schrodinger.livedesign.convert module

class schrodinger.livedesign.convert.Format(value)[source]

Bases: enum.Enum

An enumeration.

SDF = 1
SMILES = 2
CXSMILES = 3
SMARTS = 4
INCHI = 5
schrodinger.livedesign.convert.convert(data: str, input_format: schrodinger.livedesign.convert.Format, output_format: schrodinger.livedesign.convert.Format) → str[source]

Main entrypoint for converting one serialization to another. A few convience functions are provided below for common LD conversions.

Parameters

  • data – input text string

  • input_format – expected format for input string

  • output_format – desired format for output string

Returns

converted text string

schrodinger.livedesign.convert.sdf_to_rdkit(molblock: str) → Union[rdkit.Chem.rdchem.Mol, rdkit.Chem.rdChemReactions.ChemicalReaction][source]
Parameters

molblock – given SDF or RXN molblock

Returns

corresponding RDKit mol or reaction

schrodinger.livedesign.convert.rdkit_to_sdf(mol: rdkit.Chem.rdchem.Mol, kekulize: bool = True) → str[source]
Parameters

  • input – given RDKit mol

  • kekulize – whether to kekulize mol

Returns

corresponding SDF molblock

schrodinger.livedesign.convert.rdkit_to_cxsmiles(mol: rdkit.Chem.rdchem.Mol) → str[source]
Parameters

mol – given RDKit mol

Returns

corresponding CXSMILES stripped of coordinates

schrodinger.livedesign.convert.get_sd_reader(molblock: str) → Generator[rdkit.Chem.rdchem.Mol, None, None][source]
Parameters

molblock – string of SDF molblocks

Returns

generator that provides mols from SDF molblcoks

schrodinger.livedesign.convert.atom_has_attachment_point(atom)[source]
schrodinger.livedesign.convert.reapply_molblock_wedging(mol)[source]
schrodinger.livedesign.convert.add_hs_to_aromatic_nitrogen(mol)[source]

Intended to be used with molecules which have kekulization failures due to aromatic system(s) containing Ns where the user hasn’t provided the location of the implicit Hs in the system.

This picks an arbitrary (but canonical) aromatic N to add an H to in each aromatic system.

Returns the original mol if it can’t fix it.

schrodinger.livedesign.convert.is_polymer(s_group)[source]
schrodinger.livedesign.convert.add_polymer_brackets(mol, revert_to_mol=None, keep_existing_brackets=False)[source]

Add polymer brackets back to mol.

Parameters

  • mol – RDKit mol to add polymer brackets to

  • revert_to_mol – RDKit mol to revert to if polymer brackets cannot be added correctly to provided mol. This will occur when brackets cross more than one bond.

  • keep_existing_brackets – whether to recalculate the positions of brackets that are already present

Returns

RDKit mol with polymer brackets