \OMS/cmsy/m/n/12 j\OT1/cmtt/m/n/12 referencefra
me\OMS/cmsy/m/n/12 j \OT1/cmtt/m/n/12 ('No').[] 
 []


Overfull \hbox (326.82037pt too wide) in paragraph at lines 2470--2470
[]        \OT1/cmtt/m/n/12 * group          -- a selection string specifying th
e groups of atoms on which the rigid body trajectory will be defined.[] 
 []


Overfull \hbox (129.22028pt too wide) in paragraph at lines 2473--2473
[]        \OT1/cmtt/m/n/12 * pyroserver     -- a string specifying if Pyro will
 be used and how to run the analysis.[] 
 []


Overfull \hbox (5.72021pt too wide) in paragraph at lines 2477--2477
[]    \OT1/cmtt/m/n/12 - To run the analysis do: a.runAnalysis() where a is the
 analysis object.[] 
 []


Overfull \hbox (67.47025pt too wide) in paragraph at lines 2478--2478
[]    \OT1/cmtt/m/n/12 - To estimate the analysis do: a.estimateAnalysis() wher
e a is the analysis object.[] 
 []


Overfull \hbox (166.2703pt too wide) in paragraph at lines 2479--2479
[]    \OT1/cmtt/m/n/12 - To save the analysis to 'file' file name do: a.saveAna
lysis(file) where a is the analysis object.[] 
 []

[48]
Overfull \hbox (32.37648pt too wide) in paragraph at lines 2621--2622
\OT1/cmr/m/n/12 y-sis(), set-Input-Pa-ram-e-ters(), sub-set-S-e-lec-tion(), up-
date-JobProgress(), weight-ingScheme() 
 []


Overfull \hbox (163.38611pt too wide) in paragraph at lines 2657--2667
[] 
 []

[49]
Overfull \hbox (222.337pt too wide) in paragraph at lines 2677--2677
[]    \OT1/cmtt/m/n/12 - \OMS/cmsy/m/n/12 j\OT1/cmtt/m/n/12 parameters\OMS/cmsy
/m/n/12 j \OT1/cmtt/m/n/12 -- a dictionnary of the input parameters, or 'None' 
to set up the analysis without parameters.[] 
 []


Overfull \hbox (160.09529pt too wide) in paragraph at lines 2678--2678
[]        \OT1/cmtt/m/n/12 * trajectory     -- a trajectory file name or an ins
tance of MMTK.Trajectory.Trajectory class.[] 
 []


Overfull \hbox (277.42035pt too wide) in paragraph at lines 2679--2679
[]        \OT1/cmtt/m/n/12 * timeinfo       -- a string of the form 'first:last
:step' where 'first' is an integer specifying the first frame[] 
 []


Overfull \hbox (252.72034pt too wide) in paragraph at lines 2680--2680
[]                            \OT1/cmtt/m/n/12 number to consider, 'last' is an
 integer specifying the last frame number to consider and[] 
 []


Overfull \hbox (116.87027pt too wide) in paragraph at lines 2681--2681
[]                            \OT1/cmtt/m/n/12 'step' is an integer specifying 
the step number between two frames.[] 
 []


Overfull \hbox (203.32031pt too wide) in paragraph at lines 2682--2682
[]        \OT1/cmtt/m/n/12 * referenceframe -- an integer in [1,len(trajectory)
] specifying which frame should be the reference.[] 
 []


Overfull \hbox (295.94536pt too wide) in paragraph at lines 2683--2683
[]        \OT1/cmtt/m/n/12 * stepwiserbt    -- a string being one of 'Yes' or '
No' specifying whether the reference frame for frame i should be[] 
 []


Overfull \hbox (240.86201pt too wide) in paragraph at lines 2684--2684
[]                            \OT1/cmtt/m/n/12 the frame i - 1 ('Yes') or shoul
d be a fixed frame defined with \OMS/cmsy/m/n/12 j\OT1/cmtt/m/n/12 referencefra
me\OMS/cmsy/m/n/12 j \OT1/cmtt/m/n/12 ('No').[] 
 []


Overfull \hbox (308.29536pt too wide) in paragraph at lines 2685--2685
[]        \OT1/cmtt/m/n/12 * wignerindexes  -- a string of the form 'j,m,n' whe
re 'j', 'm' and 'n' are respectively the j, m and n indexes of the[] 
 []


Overfull \hbox (326.82037pt too wide) in paragraph at lines 2687--2687
[]        \OT1/cmtt/m/n/12 * group          -- a selection string specifying th
e groups of atoms on which the rigid body trajectory will be defined.[] 
 []


Overfull \hbox (345.34538pt too wide) in paragraph at lines 2689--2689
[]        \OT1/cmtt/m/n/12 * rcf            -- the output NetCDF file name. A C
DL version of this file will also be generated with the '.cdl' extension[] 
 []


Overfull \hbox (129.22028pt too wide) in paragraph at lines 2691--2691
[]        \OT1/cmtt/m/n/12 * pyroserver     -- a string specifying if Pyro will
 be used and how to run the analysis.[] 
 []


Overfull \hbox (5.72021pt too wide) in paragraph at lines 2695--2695
[]    \OT1/cmtt/m/n/12 - To run the analysis do: a.runAnalysis() where a is the
 analysis object.[] 
 []


Overfull \hbox (67.47025pt too wide) in paragraph at lines 2696--2696
[]    \OT1/cmtt/m/n/12 - To estimate the analysis do: a.estimateAnalysis() wher
e a is the analysis object.[] 
 []


Overfull \hbox (166.2703pt too wide) in paragraph at lines 2697--2697
[]    \OT1/cmtt/m/n/12 - To save the analysis to 'file' file name do: a.saveAna
lysis(file) where a is the analysis object.[] 
 []

[50]
Overfull \hbox (32.37648pt too wide) in paragraph at lines 2839--2840
\OT1/cmr/m/n/12 y-sis(), set-Input-Pa-ram-e-ters(), sub-set-S-e-lec-tion(), up-
date-JobProgress(), weight-ingScheme() 
 []


Overfull \hbox (55.9786pt too wide) in paragraph at lines 2875--2878
\OT1/cmr/m/n/12 An in-ter-me-di-ate class used by \OMS/cmsy/m/n/12 j\OT1/cmr/m/
n/12 AngularVelocityAutoCorrelationFunction\OMS/cmsy/m/n/12 j \OT1/cmr/m/n/12 a
nd \OMS/cmsy/m/n/12 j\OT1/cmr/m/n/12 AngularDensityOfStates\OMS/cmsy/m/n/12 j
 []

[51]
Overfull \hbox (244.76756pt too wide) in paragraph at lines 2941--2958
[] 
 []


Overfull \hbox (222.337pt too wide) in paragraph at lines 2968--2968
[]    \OT1/cmtt/m/n/12 - \OMS/cmsy/m/n/12 j\OT1/cmtt/m/n/12 parameters\OMS/cmsy
/m/n/12 j \OT1/cmtt/m/n/12 -- a dictionnary of the input parameters, or 'None' 
to set up the analysis without parameters.[] 
 []


Overfull \hbox (166.2703pt too wide) in paragraph at lines 2969--2969
[]        \OT1/cmtt/m/n/12 * trajectory      -- a trajectory file name or an in
stance of MMTK.Trajectory.Trajectory class.[] 
 []


Overfull \hbox (283.59535pt too wide) in paragraph at lines 2970--2970
[]        \OT1/cmtt/m/n/12 * timeinfo        -- a string of the form 'first:las
t:step' where 'first' is an integer specifying the first frame[] 
 []


Overfull \hbox (258.89534pt too wide) in paragraph at lines 2971--2971
[]                             \OT1/cmtt/m/n/12 number to consider, 'last' is a
n integer specifying the last frame number to consider and[] 
 []


Overfull \hbox (123.04527pt too wide) in paragraph at lines 2972--2972
[]                             \OT1/cmtt/m/n/12 'step' is an integer specifying
 the step number between two frames.[] 
 []


Overfull \hbox (265.07034pt too wide) in paragraph at lines 2973--2973
[]        \OT1/cmtt/m/n/12 * differentiation -- an integer in [0,5] specifying 
the order of the differentiation used to get the velocities[] 
 []


Overfull \hbox (302.12036pt too wide) in paragraph at lines 2974--2974
[]                             \OT1/cmtt/m/n/12 out of the coordinates. 0 means
 that the velocities are already present in the trajectory loaded[] 
 []


Overfull \hbox (190.9703pt too wide) in paragraph at lines 2976--2976
[]        \OT1/cmtt/m/n/12 * projection      -- a string of the form 'vx,vy,vz'
 specifying the vector along which the analysis[] 
 []


Overfull \hbox (289.77036pt too wide) in paragraph at lines 2977--2977
[]                             \OT1/cmtt/m/n/12 will be computed. 'vx', 'vy', a
nd 'vz' are floats specifying respectively the x, y and z value[] 
 []


Overfull \hbox (209.49532pt too wide) in paragraph at lines 2979--2979
[]        \OT1/cmtt/m/n/12 * referenceframe  -- an integer in [1,len(trajectory
)] specifying which frame should be the reference.[] 
 []


Overfull \hbox (302.12036pt too wide) in paragraph at lines 2980--2980
[]        \OT1/cmtt/m/n/12 * stepwiserbt     -- a string being one of 'Yes' or 
'No' specifying whether the reference frame for frame i should be[] 
 []


Overfull \hbox (247.03702pt too wide) in paragraph at lines 2981--2981
[]                             \OT1/cmtt/m/n/12 the frame i - 1 ('Yes') or shou
ld be a fixed frame defined with \OMS/cmsy/m/n/12 j\OT1/cmtt/m/n/12 referencefr
ame\OMS/cmsy/m/n/12 j \OT1/cmtt/m/n/12 ('No').[] 
 []


Overfull \hbox (332.99538pt too wide) in paragraph at lines 2982--2982
[]        \OT1/cmtt/m/n/12 * group           -- a selection string specifying t
he groups of atoms on which the rigid body trajectory will be defined.[] 
 []


Overfull \hbox (351.52039pt too wide) in paragraph at lines 2984--2984
[]        \OT1/cmtt/m/n/12 * avacf           -- the output NetCDF file name. A 
CDL version of this file will also be generated with the '.cdl' extension[] 
 []

[52]
Overfull \hbox (135.39528pt too wide) in paragraph at lines 2986--2986
[]        \OT1/cmtt/m/n/12 * pyroserver      -- a string specifying if Pyro wil
l be used and how to run the analysis.[] 
 []


Overfull \hbox (5.72021pt too wide) in paragraph at lines 2990--2990
[]    \OT1/cmtt/m/n/12 - To run the analysis do: a.runAnalysis() where a is the
 analysis object.[] 
 []


Overfull \hbox (67.47025pt too wide) in paragraph at lines 2991--2991
[]    \OT1/cmtt/m/n/12 - To estimate the analysis do: a.estimateAnalysis() wher
e a is the analysis object.[] 
 []


Overfull \hbox (166.2703pt too wide) in paragraph at lines 2992--2992
[]    \OT1/cmtt/m/n/12 - To save the analysis to 'file' file name do: a.saveAna
lysis(file) where a is the analysis object.[] 
 []

[53]
Overfull \hbox (32.37648pt too wide) in paragraph at lines 3134--3135
\OT1/cmr/m/n/12 y-sis(), set-Input-Pa-ram-e-ters(), sub-set-S-e-lec-tion(), up-
date-JobProgress(), weight-ingScheme() 
 []


Overfull \hbox (143.75089pt too wide) in paragraph at lines 3176--3193
[] 
 []


Overfull \hbox (222.337pt too wide) in paragraph at lines 3203--3203
[]    \OT1/cmtt/m/n/12 - \OMS/cmsy/m/n/12 j\OT1/cmtt/m/n/12 parameters\OMS/cmsy
/m/n/12 j \OT1/cmtt/m/n/12 -- a dictionnary of the input parameters, or 'None' 
to set up the analysis without parameters.[] 
 []


Overfull \hbox (166.2703pt too wide) in paragraph at lines 3204--3204
[]        \OT1/cmtt/m/n/12 * trajectory      -- a trajectory file name or an in
stance of MMTK.Trajectory.Trajectory class.[] 
 []


Overfull \hbox (283.59535pt too wide) in paragraph at lines 3205--3205
[]        \OT1/cmtt/m/n/12 * timeinfo        -- a string of the form 'first:las
t:step' where 'first' is an integer specifying the first frame[] 
 []


Overfull \hbox (258.89534pt too wide) in paragraph at lines 3206--3206
[]                             \OT1/cmtt/m/n/12 number to consider, 'last' is a
n integer specifying the last frame number to consider and[] 
 []


Overfull \hbox (123.04527pt too wide) in paragraph at lines 3207--3207
[]                             \OT1/cmtt/m/n/12 'step' is an integer specifying
 the step number between two frames.[] 
 []


Overfull \hbox (265.07034pt too wide) in paragraph at lines 3208--3208
[]        \OT1/cmtt/m/n/12 * differentiation -- an integer in [0,5] specifying 
the order of the differentiation used to get the velocities[] 
 []

[54]
Overfull \hbox (302.12036pt too wide) in paragraph at lines 3209--3209
[]                             \OT1/cmtt/m/n/12 out of the coordinates. 0 means
 that the velocities are already present in the trajectory loaded[] 
 []


Overfull \hbox (190.9703pt too wide) in paragraph at lines 3211--3211
[]        \OT1/cmtt/m/n/12 * projection      -- a string of the form 'vx,vy,vz'
 specifying the vector along which the analysis[] 
 []


Overfull \hbox (289.77036pt too wide) in paragraph at lines 3212--3212
[]                             \OT1/cmtt/m/n/12 will be computed. 'vx', 'vy', a
nd 'vz' are floats specifying respectively the x, y and z value[] 
 []


Overfull \hbox (209.49532pt too wide) in paragraph at lines 3214--3214
[]        \OT1/cmtt/m/n/12 * referenceframe  -- an integer in [1,len(trajectory
)] specifying which frame should be the reference.[] 
 []


Overfull \hbox (302.12036pt too wide) in paragraph at lines 3215--3215
[]        \OT1/cmtt/m/n/12 * stepwiserbt     -- a string being one of 'Yes' or 
'No' specifying whether the reference frame for frame i should be[] 
 []


Overfull \hbox (247.03702pt too wide) in paragraph at lines 3216--3216
[]                             \OT1/cmtt/m/n/12 the frame i - 1 ('Yes') or shou
ld be a fixed frame defined with \OMS/cmsy/m/n/12 j\OT1/cmtt/m/n/12 referencefr
ame\OMS/cmsy/m/n/12 j \OT1/cmtt/m/n/12 ('No').[] 
 []


Overfull \hbox (320.64537pt too wide) in paragraph at lines 3217--3217
[]        \OT1/cmtt/m/n/12 * fftwindow       -- a float in ]0.0,100.0[ specifyi
ng the width of the gaussian, in percentage of the trajectory length[] 
 []


Overfull \hbox (332.99538pt too wide) in paragraph at lines 3219--3219
[]        \OT1/cmtt/m/n/12 * group           -- a selection string specifying t
he groups of atoms on which the rigid body trajectory will be defined.[] 
 []


Overfull \hbox (351.52039pt too wide) in paragraph at lines 3221--3221
[]        \OT1/cmtt/m/n/12 * ados            -- the output NetCDF file name. A 
CDL version of this file will also be generated with the '.cdl' extension[] 
 []


Overfull \hbox (135.39528pt too wide) in paragraph at lines 3223--3223
[]        \OT1/cmtt/m/n/12 * pyroserver      -- a string specifying if Pyro wil
l be used and how to run the analysis.[] 
 []


Overfull \hbox (5.72021pt too wide) in paragraph at lines 3227--3227
[]    \OT1/cmtt/m/n/12 - To run the analysis do: a.runAnalysis() where a is the
 analysis object.[] 
 []


Overfull \hbox (67.47025pt too wide) in paragraph at lines 3228--3228
[]    \OT1/cmtt/m/n/12 - To estimate the analysis do: a.estimateAnalysis() wher
e a is the analysis object.[] 
 []


Overfull \hbox (166.2703pt too wide) in paragraph at lines 3229--3229
[]    \OT1/cmtt/m/n/12 - To save the analysis to 'file' file name do: a.saveAna
lysis(file) where a is the analysis object.[] 
 []

[55]
Overfull \hbox (32.37648pt too wide) in paragraph at lines 3371--3372
\OT1/cmr/m/n/12 y-sis(), set-Input-Pa-ram-e-ters(), sub-set-S-e-lec-tion(), up-
date-JobProgress(), weight-ingScheme() 
 []

) [56]
\openout2 = `nMOLDYN.Analysis.NMR-module.aux'.

 (./nMOLDYN.Analysis.NMR-module.tex
Overfull \hbox (172.4453pt too wide) in paragraph at lines 23--23
[]    \OT1/cmtt/m/n/12 * OrderParameterContactModel : sets up an order paramete
r analysis using the contact model approach.[] 
 []


Overfull \hbox (25.8389pt too wide) in paragraph at lines 35--45
[] 
 []


Overfull \hbox (222.337pt too wide) in paragraph at lines 55--55
[]    \OT1/cmtt/m/n/12 - \OMS/cmsy/m/n/12 j\OT1/cmtt/m/n/12 parameters\OMS/cmsy
/m/n/12 j \OT1/cmtt/m/n/12 -- a dictionnary of the input parameters, or 'None' 
to set up the analysis without parameters.[] 
 []


Overfull \hbox (184.7953pt too wide) in paragraph at lines 56--56
[]        \OT1/cmtt/m/n/12 * trajectory         -- a trajectory file name or an
 instance of MMTK.Trajectory.Trajectory class.[] 
 []


Overfull \hbox (302.12036pt too wide) in paragraph at lines 57--57
[]        \OT1/cmtt/m/n/12 * timeinfo           -- a string of the form 'first:
last:step' where 'first' is an integer specifying the first frame[] 
 []


Overfull \hbox (277.42035pt too wide) in paragraph at lines 58--58
[]                                \OT1/cmtt/m/n/12 number to consider, 'last' i
s an integer specifying the last frame number to consider and[] 
 []


Overfull \hbox (141.57028pt too wide) in paragraph at lines 59--59
[]                                \OT1/cmtt/m/n/12 'step' is an integer specify
ing the step number between two frames.[] 
 []


Overfull \hbox (289.77036pt too wide) in paragraph at lines 60--60
[]        \OT1/cmtt/m/n/12 * group              -- a selection string specifyin
g the groups of atoms that will define the vectors on which the[] 
 []


Overfull \hbox (184.7953pt too wide) in paragraph at lines 61--61
[]                                \OT1/cmtt/m/n/12 analysis will be computed. E
ach group must contain two and only two atoms.[] 
 []


Overfull \hbox (215.67032pt too wide) in paragraph at lines 62--62
[]        \OT1/cmtt/m/n/12 * atomorder          -- a string of the form 'atom1,
atom2,atom3' where 'atom1', 'atom2' and 'atom3' are[] 
 []


Overfull \hbox (221.84532pt too wide) in paragraph at lines 63--63
[]                                \OT1/cmtt/m/n/12 respectively the MMTK atom n
ames of the atoms in the way they should be ordered.[] 
 []


Overfull \hbox (370.0454pt too wide) in paragraph at lines 64--64
[]        \OT1/cmtt/m/n/12 * op                 -- the output NetCDF file name.
 A CDL version of this file will also be generated with the '.cdl' extension[] 

 []


Overfull \hbox (153.92029pt too wide) in paragraph at lines 66--66
[]        \OT1/cmtt/m/n/12 * pyroserver         -- a string specifying if Pyro 
will be used and how to run the analysis.[] 
 []


Overfull \hbox (5.72021pt too wide) in paragraph at lines 70--70
[]    \OT1/cmtt/m/n/12 - To run the analysis do: a.runAnalysis() where a is the
 analysis object.[] 
 []


Overfull \hbox (67.47025pt too wide) in paragraph at lines 71--71
[]    \OT1/cmtt/m/n/12 - To estimate the analysis do: a.estimateAnalysis() wher
e a is the analysis object.[] 
 []


Overfull \hbox (166.2703pt too wide) in paragraph at lines 72--72
[]    \OT1/cmtt/m/n/12 - To save the analysis to 'file' file name do: a.saveAna
lysis(file) where a is the analysis object.[] 
 []

[57


]
Overfull \hbox (32.37648pt too wide) in paragraph at lines 219--220
\OT1/cmr/m/n/12 y-sis(), set-Input-Pa-ram-e-ters(), sub-set-S-e-lec-tion(), up-
date-JobProgress(), weight-ingScheme() 
 []

[58]
Overfull \hbox (109.86668pt too wide) in paragraph at lines 255--265
[] 
 []


Overfull \hbox (222.337pt too wide) in paragraph at lines 275--275
[]    \OT1/cmtt/m/n/12 - \OMS/cmsy/m/n/12 j\OT1/cmtt/m/n/12 parameters\OMS/cmsy
/m/n/12 j \OT1/cmtt/m/n/12 -- a dictionnary of the input parameters, or 'None' 
to set up the analysis without parameters.[] 
 []


Overfull \hbox (135.39528pt too wide) in paragraph at lines 276--276
[]        \OT1/cmtt/m/n/12 * trajectory -- a trajectory file name or an instanc
e of MMTK.Trajectory.Trajectory class.[] 
 []


Overfull \hbox (252.72034pt too wide) in paragraph at lines 277--277
[]        \OT1/cmtt/m/n/12 * timeinfo   -- a string of the form 'first:last:ste
p' where 'first' is an integer specifying the first frame[] 
 []


Overfull \hbox (228.02032pt too wide) in paragraph at lines 278--278
[]                        \OT1/cmtt/m/n/12 number to consider, 'last' is an int
eger specifying the last frame number to consider and[] 
 []


Overfull \hbox (92.17026pt too wide) in paragraph at lines 279--279
[]                        \OT1/cmtt/m/n/12 'step' is an integer specifying the 
step number between two frames.[] 
 []


Overfull \hbox (320.64537pt too wide) in paragraph at lines 280--280
[]        \OT1/cmtt/m/n/12 * opcm       -- the output NetCDF file name. A CDL v
ersion of this file will also be generated with the '.cdl' extension[] 
 []


Overfull \hbox (104.52026pt too wide) in paragraph at lines 282--282
[]        \OT1/cmtt/m/n/12 * pyroserver -- a string specifying if Pyro will be 
used and how to run the analysis.[] 
 []


Overfull \hbox (5.72021pt too wide) in paragraph at lines 286--286
[]    \OT1/cmtt/m/n/12 - To run the analysis do: a.runAnalysis() where a is the
 analysis object.[] 
 []


Overfull \hbox (67.47025pt too wide) in paragraph at lines 287--287
[]    \OT1/cmtt/m/n/12 - To estimate the analysis do: a.estimateAnalysis() wher
e a is the analysis object.[] 
 []


Overfull \hbox (166.2703pt too wide) in paragraph at lines 288--288
[]    \OT1/cmtt/m/n/12 - To save the analysis to 'file' file name do: a.saveAna
lysis(file) where a is the analysis object.[] 
 []


Overfull \hbox (215.67032pt too wide) in paragraph at lines 292--292
[]    \OT1/cmtt/m/n/12 - This code is adapted from the s2predict code developpe
d by F. Zhang and R. Bruschweiler and available in:[] 
 []

[59]
Overfull \hbox (209.49532pt too wide) in paragraph at lines 295--295
[]    \OT1/cmtt/m/n/12 - For more details about the method: Zhang, F., Bruschwe
iler, R. J. AM. Chem. Soc. 2002, 124, 12654-12655.[] 
 []


Overfull \hbox (32.37648pt too wide) in paragraph at lines 438--439
\OT1/cmr/m/n/12 y-sis(), set-Input-Pa-ram-e-ters(), sub-set-S-e-lec-tion(), up-
date-JobProgress(), weight-ingScheme() 
 []

[60]) [61]
\openout2 = `nMOLDYN.Analysis.Scattering-module.aux'.

