schrodinger.protein.helm.monomer_db_converter module

Script to convert an existing monomer database into a database that’s supported by the monomer apis.

As a starting point, We assume that users have monomer data in SDF (molfile), MAE, JSON, or XML format, and that they use the same fields that Pistioa does.

Use $SCHRODINGER/run python3 -m schrodinger.protein.helm.monomer_db_converter [OPTIONS] to invoke this script.

e.g.:

$SCHRODINGER/run python3 -m schrodinger.protein.helm.monomer_db_converter monomerLib2.0.sdf new.db $SCHRODINGER/run python3 -m schrodinger.protein.helm.monomer_db_converter monomers.xml new.db

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.protein.helm.monomer_db_converter.PrintFieldsAction(option_strings, dest='==SUPPRESS==', default='==SUPPRESS==', help=None, **kwargs)

Bases: Action

Help-like actuion to print the database field names and definitions.

__init__(option_strings, dest='==SUPPRESS==', default='==SUPPRESS==', help=None, **kwargs)

schrodinger.protein.helm.monomer_db_converter.add_arguments(parser)

schrodinger.protein.helm.monomer_db_converter.assign_pdb_name_to_residue(mol: Mol) → str

Assigns PDB residue name and atom names to the given RDKit molecule, assuming the structure is a single residue.

Parameters:

mol (Chem.Mol) – The RDKit molecule to assign PDB residue name to.

Returns:

The PDB residue name.

schrodinger.protein.helm.monomer_db_converter.get_mol(mol, properties: dict) → Mol

Some monomer DB have monomers as SMILES in a property on and as SDF

class schrodinger.protein.helm.monomer_db_converter.InteractiveFixer(mol, props, entry_data)

Bases: object

Wrap functions in the monomer_db_validation module to allow interaction

Wraps and exposes all validate_* functions in monomer_db_validation, retaining the same signature and functionality. However, if a validation error is raised, give the user the option to update the value.

__init__(mol, props, entry_data)

schrodinger.protein.helm.monomer_db_converter.process_monomer(mol: Mol, default: dict, mapping: dict, interactive: bool = False) → dict

schrodinger.protein.helm.monomer_db_converter.read_monomers(filename: str)

schrodinger.protein.helm.monomer_db_converter.convert_nsr(st: Structure) → Mol

Convert a Structure from a _nsr.mae file into a Mol with the conventional properties needed by the monomer database: symbol, name, monomer_type, polymer_type, as well as the atom mapping numbers used to tag the attachment points.

For the purpose of this function, the input Structure MUST consist of a single residue with a non-empty name; also, atoms SHOULD have names, at least one of which should be N or OXT, which define the attachment points.

schrodinger.protein.helm.monomer_db_converter.get_atoms_by_name(mol: Mol) → dict[str, int]

Return a dict mapping from PDB atom name to atom index.

schrodinger.protein.helm.monomer_db_converter.main(argv=None)

schrodinger.protein.helm.monomer_db_converter.core(opts)