add cycle_break attribute to molsetup Bond #254
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and tuple_to_string to fix dihedral (tuple of ints) as key problem in json
Use utility functions in jsonutils to fix #151 (dihedrals)
Revision of default templates: Fixes and Disambiguation for inconsistent residue names in CHARMM
Add keyword argument `rename_atoms` to `MoleculePreparation.prepare` and make option avail in CLI script
…g and warning msg
preparator = MoleculePreparation.from_config(config); minor edits to help msg
… MoleculePreparation.from_config(config); minor edits to help msg
minor fix in error msg
fix the special handling of some agrs that unexpectly end up with default (without referring to config)
Read Partial Charges from mol2 and SDF
docs: cli args override config file params
Format string in output file with plain line-ending character instead of os.linesep
don't max out substructure matches at 1000
in mk_prepare_ligand.py
Catch prepare errors without interrupting batch processing
graph and ring_corners
Remove dependencies from setup.py
…ol() to reduce overhead
Remove from class Ring the unused attributes to reduce overhead in molecule preparation
4 tasks
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This is to support a more general macrocyle bond breaking scheme in future autodock, which does not depend on atom types such as CG0/G0. Adds option
untyped_macrocycletoMoleculePreparationto skip assigning the CG/G types, and to allow any rotatable bond to be broken for macrocycle sampling, instead of allowing only bonds between atoms of type C.