 (./nMOLDYN.Analysis.Scattering-module.tex
Overfull \hbox (11.89522pt too wide) in paragraph at lines 18--18
[]\OT1/cmtt/m/n/12 Collections of classes for the determination of scattering-r
elated properties.[] 
 []


Overfull \hbox (160.09529pt too wide) in paragraph at lines 21--21
[]    \OT1/cmtt/m/n/12 * DynamicCoherentStructureFactor           : sets up a D
ynamic Coherent Structure Factor analysis.[] 
 []


Overfull \hbox (351.52039pt too wide) in paragraph at lines 22--22
[]    \OT1/cmtt/m/n/12 * DynamicCoherentStructureFactorARModel    : sets up a D
ynamic Coherent Structure Factor analysis using an Auto Regressive model.[] 
 []


Overfull \hbox (178.6203pt too wide) in paragraph at lines 23--23
[]    \OT1/cmtt/m/n/12 * DynamicIncoherentStructureFactor         : sets up an 
Dynamic Incoherent Structure Factor analysis.[] 
 []


Overfull \hbox (370.0454pt too wide) in paragraph at lines 24--24
[]    \OT1/cmtt/m/n/12 * DynamicIncoherentStructureFactorGaussian : sets up an 
Dynamic Incoherent Structure Factor analysis using a Gaussian approximation.[] 

 []


Overfull \hbox (370.0454pt too wide) in paragraph at lines 25--25
[]    \OT1/cmtt/m/n/12 * IncoherentStructureFactorARModel         : sets up an 
Dynamic Incoherent Structure Factor analysis using an Auto Regressive model.[] 

 []


Overfull \hbox (178.6203pt too wide) in paragraph at lines 26--26
[]    \OT1/cmtt/m/n/12 * ElasticIncoherentStructureFactor         : sets up an 
Elastic Incoherent Structure Factor analysis.[] 
 []


Overfull \hbox (153.92029pt too wide) in paragraph at lines 27--27
[]    \OT1/cmtt/m/n/12 * StaticCoherentStructureFactor            : sets up a S
tatic Coherent Structure Factor analysis.[] 
 []


Overfull \hbox (156.36665pt too wide) in paragraph at lines 92--102
[] 
 []

[62


]
Overfull \hbox (222.337pt too wide) in paragraph at lines 112--112
[]    \OT1/cmtt/m/n/12 - \OMS/cmsy/m/n/12 j\OT1/cmtt/m/n/12 parameters\OMS/cmsy
/m/n/12 j \OT1/cmtt/m/n/12 -- a dictionnary of the input parameters, or 'None' 
to set up the analysis without parameters.[] 
 []


Overfull \hbox (178.6203pt too wide) in paragraph at lines 113--113
[]        \OT1/cmtt/m/n/12 * trajectory        -- a trajectory file name or an 
instance of MMTK.Trajectory.Trajectory class.[] 
 []


Overfull \hbox (295.94536pt too wide) in paragraph at lines 114--114
[]        \OT1/cmtt/m/n/12 * timeinfo          -- a string of the form 'first:l
ast:step' where 'first' is an integer specifying the first frame[] 
 []


Overfull \hbox (271.24535pt too wide) in paragraph at lines 115--115
[]                               \OT1/cmtt/m/n/12 number to consider, 'last' is
 an integer specifying the last frame number to consider and[] 
 []


Overfull \hbox (135.39528pt too wide) in paragraph at lines 116--116
[]                               \OT1/cmtt/m/n/12 'step' is an integer specifyi
ng the step number between two frames.[] 
 []


Overfull \hbox (252.72034pt too wide) in paragraph at lines 117--117
[]        \OT1/cmtt/m/n/12 * qshellvalues      -- a string of the form 'qmin1:q
max1:dq1;qmin2:qmax2:dq2...' where 'qmin1', 'qmin2' ... ,[] 
 []


Overfull \hbox (221.84532pt too wide) in paragraph at lines 118--118
[]                               \OT1/cmtt/m/n/12 'qmax1', 'qmax2' ... and 'dq1
', 'dq2' ... are floats that represents respectively[] 
 []


Overfull \hbox (141.57028pt too wide) in paragraph at lines 119--119
[]                               \OT1/cmtt/m/n/12 the q minimum, the q maximum 
and the q steps for q interval 1, 2 ...[] 
 []


Overfull \hbox (135.39528pt too wide) in paragraph at lines 121--121
[]        \OT1/cmtt/m/n/12 * qvectorspershell  -- a float specifying the number
 of q vectors to generate per q shell.[] 
 []


Overfull \hbox (308.29536pt too wide) in paragraph at lines 122--122
[]        \OT1/cmtt/m/n/12 * qvectorsgenerator -- a string being one of 'isotro
pic', 'anisotropic' or 'explicit' specifying the way the q vectors[] 
 []


Overfull \hbox (302.12036pt too wide) in paragraph at lines 124--124
[]        \OT1/cmtt/m/n/12 * qvectorsdirection -- a string of the form 'v1x,v1y
,v1z;v2x,v2y,v2z...' where 'v1x', 'v2x' ..., 'v1y', 'v2y' ... and[] 
 []


Overfull \hbox (332.99538pt too wide) in paragraph at lines 125--125
[]                               \OT1/cmtt/m/n/12 'v1z', 'v2z' ... are floats t
hat represents respectively the x, y and z values of the vectord along[] 
 []


Overfull \hbox (332.99538pt too wide) in paragraph at lines 127--127
[]        \OT1/cmtt/m/n/12 * fftwindow         -- a float in ]0.0,100.0[ specif
ying the width of the gaussian, in percentage of the trajectory length[] 
 []


Overfull \hbox (147.74529pt too wide) in paragraph at lines 129--129
[]        \OT1/cmtt/m/n/12 * subset            -- a selection string specifying
 the atoms to consider for the analysis.[] 
 []


Overfull \hbox (363.87039pt too wide) in paragraph at lines 130--130
[]        \OT1/cmtt/m/n/12 * deuteration       -- a selection string specifying
 the hydrogen atoms whose atomic parameters will be those of the deuterium.[] 
 []


Overfull \hbox (382.3954pt too wide) in paragraph at lines 131--131
[]        \OT1/cmtt/m/n/12 * weights           -- a string equal to 'equal', 'm
ass', 'coherent' , 'incoherent' or 'atomicNumber' that specifies the weighting[
] 
 []


Overfull \hbox (147.74529pt too wide) in paragraph at lines 133--133
[]        \OT1/cmtt/m/n/12 * dcsf              -- the output NetCDF file name f
or the intermediate scattering function.[] 
 []


Overfull \hbox (147.74529pt too wide) in paragraph at lines 134--134
[]        \OT1/cmtt/m/n/12 * pyroserver        -- a string specifying if Pyro w
ill be used and how to run the analysis.[] 
 []


Overfull \hbox (5.72021pt too wide) in paragraph at lines 138--138
[]    \OT1/cmtt/m/n/12 - To run the analysis do: a.runAnalysis() where a is the
 analysis object.[] 
 []


Overfull \hbox (67.47025pt too wide) in paragraph at lines 139--139
[]    \OT1/cmtt/m/n/12 - To estimate the analysis do: a.estimateAnalysis() wher
e a is the analysis object.[] 
 []


Overfull \hbox (166.2703pt too wide) in paragraph at lines 140--140
[]    \OT1/cmtt/m/n/12 - To save the analysis to 'file' file name do: a.saveAna
lysis(file) where a is the analysis object.[] 
 []

[63]
Overfull \hbox (32.37648pt too wide) in paragraph at lines 283--284
\OT1/cmr/m/n/12 y-sis(), set-Input-Pa-ram-e-ters(), sub-set-S-e-lec-tion(), up-
date-JobProgress(), weight-ingScheme() 
 []

[64]
Overfull \hbox (138.14442pt too wide) in paragraph at lines 322--332
[] 
 []


Overfull \hbox (222.337pt too wide) in paragraph at lines 342--342
[]    \OT1/cmtt/m/n/12 - \OMS/cmsy/m/n/12 j\OT1/cmtt/m/n/12 parameters\OMS/cmsy
/m/n/12 j \OT1/cmtt/m/n/12 -- a dictionnary of the input parameters, or 'None' 
to set up the analysis without parameters.[] 
 []


Overfull \hbox (178.6203pt too wide) in paragraph at lines 343--343
[]        \OT1/cmtt/m/n/12 * trajectory        -- a trajectory file name or an 
instance of MMTK.Trajectory.Trajectory class.[] 
 []


Overfull \hbox (295.94536pt too wide) in paragraph at lines 344--344
[]        \OT1/cmtt/m/n/12 * timeinfo          -- a string of the form 'first:l
ast:step' where 'first' is an integer specifying the first frame[] 
 []


Overfull \hbox (271.24535pt too wide) in paragraph at lines 345--345
[]                               \OT1/cmtt/m/n/12 number to consider, 'last' is
 an integer specifying the last frame number to consider and[] 
 []


Overfull \hbox (135.39528pt too wide) in paragraph at lines 346--346
[]                               \OT1/cmtt/m/n/12 'step' is an integer specifyi
ng the step number between two frames.[] 
 []


Overfull \hbox (252.72034pt too wide) in paragraph at lines 347--347
[]        \OT1/cmtt/m/n/12 * qshellvalues      -- a string of the form 'qmin1:q
max1:dq1;qmin2:qmax2:dq2...' where 'qmin1', 'qmin2' ... ,[] 
 []


Overfull \hbox (221.84532pt too wide) in paragraph at lines 348--348
[]                               \OT1/cmtt/m/n/12 'qmax1', 'qmax2' ... and 'dq1
', 'dq2' ... are floats that represents respectively[] 
 []


Overfull \hbox (141.57028pt too wide) in paragraph at lines 349--349
[]                               \OT1/cmtt/m/n/12 the q minimum, the q maximum 
and the q steps for q interval 1, 2 ...[] 
 []


Overfull \hbox (135.39528pt too wide) in paragraph at lines 351--351
[]        \OT1/cmtt/m/n/12 * qvectorspershell  -- a float specifying the number
 of q vectors to generate per q shell.[] 
 []


Overfull \hbox (308.29536pt too wide) in paragraph at lines 352--352
[]        \OT1/cmtt/m/n/12 * qvectorsgenerator -- a string being one of 'isotro
pic', 'anisotropic' or 'explicit' specifying the way the q vectors[] 
 []


Overfull \hbox (302.12036pt too wide) in paragraph at lines 354--354
[]        \OT1/cmtt/m/n/12 * qvectorsdirection -- a string of the form 'v1x,v1y
,v1z;v2x,v2y,v2z...' where 'v1x', 'v2x' ..., 'v1y', 'v2y' ... and[] 
 []


Overfull \hbox (332.99538pt too wide) in paragraph at lines 355--355
[]                               \OT1/cmtt/m/n/12 'v1z', 'v2z' ... are floats t
hat represents respectively the x, y and z values of the vectord along[] 
 []


Overfull \hbox (332.99538pt too wide) in paragraph at lines 357--357
[]        \OT1/cmtt/m/n/12 * fftwindow         -- a float in ]0.0,100.0[ specif
ying the width of the gaussian, in percentage of the trajectory length[] 
 []


Overfull \hbox (147.74529pt too wide) in paragraph at lines 359--359
[]        \OT1/cmtt/m/n/12 * subset            -- a selection string specifying
 the atoms to consider for the analysis.[] 
 []


Overfull \hbox (363.87039pt too wide) in paragraph at lines 360--360
[]        \OT1/cmtt/m/n/12 * deuteration       -- a selection string specifying
 the hydrogen atoms whose atomic parameters will be those of the deuterium.[] 
 []


Overfull \hbox (382.3954pt too wide) in paragraph at lines 361--361
[]        \OT1/cmtt/m/n/12 * weights           -- a string equal to 'equal', 'm
ass', 'coherent' , 'incoherent' or 'atomicNumber' that specifies the weighting[
] 
 []


Overfull \hbox (147.74529pt too wide) in paragraph at lines 363--363
[]        \OT1/cmtt/m/n/12 * csf               -- the output NetCDF file name f
or the intermediate scattering function.[] 
 []


Overfull \hbox (147.74529pt too wide) in paragraph at lines 364--364
[]        \OT1/cmtt/m/n/12 * pyroserver        -- a string specifying if Pyro w
ill be used and how to run the analysis.[] 
 []

[65]
Overfull \hbox (5.72021pt too wide) in paragraph at lines 368--368
[]    \OT1/cmtt/m/n/12 - To run the analysis do: a.runAnalysis() where a is the
 analysis object.[] 
 []


Overfull \hbox (67.47025pt too wide) in paragraph at lines 369--369
[]    \OT1/cmtt/m/n/12 - To estimate the analysis do: a.estimateAnalysis() wher
e a is the analysis object.[] 
 []


Overfull \hbox (166.2703pt too wide) in paragraph at lines 370--370
[]    \OT1/cmtt/m/n/12 - To save the analysis to 'file' file name do: a.saveAna
lysis(file) where a is the analysis object.[] 
 []

[66]
Overfull \hbox (32.37648pt too wide) in paragraph at lines 513--514
\OT1/cmr/m/n/12 y-sis(), set-Input-Pa-ram-e-ters(), sub-set-S-e-lec-tion(), up-
date-JobProgress(), weight-ingScheme() 
 []


Overfull \hbox (176.63055pt too wide) in paragraph at lines 552--562
[] 
 []


Overfull \hbox (48.94524pt too wide) in paragraph at lines 564--564
[]\OT1/cmtt/m/n/12 Sets up a Dynamic Coherent Structure Factor analysis using a
n Auto Regressive model.[] 
 []


Overfull \hbox (222.337pt too wide) in paragraph at lines 572--572
[]    \OT1/cmtt/m/n/12 - \OMS/cmsy/m/n/12 j\OT1/cmtt/m/n/12 parameters\OMS/cmsy
/m/n/12 j \OT1/cmtt/m/n/12 -- a dictionnary of the input parameters, or 'None' 
to set up the analysis without parameters.[] 
 []


Overfull \hbox (178.6203pt too wide) in paragraph at lines 573--573
[]        \OT1/cmtt/m/n/12 * trajectory        -- a trajectory file name or an 
instance of MMTK.Trajectory.Trajectory class.[] 
 []


Overfull \hbox (295.94536pt too wide) in paragraph at lines 574--574
[]        \OT1/cmtt/m/n/12 * timeinfo          -- a string of the form 'first:l
ast:step' where 'first' is an integer specifying the first frame[] 
 []


Overfull \hbox (271.24535pt too wide) in paragraph at lines 575--575
[]                               \OT1/cmtt/m/n/12 number to consider, 'last' is
 an integer specifying the last frame number to consider and[] 
 []


Overfull \hbox (135.39528pt too wide) in paragraph at lines 576--576
[]                               \OT1/cmtt/m/n/12 'step' is an integer specifyi
ng the step number between two frames.[] 
 []


Overfull \hbox (141.57028pt too wide) in paragraph at lines 577--577
[]        \OT1/cmtt/m/n/12 * armodelorder      -- an integer in [1, len(traject
ory)[ specifying the order of the model[] 
 []


Overfull \hbox (252.72034pt too wide) in paragraph at lines 578--578
[]        \OT1/cmtt/m/n/12 * qshellvalues      -- a string of the form 'qmin1:q
max1:dq1;qmin2:qmax2:dq2...' where 'qmin1', 'qmin2' ... ,[] 
 []


Overfull \hbox (221.84532pt too wide) in paragraph at lines 579--579
[]                               \OT1/cmtt/m/n/12 'qmax1', 'qmax2' ... and 'dq1
', 'dq2' ... are floats that represents respectively[] 
 []


Overfull \hbox (141.57028pt too wide) in paragraph at lines 580--580
[]                               \OT1/cmtt/m/n/12 the q minimum, the q maximum 
and the q steps for q interval 1, 2 ...[] 
 []

[67]
Overfull \hbox (135.39528pt too wide) in paragraph at lines 582--582
[]        \OT1/cmtt/m/n/12 * qvectorspershell  -- a float specifying the number
 of q vectors to generate per q shell.[] 
 []


Overfull \hbox (308.29536pt too wide) in paragraph at lines 583--583
[]        \OT1/cmtt/m/n/12 * qvectorsgenerator -- a string being one of 'isotro
pic', 'anisotropic' or 'explicit' specifying the way the q vectors[] 
 []


Overfull \hbox (302.12036pt too wide) in paragraph at lines 585--585
[]        \OT1/cmtt/m/n/12 * qvectorsdirection -- a string of the form 'v1x,v1y
,v1z;v2x,v2y,v2z...' where 'v1x', 'v2x' ..., 'v1y', 'v2y' ... and[] 
 []


Overfull \hbox (332.99538pt too wide) in paragraph at lines 586--586
[]                               \OT1/cmtt/m/n/12 'v1z', 'v2z' ... are floats t
hat represents respectively the x, y and z values of the vectord along[] 
 []


Overfull \hbox (147.74529pt too wide) in paragraph at lines 588--588
[]        \OT1/cmtt/m/n/12 * subset            -- a selection string specifying
 the atoms to consider for the analysis.[] 
 []


Overfull \hbox (363.87039pt too wide) in paragraph at lines 589--589
[]        \OT1/cmtt/m/n/12 * deuteration       -- a selection string specifying
 the hydrogen atoms whose atomic parameters will be those of the deuterium.[] 
 []


Overfull \hbox (382.3954pt too wide) in paragraph at lines 590--590
[]        \OT1/cmtt/m/n/12 * weights           -- a string equal to 'equal', 'm
ass', 'coherent' , 'incoherent' or 'atomicNumber' that specifies the weighting[
] 
 []


Overfull \hbox (147.74529pt too wide) in paragraph at lines 593--593
[]        \OT1/cmtt/m/n/12 * pyroserver        -- a string specifying if Pyro w
ill be used and how to run the analysis.[] 
 []


Overfull \hbox (5.72021pt too wide) in paragraph at lines 597--597
[]    \OT1/cmtt/m/n/12 - To run the analysis do: a.runAnalysis() where a is the
 analysis object.[] 
 []


Overfull \hbox (67.47025pt too wide) in paragraph at lines 598--598
[]    \OT1/cmtt/m/n/12 - To estimate the analysis do: a.estimateAnalysis() wher
e a is the analysis object.[] 
 []


Overfull \hbox (166.2703pt too wide) in paragraph at lines 599--599
[]    \OT1/cmtt/m/n/12 - To save the analysis to 'file' file name do: a.saveAna
lysis(file) where a is the analysis object.[] 
 []

[68]
Overfull \hbox (32.37648pt too wide) in paragraph at lines 742--743
\OT1/cmr/m/n/12 y-sis(), set-Input-Pa-ram-e-ters(), sub-set-S-e-lec-tion(), up-
date-JobProgress(), weight-ingScheme() 
 []


Overfull \hbox (165.14444pt too wide) in paragraph at lines 781--791
[] 
 []

[69]
Overfull \hbox (222.337pt too wide) in paragraph at lines 801--801
[]    \OT1/cmtt/m/n/12 - \OMS/cmsy/m/n/12 j\OT1/cmtt/m/n/12 parameters\OMS/cmsy
/m/n/12 j \OT1/cmtt/m/n/12 -- a dictionnary of the input parameters, or 'None' 
to set up the analysis without parameters.[] 
 []


Overfull \hbox (178.6203pt too wide) in paragraph at lines 802--802
[]        \OT1/cmtt/m/n/12 * trajectory        -- a trajectory file name or an 
instance of MMTK.Trajectory.Trajectory class.[] 
 []


Overfull \hbox (295.94536pt too wide) in paragraph at lines 803--803
[]        \OT1/cmtt/m/n/12 * timeinfo          -- a string of the form 'first:l
ast:step' where 'first' is an integer specifying the first frame[] 
 []


Overfull \hbox (271.24535pt too wide) in paragraph at lines 804--804
[]                               \OT1/cmtt/m/n/12 number to consider, 'last' is
 an integer specifying the last frame number to consider and[] 
 []


Overfull \hbox (135.39528pt too wide) in paragraph at lines 805--805
[]                               \OT1/cmtt/m/n/12 'step' is an integer specifyi
ng the step number between two frames.[] 
 []


Overfull \hbox (252.72034pt too wide) in paragraph at lines 806--806
[]        \OT1/cmtt/m/n/12 * qshellvalues      -- a string of the form 'qmin1:q
max1:dq1;qmin2:qmax2:dq2...' where 'qmin1', 'qmin2' ... ,[] 
 []


Overfull \hbox (221.84532pt too wide) in paragraph at lines 807--807
[]                               \OT1/cmtt/m/n/12 'qmax1', 'qmax2' ... and 'dq1
', 'dq2' ... are floats that represents respectively[] 
 []


Overfull \hbox (141.57028pt too wide) in paragraph at lines 808--808
[]                               \OT1/cmtt/m/n/12 the q minimum, the q maximum 
and the q steps for q interval 1, 2 ...[] 
 []


Overfull \hbox (135.39528pt too wide) in paragraph at lines 810--810
[]        \OT1/cmtt/m/n/12 * qvectorspershell  -- a float specifying the number
 of q vectors to generate per q shell.[] 
 []


Overfull \hbox (308.29536pt too wide) in paragraph at lines 811--811
[]        \OT1/cmtt/m/n/12 * qvectorsgenerator -- a string being one of 'isotro
pic', 'anisotropic' or 'explicit' specifying the way the q vectors[] 
 []


Overfull \hbox (302.12036pt too wide) in paragraph at lines 813--813
[]        \OT1/cmtt/m/n/12 * qvectorsdirection -- a string of the form 'v1x,v1y
,v1z;v2x,v2y,v2z...' where 'v1x', 'v2x' ..., 'v1y', 'v2y' ... and[] 
 []


Overfull \hbox (332.99538pt too wide) in paragraph at lines 814--814
[]                               \OT1/cmtt/m/n/12 'v1z', 'v2z' ... are floats t
hat represents respectively the x, y and z values of the vectord along[] 
 []


Overfull \hbox (332.99538pt too wide) in paragraph at lines 816--816
[]        \OT1/cmtt/m/n/12 * fftwindow         -- a float in ]0.0,100.0[ specif
ying the width of the gaussian, in percentage of the trajectory length[] 
 []


Overfull \hbox (147.74529pt too wide) in paragraph at lines 818--818
[]        \OT1/cmtt/m/n/12 * subset            -- a selection string specifying
 the atoms to consider for the analysis.[] 
 []


Overfull \hbox (363.87039pt too wide) in paragraph at lines 819--819
[]        \OT1/cmtt/m/n/12 * deuteration       -- a selection string specifying
 the hydrogen atoms whose atomic parameters will be those of the deuterium.[] 
 []


Overfull \hbox (382.3954pt too wide) in paragraph at lines 820--820
[]        \OT1/cmtt/m/n/12 * weights           -- a string equal to 'equal', 'm
ass', 'coherent' , 'incoherent' or 'atomicNumber' that specifies the weighting[
] 
 []


Overfull \hbox (147.74529pt too wide) in paragraph at lines 822--822
[]        \OT1/cmtt/m/n/12 * disf              -- the output NetCDF file name f
or the intermediate scattering function.[] 
 []


Overfull \hbox (147.74529pt too wide) in paragraph at lines 823--823
[]        \OT1/cmtt/m/n/12 * pyroserver        -- a string specifying if Pyro w
ill be used and how to run the analysis.[] 
 []


Overfull \hbox (5.72021pt too wide) in paragraph at lines 827--827
[]    \OT1/cmtt/m/n/12 - To run the analysis do: a.runAnalysis() where a is the
 analysis object.[] 
 []


Overfull \hbox (67.47025pt too wide) in paragraph at lines 828--828
[]    \OT1/cmtt/m/n/12 - To estimate the analysis do: a.estimateAnalysis() wher
e a is the analysis object.[] 
 []


Overfull \hbox (166.2703pt too wide) in paragraph at lines 829--829
[]    \OT1/cmtt/m/n/12 - To save the analysis to 'file' file name do: a.saveAna
lysis(file) where a is the analysis object.[] 
 []

[70]
Overfull \hbox (32.37648pt too wide) in paragraph at lines 972--973
\OT1/cmr/m/n/12 y-sis(), set-Input-Pa-ram-e-ters(), sub-set-S-e-lec-tion(), up-
date-JobProgress(), weight-ingScheme() 
 []

[71]
Overfull \hbox (185.40834pt too wide) in paragraph at lines 1011--1021
[] 
 []


Overfull \hbox (67.47025pt too wide) in paragraph at lines 1023--1023
[]\OT1/cmtt/m/n/12 Sets up an Dynamic Incoherent Structure Factor analysis usin
g an Auto Regressive model.[] 
 []


Overfull \hbox (222.337pt too wide) in paragraph at lines 1031--1031
[]    \OT1/cmtt/m/n/12 - \OMS/cmsy/m/n/12 j\OT1/cmtt/m/n/12 parameters\OMS/cmsy
/m/n/12 j \OT1/cmtt/m/n/12 -- a dictionnary of the input parameters, or 'None' 
to set up the analysis without parameters.[] 
 []


