Parametric time-lagged tSNE. The code fits the input trajectory to a reference PDB file. Next, it introduces a time lag in the spirit of time-lagged independent component analysis (TICA) method. Finally, it optimizes parameters of an artificial neural network to provide tSNE representation as the output. It is possible to specify box that fits the molecule, time lag and neural network hyperparameters.
It uses Keras, PyTorch, MDtraj, and numpy.
Usage:
-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!
-lag LAGTIME Time lag in number of frames (default 1)
-maxpcs MAXPCS Number of TICA coordinates to be passed to t-SNE
(default 50)
-dim EMBED_DIM Number of output dimensions (default 2)
-perplex PERPLEX Value of t-SNE perplexity (default 30.0)
-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)
-nofit NOFIT Disable fitting, the trajectory must be properly fited
(default False)
-layers LAYERS Number of hidden layers (allowed values 1-3, default =
1)
-layer1 LAYER1 Number of neurons in the first encoding layer (default
= 256)
-layer2 LAYER2 Number of neurons in the second encoding layer
(default = 256)
-layer3 LAYER3 Number of neurons in the third encoding layer (default
= 256)
-actfun1 ACTFUN1 Activation function of the first layer (default =
sigmoid, for options see keras documentation)
-actfun2 ACTFUN2 Activation function of the second layer (default =
linear, for options see keras documentation)
-actfun3 ACTFUN3 Activation function of the third layer (default =
linear, for options see keras documentation)
-optim OPTIM Optimizer (default = adam, for options see keras
documentation)
-epochs EPOCHS Number of epochs (default = 100, >1000 may be
necessary for real life applications)
-shuffle_interval SHUFFLE_INTERVAL
Shuffle interval (default = number of epochs + 1)
-batch BATCH_SIZE Batch size (0 = no batches, default = 0)
-o OFILE Output file with values of t-SNE embeddings (txt,
default = no output)
-plumed PLUMEDFILE Output file for Plumed (default = plumed.dat)
-plumed2 PLUMEDFILE2 Output file for Plumed >= 2.6 (default - no output)