e3fp.conformer.util module¶
Utilities for handling SMILES strings and RDKit mols and conformers.
Author: Seth Axen E-mail: seth.axen@gmail.com
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class
MolItemName
(mol_name=None, proto_state_num=None, conf_num=None, proto_delim='-', conf_delim='_')[source]¶ Bases:
object
Class for parsing mol item names and converting to various formats.
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property
conf_name
¶
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classmethod
from_str
(mol_item_name, mol_item_regex=re.compile('(?P<mol_name>.+?)(?:-(?P<proto_state_num>\\d+))?(?:_(?P<conf_num>\\d+))?$'), mol_item_fields=('mol_name', 'proto_state_num', 'conf_num'), **kwargs)[source]¶
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property
mol_item_name
¶
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static
mol_item_name_to_dict
(mol_item_name, mol_item_regex=re.compile('(?P<mol_name>.+?)(?:-(?P<proto_state_num>\\d+))?(?:_(?P<conf_num>\\d+))?$'), mol_item_fields=('mol_name', 'proto_state_num', 'conf_num'))[source]¶
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property
mol_name
¶
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property
proto_name
¶
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property
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class
MolItemTuple
(mol_name, proto_state_num, conf_num)¶ Bases:
tuple
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property
conf_num
¶ Alias for field number 2
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property
mol_name
¶ Alias for field number 0
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property
proto_state_num
¶ Alias for field number 1
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property
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add_conformer_energies_to_mol
(mol, energies)[source]¶ Add conformer energies as mol property.
See discussion at https://sourceforge.net/p/rdkit/mailman/message/27547551/
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mol2_generator
(*filenames)[source]¶ Parse name from mol2 filename and return generator.
- Parameters
files (iterable object) – List of mol2 files, where filename should be molecule name followed by “.mol2”
- Yields
tuple – tuple of the format (file, name).
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mol_from_mol2
(mol2_file, name=None, standardise=False)[source]¶ Read a mol2 file into an RDKit
PropertyMol
.- Parameters
mol2_file (str) – path to a mol2 file
name (str, optional) – Name of molecule. If not provided, uses file basename as name
standardise (bool) – Clean mol through standardisation
- Returns
RDKit PropertyMol
- Return type
Molecule.
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mol_from_sdf
(sdf_file, conf_num=None, standardise=False)[source]¶ Read SDF file into an RDKit Mol object.
- Parameters
sdf_file (str) – Path to an SDF file
conf_num (int or None, optional) – Maximum number of conformers to read from file. Defaults to all.
standardise (bool (default False)) – Clean mol through standardisation
- Returns
RDKit Mol
- Return type
Mol object with each molecule in SDF file as a conformer
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mol_from_smiles
(smiles, name, standardise=False)[source]¶ Generate a n RDKit
PropertyMol
from SMILES string.- Parameters
smile (str) – SMILES string
name (str) – Name of molecule
standardise (bool) – Clean Mol through standardisation
- Returns
RDKit PropertyMol
- Return type
Molecule.
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mol_to_sdf
(mol, out_file, conf_num=None)[source]¶ Write RDKit Mol objects to an SDF file.
- Parameters
mol (RDKit Mol) – A molecule containing 1 or more conformations to write to file.
out_file (str) – Path to save SDF file.
conf_num (int or None, optional) – Maximum number of conformers to save to file. Defaults to all.