Overfull \hbox (178.6203pt too wide) in paragraph at lines 1032--1032
[]        \OT1/cmtt/m/n/12 * trajectory        -- a trajectory file name or an 
instance of MMTK.Trajectory.Trajectory class.[] 
 []


Overfull \hbox (295.94536pt too wide) in paragraph at lines 1033--1033
[]        \OT1/cmtt/m/n/12 * timeinfo          -- a string of the form 'first:l
ast:step' where 'first' is an integer specifying the first frame[] 
 []


Overfull \hbox (271.24535pt too wide) in paragraph at lines 1034--1034
[]                               \OT1/cmtt/m/n/12 number to consider, 'last' is
 an integer specifying the last frame number to consider and[] 
 []


Overfull \hbox (135.39528pt too wide) in paragraph at lines 1035--1035
[]                               \OT1/cmtt/m/n/12 'step' is an integer specifyi
ng the step number between two frames.[] 
 []


Overfull \hbox (141.57028pt too wide) in paragraph at lines 1036--1036
[]        \OT1/cmtt/m/n/12 * armodelorder      -- an integer in [1, len(traject
ory)[ specifying the order of the model[] 
 []


Overfull \hbox (252.72034pt too wide) in paragraph at lines 1037--1037
[]        \OT1/cmtt/m/n/12 * qshellvalues      -- a string of the form 'qmin1:q
max1:dq1;qmin2:qmax2:dq2...' where 'qmin1', 'qmin2' ... ,[] 
 []


Overfull \hbox (221.84532pt too wide) in paragraph at lines 1038--1038
[]                               \OT1/cmtt/m/n/12 'qmax1', 'qmax2' ... and 'dq1
', 'dq2' ... are floats that represents respectively[] 
 []


Overfull \hbox (141.57028pt too wide) in paragraph at lines 1039--1039
[]                               \OT1/cmtt/m/n/12 the q minimum, the q maximum 
and the q steps for q interval 1, 2 ...[] 
 []


Overfull \hbox (135.39528pt too wide) in paragraph at lines 1041--1041
[]        \OT1/cmtt/m/n/12 * qvectorspershell  -- a float specifying the number
 of q vectors to generate per q shell.[] 
 []


Overfull \hbox (308.29536pt too wide) in paragraph at lines 1042--1042
[]        \OT1/cmtt/m/n/12 * qvectorsgenerator -- a string being one of 'isotro
pic', 'anisotropic' or 'explicit' specifying the way the q vectors[] 
 []


Overfull \hbox (302.12036pt too wide) in paragraph at lines 1044--1044
[]        \OT1/cmtt/m/n/12 * qvectorsdirection -- a string of the form 'v1x,v1y
,v1z;v2x,v2y,v2z...' where 'v1x', 'v2x' ..., 'v1y', 'v2y' ... and[] 
 []


Overfull \hbox (332.99538pt too wide) in paragraph at lines 1045--1045
[]                               \OT1/cmtt/m/n/12 'v1z', 'v2z' ... are floats t
hat represents respectively the x, y and z values of the vectord along[] 
 []


Overfull \hbox (147.74529pt too wide) in paragraph at lines 1047--1047
[]        \OT1/cmtt/m/n/12 * subset            -- a selection string specifying
 the atoms to consider for the analysis.[] 
 []


Overfull \hbox (363.87039pt too wide) in paragraph at lines 1048--1048
[]        \OT1/cmtt/m/n/12 * deuteration       -- a selection string specifying
 the hydrogen atoms whose atomic parameters will be those of the deuterium.[] 
 []


Overfull \hbox (382.3954pt too wide) in paragraph at lines 1049--1049
[]        \OT1/cmtt/m/n/12 * weights           -- a string equal to 'equal', 'm
ass', 'coherent' , 'incoherent' or 'atomicNumber' that specifies the weighting[
] 
 []


Overfull \hbox (147.74529pt too wide) in paragraph at lines 1051--1051
[]        \OT1/cmtt/m/n/12 * disfar            -- the output NetCDF file name f
or the intermediate scattering function.[] 
 []


Overfull \hbox (147.74529pt too wide) in paragraph at lines 1052--1052
[]        \OT1/cmtt/m/n/12 * pyroserver        -- a string specifying if Pyro w
ill be used and how to run the analysis.[] 
 []

[72]
Overfull \hbox (5.72021pt too wide) in paragraph at lines 1056--1056
[]    \OT1/cmtt/m/n/12 - To run the analysis do: a.runAnalysis() where a is the
 analysis object.[] 
 []


Overfull \hbox (67.47025pt too wide) in paragraph at lines 1057--1057
[]    \OT1/cmtt/m/n/12 - To estimate the analysis do: a.estimateAnalysis() wher
e a is the analysis object.[] 
 []


Overfull \hbox (166.2703pt too wide) in paragraph at lines 1058--1058
[]    \OT1/cmtt/m/n/12 - To save the analysis to 'file' file name do: a.saveAna
lysis(file) where a is the analysis object.[] 
 []

[73]
Overfull \hbox (32.37648pt too wide) in paragraph at lines 1201--1202
\OT1/cmr/m/n/12 y-sis(), set-Input-Pa-ram-e-ters(), sub-set-S-e-lec-tion(), up-
date-JobProgress(), weight-ingScheme() 
 []


Overfull \hbox (218.28056pt too wide) in paragraph at lines 1240--1250
[] 
 []


Overfull \hbox (61.29524pt too wide) in paragraph at lines 1252--1252
[]\OT1/cmtt/m/n/12 Sets up an Dynamic Incoherent Structure Factor analysis with
in Gaussian approximation.[] 
 []


Overfull \hbox (222.337pt too wide) in paragraph at lines 1260--1260
[]    \OT1/cmtt/m/n/12 - \OMS/cmsy/m/n/12 j\OT1/cmtt/m/n/12 parameters\OMS/cmsy
/m/n/12 j \OT1/cmtt/m/n/12 -- a dictionnary of the input parameters, or 'None' 
to set up the analysis without parameters.[] 
 []


Overfull \hbox (147.74529pt too wide) in paragraph at lines 1261--1261
[]        \OT1/cmtt/m/n/12 * trajectory   -- a trajectory file name or an insta
nce of MMTK.Trajectory.Trajectory class.[] 
 []


Overfull \hbox (265.07034pt too wide) in paragraph at lines 1262--1262
[]        \OT1/cmtt/m/n/12 * timeinfo     -- a string of the form 'first:last:s
tep' where 'first' is an integer specifying the first frame[] 
 []


Overfull \hbox (240.37033pt too wide) in paragraph at lines 1263--1263
[]                          \OT1/cmtt/m/n/12 number to consider, 'last' is an i
nteger specifying the last frame number to consider and[] 
 []


Overfull \hbox (104.52026pt too wide) in paragraph at lines 1264--1264
[]                          \OT1/cmtt/m/n/12 'step' is an integer specifying th
e step number between two frames.[] 
 []


Overfull \hbox (221.84532pt too wide) in paragraph at lines 1265--1265
[]        \OT1/cmtt/m/n/12 * qshellvalues -- a string of the form 'qmin1:qmax1:
dq1;qmin2:qmax2:dq2...' where 'qmin1', 'qmin2' ... ,[] 
 []


Overfull \hbox (190.9703pt too wide) in paragraph at lines 1266--1266
[]                          \OT1/cmtt/m/n/12 'qmax1', 'qmax2' ... and 'dq1', 'd
q2' ... are floats that represents respectively[] 
 []


Overfull \hbox (110.69527pt too wide) in paragraph at lines 1267--1267
[]                          \OT1/cmtt/m/n/12 the q minimum, the q maximum and t
he q steps for q interval 1, 2 ...[] 
 []


Overfull \hbox (302.12036pt too wide) in paragraph at lines 1268--1268
[]        \OT1/cmtt/m/n/12 * fftwindow    -- a float in ]0.0,100.0[ specifying 
the width of the gaussian, in percentage of the trajectory length[] 
 []


Overfull \hbox (116.87027pt too wide) in paragraph at lines 1270--1270
[]        \OT1/cmtt/m/n/12 * subset       -- a selection string specifying the 
atoms to consider for the analysis.[] 
 []


Overfull \hbox (332.99538pt too wide) in paragraph at lines 1271--1271
[]        \OT1/cmtt/m/n/12 * deuteration  -- a selection string specifying the 
hydrogen atoms whose atomic parameters will be those of the deuterium.[] 
 []


Overfull \hbox (351.52039pt too wide) in paragraph at lines 1272--1272
[]        \OT1/cmtt/m/n/12 * weights      -- a string equal to 'equal', 'mass',
 'coherent' , 'incoherent' or 'atomicNumber' that specifies the weighting[] 
 []


Overfull \hbox (116.87027pt too wide) in paragraph at lines 1274--1274
[]        \OT1/cmtt/m/n/12 * disfg        -- the output NetCDF file name for th
e intermediate scattering function.[] 
 []

[74]
Overfull \hbox (116.87027pt too wide) in paragraph at lines 1275--1275
[]        \OT1/cmtt/m/n/12 * pyroserver   -- a string specifying if Pyro will b
e used and how to run the analysis.[] 
 []


Overfull \hbox (5.72021pt too wide) in paragraph at lines 1279--1279
[]    \OT1/cmtt/m/n/12 - To run the analysis do: a.runAnalysis() where a is the
 analysis object.[] 
 []


Overfull \hbox (67.47025pt too wide) in paragraph at lines 1280--1280
[]    \OT1/cmtt/m/n/12 - To estimate the analysis do: a.estimateAnalysis() wher
e a is the analysis object.[] 
 []


Overfull \hbox (166.2703pt too wide) in paragraph at lines 1281--1281
[]    \OT1/cmtt/m/n/12 - To save the analysis to 'file' file name do: a.saveAna
lysis(file) where a is the analysis object.[] 
 []

[75]
Overfull \hbox (32.37648pt too wide) in paragraph at lines 1445--1446
\OT1/cmr/m/n/12 y-sis(), set-Input-Pa-ram-e-ters(), sub-set-S-e-lec-tion(), up-
date-JobProgress(), weight-ingScheme() 
 []


Overfull \hbox (152.10834pt too wide) in paragraph at lines 1484--1494
[] 
 []


Overfull \hbox (222.337pt too wide) in paragraph at lines 1504--1504
[]    \OT1/cmtt/m/n/12 - \OMS/cmsy/m/n/12 j\OT1/cmtt/m/n/12 parameters\OMS/cmsy
/m/n/12 j \OT1/cmtt/m/n/12 -- a dictionnary of the input parameters, or 'None' 
to set up the analysis without parameters.[] 
 []


Overfull \hbox (178.6203pt too wide) in paragraph at lines 1505--1505
[]        \OT1/cmtt/m/n/12 * trajectory        -- a trajectory file name or an 
instance of MMTK.Trajectory.Trajectory class.[] 
 []


Overfull \hbox (295.94536pt too wide) in paragraph at lines 1506--1506
[]        \OT1/cmtt/m/n/12 * timeinfo          -- a string of the form 'first:l
ast:step' where 'first' is an integer specifying the first frame[] 
 []


Overfull \hbox (271.24535pt too wide) in paragraph at lines 1507--1507
[]                               \OT1/cmtt/m/n/12 number to consider, 'last' is
 an integer specifying the last frame number to consider and[] 
 []

[76]
Overfull \hbox (135.39528pt too wide) in paragraph at lines 1508--1508
[]                               \OT1/cmtt/m/n/12 'step' is an integer specifyi
ng the step number between two frames.[] 
 []


Overfull \hbox (252.72034pt too wide) in paragraph at lines 1509--1509
[]        \OT1/cmtt/m/n/12 * qshellvalues      -- a string of the form 'qmin1:q
max1:dq1;qmin2:qmax2:dq2...' where 'qmin1', 'qmin2' ... ,[] 
 []


Overfull \hbox (221.84532pt too wide) in paragraph at lines 1510--1510
[]                               \OT1/cmtt/m/n/12 'qmax1', 'qmax2' ... and 'dq1
', 'dq2' ... are floats that represents respectively[] 
 []


Overfull \hbox (141.57028pt too wide) in paragraph at lines 1511--1511
[]                               \OT1/cmtt/m/n/12 the q minimum, the q maximum 
and the q steps for q interval 1, 2 ...[] 
 []


Overfull \hbox (135.39528pt too wide) in paragraph at lines 1513--1513
[]        \OT1/cmtt/m/n/12 * qvectorspershell  -- a float specifying the number
 of q vectors to generate per q shell.[] 
 []


Overfull \hbox (308.29536pt too wide) in paragraph at lines 1514--1514
[]        \OT1/cmtt/m/n/12 * qvectorsgenerator -- a string being one of 'isotro
pic', 'anisotropic' or 'explicit' specifying the way the q vectors[] 
 []


Overfull \hbox (302.12036pt too wide) in paragraph at lines 1516--1516
[]        \OT1/cmtt/m/n/12 * qvectorsdirection -- a string of the form 'v1x,v1y
,v1z;v2x,v2y,v2z...' where 'v1x', 'v2x' ..., 'v1y', 'v2y' ... and[] 
 []


Overfull \hbox (332.99538pt too wide) in paragraph at lines 1517--1517
[]                               \OT1/cmtt/m/n/12 'v1z', 'v2z' ... are floats t
hat represents respectively the x, y and z values of the vectord along[] 
 []


Overfull \hbox (147.74529pt too wide) in paragraph at lines 1519--1519
[]        \OT1/cmtt/m/n/12 * subset            -- a selection string specifying
 the atoms to consider for the analysis.[] 
 []


Overfull \hbox (363.87039pt too wide) in paragraph at lines 1520--1520
[]        \OT1/cmtt/m/n/12 * deuteration       -- a selection string specifying
 the hydrogen atoms whose atomic parameters will be those of the deuterium.[] 
 []


Overfull \hbox (382.3954pt too wide) in paragraph at lines 1521--1521
[]        \OT1/cmtt/m/n/12 * weights           -- a string equal to 'equal', 'm
ass', 'coherent' , 'incoherent' or 'atomicNumber' that specifies the weighting[
] 
 []


Overfull \hbox (363.87039pt too wide) in paragraph at lines 1523--1523
[]        \OT1/cmtt/m/n/12 * eisf              -- the output NetCDF file name. 
A CDL version of this file will also be generated with the '.cdl' extension[] 
 []


Overfull \hbox (147.74529pt too wide) in paragraph at lines 1525--1525
[]        \OT1/cmtt/m/n/12 * pyroserver        -- a string specifying if Pyro w
ill be used and how to run the analysis.[] 
 []


Overfull \hbox (5.72021pt too wide) in paragraph at lines 1529--1529
[]    \OT1/cmtt/m/n/12 - To run the analysis do: a.runAnalysis() where a is the
 analysis object.[] 
 []


Overfull \hbox (67.47025pt too wide) in paragraph at lines 1530--1530
[]    \OT1/cmtt/m/n/12 - To estimate the analysis do: a.estimateAnalysis() wher
e a is the analysis object.[] 
 []


Overfull \hbox (166.2703pt too wide) in paragraph at lines 1531--1531
[]    \OT1/cmtt/m/n/12 - To save the analysis to 'file' file name do: a.saveAna
lysis(file) where a is the analysis object.[] 
 []

[77]
Overfull \hbox (32.37648pt too wide) in paragraph at lines 1674--1675
\OT1/cmr/m/n/12 y-sis(), set-Input-Pa-ram-e-ters(), sub-set-S-e-lec-tion(), up-
date-JobProgress(), weight-ingScheme() 
 []


Overfull \hbox (197.17914pt too wide) in paragraph at lines 1713--1723
[] 
 []

[78]
Overfull \hbox (222.337pt too wide) in paragraph at lines 1733--1733
[]    \OT1/cmtt/m/n/12 - \OMS/cmsy/m/n/12 j\OT1/cmtt/m/n/12 parameters\OMS/cmsy
/m/n/12 j \OT1/cmtt/m/n/12 -- a dictionnary of the input parameters, or 'None' 
to set up the analysis without parameters.[] 
 []


Overfull \hbox (178.6203pt too wide) in paragraph at lines 1734--1734
[]        \OT1/cmtt/m/n/12 * trajectory        -- a trajectory file name or an 
instance of MMTK.Trajectory.Trajectory class.[] 
 []


Overfull \hbox (295.94536pt too wide) in paragraph at lines 1735--1735
[]        \OT1/cmtt/m/n/12 * timeinfo          -- a string of the form 'first:l
ast:step' where 'first' is an integer specifying the first frame[] 
 []


Overfull \hbox (271.24535pt too wide) in paragraph at lines 1736--1736
[]                               \OT1/cmtt/m/n/12 number to consider, 'last' is
 an integer specifying the last frame number to consider and[] 
 []


Overfull \hbox (135.39528pt too wide) in paragraph at lines 1737--1737
[]                               \OT1/cmtt/m/n/12 'step' is an integer specifyi
ng the step number between two frames.[] 
 []


Overfull \hbox (252.72034pt too wide) in paragraph at lines 1738--1738
[]        \OT1/cmtt/m/n/12 * qshellvalues      -- a string of the form 'qmin1:q
max1:dq1;qmin2:qmax2:dq2...' where 'qmin1', 'qmin2' ... ,[] 
 []


Overfull \hbox (221.84532pt too wide) in paragraph at lines 1739--1739
[]                               \OT1/cmtt/m/n/12 'qmax1', 'qmax2' ... and 'dq1
', 'dq2' ... are floats that represents respectively[] 
 []


Overfull \hbox (141.57028pt too wide) in paragraph at lines 1740--1740
[]                               \OT1/cmtt/m/n/12 the q minimum, the q maximum 
and the q steps for q interval 1, 2 ...[] 
 []


Overfull \hbox (147.74529pt too wide) in paragraph at lines 1741--1741
[]        \OT1/cmtt/m/n/12 * subset            -- a selection string specifying
 the atoms to consider for the analysis.[] 
 []


Overfull \hbox (363.87039pt too wide) in paragraph at lines 1742--1742
[]        \OT1/cmtt/m/n/12 * deuteration       -- a selection string specifying
 the hydrogen atoms whose atomic parameters will be those of the deuterium.[] 
 []


Overfull \hbox (382.3954pt too wide) in paragraph at lines 1743--1743
[]        \OT1/cmtt/m/n/12 * weights           -- a string equal to 'equal', 'm
ass', 'coherent' , 'incoherent' or 'atomicNumber' that specifies the weighting[
] 
 []


Overfull \hbox (363.87039pt too wide) in paragraph at lines 1745--1745
[]        \OT1/cmtt/m/n/12 * scsf              -- the output NetCDF file name. 
A CDL version of this file will also be generated with the '.cdl' extension[] 
 []


Overfull \hbox (147.74529pt too wide) in paragraph at lines 1747--1747
[]        \OT1/cmtt/m/n/12 * pyroserver        -- a string specifying if Pyro w
ill be used and how to run the analysis.[] 
 []


Overfull \hbox (5.72021pt too wide) in paragraph at lines 1751--1751
[]    \OT1/cmtt/m/n/12 - To run the analysis do: a.runAnalysis() where a is the
 analysis object.[] 
 []


Overfull \hbox (67.47025pt too wide) in paragraph at lines 1752--1752
[]    \OT1/cmtt/m/n/12 - To estimate the analysis do: a.estimateAnalysis() wher
e a is the analysis object.[] 
 []


Overfull \hbox (166.2703pt too wide) in paragraph at lines 1753--1753
[]    \OT1/cmtt/m/n/12 - To save the analysis to 'file' file name do: a.saveAna
lysis(file) where a is the analysis object.[] 
 []


Overfull \hbox (160.09529pt too wide) in paragraph at lines 1757--1757
[]    \OT1/cmtt/m/n/12 - The analysis is based on the angular averaged coherent
 static structure factor formula where the[] 
 []


Overfull \hbox (178.6203pt too wide) in paragraph at lines 1758--1758
[]      \OT1/cmtt/m/n/12 summation over the q vectors is replaced by an integra
l over the q space. The formula used is taken[] 
 []


Overfull \hbox (11.89522pt too wide) in paragraph at lines 1759--1759
[]      \OT1/cmtt/m/n/12 from equation 2.35 of Fischer et al. Rep. Prog. Phys. 
69 (2006) 233-299.[] 
 []

[79]
Overfull \hbox (32.37648pt too wide) in paragraph at lines 1903--1904
\OT1/cmr/m/n/12 y-sis(), set-Input-Pa-ram-e-ters(), sub-set-S-e-lec-tion(), up-
date-JobProgress(), weight-ingScheme() 
 []

[80]) [81]
\openout2 = `nMOLDYN.Analysis.Slave-module.aux'.

 (./nMOLDYN.Analysis.Slave-module.tex
Overfull \hbox (48.94524pt too wide) in paragraph at lines 18--18
[]\OT1/cmtt/m/n/12 This modules contains the functions used by Pyro slave to pe
rform analysis remotely.[] 
 []

LaTeX Font Info:    Font shape `OMS/cmr/m/it' in size <12> not available
(Font)              Font shape `OMS/cmsy/m/n' tried instead on input line 65.

Overfull \hbox (190.51923pt too wide) in paragraph at lines 65--66
[]\OT1/cmr/m/it/12 (type=MMTK.Atom\OMS/cmsy/m/n/12 j\OT1/cmr/m/it/12 integer\OM
S/cmsy/m/n/12 j\OT1/cmr/m/it/12 MMTK.Collections.Collection\OMS/cmsy/m/n/12 j\O
T1/cmr/m/it/12 nMOLDYN.Mathematics.QVectors)  
 []

) [82


]
\openout2 = `nMOLDYN.Analysis.Structure-module.aux'.

