Complete

API

rdworks.stereoisomers

Functions

correct_wedged_bonds(rdmol)

Corrects wedged bonds for chiral centers. Args: rdmol (Chem.Mol): input molecule.

1. Clear all stereochemistry information
2. Identify chiral centers and non-chiral atoms/bonds
3. Reassign stereochemistry only where appropriate
4. Return the modified molecule

enumerate_ring_bond_stereoisomers(rdmol, ring_bond_stereo_info, override=False)

Enumerates unspecified double bond stereochemistry (cis/trans).

Small rings (< 8 atoms): RDKit does NOT enumerate E/Z stereochemistry for double bonds because the ring constraints make one configuration impossible

Macrocycles (≥ 8 atoms): RDKit CAN enumerate E/Z stereochemistry for double bonds since both configurations are geometrically feasible

Parameters:

• rdmol (Mol) –

  input molecule.

• ring_bond_stereo_info (List[Tuple]) –

  ring_bond_stereo_info will be set when .remove_stereo() is called. bond_stereo_info = [(bond_idx, bond_stereo_descriptor), ..] where bond_stereo_descriptor is Chem.StereoDescriptor.Bond_Cis or Chem.StereoDescriptor.Bond_Trans, or Chem.StereoDescriptor.NoValue.

• override (bool, default: False ) –

  description. Defaults to False.

Returns:

• list[Mol] –

  List[Chem.Mol]: list of enumerated stereoisomers.

enumerate_stereoisomers(rdmol)

Returns enumerated stereoisomers.

Parameters:

• rdmol (Mol) –

  input molecule.

Returns:

• list[Mol] –

  List[Chem.Mol]: a list of enumerated stereoisomers.

rdworks.tautomerism

Reference:

D. K. Dhaked, W.-D. Ihlenfeldt, H. Patel, V. Delannée, M. C. Nicklaus, Toward a Comprehensive Treatment of Tautomerism in Chemoinformatics Including in InChI V2. J. Chem. Inf. Model. (2020). https://doi.org/10.1021/acs.jcim.9b01080.

https://github.com/xundrug/moltaut

Classes

ComprehensiveTautomers

Comprehensive tautomer enumeration based on MolTaut implementation D. K. Dhaked, W.-D. Ihlenfeldt, H. Patel, V. Delannée, M. C. Nicklaus, Toward a Comprehensive Treatment of Tautomerism in Chemoinformatics Including in InChI V2. J. Chem. Inf. Model. (2020). https://doi.org/10.1021/acs.jcim.9b01080.

Attributes

device = None instance-attribute

dict = {'self': [self.smiles]} instance-attribute

enumerated = [] instance-attribute

forbidden = ['O=[N+]([O-])'] class-attribute instance-attribute

forbidden_patterns = [(Chem.MolFromSmarts(_)) for _ in forbidden] class-attribute instance-attribute

imodel = None instance-attribute

microstates = [] instance-attribute

nmodel = None instance-attribute

num_confs = None instance-attribute

optimizer = None instance-attribute

ordered = [] instance-attribute

popular = [] instance-attribute

ps = Chem.SmilesParserParams() class-attribute instance-attribute

rdmol = Chem.MolFromSmiles(smiles) instance-attribute

revdict = defaultdict(list) instance-attribute

smiles = smiles instance-attribute

smirks = [(line.strip().split('\t')) for line in contents] instance-attribute

states = [] instance-attribute

uncharger = rdMolStandardize.Uncharger() class-attribute instance-attribute

Functions

enumerate()

RdkTautomers

RDKit built-in tautomer enumeration

M. Sitzmann, W.-D. Ihlenfeldt, M. C. Nicklaus, Tautomerism in large databases. J. Comput. Aided Mol. Des. 24, 521-551 (2010).

Attributes

enumerator = rdMolStandardize.TautomerEnumerator() instance-attribute

rdmol = Chem.MolFromSmiles(smiles) instance-attribute

smiles = smiles instance-attribute

Functions

canonicalize()

enumerate()

rdworks.std

Functions

clean_2d(rdmol, reset_isotope=True, remove_H=True)

Clean molecule for 2D depiction.

Parameters:

• rdmol (Mol) –

  molecule (not to be modified)

• reset_isotope (bool, default: True ) –

  whether to reset isotope information. Defaults to True.

• remove_H (bool, default: True ) –

  whether to remove implicit hydrogens. Defaults to True.

Returns:

• tuple[Mol, list[Mol]] –

  (cleaned copy of molecule, list of Chem.Mol.Conformers from molecule)

desalt_smiles(smiles)

Remove salt(s) from SMILES.

Parameters:

• smiles (str) –

  SMILES.

Returns:

• tuple[str, Mol] –

  (desalted SMILES, desalted Chem.Mol)

generate_inchi_key(rdmol)

Generate InChIKey.

Note

• An InChIKey is a 27-character string consisting of three parts:
  • 14 characters: Derived from the connectivity layer of the InChI.
  • Hyphen (-): Separates the first two blocks.
  • 9 characters: Derived from the remaining InChI layers.
  • A hyphen (-): Separates the second and third blocks.
  • A final checksum character: Ensures the integrity of the key.

Parameters:

• rdmol (Mol) –

  input molecule

Returns:

• str ( str ) –

  27-character InChIKey

neutralize_atoms(rdmol)

Neutralizes atoms.

It is adapted from Noel O'Boyle's nocharge code: rdkit cookbook, no charge. It is a neutralization by atom approach and neutralizes atoms with a +1 or -1 charge by removing or adding hydrogen where possible. The SMARTS pattern checks for a hydrogen in +1 charged atoms and checks for no neighbors with a negative charge (for +1 atoms) and no neighbors with a positive charge (for -1 atoms), this is to avoid altering molecules with charge separation (e.g., nitro groups).

The neutralize_atoms() function differs from the rdMolStandardize.Uncharger behavior. See the MolVS documentation for Uncharger.

This class uncharges molecules by adding and/or removing hydrogens. In cases where there is a positive charge that is not neutralizable, any corresponding negative charge is also preserved. As an example, rdMolStandardize.Uncharger will not change charges on CN+(C)CCC([O-])=O, as there is a positive charge that is not neutralizable. In contrast, the neutralize_atoms() function will attempt to neutralize any atoms it can (in this case to CN+(C)CCC(=O)O). That is, neutralize_atoms() ignores the overall charge on the molecule, and attempts to neutralize charges even if the neutralization introduces an overall formal charge on the molecule.

Parameters:

• rdmol (Chem.Mol) –

  molecule (not to be modified).

Returns:

• Mol –

  Chem.Mol: neutralized copy of molecule.

standardize(rdmol)

Returns standardized rdkit.Chem.Mol object.

Parameters:

• smiles (str) –

  input SMILES string.

Returns:

• Mol –

  Chem.Mol: standardized rdkit.Chem.Mol object.

standardize_smiles(smiles)

Returns standardized SMILES string.

The rdMolStandardize.StandardizeSmiles() function performs the following steps:

1. mol = Chem.MolFromSmiles(sm)
2. Chem.SanitizeMol(mol)
3. mol = Chem.RemoveHs(mol)
4. mol = rdMolStandardize.MetalDisconnector().Disconnect(mol)
5. mol = rdMolStandardize.Normalize(mol)
6. mol = rdMolStandardize.Reionize(mol)
7. Chem.AssignStereochemistry(mol, force=True, cleanIt=True)
8. Chem.MolToSmiles(mol)

See rdkit notebook and greg's notebook, and youtube video.

Parameters:

• smiles (str) –

  input SMILES string.

Returns:

• str ( str ) –

  standardized SMILES string.