Package: chytorch
Chytorch [kʌɪtɔːrtʃ]Library for modeling molecules and reactions in torch way.InstallationUsepip install chytorchto install release version.Orpip install .in source code directory to install DEV version.Pretrained modelsChytorch main package doesn't include models zoo.
Each model has its own named package and can be installed separately.
Installed models can be imported asfrom chytorch.zoo.<model_name> import Model.Usagechytorch.nn.MoleculeEncoderandchytorch.nn.ReactionEncoder- core graphormer layers for molecules and reactions.
API is combination oftorch.nn.TransformerEncoderLayerwithtorch.nn.TransformerEncoder.Batch preparation:chytorch.utils.data.MoleculeDatasetandchytorch.utils.data.ReactionDataset- Map-like on-the-fly dataset generators for molecules and reactions.
Supportedchython.MoleculeContainerandchython.ReactionContainerobjects, and bytes-packed structures.chytorch.utils.data.collate_moleculesandchytorch.utils.data.collate_reactions- collate functions fortorch.utils.data.DataLoader.Note: torch DataLoader automatically do proper collation since 1.13 release.Example:from chytorch.utils.data import MoleculeDataset, SMILESDataset
from torch.utils.data import DataLoader

data = ['CCO', 'CC=O']
ds = MoleculeDataset(SMILESDataset(data, cache={}))
dl = DataLoader(ds, batch_size=10)Forward call:Molecules coded as tensors of:atoms numbers shifted by 2 (e.g. hydrogen = 3).
0 - reserved for padding, 1 - reserved for CLS token, 2 - extra reservation.neighbors count, including implicit hydrogens shifted by 2 (e.g. CO = CH3OH = [6, 4]).
0 - reserved for padding, 1 - extra reservation, 2 - no-neighbors, 3 - one neighbor.topological distances' matrix shifted by 2 with upper limit.
0 - reserved for padding, 1 - reserved for not-connected graph components coding, 2 - self-loop, 3 - connected atoms.Reactions coded in similar way. Molecules atoms and neighbors matrices just stacked. Distance matrices stacked on diagonal.
Reactions include additional tensor with reaction role codes for each token.
0 - padding, 1 - reaction CLS, 2 - reactants, 3 - products.from chytorch.nn import MoleculeEncoder

encoder = MoleculeEncoder()
for b in dl:
    encoder(b)Combine molecules and labels:chytorch.utils.data.chained_collate- helper for combining different data parts. Useful for tricky input.from torch import stack
from torch.utils.data import DataLoader, TensorDataset
from chytorch.utils.data import chained_collate, collate_molecules, MoleculeDataset

dl = DataLoader(TensorDataset(MoleculeDataset(molecules_list), properties_tensor),
    collate_fn=chained_collate(collate_molecules, stack))Scheduler:chytorch.optim.lr_scheduler.WarmUpCosine- Linear warmup followed with cosine-function for 0-pi range rescaled to lr_rate - decrease_coef * lr_rate interval.Voting NN with single hidden layer:chytorch.nn.VotingClassifier,chytorch.nn.BinaryVotingClassifierandchytorch.nn.VotingRegressor- speed optimized multiple heads for ensemble predictions.Helper Modules:chytorch.nn.Slicer- do tensor slicing. Useful for transformer's CLS token extraction intorch.nn.Sequence.Data Wrappers:Inchytorch.utils.datamodule stored different data wrappers for simplifying ML workflows.
All wrappers havetorch.utils.data.Datasetinterface.SizedList- list wrapper withsize()method. Useful withtorch.utils.data.TensorDataset.SMILESDataset- on-the-fly smiles tochython.MoleculeContainerorchython.ReactionContainerparser.LMDBMapper- LMDB KV storage to dataset mapper.PostgresMapper- Postgres DB table to dataset mapper.SMILESTokenizerDataset- on-the-fly generator of tokenized SMILES.TensorUnpack,StructUnpack,PickleUnpack- bytes to tensor/object unpackersPublications1Bidirectional Graphormer for Reactivity Understanding: Neural Network Trained to Reaction Atom-to-Atom Mapping Task