 (./nMOLDYN.Analysis.Structure-module.tex
Overfull \hbox (5.72021pt too wide) in paragraph at lines 18--18
[]\OT1/cmtt/m/n/12 Collections of classes for the determination of structure-re
lated properties.[] 
 []


Overfull \hbox (18.07022pt too wide) in paragraph at lines 22--22
[]    \OT1/cmtt/m/n/12 * PairDistributionFunction : sets up a Pair Distribution
 Function Analysis.[] 
 []


Overfull \hbox (100.42085pt too wide) in paragraph at lines 37--47
[] 
 []


Overfull \hbox (222.337pt too wide) in paragraph at lines 57--57
[]    \OT1/cmtt/m/n/12 - \OMS/cmsy/m/n/12 j\OT1/cmtt/m/n/12 parameters\OMS/cmsy
/m/n/12 j \OT1/cmtt/m/n/12 -- a dictionnary of the input parameters, or 'None' 
to set up the analysis without parameters.[] 
 []


Overfull \hbox (141.57028pt too wide) in paragraph at lines 58--58
[]        \OT1/cmtt/m/n/12 * trajectory  -- a trajectory file name or an instan
ce of MMTK.Trajectory.Trajectory class.[] 
 []


Overfull \hbox (258.89534pt too wide) in paragraph at lines 59--59
[]        \OT1/cmtt/m/n/12 * timeinfo    -- a string of the form 'first:last:st
ep' where 'first' is an integer specifying the first frame[] 
 []


Overfull \hbox (234.19533pt too wide) in paragraph at lines 60--60
[]                         \OT1/cmtt/m/n/12 number to consider, 'last' is an in
teger specifying the last frame number to consider and[] 
 []


Overfull \hbox (98.34526pt too wide) in paragraph at lines 61--61
[]                         \OT1/cmtt/m/n/12 'step' is an integer specifying the
 step number between two frames.[] 
 []


Overfull \hbox (265.07034pt too wide) in paragraph at lines 62--62
[]        \OT1/cmtt/m/n/12 * rvalues     -- a string of the form 'rmin:rmax:dr'
 where 'rmin' is a float specifying the minimum distance to[] 
 []


Overfull \hbox (283.59535pt too wide) in paragraph at lines 63--63
[]                         \OT1/cmtt/m/n/12 consider, 'rmax' is a float specify
ing the maximum distance value to consider and 'dr' is a float[] 
 []


Overfull \hbox (110.69527pt too wide) in paragraph at lines 65--65
[]        \OT1/cmtt/m/n/12 * subset      -- a selection string specifying the a
toms to consider for the analysis.[] 
 []


Overfull \hbox (326.82037pt too wide) in paragraph at lines 66--66
[]        \OT1/cmtt/m/n/12 * deuteration -- a selection string specifying the h
ydrogen atoms whose atomic parameters will be those of the deuterium.[] 
 []


Overfull \hbox (345.34538pt too wide) in paragraph at lines 67--67
[]        \OT1/cmtt/m/n/12 * weights     -- a string equal to 'equal', 'mass', 
'coherent' , 'incoherent' or 'atomicNumber' that specifies the weighting[] 
 []


Overfull \hbox (326.82037pt too wide) in paragraph at lines 69--69
[]        \OT1/cmtt/m/n/12 * pdf         -- the output NetCDF file name. A CDL 
version of this file will also be generated with the '.cdl' extension[] 
 []


Overfull \hbox (110.69527pt too wide) in paragraph at lines 71--71
[]        \OT1/cmtt/m/n/12 * pyroserver  -- a string specifying if Pyro will be
 used and how to run the analysis.[] 
 []


Overfull \hbox (5.72021pt too wide) in paragraph at lines 75--75
[]    \OT1/cmtt/m/n/12 - To run the analysis do: a.runAnalysis() where a is the
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[83


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[]    \OT1/cmtt/m/n/12 - To estimate the analysis do: a.estimateAnalysis() wher
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[]    \OT1/cmtt/m/n/12 - To save the analysis to 'file' file name do: a.saveAna
lysis(file) where a is the analysis object.[] 
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[]    \OT1/cmtt/m/n/12 - This code contains a pyrex function for the distance h
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[84]
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[]    \OT1/cmtt/m/n/12 - \OMS/cmsy/m/n/12 j\OT1/cmtt/m/n/12 parameters\OMS/cmsy
/m/n/12 j \OT1/cmtt/m/n/12 -- a dictionnary of the input parameters, or 'None' 
to set up the analysis without parameters.[] 
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[]        \OT1/cmtt/m/n/12 * trajectory  -- a trajectory file name or an instan
ce of MMTK.Trajectory.Trajectory class.[] 
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[]        \OT1/cmtt/m/n/12 * timeinfo    -- a string of the form 'first:last:st
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[]        \OT1/cmtt/m/n/12 * rvalues     -- a string of the form 'rmin:rmax:dr'
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[]        \OT1/cmtt/m/n/12 * group       -- a selection string specifying the g
roups of atoms that will be used to define the points around which[] 
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[]                         \OT1/cmtt/m/n/12 the coordination number will be com
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[85]
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[]        \OT1/cmtt/m/n/12 * subset      -- a selection string specifying the a
toms to consider for the analysis.[] 
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[]        \OT1/cmtt/m/n/12 * deuteration -- a selection string specifying the h
ydrogen atoms whose atomic parameters will be those of the deuterium.[] 
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[]        \OT1/cmtt/m/n/12 * cn          -- the output NetCDF file name. A CDL 
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[]        \OT1/cmtt/m/n/12 * pyroserver  -- a string specifying if Pyro will be
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[]    \OT1/cmtt/m/n/12 - To estimate the analysis do: a.estimateAnalysis() wher
e a is the analysis object.[] 
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lysis(file) where a is the analysis object.[] 
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[]    \OT1/cmtt/m/n/12 - To estimate the analysis do: a.estimateAnalysis() wher
e a is the analysis object.[] 
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lysis(file) where a is the analysis object.[] 
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[]    \OT1/cmtt/m/n/12 - For more details: Kneller, G.R., Calligari, P. Acta Cr
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om3' where 'atom1', 'atom2' and 'atom3' are[] 
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ersion of this file will also be generated with the '.cdl' extension[] 
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used and how to run the analysis.[] 
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e a is the analysis object.[] 
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lysis(file) where a is the analysis object.[] 
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[90]
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) [150]
\openout2 = `nMOLDYN.Core-module.aux'.

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]
\openout2 = `nMOLDYN.Core.Chemistry-module.aux'.

 (./nMOLDYN.Core.Chemistry-module.tex
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[]\OT1/cmtt/m/n/12 This modules implements the functions and procedures that ar
e related to chemistry.[] 
 []


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[]    \OT1/cmtt/m/n/12 * belongToAnAmine  : this function determine whether or 
not \OMS/cmsy/m/n/12 j\OT1/cmtt/m/n/12 atom\OMS/cmsy/m/n/12 j \OT1/cmtt/m/n/12 
is part of an amine group.[] 
 []


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[]    \OT1/cmtt/m/n/12 * belongToAHydroxy : this function determine whether or 
not \OMS/cmsy/m/n/12 j\OT1/cmtt/m/n/12 atom\OMS/cmsy/m/n/12 j \OT1/cmtt/m/n/12 
is part of a hydroxy group.[] 
 []


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[]    \OT1/cmtt/m/n/12 * belongToAMethyl  : this function determine whether or 
not \OMS/cmsy/m/n/12 j\OT1/cmtt/m/n/12 atom\OMS/cmsy/m/n/12 j \OT1/cmtt/m/n/12 
is part of a mathyl group.[] 
 []


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[]    \OT1/cmtt/m/n/12 * belongToAThiol   : this function determine whether or 
not \OMS/cmsy/m/n/12 j\OT1/cmtt/m/n/12 atom\OMS/cmsy/m/n/12 j \OT1/cmtt/m/n/12 
is part of a thiol group.[] 
 []

) [152


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\openout2 = `nMOLDYN.Core.Config-module.aux'.

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[]\OT1/cmtt/m/n/12 @param cfgFilename: if not None, the name of the PREFERENCES
 file to save else the configuration file[] 
 []


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[]        \OT1/cmtt/m/n/12 -$USERPROFILE/Application Data/nMOLDYN/nMOLDYN.ini o
n Windows[] 
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[]\OT1/cmtt/m/n/12 @param config: the configuration to save. By default, the de
fault PREFERENCES stored in[] 
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t be the ones defined in[] 
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[]\OT1/cmtt/m/n/12 Loads a configuration from \OMS/cmsy/m/n/12 j\OT1/cmtt/m/n/1
2 cfgFilename\OMS/cmsy/m/n/12 j \OT1/cmtt/m/n/12 file name and updates \OMS/cms
y/m/n/12 j\OT1/cmtt/m/n/12 config\OMS/cmsy/m/n/12 j \OT1/cmtt/m/n/12 PREFERENCE
S.[] 
 []


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[]\OT1/cmtt/m/n/12 @param cfgFilename: if not None, the name of the PREFERENCES
 file to load else the configuration file[] 
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n Windows[] 
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]
\openout2 = `nMOLDYN.Core.Error-module.aux'.

 (./nMOLDYN.Core.Error-module.tex) [154


]
\openout2 = `nMOLDYN.Core.IOFiles-module.aux'.


(./nMOLDYN.Core.IOFiles-module.tex
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[]    \OT1/cmtt/m/n/12 * TemporaryFile            : creates a temporary file st
roring the evolution of an analysis.[] 
 []

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[]    \OT1/cmtt/m/n/12 * AmberNetCDFConverter     : converts a trajectory from 
Amber \OML/cmm/m/it/12 > \OT1/cmtt/m/n/12 9 to a MMTK NetCDF trajectory.[] 
 []


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[]    \OT1/cmtt/m/n/12 * CHARMMConverter          : converts a trajectory from 
CHARMM to a MMTK NetCDF trajectory.[] 
 []


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[]    \OT1/cmtt/m/n/12 * DL[]POLYConverter         : converts a trajectory from
 DL[]POLY \OML/cmtt/m/n/12 > \OT1/cmtt/m/n/12 9 to a MMTK NetCDF trajectory.[] 

 []


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[]    \OT1/cmtt/m/n/12 * MaterialsStudioConverter : converts a trajectory from 
MaterialsStudio \OML/cmtt/m/n/12 > \OT1/cmtt/m/n/12 9 to a MMTK NetCDF trajecto
ry.[] 
 []


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[]    \OT1/cmtt/m/n/12 * NAMDConverter            : converts a trajectory from 
NAMD to a MMTK NetCDF trajectory.[] 
 []


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[]    \OT1/cmtt/m/n/12 * VASPConverter            : converts a trajectory from 
VASP \OML/cmtt/m/n/12 > \OT1/cmtt/m/n/12 9 to a MMTK NetCDF trajectory.[] 
 []

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] [156] [157] [158] [159] [160] [161]
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\openout2 = `nMOLDYN.Core.Logger-module.aux'.

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[]    \OT1/cmtt/m/n/12 * LogMessage   : displays a logging message of a specifi
ed logging level to the specified logger(s).[] 
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\openout2 = `nMOLDYN.Core.Mathematics-module.aux'.

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[]\OT1/cmtt/m/n/12 This modules implements the mathematics-related classes, fun
ctions and procedures.[] 
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[]    \OT1/cmtt/m/n/12 * differentiate      : performs a numerical differentiat
ion of 1D Numeric array[] 
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[]    \OT1/cmtt/m/n/12 * correlation        : performs the numerical correlatio
n between two 1D Numeric arrays[] 
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[]    \OT1/cmtt/m/n/12 * convolution        : performs the numerical convolutio
n between two 1D Numeric arrays[] 
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[]    \OT1/cmtt/m/n/12 * gaussianWindow     : performs a Gaussian smoothing of 
1D Numeric array.[] 
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[]    \OT1/cmtt/m/n/12 * basisVectors       : computes the basis vectors of the
 simulation cell from a set of values defining its geometry (3 distances and 3 
angles).[] 
 []


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[]    \OT1/cmtt/m/n/12 * randomPointInCircle: returns a vector within a circle 
of radius \OMS/cmsy/m/n/12 j\OT1/cmtt/m/n/12 r\OMS/cmsy/m/n/12 j \OT1/cmtt/m/n/
12 and orthogonal to a given direction.[] 
 []


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[]    \OT1/cmtt/m/n/12 * randomDirection2D  : returns a normalized vector gener
ated from a unit circle orthogonal to a given direction.[] 
 []


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[]    \OT1/cmtt/m/n/12 * randomPlane2D      : generates a normalized random q-v
ector on a plane defined by vect1, vect2.[] 
 []


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[]    \OT1/cmtt/m/n/12 * qVectorGenerator   : sets up and returns a set of q ve
ctors generated from different user-defined parameters.[] 
 []


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[]    \OT1/cmtt/m/n/12 * sphericalHarmonics : calculates the spherical function
s Y from a set of j, m, n Wigner indexes[] 
 []

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] [171] [172] [173] [174] [175]) [176]
\openout2 = `nMOLDYN.Core.Misc-module.aux'.

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[]\OT1/cmtt/m/n/12 This modules implements the functions and procedures that ca
n not be classified anywhere else in[] 
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[]    \OT1/cmtt/m/n/12 * findNestedDirectories : parses recursively a directory
 tree appending each nested subdirectory found in a list.[] 
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[]    \OT1/cmtt/m/n/12 * findExecutable        : searches for an executable in 
OS dependant classical paths.[] 
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\openout2 = `nMOLDYN.Core.Preferences-module.aux'.

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\openout2 = `nMOLDYN.GUI-module.aux'.


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[]\OT1/cmr/bx/n/12 GeneralInformationsDialog\OT1/cmr/m/n/12 : This mod-ules im-
ple-ments I\OMS/cmsy/m/n/12 f\OT1/cmr/m/n/12 Help--\OML/cmm/m/it/12 >\OT1/cmr/m
/n/12 About nMOL-DYN\OMS/cmsy/m/n/12 g
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\openout2 = `nMOLDYN.GUI.ASCIIToNetCDFConversionDialog-module.aux'.

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[]    \OT1/cmtt/m/n/12 * ASCIIToNetCDFConversionDialog: creates I\OMS/cmsy/m/n/
12 f\OT1/cmtt/m/n/12 File--\OML/cmm/m/it/12 >\OT1/cmtt/m/n/12 Convert ASCII to 
NetCDF\OMS/cmsy/m/n/12 g \OT1/cmtt/m/n/12 dialog used to[] 
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\openout2 = `nMOLDYN.GUI.AnalysisBenchmarkDialog-module.aux'.

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[]    \OT1/cmtt/m/n/12 * AnalysisBenchmarkDialog: creates I\OMS/cmsy/m/n/12 f\O
T1/cmtt/m/n/12 Help--\OML/cmm/m/it/12 >\OT1/cmtt/m/n/12 nMOLDYN benchmark\OMS/c
msy/m/n/12 g \OT1/cmtt/m/n/12 dialog used to run the stability tests[] 
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\openout2 = `nMOLDYN.GUI.AnalysisDialog-module.aux'.

 (./nMOLDYN.GUI.AnalysisDialog-module.tex
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[]    \OT1/cmtt/m/n/12 * AnalysisDialog: creates I\OMS/cmsy/m/n/12 f\OT1/cmtt/m
/n/12 Analysis--\OML/cmm/m/it/12 >\OT1/cmtt/m/n/12 selected analysis\OMS/cmsy/m
/n/12 g \OT1/cmtt/m/n/12 dialog used to setup and/orrun[] 
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\openout2 = `nMOLDYN.GUI.AnimationDialog-module.aux'.

 (./nMOLDYN.GUI.AnimationDialog-module.tex
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[]    \OT1/cmtt/m/n/12 * AnimationDialog: creates I\OMS/cmsy/m/n/12 f\OT1/cmtt/
m/n/12 View--\OML/cmm/m/it/12 >\OT1/cmtt/m/n/12 Animation\OMS/cmsy/m/n/12 g \OT
1/cmtt/m/n/12 dialog used to view an animation of a trajectory.[] 
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[] 
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\OT1/cmr/m/n/12 ure(), deletecom-mand(), event[]add(), event[]delete(), event[]
generate(), event[]info(),
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\OT1/cmr/m/n/12 fo-cus(), fo-cus[]displayof(), fo-cus[]force(), fo-cus[]get(), 
fo-cus[]lastfor(), fo-cus[]set(), get-
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\OT1/cmr/m/n/12 grab[]status(), grid[]bbox(), grid[]columnconfigure(), grid[]lo
cation(), grid[]propagate(),
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\OT1/cmr/m/n/12 grid[]rowconfigure(), grid[]size(), grid[]slaves(), im-age[]nam
es(), im-age[]types(), keys(),
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\OT1/cmr/m/n/12 lift(), lower(), main-loop(), name-towid-get(), op-tion[]add(),
 op-tion[]clear(), op-tion[]get(),
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\OT1/cmr/m/n/12 op-tion[]readfile(), pack[]propagate(), pack[]slaves(), place[]
slaves(), prop-a-gate(), quit(),
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\OT1/cmr/m/n/12 tk[]focusFollowsMouse(), tk[]focusNext(), tk[]focusPrev(), tk[]
menuBar(), tk[]setPalette(),
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\OT1/cmr/m/n/12 date[]idletasks(), wait[]variable(), wait[]visibility(), wait[]
window(), wait-var(), winfo[]atom(),
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\OT1/cmr/m/n/12 winfo[]atomname(), winfo[]cells(), winfo[]children(), winfo[]cl
ass(), winfo[]colormapfull(),
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\OT1/cmr/m/n/12 winfo[]containing(), winfo[]depth(), winfo[]exists(), winfo[]fp
ixels(), winfo[]geometry(),
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\OT1/cmr/m/n/12 winfo[]height(), winfo[]id(), winfo[]interps(), winfo[]ismapped
(), winfo[]manager(), winfo[]name(),
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\OT1/cmr/m/n/12 winfo[]parent(), winfo[]pathname(), winfo[]pixels(), winfo[]poi
nterx(), winfo[]pointerxy(),
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\OT1/cmr/m/n/12 winfo[]rooty(), winfo[]screen(), winfo[]screencells(), winfo[]s
creendepth(), winfo[]screenheight(),
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isual(), winfo[]screenwidth(),
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[190]
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\OT1/cmr/m/n/12 draw(), wm[]aspect(), wm[]attributes(), wm[]client(), wm[]color
mapwindows(), wm[]command(),
 []


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\OT1/cmr/m/n/12 wm[]deiconify(), wm[]focusmodel(), wm[]frame(), wm[]geometry(),
 wm[]grid(), wm[]group(),
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\OT1/cmr/m/n/12 wm[]iconbitmap(), wm[]iconify(), wm[]iconmask(), wm[]iconname()
, wm[]iconposition(),
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\OT1/cmr/m/n/12 wm[]iconwindow(), wm[]maxsize(), wm[]minsize(), wm[]overridered
irect(), wm[]positionfrom(),
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\OT1/cmr/m/n/12 wm[]protocol(), wm[]resizable(), wm[]sizefrom(), wm[]state(), w
m[]title(), wm[]transient(),
 []

) [191]
\openout2 = `nMOLDYN.GUI.CheckJobsStatusDialog-module.aux'.

 (./nMOLDYN.GUI.CheckJobsStatusDialog-module.tex
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[]    \OT1/cmtt/m/n/12 * CheckJobsStatusDialog: creates I\OMS/cmsy/m/n/12 f\OT1
/cmtt/m/n/12 Help--\OML/cmm/m/it/12 >\OT1/cmtt/m/n/12 Check job status\OMS/cmsy
/m/n/12 g \OT1/cmtt/m/n/12 dialog used to[] 
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\OT1/cmr/m/n/12 ure(), deletecom-mand(), event[]add(), event[]delete(), event[]
generate(), event[]info(),
 []


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\OT1/cmr/m/n/12 fo-cus(), fo-cus[]displayof(), fo-cus[]force(), fo-cus[]get(), 
fo-cus[]lastfor(), fo-cus[]set(), get-
 []


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\OT1/cmr/m/n/12 grab[]status(), grid[]bbox(), grid[]columnconfigure(), grid[]lo
cation(), grid[]propagate(),
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\OT1/cmr/m/n/12 grid[]rowconfigure(), grid[]size(), grid[]slaves(), im-age[]nam
es(), im-age[]types(), keys(),
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\OT1/cmr/m/n/12 lift(), lower(), main-loop(), name-towid-get(), op-tion[]add(),
 op-tion[]clear(), op-tion[]get(),
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slaves(), prop-a-gate(), quit(),
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\OT1/cmr/m/n/12 tk[]focusFollowsMouse(), tk[]focusNext(), tk[]focusPrev(), tk[]
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 []


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\OT1/cmr/m/n/12 date[]idletasks(), wait[]variable(), wait[]visibility(), wait[]
window(), wait-var(), winfo[]atom(),
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\OT1/cmr/m/n/12 winfo[]atomname(), winfo[]cells(), winfo[]children(), winfo[]cl
ass(), winfo[]colormapfull(),
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\OT1/cmr/m/n/12 winfo[]containing(), winfo[]depth(), winfo[]exists(), winfo[]fp
ixels(), winfo[]geometry(),
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\OT1/cmr/m/n/12 winfo[]height(), winfo[]id(), winfo[]interps(), winfo[]ismapped
(), winfo[]manager(), winfo[]name(),
 []


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\OT1/cmr/m/n/12 winfo[]parent(), winfo[]pathname(), winfo[]pixels(), winfo[]poi
nterx(), winfo[]pointerxy(),
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\OT1/cmr/m/n/12 winfo[]rooty(), winfo[]screen(), winfo[]screencells(), winfo[]s
creendepth(), winfo[]screenheight(),
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\OT1/cmr/m/n/12 winfo[]screenmmheight(), winfo[]screenmmwidth(), winfo[]screenv
isual(), winfo[]screenwidth(),
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[193]
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\OT1/cmr/m/n/12 draw(), wm[]aspect(), wm[]attributes(), wm[]client(), wm[]color
mapwindows(), wm[]command(),
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\OT1/cmr/m/n/12 wm[]deiconify(), wm[]focusmodel(), wm[]frame(), wm[]geometry(),
 wm[]grid(), wm[]group(),
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\OT1/cmr/m/n/12 wm[]iconbitmap(), wm[]iconify(), wm[]iconmask(), wm[]iconname()
, wm[]iconposition(),
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\OT1/cmr/m/n/12 wm[]iconwindow(), wm[]maxsize(), wm[]minsize(), wm[]overridered
irect(), wm[]positionfrom(),
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\OT1/cmr/m/n/12 wm[]protocol(), wm[]resizable(), wm[]sizefrom(), wm[]state(), w
m[]title(), wm[]transient(),
 []

) [194]
\openout2 = `nMOLDYN.GUI.GeneralInformationsDialog-module.aux'.

 (./nMOLDYN.GUI.GeneralInformationsDialog-module.tex
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[] 
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\OT1/cmr/m/n/12 ure(), deletecom-mand(), event[]add(), event[]delete(), event[]
generate(), event[]info(),
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\OT1/cmr/m/n/12 fo-cus(), fo-cus[]displayof(), fo-cus[]force(), fo-cus[]get(), 
fo-cus[]lastfor(), fo-cus[]set(), get-
 []


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\OT1/cmr/m/n/12 grab[]status(), grid[]bbox(), grid[]columnconfigure(), grid[]lo
cation(), grid[]propagate(),
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\OT1/cmr/m/n/12 grid[]rowconfigure(), grid[]size(), grid[]slaves(), im-age[]nam
es(), im-age[]types(), keys(),
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\OT1/cmr/m/n/12 lift(), lower(), main-loop(), name-towid-get(), op-tion[]add(),
 op-tion[]clear(), op-tion[]get(),
 []


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\OT1/cmr/m/n/12 op-tion[]readfile(), pack[]propagate(), pack[]slaves(), place[]
slaves(), prop-a-gate(), quit(),
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\OT1/cmr/m/n/12 tk[]focusFollowsMouse(), tk[]focusNext(), tk[]focusPrev(), tk[]
menuBar(), tk[]setPalette(),
 []


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\OT1/cmr/m/n/12 date[]idletasks(), wait[]variable(), wait[]visibility(), wait[]
window(), wait-var(), winfo[]atom(),
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\OT1/cmr/m/n/12 winfo[]atomname(), winfo[]cells(), winfo[]children(), winfo[]cl
ass(), winfo[]colormapfull(),
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\OT1/cmr/m/n/12 winfo[]containing(), winfo[]depth(), winfo[]exists(), winfo[]fp
ixels(), winfo[]geometry(),
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\OT1/cmr/m/n/12 winfo[]height(), winfo[]id(), winfo[]interps(), winfo[]ismapped
(), winfo[]manager(), winfo[]name(),
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\OT1/cmr/m/n/12 winfo[]parent(), winfo[]pathname(), winfo[]pixels(), winfo[]poi
nterx(), winfo[]pointerxy(),
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\OT1/cmr/m/n/12 winfo[]rooty(), winfo[]screen(), winfo[]screencells(), winfo[]s
creendepth(), winfo[]screenheight(),
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\OT1/cmr/m/n/12 winfo[]screenmmheight(), winfo[]screenmmwidth(), winfo[]screenv
isual(), winfo[]screenwidth(),
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[196]
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\OT1/cmr/m/n/12 draw(), wm[]aspect(), wm[]attributes(), wm[]client(), wm[]color
mapwindows(), wm[]command(),
 []


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\OT1/cmr/m/n/12 wm[]deiconify(), wm[]focusmodel(), wm[]frame(), wm[]geometry(),
 wm[]grid(), wm[]group(),
 []


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\OT1/cmr/m/n/12 wm[]iconbitmap(), wm[]iconify(), wm[]iconmask(), wm[]iconname()
, wm[]iconposition(),
 []


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\OT1/cmr/m/n/12 wm[]iconwindow(), wm[]maxsize(), wm[]minsize(), wm[]overridered
irect(), wm[]positionfrom(),
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\OT1/cmr/m/n/12 wm[]protocol(), wm[]resizable(), wm[]sizefrom(), wm[]state(), w
m[]title(), wm[]transient(),
 []

) [197]
\openout2 = `nMOLDYN.GUI.HTMLReader-module.aux'.

 (./nMOLDYN.GUI.HTMLReader-module.tex) [198


]
\openout2 = `nMOLDYN.GUI.HTMLReader.mfxtools-module.aux'.


(./nMOLDYN.GUI.HTMLReader.mfxtools-module.tex) [199


]
\openout2 = `nMOLDYN.GUI.HTMLReader.mfxutil-module.aux'.


(./nMOLDYN.GUI.HTMLReader.mfxutil-module.tex [200


]
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[] 
 []

[201]) [202] [203]
\openout2 = `nMOLDYN.GUI.HTMLReader.tkconst-module.aux'.

 (./nMOLDYN.GUI.HTMLReader.tkconst-module.tex) [204


]
\openout2 = `nMOLDYN.GUI.HTMLReader.tkfont-module.aux'.


(./nMOLDYN.GUI.HTMLReader.tkfont-module.tex) [205


]
\openout2 = `nMOLDYN.GUI.HTMLReader.tkhtml-module.aux'.


