To use this you will need to install either:
into your python environment.
Then:
-
download(git clone) this source code
-
install it into your python environment: cd into thee root directory of this package
pip install .
General purpose helper classes around the RDKit and openeye toolkits for handling molecular input files. This packages tries to abstract the toolkits away and thus provides a toolkit independent interface to dealing with molecular files and, to some extend, with molecule objects.
The underlying toolkit used can be determined with the CDDLIB_TOOLKIT enviroment variable. It defaults to openeye, but if loading the openeye package fails it will try to fall back to the RDKit library.
The package is still under development but here is an example on how to get started:
from cddlib.chem.io import get_mol_input_stream, get_mol_output_stream
# open input and output files
# Note: output will be to stdout as only file extension is given
with get_mol_input_stream('tests/data/test_CCCO_confs.sdf') as inFile, \
get_mol_output_stream('.sdf') as outFile:
# loop over input molecules
for mol in inFile:
mol['numAtoms'] = len(mol.atoms) # set new sd tag value
outFile.write_mol(mol) # write to output file
Various utility modules.
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