Requires numpy, keras and mdtraj
Example:
encodetraj -i traj_fit.xtc -p reference.pdb -boxx 1 -boxy 1 -boxz 1 -testset 0.2 \
-low low.txt -high high.txt -filter filtered -model model -epochs 1000
Usage:
usage: encodetraj [-h] [-i INFILE] [-p INTOP] [-boxx BOXX] [-boxy BOXY]
[-boxz BOXZ] [-testset TESTSET] [-shuffle SHUFFLE]
[-layers LAYERS] [-layer1 LAYER1] [-layer2 LAYER2]
[-encdim ENCDIM] [-actfun1 ACTFUN1] [-actfun2 ACTFUN2]
[-optim OPTIM] [-loss LOSS] [-epochs EPOCHS]
[-batch BATCH] [-low LOWFILE] [-high HIGHFILE]
[-filter FILTERFILE] [-model MODELFILE]
[-plumed PLUMEDFILE]
Autoencoders for molecular trajectory analysis, requires numpy, keras and mdtraj
optional arguments:
-h, --help show this help message and exit
-i INFILE Input trajectory in pdb, xtc, trr, dcd, netcdf or mdcrd,
WARNING: the trajectory must be 1. centered in the PBC
box, 2. fitted to a reference structure and 3. must
contain only atoms to be analysed!
-p INTOP Input topology in pdb, WARNING: the structure must be 1.
centered in the PBC box and 2. must contain only atoms
to be analysed!
-boxx BOXX Size of x coordinate of PBC box (from 0 to set value in
nm)
-boxy BOXY Size of y coordinate of PBC box (from 0 to set value in
nm)
-boxz BOXZ Size of z coordinate of PBC box (from 0 to set value in
nm)
-testset TESTSET Size of test set (fraction of the trajectory, default =
0.1)
-shuffle SHUFFLE Shuffle trajectory frames to obtain training and test
set (default True)
-layers LAYERS Number of encoding layers (same as number of decoding,
allowed values 2-3, default = 2)
-layer1 LAYER1 Number of neurons in the second encoding layer (default
= 256)
-layer2 LAYER2 Number of neurons in the third encoding layer (default =
256)
-encdim ENCDIM Encoding dimension (default = 3)
-actfun1 ACTFUN1 Activation function of the first layer (default =
sigmoid, for options see keras documentation)
-actfun2 ACTFUN2 Activation function of the second layer (default =
sigmoid, for options see keras documentation)
-optim OPTIM Optimizer (default = adam, for options see keras
documentation)
-loss LOSS Loss function (default = mean_squared_error, for options
see keras documentation)
-epochs EPOCHS Number of epochs (default = 100, >1000 may be necessary
for real life applications)
-batch BATCH Batchsize (0 = no batches, default = 256)
-low LOWFILE Output file with low-dimensional embedings (xvg or txt,
default = no output)
-high HIGHFILE Output file with original coordinates and encoded-
decoded coordinates (xvg or txt, default = no output)
-filter FILTERFILE Output file with encoded-decoded trajectory in .xtc
format (default = no output)
-model MODELFILE Prefix for output model files (experimental, default =
no output)
-plot PLOTFILE Model plot file in png (default = no output)
-plumed PLUMEDFILE Output file for Plumed (default = no output)