(./nMOLDYN.GUI.HTMLReader.tkhtml-module.tex
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et(), im-age[]cget(), im-age[]configure(),
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\OT1/cmr/m/n/12 mark[]next(), mark[]previous(), mark[]set(), mark[]unset(), sca
n[]dragto(), scan[]mark(),
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\OT1/cmr/m/n/12 search(), see(), tag[]add(), tag[]bind(), tag[]cget(), tag[]con
fig(), tag[]configure(), tag[]delete(),
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\OT1/cmr/m/n/12 tag[]lower(), tag[]names(), tag[]nextrange(), tag[]prevrange(),
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\OT1/cmr/m/n/12 tag[]remove(), tag[]unbind(), tk[]textBackspace(), tk[]textInde
xCloser(), tk[]textResetAnchor(),
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\OT1/cmr/m/n/12 tk[]textSelectTo(), win-dow[]cget(), win-dow[]config(), win-dow
[]configure(), win-dow[]create(),
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[][][]\OT1/cmr/m/n/12 getitem[][](), [][]setitem[][](), [][]str[][](), af-ter()
, af-ter[]cancel(), af-ter[]idle(), bell(), bind(),
 []


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\OT1/cmr/m/n/12 get-var(), grab[]current(), grab[]release(), grab[]set(), grab[
]set[]global(), grab[]status(),
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\OT1/cmr/m/n/12 grid[]bbox(), grid[]columnconfigure(), grid[]location(), grid[]
propagate(), grid[]rowconfigure(),
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\OT1/cmr/m/n/12 towid-get(), op-tion[]add(), op-tion[]clear(), op-tion[]get(), 
op-tion[]readfile(), pack[]propagate(),
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\OT1/cmr/m/n/12 tion[]clear(), se-lec-tion[]get(), se-lec-tion[]handle(), se-le
c-tion[]own(), se-lec-tion[]own[]get(),
 []


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\OT1/cmr/m/n/12 send(), set-var(), size(), slaves(), tk[]bisque(), tk[]focusFol
lowsMouse(), tk[]focusNext(),
 []


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\OT1/cmr/m/n/12 tk[]focusPrev(), tk[]menuBar(), tk[]setPalette(), tk[]strictMot
if(), tkraise(), un-bind(),
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\OT1/cmr/m/n/12 un-bind[]all(), un-bind[]class(), up-date(), up-date[]idletasks
(), wait[]variable(), wait[]visibility(),
 []


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\OT1/cmr/m/n/12 wait[]window(), wait-var(), winfo[]atom(), winfo[]atomname(), w
info[]cells(), winfo[]children(),
 []


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\OT1/cmr/m/n/12 winfo[]class(), winfo[]colormapfull(), winfo[]containing(), win
fo[]depth(), winfo[]exists(),
 []


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\OT1/cmr/m/n/12 winfo[]fpixels(), winfo[]geometry(), winfo[]height(), winfo[]id
(), winfo[]interps(), winfo[]ismapped(),
 []


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\OT1/cmr/m/n/12 winfo[]pointerx(), winfo[]pointerxy(), winfo[]pointery(), winfo
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\OT1/cmr/m/n/12 winfo[]rgb(), winfo[]rootx(), winfo[]rooty(), winfo[]screen(), 
winfo[]screencells(), winfo[]screendepth(),
 []


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\OT1/cmr/m/n/12 winfo[]screenheight(), winfo[]screenmmheight(), winfo[]screenmm
width(), winfo[]screenvisual(),
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\OT1/cmr/m/n/12 winfo[]screenwidth(), winfo[]server(), winfo[]toplevel(), winfo
[]viewable(), winfo[]visual(),
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[208]
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xt(Section
 []


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\OT1/cmr/m/n/12 edit[]redo(), edit[]reset(), edit[]separator(), edit[]undo(), g
et(), im-age[]cget(), im-age[]configure(),
 []


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\OT1/cmr/m/n/12 mark[]next(), mark[]previous(), mark[]set(), mark[]unset(), sca
n[]dragto(), scan[]mark(),
 []


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\OT1/cmr/m/n/12 search(), see(), tag[]add(), tag[]bind(), tag[]cget(), tag[]con
fig(), tag[]configure(), tag[]delete(),
 []


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\OT1/cmr/m/n/12 tag[]lower(), tag[]names(), tag[]nextrange(), tag[]prevrange(),
 tag[]raise(), tag[]ranges(),
 []


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\OT1/cmr/m/n/12 tag[]remove(), tag[]unbind(), tk[]textBackspace(), tk[]textInde
xCloser(), tk[]textResetAnchor(),
 []


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\OT1/cmr/m/n/12 tk[]textSelectTo(), win-dow[]cget(), win-dow[]config(), win-dow
[]configure(), win-dow[]create(),
 []

[211]
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[][][]\OT1/cmr/m/n/12 getitem[][](), [][]setitem[][](), [][]str[][](), af-ter()
, af-ter[]cancel(), af-ter[]idle(), bell(), bind(),
 []


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\OT1/cmr/m/n/12 get-var(), grab[]current(), grab[]release(), grab[]set(), grab[
]set[]global(), grab[]status(),
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\OT1/cmr/m/n/12 grid[]bbox(), grid[]columnconfigure(), grid[]location(), grid[]
propagate(), grid[]rowconfigure(),
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\OT1/cmr/m/n/12 towid-get(), op-tion[]add(), op-tion[]clear(), op-tion[]get(), 
op-tion[]readfile(), pack[]propagate(),
 []


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\OT1/cmr/m/n/12 tion[]clear(), se-lec-tion[]get(), se-lec-tion[]handle(), se-le
c-tion[]own(), se-lec-tion[]own[]get(),
 []


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\OT1/cmr/m/n/12 send(), set-var(), size(), slaves(), tk[]bisque(), tk[]focusFol
lowsMouse(), tk[]focusNext(),
 []


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\OT1/cmr/m/n/12 tk[]focusPrev(), tk[]menuBar(), tk[]setPalette(), tk[]strictMot
if(), tkraise(), un-bind(),
 []


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\OT1/cmr/m/n/12 un-bind[]all(), un-bind[]class(), up-date(), up-date[]idletasks
(), wait[]variable(), wait[]visibility(),
 []


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\OT1/cmr/m/n/12 wait[]window(), wait-var(), winfo[]atom(), winfo[]atomname(), w
info[]cells(), winfo[]children(),
 []


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\OT1/cmr/m/n/12 winfo[]class(), winfo[]colormapfull(), winfo[]containing(), win
fo[]depth(), winfo[]exists(),
 []


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\OT1/cmr/m/n/12 winfo[]fpixels(), winfo[]geometry(), winfo[]height(), winfo[]id
(), winfo[]interps(), winfo[]ismapped(),
 []


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\OT1/cmr/m/n/12 winfo[]pointerx(), winfo[]pointerxy(), winfo[]pointery(), winfo
[]reqheight(), winfo[]reqwidth(),
 []


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\OT1/cmr/m/n/12 winfo[]rgb(), winfo[]rootx(), winfo[]rooty(), winfo[]screen(), 
winfo[]screencells(), winfo[]screendepth(),
 []


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\OT1/cmr/m/n/12 winfo[]screenheight(), winfo[]screenmmheight(), winfo[]screenmm
width(), winfo[]screenvisual(),
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\OT1/cmr/m/n/12 winfo[]screenwidth(), winfo[]server(), winfo[]toplevel(), winfo
[]viewable(), winfo[]visual(),
 []


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\OT1/cmr/m/n/12 winfo[]visualid(), winfo[]visualsavailable(), winfo[]vrootheigh
t(), winfo[]vrootwidth(),
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[] 
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[212] [213]
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\OT1/cmr/m/n/12 do[]li(), do[]link(), do[]meta(), do[]nextid(), do[]p(), do[]pl
aintext(), end[]a(), end[]address(),
 []


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\OT1/cmr/m/n/12 end[]html(), end[]i(), end[]kbd(), end[]listing(), end[]menu(),
 end[]ol(), end[]pre(), end[]samp(),
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\OT1/cmr/m/n/12 dle[]data(), re-set(), save[]bgn(), save[]end(), start[]a(), st
art[]address(), start[]b(), start[]blockquote(),
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\OT1/cmr/m/n/12 start[]body(), start[]cite(), start[]code(), start[]dir(), star
t[]dl(), start[]em(), start[]h1(),
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\OT1/cmr/m/n/12 start[]i(), start[]kbd(), start[]listing(), start[]menu(), star
t[]ol(), start[]pre(), start[]samp(),
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\OT1/cmr/m/n/12 start[]strong(), start[]title(), start[]tt(), start[]ul(), star
t[]var(), start[]xmp(), un-known[]endtag(),
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[]\OT1/cmr/m/n/12 close(), con-vert[]charref(), con-vert[]codepoint(), con-vert
[]entityref(), feed(), fin-ish[]endtag(),
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\OT1/cmr/m/n/12 fin-ish[]shorttag(), fin-ish[]starttag(), get[]starttag[]text()
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[]\OT1/cmr/m/n/12 getpos(), parse[]comment(), parse[]declaration(), parse[]mark
ed[]section(), un-known[]decl(),
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[215]) [216] [217]
\openout2 = `nMOLDYN.GUI.HTMLReader.tkinit-module.aux'.

 (./nMOLDYN.GUI.HTMLReader.tkinit-module.tex [218


]) [219]
\openout2 = `nMOLDYN.GUI.HTMLReader.tkutil-module.aux'.


(./nMOLDYN.GUI.HTMLReader.tkutil-module.tex) [220


]
\openout2 = `nMOLDYN.GUI.HTMLReader.tkwidget-module.aux'.


(./nMOLDYN.GUI.HTMLReader.tkwidget-module.tex
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[]\OT1/cmr/bx/it/12 Inherited from nMOL-DYN.GUI.HTMLReader.tkwidget.MfxDialog(S
ection [][][][][][]) 
 []


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[] 
 []

[222]
Overfull \hbox (14.67714pt too wide) in paragraph at lines 318--319
[]\OT1/cmr/bx/it/12 Inherited from nMOL-DYN.GUI.HTMLReader.tkwidget.MfxDialog(S
ection [][][][][][]) 
 []


Overfull \hbox (248.57906pt too wide) in paragraph at lines 357--387
[] 
 []


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[]\OT1/cmr/bx/it/12 Inherited from nMOL-DYN.GUI.HTMLReader.tkwidget.MfxSimpleSl
ider(Section
 []


Overfull \hbox (14.67714pt too wide) in paragraph at lines 414--415
[]\OT1/cmr/bx/it/12 Inherited from nMOL-DYN.GUI.HTMLReader.tkwidget.MfxDialog(S
ection [][][][][][]) 
 []

[223] [224]) [225]
\openout2 = `nMOLDYN.GUI.HTMLReader.util-module.aux'.

 (./nMOLDYN.GUI.HTMLReader.util-module.tex [226


]) [227]
\openout2 = `nMOLDYN.GUI.HTMLReader.version-module.aux'.


(./nMOLDYN.GUI.HTMLReader.version-module.tex) [228


]
\openout2 = `nMOLDYN.GUI.MainDialog-module.aux'.


(./nMOLDYN.GUI.MainDialog-module.tex
Overfull \hbox (123.04527pt too wide) in paragraph at lines 21--21
[]    \OT1/cmtt/m/n/12 * MainDialog: The class that defines the nMOLDYN GUI mai
n window and its associated actions.[] 
 []

[229


] [230]
Overfull \hbox (1.55647pt too wide) in paragraph at lines 465--466
\OT1/cmr/m/n/12 ure(), deletecom-mand(), event[]add(), event[]delete(), event[]
generate(), event[]info(),
 []


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\OT1/cmr/m/n/12 fo-cus(), fo-cus[]displayof(), fo-cus[]force(), fo-cus[]get(), 
fo-cus[]lastfor(), fo-cus[]set(), get-
 []


Overfull \hbox (9.89888pt too wide) in paragraph at lines 465--466
\OT1/cmr/m/n/12 grab[]status(), grid[]bbox(), grid[]columnconfigure(), grid[]lo
cation(), grid[]propagate(),
 []


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\OT1/cmr/m/n/12 grid[]rowconfigure(), grid[]size(), grid[]slaves(), im-age[]nam
es(), im-age[]types(), keys(),
 []


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\OT1/cmr/m/n/12 lift(), lower(), main-loop(), name-towid-get(), op-tion[]add(),
 op-tion[]clear(), op-tion[]get(),
 []


Overfull \hbox (9.65083pt too wide) in paragraph at lines 465--466
\OT1/cmr/m/n/12 op-tion[]readfile(), pack[]propagate(), pack[]slaves(), place[]
slaves(), prop-a-gate(), quit(),
 []


Overfull \hbox (24.17793pt too wide) in paragraph at lines 465--466
\OT1/cmr/m/n/12 tk[]focusFollowsMouse(), tk[]focusNext(), tk[]focusPrev(), tk[]
menuBar(), tk[]setPalette(),
 []


Overfull \hbox (36.98888pt too wide) in paragraph at lines 465--466
\OT1/cmr/m/n/12 date[]idletasks(), wait[]variable(), wait[]visibility(), wait[]
window(), wait-var(), winfo[]atom(),
 []


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\OT1/cmr/m/n/12 winfo[]atomname(), winfo[]cells(), winfo[]children(), winfo[]cl
ass(), winfo[]colormapfull(),
 []


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\OT1/cmr/m/n/12 winfo[]containing(), winfo[]depth(), winfo[]exists(), winfo[]fp
ixels(), winfo[]geometry(),
 []


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\OT1/cmr/m/n/12 winfo[]height(), winfo[]id(), winfo[]interps(), winfo[]ismapped
(), winfo[]manager(), winfo[]name(),
 []


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\OT1/cmr/m/n/12 winfo[]parent(), winfo[]pathname(), winfo[]pixels(), winfo[]poi
nterx(), winfo[]pointerxy(),
 []


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\OT1/cmr/m/n/12 winfo[]rooty(), winfo[]screen(), winfo[]screencells(), winfo[]s
creendepth(), winfo[]screenheight(),
 []


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\OT1/cmr/m/n/12 winfo[]screenmmheight(), winfo[]screenmmwidth(), winfo[]screenv
isual(), winfo[]screenwidth(),
 []

[231]
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\OT1/cmr/m/n/12 draw(), wm[]aspect(), wm[]attributes(), wm[]client(), wm[]color
mapwindows(), wm[]command(),
 []


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\OT1/cmr/m/n/12 wm[]deiconify(), wm[]focusmodel(), wm[]frame(), wm[]geometry(),
 wm[]grid(), wm[]group(),
 []


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\OT1/cmr/m/n/12 wm[]iconbitmap(), wm[]iconify(), wm[]iconmask(), wm[]iconname()
, wm[]iconposition(),
 []


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\OT1/cmr/m/n/12 wm[]iconwindow(), wm[]maxsize(), wm[]minsize(), wm[]overridered
irect(), wm[]positionfrom(),
 []


Overfull \hbox (23.3329pt too wide) in paragraph at lines 471--472
\OT1/cmr/m/n/12 wm[]protocol(), wm[]resizable(), wm[]sizefrom(), wm[]state(), w
m[]title(), wm[]transient(),
 []

) [232]
\openout2 = `nMOLDYN.GUI.NetCDFToASCIIConversionDialog-module.aux'.

 (./nMOLDYN.GUI.NetCDFToASCIIConversionDialog-module.tex
Overfull \hbox (107.13408pt too wide) in paragraph at lines 21--21
[]    \OT1/cmtt/m/n/12 * NetCDFToASCIIConversionDialog: creates I\OMS/cmsy/m/n/
12 f\OT1/cmtt/m/n/12 File--\OML/cmm/m/it/12 >\OT1/cmtt/m/n/12 Convert NetCDF to
 ASCII\OMS/cmsy/m/n/12 g \OT1/cmtt/m/n/12 dialog used to[] 
 []


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[] 
 []

[233


]
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[]\OT1/cmtt/m/n/12 This method opens a NetCDF file and updates the dialog with 
the data read from that file.[] 
 []

) [234]
\openout2 = `nMOLDYN.GUI.PDBSnapshotGeneratorDialog-module.aux'.

 (./nMOLDYN.GUI.PDBSnapshotGeneratorDialog-module.tex
Overfull \hbox (33.03404pt too wide) in paragraph at lines 21--21
[]    \OT1/cmtt/m/n/12 * PDBSnapshotGeneratorDialog: creates I\OMS/cmsy/m/n/12 
f\OT1/cmtt/m/n/12 File--\OML/cmm/m/it/12 >\OT1/cmtt/m/n/12 Frame snapshot\OMS/c
msy/m/n/12 g \OT1/cmtt/m/n/12 dialog used to[] 
 []


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[] 
 []

[235


]) [236]
\openout2 = `nMOLDYN.GUI.PlotNetCDFVariableDialog-module.aux'.

 (./nMOLDYN.GUI.PlotNetCDFVariableDialog-module.tex
Overfull \hbox (131.83409pt too wide) in paragraph at lines 22--22
[]    \OT1/cmtt/m/n/12 * ASCIIToNetCDFConversionDialog: creates I\OMS/cmsy/m/n/
12 f\OT1/cmtt/m/n/12 View--\OML/cmm/m/it/12 >\OT1/cmtt/m/n/12 Plot\OMS/cmsy/m/n
/12 g \OT1/cmtt/m/n/12 dialog used to plot NetCDF variables.[] 
 []


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[] 
 []

[237


]
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[] 
 []

[238] [239]
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[]\OT1/cmtt/m/n/12 This method opens a NetCDF file and updates the dialog with 
the data read from that file.[] 
 []

) [240]
\openout2 = `nMOLDYN.GUI.PreferencesDialog-module.aux'.

 (./nMOLDYN.GUI.PreferencesDialog-module.tex
Overfull \hbox (212.10913pt too wide) in paragraph at lines 21--21
[]    \OT1/cmtt/m/n/12 * PreferencesDialog: creates I\OMS/cmsy/m/n/12 f\OT1/cmt
t/m/n/12 File--\OML/cmm/m/it/12 >\OT1/cmtt/m/n/12 Preferences\OMS/cmsy/m/n/12 g
 \OT1/cmtt/m/n/12 dialog used to to set up nMOLDYN PREFERENCES variables.[] 
 []


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[] 
 []

[241


]) [242]
\openout2 = `nMOLDYN.GUI.PyroServerDialog-module.aux'.

 (./nMOLDYN.GUI.PyroServerDialog-module.tex
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[] 
 []

[243


]
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[]\OT1/cmtt/m/n/12 Reads a pyro server configuration file that contains informa
tion about the nodes of the cluster that will[] 
 []


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[]\OT1/cmtt/m/n/12 A pyro server configuration file is an ASCII file that conta
ins either:[] 
 []


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[]    \OT1/cmtt/m/n/12 -a single line 'host node-name-1 node-name-2 node-name-3
...' for an explicit declaration of[] 
 []


Overfull \hbox (243.12576pt too wide) in paragraph at lines 250--250
[]        \OT1/cmtt/m/n/12 *'number number1-number2 number3-number4 ...' for a 
contracted declaration of the nodes that will[] 
 []


Overfull \hbox (88.75069pt too wide) in paragraph at lines 251--251
[]        \OT1/cmtt/m/n/12 be checked. E.g. conveneient if the node names are n
ode1 node2 node3 ...[] 
 []


Overfull \hbox (1.55647pt too wide) in paragraph at lines 323--324
\OT1/cmr/m/n/12 ure(), deletecom-mand(), event[]add(), event[]delete(), event[]
generate(), event[]info(),
 []


Overfull \hbox (1.73924pt too wide) in paragraph at lines 323--324
\OT1/cmr/m/n/12 fo-cus(), fo-cus[]displayof(), fo-cus[]force(), fo-cus[]get(), 
fo-cus[]lastfor(), fo-cus[]set(), get-
 []


Overfull \hbox (9.89888pt too wide) in paragraph at lines 323--324
\OT1/cmr/m/n/12 grab[]status(), grid[]bbox(), grid[]columnconfigure(), grid[]lo
cation(), grid[]propagate(),
 []


Overfull \hbox (4.21977pt too wide) in paragraph at lines 323--324
\OT1/cmr/m/n/12 grid[]rowconfigure(), grid[]size(), grid[]slaves(), im-age[]nam
es(), im-age[]types(), keys(),
 []


Overfull \hbox (13.9069pt too wide) in paragraph at lines 323--324
\OT1/cmr/m/n/12 lift(), lower(), main-loop(), name-towid-get(), op-tion[]add(),
 op-tion[]clear(), op-tion[]get(),
 []


Overfull \hbox (9.65083pt too wide) in paragraph at lines 323--324
\OT1/cmr/m/n/12 op-tion[]readfile(), pack[]propagate(), pack[]slaves(), place[]
slaves(), prop-a-gate(), quit(),
 []


Overfull \hbox (24.17793pt too wide) in paragraph at lines 323--324
\OT1/cmr/m/n/12 tk[]focusFollowsMouse(), tk[]focusNext(), tk[]focusPrev(), tk[]
menuBar(), tk[]setPalette(),
 []


Overfull \hbox (36.98888pt too wide) in paragraph at lines 323--324
\OT1/cmr/m/n/12 date[]idletasks(), wait[]variable(), wait[]visibility(), wait[]
window(), wait-var(), winfo[]atom(),
 []


Overfull \hbox (16.81825pt too wide) in paragraph at lines 323--324
\OT1/cmr/m/n/12 winfo[]atomname(), winfo[]cells(), winfo[]children(), winfo[]cl
ass(), winfo[]colormapfull(),
 []


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\OT1/cmr/m/n/12 winfo[]containing(), winfo[]depth(), winfo[]exists(), winfo[]fp
ixels(), winfo[]geometry(),
 []


Overfull \hbox (57.14644pt too wide) in paragraph at lines 323--324
\OT1/cmr/m/n/12 winfo[]height(), winfo[]id(), winfo[]interps(), winfo[]ismapped
(), winfo[]manager(), winfo[]name(),
 []


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\OT1/cmr/m/n/12 winfo[]parent(), winfo[]pathname(), winfo[]pixels(), winfo[]poi
nterx(), winfo[]pointerxy(),
 []


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\OT1/cmr/m/n/12 winfo[]rooty(), winfo[]screen(), winfo[]screencells(), winfo[]s
creendepth(), winfo[]screenheight(),
 []


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\OT1/cmr/m/n/12 winfo[]screenmmheight(), winfo[]screenmmwidth(), winfo[]screenv
isual(), winfo[]screenwidth(),
 []

[244]
Overfull \hbox (56.89839pt too wide) in paragraph at lines 329--330
\OT1/cmr/m/n/12 draw(), wm[]aspect(), wm[]attributes(), wm[]client(), wm[]color
mapwindows(), wm[]command(),
 []


Overfull \hbox (32.92863pt too wide) in paragraph at lines 329--330
\OT1/cmr/m/n/12 wm[]deiconify(), wm[]focusmodel(), wm[]frame(), wm[]geometry(),
 wm[]grid(), wm[]group(),
 []


Overfull \hbox (14.79466pt too wide) in paragraph at lines 329--330
\OT1/cmr/m/n/12 wm[]iconbitmap(), wm[]iconify(), wm[]iconmask(), wm[]iconname()
, wm[]iconposition(),
 []


Overfull \hbox (48.47765pt too wide) in paragraph at lines 329--330
\OT1/cmr/m/n/12 wm[]iconwindow(), wm[]maxsize(), wm[]minsize(), wm[]overridered
irect(), wm[]positionfrom(),
 []


Overfull \hbox (23.3329pt too wide) in paragraph at lines 329--330
\OT1/cmr/m/n/12 wm[]protocol(), wm[]resizable(), wm[]sizefrom(), wm[]state(), w
m[]title(), wm[]transient(),
 []

) [245]
\openout2 = `nMOLDYN.GUI.SelectionDialog-module.aux'.

