schrodinger.livedesign.convert module

schrodinger.livedesign.convert.convert(data: str, input_format: schrodinger.rdkit_extensions.Format, output_format: schrodinger.rdkit_extensions.Format, additional_properties: Optional[Dict] = None) → str

Main entrypoint for converting one serialization to another. A few convenience 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.set_properties(mol: rdkit.Chem.rdchem.Mol, new_props: dict)
Parameters

  • mol – molecule to set given properties on

  • new_props – map of properties to add onto the molecule

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

molblock – given MDL or MDL RXN

Returns

corresponding RDKit mol or reaction

schrodinger.livedesign.convert.rdkit_to_sdf(mol: rdkit.Chem.rdchem.Mol) → str
Parameters

input – given RDKit mol

Returns

corresponding sdf molblock

schrodinger.livedesign.convert.get_sd_reader(molblocks: str) → Iterator[Union[rdkit.Chem.rdchem.Mol, ValueError]]
Parameters

molblocks – string of sdf molblocks

Returns

generator that provides mols from sdf molblocks or ValueError if the SDF cannot be read

schrodinger.livedesign.convert.add_hs_to_aromatic_nitrogen(mol)

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)
schrodinger.livedesign.convert.clean_up_polymer_brackets(mol, revert_to_mol=None, keep_existing_brackets=False)

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

schrodinger.livedesign.convert.rdkit_to_fasta(mol: rdkit.Chem.rdchem.Mol) → str

Stub function intended to eventually call an rdkit-based polymer sequence extraction function to convert an rdmol into a FASTA sequence file.

For now, it expects a single coarse-grain rdmol with single-letter monomer names. It treats all sequences as proteins for the convenience of using ProteinAlignment.

Parameters

input – given RDKit mol

Returns

corresponding FASTA string

schrodinger.livedesign.convert.get_nucleobase_atoms(atoms: iter[Chem.rdchem.Atom]) → list[Chem.rdchem.Atom]

Get the nucleobase atoms from a list of atoms

Parameters

atoms – a list of course-grain atoms

Returns

a list of nucleobase atoms

schrodinger.livedesign.convert.get_monomer_names(atoms: iter[Chem.rdchem.Atom]) → list[str]

Get the monomer names from a list of atoms

Parameters

atoms – a list of course-grain atoms

Returns

a list of monomer names

schrodinger.livedesign.convert.get_seq_object(monomer_names: list[str], polymer_type: PolymerType) → sequence.Sequence

Get a sequence object of the appropriate type from a list of monomer names

Parameters

  • monomer_names – a list of single-letter monomer names

  • polymer_type – the origin polymer type of the monomers

Returns

a sequence object consisting of the supplied monomers