 (./nMOLDYN.GUI.SelectionDialog-module.tex
Overfull \hbox (61.29524pt too wide) in paragraph at lines 18--18
[]\OT1/cmtt/m/n/12 This modules implements the atom selection dialog used in al
most all nMOLDYN analysis.[] 
 []


Overfull \hbox (228.02032pt too wide) in paragraph at lines 20--20
[]\OT1/cmtt/m/n/12 The atom selection can be performed for various purposes suc
h as selection of atoms for the simulation, selection[] 
 []


Overfull \hbox (197.14531pt too wide) in paragraph at lines 21--21
[]\OT1/cmtt/m/n/12 of hydrogen atoms to deuterate or selection of several group
 of atoms on which an analysis will be performed[] 
 []


Overfull \hbox (55.12024pt too wide) in paragraph at lines 25--25
[]    \OT1/cmtt/m/n/12 * SelectionDialog: sets up a selection dialog in the sco
pe of an analysis dialog.[] 
 []

[246


] [247] [248]
Overfull \hbox (1.55647pt too wide) in paragraph at lines 589--590
\OT1/cmr/m/n/12 ure(), deletecom-mand(), event[]add(), event[]delete(), event[]
generate(), event[]info(),
 []


Overfull \hbox (1.73924pt too wide) in paragraph at lines 589--590
\OT1/cmr/m/n/12 fo-cus(), fo-cus[]displayof(), fo-cus[]force(), fo-cus[]get(), 
fo-cus[]lastfor(), fo-cus[]set(), get-
 []


Overfull \hbox (9.89888pt too wide) in paragraph at lines 589--590
\OT1/cmr/m/n/12 grab[]status(), grid[]bbox(), grid[]columnconfigure(), grid[]lo
cation(), grid[]propagate(),
 []


Overfull \hbox (4.21977pt too wide) in paragraph at lines 589--590
\OT1/cmr/m/n/12 grid[]rowconfigure(), grid[]size(), grid[]slaves(), im-age[]nam
es(), im-age[]types(), keys(),
 []


Overfull \hbox (13.9069pt too wide) in paragraph at lines 589--590
\OT1/cmr/m/n/12 lift(), lower(), main-loop(), name-towid-get(), op-tion[]add(),
 op-tion[]clear(), op-tion[]get(),
 []


Overfull \hbox (9.65083pt too wide) in paragraph at lines 589--590
\OT1/cmr/m/n/12 op-tion[]readfile(), pack[]propagate(), pack[]slaves(), place[]
slaves(), prop-a-gate(), quit(),
 []


Overfull \hbox (24.17793pt too wide) in paragraph at lines 589--590
\OT1/cmr/m/n/12 tk[]focusFollowsMouse(), tk[]focusNext(), tk[]focusPrev(), tk[]
menuBar(), tk[]setPalette(),
 []


Overfull \hbox (36.98888pt too wide) in paragraph at lines 589--590
\OT1/cmr/m/n/12 date[]idletasks(), wait[]variable(), wait[]visibility(), wait[]
window(), wait-var(), winfo[]atom(),
 []


Overfull \hbox (16.81825pt too wide) in paragraph at lines 589--590
\OT1/cmr/m/n/12 winfo[]atomname(), winfo[]cells(), winfo[]children(), winfo[]cl
ass(), winfo[]colormapfull(),
 []


Overfull \hbox (4.74199pt too wide) in paragraph at lines 589--590
\OT1/cmr/m/n/12 winfo[]containing(), winfo[]depth(), winfo[]exists(), winfo[]fp
ixels(), winfo[]geometry(),
 []


Overfull \hbox (57.14644pt too wide) in paragraph at lines 589--590
\OT1/cmr/m/n/12 winfo[]height(), winfo[]id(), winfo[]interps(), winfo[]ismapped
(), winfo[]manager(), winfo[]name(),
 []


Overfull \hbox (18.31963pt too wide) in paragraph at lines 589--590
\OT1/cmr/m/n/12 winfo[]parent(), winfo[]pathname(), winfo[]pixels(), winfo[]poi
nterx(), winfo[]pointerxy(),
 []


Overfull \hbox (48.93459pt too wide) in paragraph at lines 589--590
\OT1/cmr/m/n/12 winfo[]rooty(), winfo[]screen(), winfo[]screencells(), winfo[]s
creendepth(), winfo[]screenheight(),
 []


Overfull \hbox (50.31847pt too wide) in paragraph at lines 589--590
\OT1/cmr/m/n/12 winfo[]screenmmheight(), winfo[]screenmmwidth(), winfo[]screenv
isual(), winfo[]screenwidth(),
 []

[249]
Overfull \hbox (56.89839pt too wide) in paragraph at lines 595--596
\OT1/cmr/m/n/12 draw(), wm[]aspect(), wm[]attributes(), wm[]client(), wm[]color
mapwindows(), wm[]command(),
 []


Overfull \hbox (32.92863pt too wide) in paragraph at lines 595--596
\OT1/cmr/m/n/12 wm[]deiconify(), wm[]focusmodel(), wm[]frame(), wm[]geometry(),
 wm[]grid(), wm[]group(),
 []


Overfull \hbox (14.79466pt too wide) in paragraph at lines 595--596
\OT1/cmr/m/n/12 wm[]iconbitmap(), wm[]iconify(), wm[]iconmask(), wm[]iconname()
, wm[]iconposition(),
 []


Overfull \hbox (48.47765pt too wide) in paragraph at lines 595--596
\OT1/cmr/m/n/12 wm[]iconwindow(), wm[]maxsize(), wm[]minsize(), wm[]overridered
irect(), wm[]positionfrom(),
 []


Overfull \hbox (23.3329pt too wide) in paragraph at lines 595--596
\OT1/cmr/m/n/12 wm[]protocol(), wm[]resizable(), wm[]sizefrom(), wm[]state(), w
m[]title(), wm[]transient(),
 []

) [250]
\openout2 = `nMOLDYN.GUI.Tags-module.aux'.

 (./nMOLDYN.GUI.Tags-module.tex) [251


]
\openout2 = `nMOLDYN.GUI.TrajectoryConversionDialog-module.aux'.


(./nMOLDYN.GUI.TrajectoryConversionDialog-module.tex
Overfull \hbox (23.64783pt too wide) in paragraph at lines 18--18
[]\OT1/cmtt/m/n/12 This modules implements I\OMS/cmsy/m/n/12 f\OT1/cmtt/m/n/12 
File --\OML/cmm/m/it/12 > \OT1/cmtt/m/n/12 Trajectory conversion --\OML/cmm/m/i
t/12 > \OT1/cmtt/m/n/12 converter\OMS/cmsy/m/n/12 g \OT1/cmtt/m/n/12 dialog.[] 

 []


Overfull \hbox (233.59793pt too wide) in paragraph at lines 21--21
[]    \OT1/cmtt/m/n/12 * AmberNetCDFConverterDialog: sets up I\OMS/cmsy/m/n/12 
f\OT1/cmtt/m/n/12 File--\OML/cmm/m/it/12 >\OT1/cmtt/m/n/12 Trajectory conversio
n --\OML/cmm/m/it/12 > \OT1/cmtt/m/n/12 Amber NetCDF to MMTK\OMS/cmsy/m/n/12 g 
\OT1/cmtt/m/n/12 dialog used to[] 
 []


Overfull \hbox (208.89792pt too wide) in paragraph at lines 23--23
[]    \OT1/cmtt/m/n/12 * CHARMMConverterDialog: sets up I\OMS/cmsy/m/n/12 f\OT1
/cmtt/m/n/12 File--\OML/cmm/m/it/12 >\OT1/cmtt/m/n/12 Trajectory conversion --\
OML/cmm/m/it/12 > \OT1/cmtt/m/n/12 CHARMM/X-PLOR to MMTK\OMS/cmsy/m/n/12 g \OT1
/cmtt/m/n/12 dialog used to[] 
 []


Overfull \hbox (174.5649pt too wide) in paragraph at lines 25--25
[]    \OT1/cmtt/m/n/12 * DL[]POLYConverterDialog: sets up I\OMS/cmsy/m/n/12 f\O
T1/cmtt/m/n/12 File--\OML/cmm/m/it/12 >\OT1/cmtt/m/n/12 Trajectory conversion -
-\OML/cmm/m/it/12 > \OT1/cmtt/m/n/12 DL[]POLY to MMTK\OMS/cmsy/m/n/12 g \OT1/cm
tt/m/n/12 dialog used to[] 
 []


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[]    \OT1/cmtt/m/n/12 * MaterialsStudioConverterDialog: sets up I\OMS/cmsy/m/n
/12 f\OT1/cmtt/m/n/12 File--\OML/cmm/m/it/12 >\OT1/cmtt/m/n/12 Trajectory conve
rsion --\OML/cmm/m/it/12 > \OT1/cmtt/m/n/12 MaterialsStudio --\OML/cmm/m/it/12 
> \OT1/cmtt/m/n/12 Discover to MMTK\OMS/cmsy/m/n/12 g \OT1/cmtt/m/n/12 or[] 
 []


Overfull \hbox (261.26173pt too wide) in paragraph at lines 28--28
[]      \OT1/cmtt/m/n/12 I\OMS/cmsy/m/n/12 f\OT1/cmtt/m/n/12 File--\OML/cmm/m/i
t/12 >\OT1/cmtt/m/n/12 Trajectory conversion --\OML/cmm/m/it/12 > \OT1/cmtt/m/n
/12 MaterialsStudio --\OML/cmm/m/it/12 > \OT1/cmtt/m/n/12 Forcite to MMTK\OMS/c
msy/m/n/12 g \OT1/cmtt/m/n/12 dialogs used to convert a Discover or a[] 
 []


Overfull \hbox (140.97289pt too wide) in paragraph at lines 30--30
[]    \OT1/cmtt/m/n/12 * NAMDConverterDialog: sets up I\OMS/cmsy/m/n/12 f\OT1/c
mtt/m/n/12 File--\OML/cmm/m/it/12 >\OT1/cmtt/m/n/12 Trajectory conversion --\OM
L/cmm/m/it/12 > \OT1/cmtt/m/n/12 NAMD to MMTK\OMS/cmsy/m/n/12 g \OT1/cmtt/m/n/1
2 dialog used to[] 
 []


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[]    \OT1/cmtt/m/n/12 * VASPConverterDialog: sets up I\OMS/cmsy/m/n/12 f\OT1/c
mtt/m/n/12 File--\OML/cmm/m/it/12 >\OT1/cmtt/m/n/12 Trajectory conversion --\OM
L/cmm/m/it/12 > \OT1/cmtt/m/n/12 VASP to MMTK\OMS/cmsy/m/n/12 g \OT1/cmtt/m/n/1
2 dialog used to[] 
 []


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[] 
 []

[252


]
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[] 
 []

[253]
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[] 
 []

[254]
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[] 
 []

[255]
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[] 
 []

[256]
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[] 
 []

) [257]
\openout2 = `nMOLDYN.GUI.ViewEffectiveModeDialog-module.aux'.

 (./nMOLDYN.GUI.ViewEffectiveModeDialog-module.tex
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[]    \OT1/cmtt/m/n/12 * ViewEffectiveModeDialog: creates I\OMS/cmsy/m/n/12 f\O
T1/cmtt/m/n/12 View --\OML/cmm/m/it/12 > \OT1/cmtt/m/n/12 Effective Mode\OMS/cm
sy/m/n/12 g \OT1/cmtt/m/n/12 dialog used to[] 
 []


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[]      \OT1/cmtt/m/n/12 view an animation of the effective modes resulting fro
m a Quasi Harmonic Analysis.[] 
 []


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[] 
 []

[258


]
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\OT1/cmr/m/n/12 ure(), deletecom-mand(), event[]add(), event[]delete(), event[]
generate(), event[]info(),
 []


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\OT1/cmr/m/n/12 fo-cus(), fo-cus[]displayof(), fo-cus[]force(), fo-cus[]get(), 
fo-cus[]lastfor(), fo-cus[]set(), get-
 []


Overfull \hbox (9.89888pt too wide) in paragraph at lines 244--245
\OT1/cmr/m/n/12 grab[]status(), grid[]bbox(), grid[]columnconfigure(), grid[]lo
cation(), grid[]propagate(),
 []


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\OT1/cmr/m/n/12 grid[]rowconfigure(), grid[]size(), grid[]slaves(), im-age[]nam
es(), im-age[]types(), keys(),
 []


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\OT1/cmr/m/n/12 lift(), lower(), main-loop(), name-towid-get(), op-tion[]add(),
 op-tion[]clear(), op-tion[]get(),
 []


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\OT1/cmr/m/n/12 op-tion[]readfile(), pack[]propagate(), pack[]slaves(), place[]
slaves(), prop-a-gate(), quit(),
 []


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\OT1/cmr/m/n/12 tk[]focusFollowsMouse(), tk[]focusNext(), tk[]focusPrev(), tk[]
menuBar(), tk[]setPalette(),
 []


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\OT1/cmr/m/n/12 date[]idletasks(), wait[]variable(), wait[]visibility(), wait[]
window(), wait-var(), winfo[]atom(),
 []


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\OT1/cmr/m/n/12 winfo[]atomname(), winfo[]cells(), winfo[]children(), winfo[]cl
ass(), winfo[]colormapfull(),
 []


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\OT1/cmr/m/n/12 winfo[]containing(), winfo[]depth(), winfo[]exists(), winfo[]fp
ixels(), winfo[]geometry(),
 []


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\OT1/cmr/m/n/12 winfo[]height(), winfo[]id(), winfo[]interps(), winfo[]ismapped
(), winfo[]manager(), winfo[]name(),
 []


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\OT1/cmr/m/n/12 winfo[]parent(), winfo[]pathname(), winfo[]pixels(), winfo[]poi
nterx(), winfo[]pointerxy(),
 []


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\OT1/cmr/m/n/12 winfo[]rooty(), winfo[]screen(), winfo[]screencells(), winfo[]s
creendepth(), winfo[]screenheight(),
 []


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\OT1/cmr/m/n/12 winfo[]screenmmheight(), winfo[]screenmmwidth(), winfo[]screenv
isual(), winfo[]screenwidth(),
 []


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\OT1/cmr/m/n/12 draw(), wm[]aspect(), wm[]attributes(), wm[]client(), wm[]color
mapwindows(), wm[]command(),
 []


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\OT1/cmr/m/n/12 wm[]deiconify(), wm[]focusmodel(), wm[]frame(), wm[]geometry(),
 wm[]grid(), wm[]group(),
 []


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\OT1/cmr/m/n/12 wm[]iconbitmap(), wm[]iconify(), wm[]iconmask(), wm[]iconname()
, wm[]iconposition(),
 []


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\OT1/cmr/m/n/12 wm[]iconwindow(), wm[]maxsize(), wm[]minsize(), wm[]overridered
irect(), wm[]positionfrom(),
 []


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\OT1/cmr/m/n/12 wm[]protocol(), wm[]resizable(), wm[]sizefrom(), wm[]state(), w
m[]title(), wm[]transient(),
 []

[259]) [260]
\openout2 = `nMOLDYN.GUI.Widgets-module.aux'.

 (./nMOLDYN.GUI.Widgets-module.tex
Overfull \hbox (92.17026pt too wide) in paragraph at lines 20--20
[]\OT1/cmtt/m/n/12 A combo widget can be defined as a label frame encapsulating
 several other Tkinter widgets.[] 
 []


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[]    \OT1/cmtt/m/n/12 * ValidatingEntry   : sets up a Tkinter Entry widget tha
t checks its contents whenever it is changed.[] 
 []


Overfull \hbox (135.39528pt too wide) in paragraph at lines 24--24
[]    \OT1/cmtt/m/n/12 * IntegerEntry      : sets up a Tkinter Entry widget tha
t checks that the input is an integer.[] 
 []


Overfull \hbox (116.87027pt too wide) in paragraph at lines 25--25
[]    \OT1/cmtt/m/n/12 * FloatEntry        : sets up a Tkinter Entry widget tha
t checks that the input is a float.[] 
 []


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[]    \OT1/cmtt/m/n/12 * StringEntry       : sets up a Tkinter Entry widget tha
t checks that the input is a string matching a given pattern.[] 
 []


Overfull \hbox (271.24535pt too wide) in paragraph at lines 27--27
[]    \OT1/cmtt/m/n/12 * ComboLabelEntry   : sets up a combo widget made of a T
kinter Label widget embedded in a Tkinter LabelFrame widget.[] 
 []


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[]    \OT1/cmtt/m/n/12 * ComboIntegerEntry : sets up a combo widget made of a T
kinter Label widget and IntegerEntry combo widget embedded[] 
 []


Overfull \hbox (246.54533pt too wide) in paragraph at lines 30--30
[]    \OT1/cmtt/m/n/12 * ComboFloatEntry   : sets up a combo widget made of a T
kinter Label widget and FloatEntry embedded in a Tkinter[] 
 []


Overfull \hbox (252.72034pt too wide) in paragraph at lines 32--32
[]    \OT1/cmtt/m/n/12 * ComboStringEntry  : sets up a combo widget made of a T
kinter Label widget and StringEntry embedded in a Tkinter[] 
 []


Overfull \hbox (271.24535pt too wide) in paragraph at lines 34--34
[]    \OT1/cmtt/m/n/12 * ComboRadiobutton  : sets up a combo widget made of a T
kinter Label widget and a set of Tkinter RadioButton widgets[] 
 []


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[]    \OT1/cmtt/m/n/12 * ComboCheckbutton  : sets up a combo widget made of a T
kinter Label widget and a Tkinter CheckButton widget embedded[] 
 []


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[]    \OT1/cmtt/m/n/12 * ComboOptionMenu   : sets up a combo widget made of a T
kinter Label widget and a Tkinter OptionMenu widget embedded[] 
 []


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[]    \OT1/cmtt/m/n/12 * ComboSpinbox      : sets up a combo widget made of a T
kinter Label widget and a Tkinter Spinbox widget embedded in[] 
 []


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[]    \OT1/cmtt/m/n/12 * ComboScale        : sets up a combo widget made of a T
kinter Label widget and a Tkinter Scale widget embedded in[] 
 []


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[]    \OT1/cmtt/m/n/12 * ComboButton       : sets up a combo widget made of a T
kinter Button widget and optionnally a Tkinter Entry widget embedded[] 
 []


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[]    \OT1/cmtt/m/n/12 * ComboFileBrowser  : sets up a combo widget made of a T
kinter Label widget, a StringEntry widget and a Tkinter Button[] 
 []


Overfull \hbox (345.34538pt too wide) in paragraph at lines 48--48
[]    \OT1/cmtt/m/n/12 * ComboText         : sets up a combo widget made of a T
kinter Text and a vertical Tkinter Scrollbar widget widget embedded in a[] 
 []


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[]    \OT1/cmtt/m/n/12 * ComboListbox      : sets up a combo widget made of a T
kinter Listbox widget and a vertical Tkinter Scrollbar widget embedded[] 
 []


Overfull \hbox (190.9703pt too wide) in paragraph at lines 52--52
[]    \OT1/cmtt/m/n/12 * StatusBar         : sets up a combo widget made of a T
kinter Scale widget embedded in a Tkinter Frame[] 
 []


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[]\OT1/cmtt/m/n/12 The following classes were adapted from the implementation o
f Frederic Lundh:[] 
 []

[261


] [262]
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[]\OT1/cmr/m/n/12 delete(), get(), icur-sor(), in-dex(), in-sert(), scan[]dragt
o(), scan[]mark(), se-lect[]adjust(),
 []


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\OT1/cmr/m/n/12 se-lect[]clear(), se-lect[]from(), se-lect[]present(), se-lect[
]range(), se-lect[]to(), se-lec-tion[]adjust(),
 []


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\OT1/cmr/m/n/12 se-lec-tion[]clear(), se-lec-tion[]from(), se-lec-tion[]present
(), se-lec-tion[]range(), se-lec-tion[]to(),
 []

[263]
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\OT1/cmr/m/n/12 ure(), deletecom-mand(), event[]add(), event[]delete(), event[]
generate(), event[]info(),
 []


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\OT1/cmr/m/n/12 fo-cus(), fo-cus[]displayof(), fo-cus[]force(), fo-cus[]get(), 
fo-cus[]lastfor(), fo-cus[]set(), get-
 []


Overfull \hbox (9.89888pt too wide) in paragraph at lines 387--388
\OT1/cmr/m/n/12 grab[]status(), grid[]bbox(), grid[]columnconfigure(), grid[]lo
cation(), grid[]propagate(),
 []


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\OT1/cmr/m/n/12 grid[]rowconfigure(), grid[]size(), grid[]slaves(), im-age[]nam
es(), im-age[]types(), keys(),
 []


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\OT1/cmr/m/n/12 lift(), lower(), main-loop(), name-towid-get(), op-tion[]add(),
 op-tion[]clear(), op-tion[]get(),
 []


Overfull \hbox (9.65083pt too wide) in paragraph at lines 387--388
\OT1/cmr/m/n/12 op-tion[]readfile(), pack[]propagate(), pack[]slaves(), place[]
slaves(), prop-a-gate(), quit(),
 []


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\OT1/cmr/m/n/12 lec-tion[]own[]get(), send(), set-var(), size(), slaves(), tk[]
bisque(), tk[]focusFollowsMouse(),
 []


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\OT1/cmr/m/n/12 tk[]focusNext(), tk[]focusPrev(), tk[]menuBar(), tk[]setPalette
(), tk[]strictMotif(), tkraise(),
 []


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\OT1/cmr/m/n/12 un-bind(), un-bind[]all(), un-bind[]class(), up-date(), up-date
[]idletasks(), wait[]variable(),
 []


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\OT1/cmr/m/n/12 wait[]visibility(), wait[]window(), wait-var(), winfo[]atom(), 
winfo[]atomname(), winfo[]cells(),
 []


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\OT1/cmr/m/n/12 winfo[]children(), winfo[]class(), winfo[]colormapfull(), winfo
[]containing(), winfo[]depth(),
 []


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\OT1/cmr/m/n/12 winfo[]exists(), winfo[]fpixels(), winfo[]geometry(), winfo[]he
ight(), winfo[]id(), winfo[]interps(),
 []


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\OT1/cmr/m/n/12 winfo[]ismapped(), winfo[]manager(), winfo[]name(), winfo[]pare
nt(), winfo[]pathname(),
 []


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\OT1/cmr/m/n/12 winfo[]pixels(), winfo[]pointerx(), winfo[]pointerxy(), winfo[]
pointery(), winfo[]reqheight(),
 []


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\OT1/cmr/m/n/12 winfo[]reqwidth(), winfo[]rgb(), winfo[]rootx(), winfo[]rooty()
, winfo[]screen(), winfo[]screencells(),
 []


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\OT1/cmr/m/n/12 winfo[]screendepth(), winfo[]screenheight(), winfo[]screenmmhei
ght(), winfo[]screenmmwidth(),
 []


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\OT1/cmr/m/n/12 winfo[]screenvisual(), winfo[]screenwidth(), winfo[]server(), w
info[]toplevel(), winfo[]viewable(),
 []


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\OT1/cmr/m/n/12 winfo[]visual(), winfo[]visualid(), winfo[]visualsavailable(), 
winfo[]vrootheight(), winfo[]vrootwidth(),
 []

[264]
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[] 
 []

[265]
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[]\OT1/cmr/m/n/12 delete(), get(), icur-sor(), in-dex(), in-sert(), scan[]dragt
o(), scan[]mark(), se-lect[]adjust(),
 []


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\OT1/cmr/m/n/12 se-lect[]clear(), se-lect[]from(), se-lect[]present(), se-lect[
]range(), se-lect[]to(), se-lec-tion[]adjust(),
 []


Overfull \hbox (17.34047pt too wide) in paragraph at lines 633--634
\OT1/cmr/m/n/12 se-lec-tion[]clear(), se-lec-tion[]from(), se-lec-tion[]present
(), se-lec-tion[]range(), se-lec-tion[]to(),
 []


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\OT1/cmr/m/n/12 ure(), deletecom-mand(), event[]add(), event[]delete(), event[]
generate(), event[]info(),
 []


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\OT1/cmr/m/n/12 fo-cus(), fo-cus[]displayof(), fo-cus[]force(), fo-cus[]get(), 
fo-cus[]lastfor(), fo-cus[]set(), get-
 []


Overfull \hbox (9.89888pt too wide) in paragraph at lines 645--646
\OT1/cmr/m/n/12 grab[]status(), grid[]bbox(), grid[]columnconfigure(), grid[]lo
cation(), grid[]propagate(),
 []


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\OT1/cmr/m/n/12 grid[]rowconfigure(), grid[]size(), grid[]slaves(), im-age[]nam
es(), im-age[]types(), keys(),
 []


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\OT1/cmr/m/n/12 lift(), lower(), main-loop(), name-towid-get(), op-tion[]add(),
 op-tion[]clear(), op-tion[]get(),
 []


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\OT1/cmr/m/n/12 op-tion[]readfile(), pack[]propagate(), pack[]slaves(), place[]
slaves(), prop-a-gate(), quit(),
 []


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\OT1/cmr/m/n/12 lec-tion[]own[]get(), send(), set-var(), size(), slaves(), tk[]
bisque(), tk[]focusFollowsMouse(),
 []


Overfull \hbox (31.71951pt too wide) in paragraph at lines 645--646
\OT1/cmr/m/n/12 tk[]focusNext(), tk[]focusPrev(), tk[]menuBar(), tk[]setPalette
(), tk[]strictMotif(), tkraise(),
 []


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\OT1/cmr/m/n/12 un-bind(), un-bind[]all(), un-bind[]class(), up-date(), up-date
[]idletasks(), wait[]variable(),
 []


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\OT1/cmr/m/n/12 wait[]visibility(), wait[]window(), wait-var(), winfo[]atom(), 
winfo[]atomname(), winfo[]cells(),
 []


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\OT1/cmr/m/n/12 winfo[]children(), winfo[]class(), winfo[]colormapfull(), winfo
[]containing(), winfo[]depth(),
 []


Overfull \hbox (45.8535pt too wide) in paragraph at lines 645--646
\OT1/cmr/m/n/12 winfo[]exists(), winfo[]fpixels(), winfo[]geometry(), winfo[]he
ight(), winfo[]id(), winfo[]interps(),
 []


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\OT1/cmr/m/n/12 winfo[]ismapped(), winfo[]manager(), winfo[]name(), winfo[]pare
nt(), winfo[]pathname(),
 []


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\OT1/cmr/m/n/12 winfo[]pixels(), winfo[]pointerx(), winfo[]pointerxy(), winfo[]
pointery(), winfo[]reqheight(),
 []


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\OT1/cmr/m/n/12 winfo[]reqwidth(), winfo[]rgb(), winfo[]rootx(), winfo[]rooty()
, winfo[]screen(), winfo[]screencells(),
 []


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\OT1/cmr/m/n/12 winfo[]screendepth(), winfo[]screenheight(), winfo[]screenmmhei
ght(), winfo[]screenmmwidth(),
 []


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\OT1/cmr/m/n/12 winfo[]screenvisual(), winfo[]screenwidth(), winfo[]server(), w
info[]toplevel(), winfo[]viewable(),
 []


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\OT1/cmr/m/n/12 winfo[]visual(), winfo[]visualid(), winfo[]visualsavailable(), 
winfo[]vrootheight(), winfo[]vrootwidth(),
 []

[266]
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[] 
 []

[267] [268]
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[]\OT1/cmr/m/n/12 delete(), get(), icur-sor(), in-dex(), in-sert(), scan[]dragt
o(), scan[]mark(), se-lect[]adjust(),
 []


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\OT1/cmr/m/n/12 se-lect[]clear(), se-lect[]from(), se-lect[]present(), se-lect[
]range(), se-lect[]to(), se-lec-tion[]adjust(),
 []


Overfull \hbox (17.34047pt too wide) in paragraph at lines 891--892
\OT1/cmr/m/n/12 se-lec-tion[]clear(), se-lec-tion[]from(), se-lec-tion[]present
(), se-lec-tion[]range(), se-lec-tion[]to(),
 []


Overfull \hbox (1.55647pt too wide) in paragraph at lines 903--904
\OT1/cmr/m/n/12 ure(), deletecom-mand(), event[]add(), event[]delete(), event[]
generate(), event[]info(),
 []


Overfull \hbox (1.73924pt too wide) in paragraph at lines 903--904
\OT1/cmr/m/n/12 fo-cus(), fo-cus[]displayof(), fo-cus[]force(), fo-cus[]get(), 
fo-cus[]lastfor(), fo-cus[]set(), get-
 []


Overfull \hbox (9.89888pt too wide) in paragraph at lines 903--904
\OT1/cmr/m/n/12 grab[]status(), grid[]bbox(), grid[]columnconfigure(), grid[]lo
cation(), grid[]propagate(),
 []


Overfull \hbox (4.21977pt too wide) in paragraph at lines 903--904
\OT1/cmr/m/n/12 grid[]rowconfigure(), grid[]size(), grid[]slaves(), im-age[]nam
es(), im-age[]types(), keys(),
 []


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\OT1/cmr/m/n/12 lift(), lower(), main-loop(), name-towid-get(), op-tion[]add(),
 op-tion[]clear(), op-tion[]get(),
 []


Overfull \hbox (9.65083pt too wide) in paragraph at lines 903--904
\OT1/cmr/m/n/12 op-tion[]readfile(), pack[]propagate(), pack[]slaves(), place[]
slaves(), prop-a-gate(), quit(),
 []


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\OT1/cmr/m/n/12 lec-tion[]own[]get(), send(), set-var(), size(), slaves(), tk[]
bisque(), tk[]focusFollowsMouse(),
 []


Overfull \hbox (31.71951pt too wide) in paragraph at lines 903--904
\OT1/cmr/m/n/12 tk[]focusNext(), tk[]focusPrev(), tk[]menuBar(), tk[]setPalette
(), tk[]strictMotif(), tkraise(),
 []


Overfull \hbox (6.0606pt too wide) in paragraph at lines 903--904
\OT1/cmr/m/n/12 un-bind(), un-bind[]all(), un-bind[]class(), up-date(), up-date
[]idletasks(), wait[]variable(),
 []


Overfull \hbox (39.2083pt too wide) in paragraph at lines 903--904
\OT1/cmr/m/n/12 wait[]visibility(), wait[]window(), wait-var(), winfo[]atom(), 
winfo[]atomname(), winfo[]cells(),
 []


Overfull \hbox (24.25984pt too wide) in paragraph at lines 903--904
\OT1/cmr/m/n/12 winfo[]children(), winfo[]class(), winfo[]colormapfull(), winfo
[]containing(), winfo[]depth(),
 []


Overfull \hbox (45.8535pt too wide) in paragraph at lines 903--904
\OT1/cmr/m/n/12 winfo[]exists(), winfo[]fpixels(), winfo[]geometry(), winfo[]he
ight(), winfo[]id(), winfo[]interps(),
 []


Overfull \hbox (17.34047pt too wide) in paragraph at lines 903--904
\OT1/cmr/m/n/12 winfo[]ismapped(), winfo[]manager(), winfo[]name(), winfo[]pare
nt(), winfo[]pathname(),
 []


Overfull \hbox (24.84734pt too wide) in paragraph at lines 903--904
\OT1/cmr/m/n/12 winfo[]pixels(), winfo[]pointerx(), winfo[]pointerxy(), winfo[]
pointery(), winfo[]reqheight(),
 []


Overfull \hbox (62.1075pt too wide) in paragraph at lines 903--904
\OT1/cmr/m/n/12 winfo[]reqwidth(), winfo[]rgb(), winfo[]rootx(), winfo[]rooty()
, winfo[]screen(), winfo[]screencells(),
 []


Overfull \hbox (52.86427pt too wide) in paragraph at lines 903--904
\OT1/cmr/m/n/12 winfo[]screendepth(), winfo[]screenheight(), winfo[]screenmmhei
ght(), winfo[]screenmmwidth(),
 []


Overfull \hbox (48.54292pt too wide) in paragraph at lines 903--904
\OT1/cmr/m/n/12 winfo[]screenvisual(), winfo[]screenwidth(), winfo[]server(), w
info[]toplevel(), winfo[]viewable(),
 []


Overfull \hbox (77.26485pt too wide) in paragraph at lines 903--904
\OT1/cmr/m/n/12 winfo[]visual(), winfo[]visualid(), winfo[]visualsavailable(), 
winfo[]vrootheight(), winfo[]vrootwidth(),
 []

[269]
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[] 
 []

[270]
Overfull \hbox (13.25414pt too wide) in paragraph at lines 1176--1177
[]\OT1/cmr/m/n/12 delete(), get(), icur-sor(), in-dex(), in-sert(), scan[]dragt
o(), scan[]mark(), se-lect[]adjust(),
 []


Overfull \hbox (34.03835pt too wide) in paragraph at lines 1176--1177
\OT1/cmr/m/n/12 se-lect[]clear(), se-lect[]from(), se-lect[]present(), se-lect[
]range(), se-lect[]to(), se-lec-tion[]adjust(),
 []


Overfull \hbox (17.34047pt too wide) in paragraph at lines 1176--1177
\OT1/cmr/m/n/12 se-lec-tion[]clear(), se-lec-tion[]from(), se-lec-tion[]present
(), se-lec-tion[]range(), se-lec-tion[]to(),
 []

[271]
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\OT1/cmr/m/n/12 ure(), deletecom-mand(), event[]add(), event[]delete(), event[]
generate(), event[]info(),
 []


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\OT1/cmr/m/n/12 fo-cus(), fo-cus[]displayof(), fo-cus[]force(), fo-cus[]get(), 
fo-cus[]lastfor(), fo-cus[]set(), get-
 []


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\OT1/cmr/m/n/12 grab[]status(), grid[]bbox(), grid[]columnconfigure(), grid[]lo
cation(), grid[]propagate(),
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\OT1/cmr/m/n/12 grid[]rowconfigure(), grid[]size(), grid[]slaves(), im-age[]nam
es(), im-age[]types(), keys(),
 []


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\OT1/cmr/m/n/12 lift(), lower(), main-loop(), name-towid-get(), op-tion[]add(),
 op-tion[]clear(), op-tion[]get(),
 []


Overfull \hbox (9.65083pt too wide) in paragraph at lines 1188--1189
\OT1/cmr/m/n/12 op-tion[]readfile(), pack[]propagate(), pack[]slaves(), place[]
slaves(), prop-a-gate(), quit(),
 []


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\OT1/cmr/m/n/12 lec-tion[]own[]get(), send(), set-var(), size(), slaves(), tk[]
bisque(), tk[]focusFollowsMouse(),
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\OT1/cmr/m/n/12 tk[]focusNext(), tk[]focusPrev(), tk[]menuBar(), tk[]setPalette
(), tk[]strictMotif(), tkraise(),
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\OT1/cmr/m/n/12 un-bind(), un-bind[]all(), un-bind[]class(), up-date(), up-date
[]idletasks(), wait[]variable(),
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\OT1/cmr/m/n/12 wait[]visibility(), wait[]window(), wait-var(), winfo[]atom(), 
winfo[]atomname(), winfo[]cells(),
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\OT1/cmr/m/n/12 winfo[]children(), winfo[]class(), winfo[]colormapfull(), winfo
[]containing(), winfo[]depth(),
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\OT1/cmr/m/n/12 winfo[]exists(), winfo[]fpixels(), winfo[]geometry(), winfo[]he
ight(), winfo[]id(), winfo[]interps(),
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\OT1/cmr/m/n/12 winfo[]ismapped(), winfo[]manager(), winfo[]name(), winfo[]pare
nt(), winfo[]pathname(),
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\OT1/cmr/m/n/12 winfo[]pixels(), winfo[]pointerx(), winfo[]pointerxy(), winfo[]
pointery(), winfo[]reqheight(),
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\OT1/cmr/m/n/12 winfo[]reqwidth(), winfo[]rgb(), winfo[]rootx(), winfo[]rooty()
, winfo[]screen(), winfo[]screencells(),
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\OT1/cmr/m/n/12 winfo[]screendepth(), winfo[]screenheight(), winfo[]screenmmhei
ght(), winfo[]screenmmwidth(),
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\OT1/cmr/m/n/12 winfo[]screenvisual(), winfo[]screenwidth(), winfo[]server(), w
info[]toplevel(), winfo[]viewable(),
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\OT1/cmr/m/n/12 winfo[]visual(), winfo[]visualid(), winfo[]visualsavailable(), 
winfo[]vrootheight(), winfo[]vrootwidth(),
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[272]
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\OT1/cmr/m/n/12 ure(), deletecom-mand(), event[]add(), event[]delete(), event[]
generate(), event[]info(),
 []


Overfull \hbox (1.73924pt too wide) in paragraph at lines 1364--1365
\OT1/cmr/m/n/12 fo-cus(), fo-cus[]displayof(), fo-cus[]force(), fo-cus[]get(), 
fo-cus[]lastfor(), fo-cus[]set(), get-
 []


Overfull \hbox (9.89888pt too wide) in paragraph at lines 1364--1365
\OT1/cmr/m/n/12 grab[]status(), grid[]bbox(), grid[]columnconfigure(), grid[]lo
cation(), grid[]propagate(),
 []


Overfull \hbox (4.21977pt too wide) in paragraph at lines 1364--1365
\OT1/cmr/m/n/12 grid[]rowconfigure(), grid[]size(), grid[]slaves(), im-age[]nam
es(), im-age[]types(), keys(),
 []


Overfull \hbox (13.9069pt too wide) in paragraph at lines 1364--1365
\OT1/cmr/m/n/12 lift(), lower(), main-loop(), name-towid-get(), op-tion[]add(),
 op-tion[]clear(), op-tion[]get(),
 []


Overfull \hbox (9.65083pt too wide) in paragraph at lines 1364--1365
\OT1/cmr/m/n/12 op-tion[]readfile(), pack[]propagate(), pack[]slaves(), place[]
slaves(), prop-a-gate(), quit(),
 []


Overfull \hbox (24.17793pt too wide) in paragraph at lines 1364--1365
\OT1/cmr/m/n/12 tk[]focusFollowsMouse(), tk[]focusNext(), tk[]focusPrev(), tk[]
menuBar(), tk[]setPalette(),
 []


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\OT1/cmr/m/n/12 date[]idletasks(), wait[]variable(), wait[]visibility(), wait[]
window(), wait-var(), winfo[]atom(),
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\OT1/cmr/m/n/12 winfo[]atomname(), winfo[]cells(), winfo[]children(), winfo[]cl
ass(), winfo[]colormapfull(),
 []


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\OT1/cmr/m/n/12 winfo[]containing(), winfo[]depth(), winfo[]exists(), winfo[]fp
ixels(), winfo[]geometry(),
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\OT1/cmr/m/n/12 winfo[]height(), winfo[]id(), winfo[]interps(), winfo[]ismapped
(), winfo[]manager(), winfo[]name(),
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\OT1/cmr/m/n/12 winfo[]parent(), winfo[]pathname(), winfo[]pixels(), winfo[]poi
nterx(), winfo[]pointerxy(),
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\OT1/cmr/m/n/12 winfo[]rooty(), winfo[]screen(), winfo[]screencells(), winfo[]s
creendepth(), winfo[]screenheight(),
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\OT1/cmr/m/n/12 winfo[]screenmmheight(), winfo[]screenmmwidth(), winfo[]screenv
isual(), winfo[]screenwidth(),
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[273] [274] [275]
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\OT1/cmr/m/n/12 ure(), deletecom-mand(), event[]add(), event[]delete(), event[]
generate(), event[]info(),
 []


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\OT1/cmr/m/n/12 fo-cus(), fo-cus[]displayof(), fo-cus[]force(), fo-cus[]get(), 
fo-cus[]lastfor(), fo-cus[]set(), get-
 []


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\OT1/cmr/m/n/12 grab[]status(), grid[]bbox(), grid[]columnconfigure(), grid[]lo
cation(), grid[]propagate(),
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\OT1/cmr/m/n/12 grid[]rowconfigure(), grid[]size(), grid[]slaves(), im-age[]nam
es(), im-age[]types(), keys(),
 []


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\OT1/cmr/m/n/12 lift(), lower(), main-loop(), name-towid-get(), op-tion[]add(),
 op-tion[]clear(), op-tion[]get(),
 []


Overfull \hbox (9.65083pt too wide) in paragraph at lines 1616--1617
\OT1/cmr/m/n/12 op-tion[]readfile(), pack[]propagate(), pack[]slaves(), place[]
slaves(), prop-a-gate(), quit(),
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\OT1/cmr/m/n/12 tk[]focusFollowsMouse(), tk[]focusNext(), tk[]focusPrev(), tk[]
menuBar(), tk[]setPalette(),
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\OT1/cmr/m/n/12 date[]idletasks(), wait[]variable(), wait[]visibility(), wait[]
window(), wait-var(), winfo[]atom(),
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\OT1/cmr/m/n/12 winfo[]atomname(), winfo[]cells(), winfo[]children(), winfo[]cl
ass(), winfo[]colormapfull(),
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\OT1/cmr/m/n/12 winfo[]containing(), winfo[]depth(), winfo[]exists(), winfo[]fp
ixels(), winfo[]geometry(),
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\OT1/cmr/m/n/12 winfo[]height(), winfo[]id(), winfo[]interps(), winfo[]ismapped
(), winfo[]manager(), winfo[]name(),
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\OT1/cmr/m/n/12 winfo[]parent(), winfo[]pathname(), winfo[]pixels(), winfo[]poi
nterx(), winfo[]pointerxy(),
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\OT1/cmr/m/n/12 winfo[]rooty(), winfo[]screen(), winfo[]screencells(), winfo[]s
creendepth(), winfo[]screenheight(),
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\OT1/cmr/m/n/12 winfo[]screenmmheight(), winfo[]screenmmwidth(), winfo[]screenv
isual(), winfo[]screenwidth(),
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[276]
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[] 
 []

[277]
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\OT1/cmr/m/n/12 ure(), deletecom-mand(), event[]add(), event[]delete(), event[]
generate(), event[]info(),
 []


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\OT1/cmr/m/n/12 fo-cus(), fo-cus[]displayof(), fo-cus[]force(), fo-cus[]get(), 
fo-cus[]lastfor(), fo-cus[]set(), get-
 []


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\OT1/cmr/m/n/12 grab[]status(), grid[]bbox(), grid[]columnconfigure(), grid[]lo
cation(), grid[]propagate(),
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\OT1/cmr/m/n/12 grid[]rowconfigure(), grid[]size(), grid[]slaves(), im-age[]nam
es(), im-age[]types(), keys(),
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\OT1/cmr/m/n/12 lift(), lower(), main-loop(), name-towid-get(), op-tion[]add(),
 op-tion[]clear(), op-tion[]get(),
 []


Overfull \hbox (9.65083pt too wide) in paragraph at lines 1885--1886
\OT1/cmr/m/n/12 op-tion[]readfile(), pack[]propagate(), pack[]slaves(), place[]
slaves(), prop-a-gate(), quit(),
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\OT1/cmr/m/n/12 tk[]focusFollowsMouse(), tk[]focusNext(), tk[]focusPrev(), tk[]
menuBar(), tk[]setPalette(),
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\OT1/cmr/m/n/12 date[]idletasks(), wait[]variable(), wait[]visibility(), wait[]
window(), wait-var(), winfo[]atom(),
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\OT1/cmr/m/n/12 winfo[]atomname(), winfo[]cells(), winfo[]children(), winfo[]cl
ass(), winfo[]colormapfull(),
 []


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\OT1/cmr/m/n/12 winfo[]containing(), winfo[]depth(), winfo[]exists(), winfo[]fp
ixels(), winfo[]geometry(),
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\OT1/cmr/m/n/12 winfo[]height(), winfo[]id(), winfo[]interps(), winfo[]ismapped
(), winfo[]manager(), winfo[]name(),
 []


Overfull \hbox (18.31963pt too wide) in paragraph at lines 1885--1886
\OT1/cmr/m/n/12 winfo[]parent(), winfo[]pathname(), winfo[]pixels(), winfo[]poi
nterx(), winfo[]pointerxy(),
 []


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\OT1/cmr/m/n/12 winfo[]rooty(), winfo[]screen(), winfo[]screencells(), winfo[]s
creendepth(), winfo[]screenheight(),
 []


Overfull \hbox (50.31847pt too wide) in paragraph at lines 1885--1886
\OT1/cmr/m/n/12 winfo[]screenmmheight(), winfo[]screenmmwidth(), winfo[]screenv
isual(), winfo[]screenwidth(),
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[278]
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[] 
 []

[279] [280]
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\OT1/cmr/m/n/12 ure(), deletecom-mand(), event[]add(), event[]delete(), event[]
generate(), event[]info(),
 []


Overfull \hbox (1.73924pt too wide) in paragraph at lines 2154--2155
\OT1/cmr/m/n/12 fo-cus(), fo-cus[]displayof(), fo-cus[]force(), fo-cus[]get(), 
fo-cus[]lastfor(), fo-cus[]set(), get-
 []


Overfull \hbox (9.89888pt too wide) in paragraph at lines 2154--2155
\OT1/cmr/m/n/12 grab[]status(), grid[]bbox(), grid[]columnconfigure(), grid[]lo
cation(), grid[]propagate(),
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Overfull \hbox (4.21977pt too wide) in paragraph at lines 2154--2155
\OT1/cmr/m/n/12 grid[]rowconfigure(), grid[]size(), grid[]slaves(), im-age[]nam
es(), im-age[]types(), keys(),
 []


Overfull \hbox (13.9069pt too wide) in paragraph at lines 2154--2155
\OT1/cmr/m/n/12 lift(), lower(), main-loop(), name-towid-get(), op-tion[]add(),
 op-tion[]clear(), op-tion[]get(),
 []


Overfull \hbox (9.65083pt too wide) in paragraph at lines 2154--2155
\OT1/cmr/m/n/12 op-tion[]readfile(), pack[]propagate(), pack[]slaves(), place[]
slaves(), prop-a-gate(), quit(),
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Overfull \hbox (24.17793pt too wide) in paragraph at lines 2154--2155
\OT1/cmr/m/n/12 tk[]focusFollowsMouse(), tk[]focusNext(), tk[]focusPrev(), tk[]
menuBar(), tk[]setPalette(),
 []


Overfull \hbox (36.98888pt too wide) in paragraph at lines 2154--2155
\OT1/cmr/m/n/12 date[]idletasks(), wait[]variable(), wait[]visibility(), wait[]
window(), wait-var(), winfo[]atom(),
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\OT1/cmr/m/n/12 winfo[]atomname(), winfo[]cells(), winfo[]children(), winfo[]cl
ass(), winfo[]colormapfull(),
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\OT1/cmr/m/n/12 winfo[]containing(), winfo[]depth(), winfo[]exists(), winfo[]fp
ixels(), winfo[]geometry(),
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\OT1/cmr/m/n/12 winfo[]height(), winfo[]id(), winfo[]interps(), winfo[]ismapped
(), winfo[]manager(), winfo[]name(),
 []


Overfull \hbox (18.31963pt too wide) in paragraph at lines 2154--2155
\OT1/cmr/m/n/12 winfo[]parent(), winfo[]pathname(), winfo[]pixels(), winfo[]poi
nterx(), winfo[]pointerxy(),
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\OT1/cmr/m/n/12 winfo[]rooty(), winfo[]screen(), winfo[]screencells(), winfo[]s
creendepth(), winfo[]screenheight(),
 []


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\OT1/cmr/m/n/12 winfo[]screenmmheight(), winfo[]screenmmwidth(), winfo[]screenv
isual(), winfo[]screenwidth(),
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[281]
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[] 
 []

[282]
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\OT1/cmr/m/n/12 ure(), deletecom-mand(), event[]add(), event[]delete(), event[]
generate(), event[]info(),
 []


Overfull \hbox (1.73924pt too wide) in paragraph at lines 2430--2431
\OT1/cmr/m/n/12 fo-cus(), fo-cus[]displayof(), fo-cus[]force(), fo-cus[]get(), 
fo-cus[]lastfor(), fo-cus[]set(), get-
 []


Overfull \hbox (9.89888pt too wide) in paragraph at lines 2430--2431
\OT1/cmr/m/n/12 grab[]status(), grid[]bbox(), grid[]columnconfigure(), grid[]lo
cation(), grid[]propagate(),
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Overfull \hbox (4.21977pt too wide) in paragraph at lines 2430--2431
\OT1/cmr/m/n/12 grid[]rowconfigure(), grid[]size(), grid[]slaves(), im-age[]nam
es(), im-age[]types(), keys(),
 []


Overfull \hbox (13.9069pt too wide) in paragraph at lines 2430--2431
\OT1/cmr/m/n/12 lift(), lower(), main-loop(), name-towid-get(), op-tion[]add(),
 op-tion[]clear(), op-tion[]get(),
 []


Overfull \hbox (9.65083pt too wide) in paragraph at lines 2430--2431
\OT1/cmr/m/n/12 op-tion[]readfile(), pack[]propagate(), pack[]slaves(), place[]
slaves(), prop-a-gate(), quit(),
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Overfull \hbox (24.17793pt too wide) in paragraph at lines 2430--2431
\OT1/cmr/m/n/12 tk[]focusFollowsMouse(), tk[]focusNext(), tk[]focusPrev(), tk[]
menuBar(), tk[]setPalette(),
 []


Overfull \hbox (36.98888pt too wide) in paragraph at lines 2430--2431
\OT1/cmr/m/n/12 date[]idletasks(), wait[]variable(), wait[]visibility(), wait[]
window(), wait-var(), winfo[]atom(),
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\OT1/cmr/m/n/12 winfo[]atomname(), winfo[]cells(), winfo[]children(), winfo[]cl
ass(), winfo[]colormapfull(),
 []


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\OT1/cmr/m/n/12 winfo[]containing(), winfo[]depth(), winfo[]exists(), winfo[]fp
ixels(), winfo[]geometry(),
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Overfull \hbox (57.14644pt too wide) in paragraph at lines 2430--2431
\OT1/cmr/m/n/12 winfo[]height(), winfo[]id(), winfo[]interps(), winfo[]ismapped
(), winfo[]manager(), winfo[]name(),
 []


Overfull \hbox (18.31963pt too wide) in paragraph at lines 2430--2431
\OT1/cmr/m/n/12 winfo[]parent(), winfo[]pathname(), winfo[]pixels(), winfo[]poi
nterx(), winfo[]pointerxy(),
 []


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\OT1/cmr/m/n/12 winfo[]rooty(), winfo[]screen(), winfo[]screencells(), winfo[]s
creendepth(), winfo[]screenheight(),
 []


Overfull \hbox (50.31847pt too wide) in paragraph at lines 2430--2431
\OT1/cmr/m/n/12 winfo[]screenmmheight(), winfo[]screenmmwidth(), winfo[]screenv
isual(), winfo[]screenwidth(),
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[283]
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[] 
 []

[284] [285] [286]
Overfull \hbox (1.55647pt too wide) in paragraph at lines 2717--2718
\OT1/cmr/m/n/12 ure(), deletecom-mand(), event[]add(), event[]delete(), event[]
generate(), event[]info(),
 []


Overfull \hbox (1.73924pt too wide) in paragraph at lines 2717--2718
\OT1/cmr/m/n/12 fo-cus(), fo-cus[]displayof(), fo-cus[]force(), fo-cus[]get(), 
fo-cus[]lastfor(), fo-cus[]set(), get-
 []


Overfull \hbox (9.89888pt too wide) in paragraph at lines 2717--2718
\OT1/cmr/m/n/12 grab[]status(), grid[]bbox(), grid[]columnconfigure(), grid[]lo
cation(), grid[]propagate(),
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Overfull \hbox (4.21977pt too wide) in paragraph at lines 2717--2718
\OT1/cmr/m/n/12 grid[]rowconfigure(), grid[]size(), grid[]slaves(), im-age[]nam
es(), im-age[]types(), keys(),
 []


Overfull \hbox (13.9069pt too wide) in paragraph at lines 2717--2718
\OT1/cmr/m/n/12 lift(), lower(), main-loop(), name-towid-get(), op-tion[]add(),
 op-tion[]clear(), op-tion[]get(),
 []


Overfull \hbox (9.65083pt too wide) in paragraph at lines 2717--2718
\OT1/cmr/m/n/12 op-tion[]readfile(), pack[]propagate(), pack[]slaves(), place[]
slaves(), prop-a-gate(), quit(),
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Overfull \hbox (24.17793pt too wide) in paragraph at lines 2717--2718
\OT1/cmr/m/n/12 tk[]focusFollowsMouse(), tk[]focusNext(), tk[]focusPrev(), tk[]
menuBar(), tk[]setPalette(),
 []


Overfull \hbox (36.98888pt too wide) in paragraph at lines 2717--2718
\OT1/cmr/m/n/12 date[]idletasks(), wait[]variable(), wait[]visibility(), wait[]
window(), wait-var(), winfo[]atom(),
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\OT1/cmr/m/n/12 winfo[]atomname(), winfo[]cells(), winfo[]children(), winfo[]cl
ass(), winfo[]colormapfull(),
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\OT1/cmr/m/n/12 winfo[]containing(), winfo[]depth(), winfo[]exists(), winfo[]fp
ixels(), winfo[]geometry(),
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Overfull \hbox (57.14644pt too wide) in paragraph at lines 2717--2718
\OT1/cmr/m/n/12 winfo[]height(), winfo[]id(), winfo[]interps(), winfo[]ismapped
(), winfo[]manager(), winfo[]name(),
 []


Overfull \hbox (18.31963pt too wide) in paragraph at lines 2717--2718
\OT1/cmr/m/n/12 winfo[]parent(), winfo[]pathname(), winfo[]pixels(), winfo[]poi
nterx(), winfo[]pointerxy(),
 []


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\OT1/cmr/m/n/12 winfo[]rooty(), winfo[]screen(), winfo[]screencells(), winfo[]s
creendepth(), winfo[]screenheight(),
 []


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\OT1/cmr/m/n/12 winfo[]screenmmheight(), winfo[]screenmmwidth(), winfo[]screenv
isual(), winfo[]screenwidth(),
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[287]
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[] 
 []

[288] [289]
Overfull \hbox (1.55647pt too wide) in paragraph at lines 3008--3009
\OT1/cmr/m/n/12 ure(), deletecom-mand(), event[]add(), event[]delete(), event[]
generate(), event[]info(),
 []


Overfull \hbox (1.73924pt too wide) in paragraph at lines 3008--3009
\OT1/cmr/m/n/12 fo-cus(), fo-cus[]displayof(), fo-cus[]force(), fo-cus[]get(), 
fo-cus[]lastfor(), fo-cus[]set(), get-
 []


Overfull \hbox (9.89888pt too wide) in paragraph at lines 3008--3009
\OT1/cmr/m/n/12 grab[]status(), grid[]bbox(), grid[]columnconfigure(), grid[]lo
cation(), grid[]propagate(),
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Overfull \hbox (4.21977pt too wide) in paragraph at lines 3008--3009
\OT1/cmr/m/n/12 grid[]rowconfigure(), grid[]size(), grid[]slaves(), im-age[]nam
es(), im-age[]types(), keys(),
 []


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\OT1/cmr/m/n/12 lift(), lower(), main-loop(), name-towid-get(), op-tion[]add(),
 op-tion[]clear(), op-tion[]get(),
 []


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\OT1/cmr/m/n/12 op-tion[]readfile(), pack[]propagate(), pack[]slaves(), place[]
slaves(), prop-a-gate(), quit(),
 []


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\OT1/cmr/m/n/12 tk[]focusFollowsMouse(), tk[]focusNext(), tk[]focusPrev(), tk[]
menuBar(), tk[]setPalette(),
 []


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\OT1/cmr/m/n/12 date[]idletasks(), wait[]variable(), wait[]visibility(), wait[]
window(), wait-var(), winfo[]atom(),
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\OT1/cmr/m/n/12 winfo[]atomname(), winfo[]cells(), winfo[]children(), winfo[]cl
ass(), winfo[]colormapfull(),
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\OT1/cmr/m/n/12 winfo[]containing(), winfo[]depth(), winfo[]exists(), winfo[]fp
ixels(), winfo[]geometry(),
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\OT1/cmr/m/n/12 winfo[]height(), winfo[]id(), winfo[]interps(), winfo[]ismapped
(), winfo[]manager(), winfo[]name(),
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\OT1/cmr/m/n/12 winfo[]parent(), winfo[]pathname(), winfo[]pixels(), winfo[]poi
nterx(), winfo[]pointerxy(),
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\OT1/cmr/m/n/12 winfo[]rooty(), winfo[]screen(), winfo[]screencells(), winfo[]s
creendepth(), winfo[]screenheight(),
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\OT1/cmr/m/n/12 winfo[]screenmmheight(), winfo[]screenmmwidth(), winfo[]screenv
isual(), winfo[]screenwidth(),
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[] 
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[291]
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\OT1/cmr/m/n/12 ure(), deletecom-mand(), event[]add(), event[]delete(), event[]
generate(), event[]info(),
 []


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\OT1/cmr/m/n/12 fo-cus(), fo-cus[]displayof(), fo-cus[]force(), fo-cus[]get(), 
fo-cus[]lastfor(), fo-cus[]set(), get-
 []


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\OT1/cmr/m/n/12 grab[]status(), grid[]bbox(), grid[]columnconfigure(), grid[]lo
cation(), grid[]propagate(),
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\OT1/cmr/m/n/12 grid[]rowconfigure(), grid[]size(), grid[]slaves(), im-age[]nam
es(), im-age[]types(), keys(),
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\OT1/cmr/m/n/12 lift(), lower(), main-loop(), name-towid-get(), op-tion[]add(),
 op-tion[]clear(), op-tion[]get(),
 []


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\OT1/cmr/m/n/12 op-tion[]readfile(), pack[]propagate(), pack[]slaves(), place[]
slaves(), prop-a-gate(), quit(),
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\OT1/cmr/m/n/12 tk[]focusFollowsMouse(), tk[]focusNext(), tk[]focusPrev(), tk[]
menuBar(), tk[]setPalette(),
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\OT1/cmr/m/n/12 date[]idletasks(), wait[]variable(), wait[]visibility(), wait[]
window(), wait-var(), winfo[]atom(),
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\OT1/cmr/m/n/12 winfo[]atomname(), winfo[]cells(), winfo[]children(), winfo[]cl
ass(), winfo[]colormapfull(),
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\OT1/cmr/m/n/12 winfo[]containing(), winfo[]depth(), winfo[]exists(), winfo[]fp
ixels(), winfo[]geometry(),
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\OT1/cmr/m/n/12 winfo[]height(), winfo[]id(), winfo[]interps(), winfo[]ismapped
(), winfo[]manager(), winfo[]name(),
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\OT1/cmr/m/n/12 winfo[]parent(), winfo[]pathname(), winfo[]pixels(), winfo[]poi
nterx(), winfo[]pointerxy(),
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\OT1/cmr/m/n/12 winfo[]rooty(), winfo[]screen(), winfo[]screencells(), winfo[]s
creendepth(), winfo[]screenheight(),
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\OT1/cmr/m/n/12 winfo[]screenmmheight(), winfo[]screenmmwidth(), winfo[]screenv
isual(), winfo[]screenwidth(),
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[] 
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[293] [294]
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\OT1/cmr/m/n/12 ure(), deletecom-mand(), event[]add(), event[]delete(), event[]
generate(), event[]info(),
 []


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\OT1/cmr/m/n/12 fo-cus(), fo-cus[]displayof(), fo-cus[]force(), fo-cus[]get(), 
fo-cus[]lastfor(), fo-cus[]set(), get-
 []


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\OT1/cmr/m/n/12 grab[]status(), grid[]bbox(), grid[]columnconfigure(), grid[]lo
cation(), grid[]propagate(),
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\OT1/cmr/m/n/12 grid[]rowconfigure(), grid[]size(), grid[]slaves(), im-age[]nam
es(), im-age[]types(), keys(),
 []


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\OT1/cmr/m/n/12 lift(), lower(), main-loop(), name-towid-get(), op-tion[]add(),
 op-tion[]clear(), op-tion[]get(),
 []


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\OT1/cmr/m/n/12 op-tion[]readfile(), pack[]propagate(), pack[]slaves(), place[]
slaves(), prop-a-gate(), quit(),
 []


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\OT1/cmr/m/n/12 tk[]focusFollowsMouse(), tk[]focusNext(), tk[]focusPrev(), tk[]
menuBar(), tk[]setPalette(),
 []


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\OT1/cmr/m/n/12 date[]idletasks(), wait[]variable(), wait[]visibility(), wait[]
window(), wait-var(), winfo[]atom(),
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\OT1/cmr/m/n/12 winfo[]atomname(), winfo[]cells(), winfo[]children(), winfo[]cl
ass(), winfo[]colormapfull(),
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\OT1/cmr/m/n/12 winfo[]containing(), winfo[]depth(), winfo[]exists(), winfo[]fp
ixels(), winfo[]geometry(),
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\OT1/cmr/m/n/12 winfo[]height(), winfo[]id(), winfo[]interps(), winfo[]ismapped
(), winfo[]manager(), winfo[]name(),
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\OT1/cmr/m/n/12 winfo[]parent(), winfo[]pathname(), winfo[]pixels(), winfo[]poi
nterx(), winfo[]pointerxy(),
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\OT1/cmr/m/n/12 winfo[]rooty(), winfo[]screen(), winfo[]screencells(), winfo[]s
creendepth(), winfo[]screenheight(),
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\OT1/cmr/m/n/12 winfo[]screenmmheight(), winfo[]screenmmwidth(), winfo[]screenv
isual(), winfo[]screenwidth(),
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[295] [296] [297]
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\OT1/cmr/m/n/12 ure(), deletecom-mand(), event[]add(), event[]delete(), event[]
generate(), event[]info(),
 []


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\OT1/cmr/m/n/12 fo-cus(), fo-cus[]displayof(), fo-cus[]force(), fo-cus[]get(), 
fo-cus[]lastfor(), fo-cus[]set(), get-
 []


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\OT1/cmr/m/n/12 grab[]status(), grid[]bbox(), grid[]columnconfigure(), grid[]lo
cation(), grid[]propagate(),
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\OT1/cmr/m/n/12 grid[]rowconfigure(), grid[]size(), grid[]slaves(), im-age[]nam
es(), im-age[]types(), keys(),
 []


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\OT1/cmr/m/n/12 lift(), lower(), main-loop(), name-towid-get(), op-tion[]add(),
 op-tion[]clear(), op-tion[]get(),
 []


Overfull \hbox (9.65083pt too wide) in paragraph at lines 3839--3840
\OT1/cmr/m/n/12 op-tion[]readfile(), pack[]propagate(), pack[]slaves(), place[]
slaves(), prop-a-gate(), quit(),
 []


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\OT1/cmr/m/n/12 tk[]focusFollowsMouse(), tk[]focusNext(), tk[]focusPrev(), tk[]
menuBar(), tk[]setPalette(),
 []


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\OT1/cmr/m/n/12 date[]idletasks(), wait[]variable(), wait[]visibility(), wait[]
window(), wait-var(), winfo[]atom(),
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\OT1/cmr/m/n/12 winfo[]atomname(), winfo[]cells(), winfo[]children(), winfo[]cl
ass(), winfo[]colormapfull(),
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\OT1/cmr/m/n/12 winfo[]containing(), winfo[]depth(), winfo[]exists(), winfo[]fp
ixels(), winfo[]geometry(),
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\OT1/cmr/m/n/12 winfo[]height(), winfo[]id(), winfo[]interps(), winfo[]ismapped
(), winfo[]manager(), winfo[]name(),
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\OT1/cmr/m/n/12 winfo[]parent(), winfo[]pathname(), winfo[]pixels(), winfo[]poi
nterx(), winfo[]pointerxy(),
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\OT1/cmr/m/n/12 winfo[]rooty(), winfo[]screen(), winfo[]screencells(), winfo[]s
creendepth(), winfo[]screenheight(),
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\OT1/cmr/m/n/12 winfo[]screenmmheight(), winfo[]screenmmwidth(), winfo[]screenv
isual(), winfo[]screenwidth(),
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[298]
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[] 
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[299]
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\OT1/cmr/m/n/12 ure(), deletecom-mand(), event[]add(), event[]delete(), event[]
generate(), event[]info(),
 []


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\OT1/cmr/m/n/12 fo-cus(), fo-cus[]displayof(), fo-cus[]force(), fo-cus[]get(), 
fo-cus[]lastfor(), fo-cus[]set(), get-
 []


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\OT1/cmr/m/n/12 grab[]status(), grid[]bbox(), grid[]columnconfigure(), grid[]lo
cation(), grid[]propagate(),
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\OT1/cmr/m/n/12 grid[]rowconfigure(), grid[]size(), grid[]slaves(), im-age[]nam
es(), im-age[]types(), keys(),
 []


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\OT1/cmr/m/n/12 lift(), lower(), main-loop(), name-towid-get(), op-tion[]add(),
 op-tion[]clear(), op-tion[]get(),
 []


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\OT1/cmr/m/n/12 op-tion[]readfile(), pack[]propagate(), pack[]slaves(), place[]
slaves(), prop-a-gate(), quit(),
 []


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\OT1/cmr/m/n/12 tk[]focusFollowsMouse(), tk[]focusNext(), tk[]focusPrev(), tk[]
menuBar(), tk[]setPalette(),
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\OT1/cmr/m/n/12 date[]idletasks(), wait[]variable(), wait[]visibility(), wait[]
window(), wait-var(), winfo[]atom(),
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\OT1/cmr/m/n/12 winfo[]atomname(), winfo[]cells(), winfo[]children(), winfo[]cl
ass(), winfo[]colormapfull(),
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\OT1/cmr/m/n/12 winfo[]containing(), winfo[]depth(), winfo[]exists(), winfo[]fp
ixels(), winfo[]geometry(),
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\OT1/cmr/m/n/12 winfo[]height(), winfo[]id(), winfo[]interps(), winfo[]ismapped
(), winfo[]manager(), winfo[]name(),
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\OT1/cmr/m/n/12 winfo[]parent(), winfo[]pathname(), winfo[]pixels(), winfo[]poi
nterx(), winfo[]pointerxy(),
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\OT1/cmr/m/n/12 winfo[]rooty(), winfo[]screen(), winfo[]screencells(), winfo[]s
creendepth(), winfo[]screenheight(),
 []


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\OT1/cmr/m/n/12 winfo[]screenmmheight(), winfo[]screenmmwidth(), winfo[]screenv
isual(), winfo[]screenwidth(),
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[300]
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[] 
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[301] [302] [303]
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\OT1/cmr/m/n/12 ure(), deletecom-mand(), event[]add(), event[]delete(), event[]
generate(), event[]info(),
 []


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\OT1/cmr/m/n/12 fo-cus(), fo-cus[]displayof(), fo-cus[]force(), fo-cus[]get(), 
fo-cus[]lastfor(), fo-cus[]set(), get-
 []


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\OT1/cmr/m/n/12 grab[]status(), grid[]bbox(), grid[]columnconfigure(), grid[]lo
cation(), grid[]propagate(),
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\OT1/cmr/m/n/12 grid[]rowconfigure(), grid[]size(), grid[]slaves(), im-age[]nam
es(), im-age[]types(), keys(),
 []


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\OT1/cmr/m/n/12 lift(), lower(), main-loop(), name-towid-get(), op-tion[]add(),
 op-tion[]clear(), op-tion[]get(),
 []


Overfull \hbox (9.65083pt too wide) in paragraph at lines 4419--4420
\OT1/cmr/m/n/12 op-tion[]readfile(), pack[]propagate(), pack[]slaves(), place[]
slaves(), prop-a-gate(), quit(),
 []


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\OT1/cmr/m/n/12 tk[]focusFollowsMouse(), tk[]focusNext(), tk[]focusPrev(), tk[]
menuBar(), tk[]setPalette(),
 []


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\OT1/cmr/m/n/12 date[]idletasks(), wait[]variable(), wait[]visibility(), wait[]
window(), wait-var(), winfo[]atom(),
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\OT1/cmr/m/n/12 winfo[]atomname(), winfo[]cells(), winfo[]children(), winfo[]cl
ass(), winfo[]colormapfull(),
 []


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\OT1/cmr/m/n/12 winfo[]containing(), winfo[]depth(), winfo[]exists(), winfo[]fp
ixels(), winfo[]geometry(),
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\OT1/cmr/m/n/12 winfo[]height(), winfo[]id(), winfo[]interps(), winfo[]ismapped
(), winfo[]manager(), winfo[]name(),
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\OT1/cmr/m/n/12 winfo[]parent(), winfo[]pathname(), winfo[]pixels(), winfo[]poi
nterx(), winfo[]pointerxy(),
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\OT1/cmr/m/n/12 winfo[]rooty(), winfo[]screen(), winfo[]screencells(), winfo[]s
creendepth(), winfo[]screenheight(),
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\OT1/cmr/m/n/12 winfo[]screenmmheight(), winfo[]screenmmwidth(), winfo[]screenv
isual(), winfo[]screenwidth(),
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[304] [305]
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\OT1/cmr/m/n/12 ure(), deletecom-mand(), event[]add(), event[]delete(), event[]
generate(), event[]info(),
 []


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\OT1/cmr/m/n/12 fo-cus(), fo-cus[]displayof(), fo-cus[]force(), fo-cus[]get(), 
fo-cus[]lastfor(), fo-cus[]set(), get-
 []


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\OT1/cmr/m/n/12 grab[]status(), grid[]bbox(), grid[]columnconfigure(), grid[]lo
cation(), grid[]propagate(),
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\OT1/cmr/m/n/12 grid[]rowconfigure(), grid[]size(), grid[]slaves(), im-age[]nam
es(), im-age[]types(), keys(),
 []


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\OT1/cmr/m/n/12 lift(), lower(), main-loop(), name-towid-get(), op-tion[]add(),
 op-tion[]clear(), op-tion[]get(),
 []


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\OT1/cmr/m/n/12 op-tion[]readfile(), pack[]propagate(), pack[]slaves(), place[]
slaves(), prop-a-gate(), quit(),
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\OT1/cmr/m/n/12 tk[]focusFollowsMouse(), tk[]focusNext(), tk[]focusPrev(), tk[]
menuBar(), tk[]setPalette(),
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\OT1/cmr/m/n/12 date[]idletasks(), wait[]variable(), wait[]visibility(), wait[]
window(), wait-var(), winfo[]atom(),
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\OT1/cmr/m/n/12 winfo[]atomname(), winfo[]cells(), winfo[]children(), winfo[]cl
ass(), winfo[]colormapfull(),
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\OT1/cmr/m/n/12 winfo[]containing(), winfo[]depth(), winfo[]exists(), winfo[]fp
ixels(), winfo[]geometry(),
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\OT1/cmr/m/n/12 winfo[]height(), winfo[]id(), winfo[]interps(), winfo[]ismapped
(), winfo[]manager(), winfo[]name(),
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\OT1/cmr/m/n/12 winfo[]parent(), winfo[]pathname(), winfo[]pixels(), winfo[]poi
nterx(), winfo[]pointerxy(),
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\OT1/cmr/m/n/12 winfo[]rooty(), winfo[]screen(), winfo[]screencells(), winfo[]s
creendepth(), winfo[]screenheight(),
 []


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\OT1/cmr/m/n/12 winfo[]screenmmheight(), winfo[]screenmmwidth(), winfo[]screenv
isual(), winfo[]screenwidth(),
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[306]
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[] 
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[307] [308]
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\OT1/cmr/m/n/12 ure(), deletecom-mand(), event[]add(), event[]delete(), event[]
generate(), event[]info(),
 []


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\OT1/cmr/m/n/12 fo-cus[]displayof(), fo-cus[]force(), fo-cus[]get(), fo-cus[]la
stfor(), fo-cus[]set(), get-boolean(),
 []


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\OT1/cmr/m/n/12 get-var(), grab[]current(), grab[]release(), grab[]set(), grab[
]set[]global(), grab[]status(),
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\OT1/cmr/m/n/12 grid[]bbox(), grid[]columnconfigure(), grid[]location(), grid[]
propagate(), grid[]rowconfigure(),
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\OT1/cmr/m/n/12 grid[]size(), grid[]slaves(), im-age[]names(), im-age[]types(),
 keys(), lift(), lower(), main-
 []


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\OT1/cmr/m/n/12 loop(), name-towid-get(), op-tion[]add(), op-tion[]clear(), op-
tion[]get(), op-tion[]readfile(),
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\OT1/cmr/m/n/12 se-lec-tion[]own[]get(), send(), set-var(), size(), slaves(), t
k[]bisque(), tk[]focusFollowsMouse(),
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\OT1/cmr/m/n/12 tk[]focusNext(), tk[]focusPrev(), tk[]menuBar(), tk[]setPalette
(), tk[]strictMotif(), tkraise(),
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\OT1/cmr/m/n/12 un-bind(), un-bind[]all(), un-bind[]class(), up-date(), up-date
[]idletasks(), wait[]variable(),
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\OT1/cmr/m/n/12 wait[]visibility(), wait[]window(), wait-var(), winfo[]atom(), 
winfo[]atomname(), winfo[]cells(),
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\OT1/cmr/m/n/12 winfo[]children(), winfo[]class(), winfo[]colormapfull(), winfo
[]containing(), winfo[]depth(),
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\OT1/cmr/m/n/12 winfo[]exists(), winfo[]fpixels(), winfo[]geometry(), winfo[]he
ight(), winfo[]id(), winfo[]interps(),
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\OT1/cmr/m/n/12 winfo[]ismapped(), winfo[]manager(), winfo[]name(), winfo[]pare
nt(), winfo[]pathname(),
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\OT1/cmr/m/n/12 winfo[]pixels(), winfo[]pointerx(), winfo[]pointerxy(), winfo[]
pointery(), winfo[]reqheight(),
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\OT1/cmr/m/n/12 winfo[]reqwidth(), winfo[]rgb(), winfo[]rootx(), winfo[]rooty()
, winfo[]screen(), winfo[]screencells(),
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