luna.MyBio.util module¶

biopython_entity_to_mol(entity, select=<Select all>, validate_mol=True, standardize_mol=True, template=None, add_h=False, ph=None, break_metal_bonds=False, mol_obj_type='rdkit', wrapped=True, openbabel='obabel', tmp_path=None, keep_tmp_files=False)[source]¶

Convert an object Entity to a molecular object (MolWrapper, rdkit.Chem.rdchem.Mol, or openbabel.pybel.Molecule).

Parameters

entity (Entity) – The entity to be converted.
select (Select) – Decide which atoms will be consired. By default, all atoms are accepted.
validate_mol (bool) – If True, validate the converted molecule with MolValidator.
standardize_mol (bool) – If True, standardize the converted molecule. Currently, only residues are standardized as it uses luna.mol.standardiser.ResiduesStandardiser by default.
template (luna.mol.template.Template, optional) – Fix the converted molecule’s bond order based on the bond orders in a template molecule. The template should implement assign_bond_order().
add_h (bool) – If True, add hydrogen to the converted molecule.
ph (float, optional) – Add hydrogens considering pH ph.
break_metal_bonds (bool) – If True, remove covalent bonds between residues and metals and fix the residue bond order.
mol_obj_type ({“rdkit”, “openbabel”}) – If “rdkit”, parse the converted molecule with RDKit and return an instance of rdkit.Chem.rdchem.Mol. If “openbabel”, parse the converted molecule with Open Babel and return an instance of openbabel.pybel.Molecule. If wrapped is True, the molecular object will be wrapped with MolWrapper.
wrapped (bool) – If True, wrap the molecular object with MolWrapper.
openbabel (str) – Pathname to Open Babel. Even if mol_obj_type is set to ‘rdkit’, this function uses Open Babel to properly parse PDB files and to add hydrogens to the molecule considering different pHs.
tmp_path (str) – A temporary directory to where temporary files will be saved. If not provided, the system’s default temporary directory will be used instead.
keep_tmp_files (bool) – If True, keep all temporary files. Otherwise, removes them in the end.

Returns

mol_obj (MolWrapper, rdkit.Chem.rdchem.Mol, or openbabel.pybel.Molecule) – The converted molecule.
ignored_atoms (list) – List of ignored atoms. Currently, ignored atoms may contain only metals.

download_pdb(pdb_id, output_path='.', overwrite=False)[source]¶

Download a PDB file from RCSB.org.

Parameters

pdb_id (str) – 4-symbols structure Id from PDB (e.g. 3J92).
output_path (str) – Put the PDB file in this directory.
overwrite (bool) – If True, overwrite any existing PDB files.

entity_to_string(entity, select=<Select all>, write_conects=True, write_end=True, preserve_atom_numbering=True)[source]¶

Convert a Structure object (or a subset of a Structure object) to string.

This function works on a structural level. That means if entity is not a Structure object, the structure will be recovered directly from entity. Therefore, use select to select specific chains, residues, and atoms from the structure object.

Parameters

entity (Entity) – The PDB object to be converted.
select (Select) – Decides which atoms will be saved at the output. By default, all atoms are accepted.
write_conects (bool) – If True, writes CONECT records.
write_end (bool) – If True, writes the END record.
preserve_atom_numbering (bool) – If True, preserve the atom numbering. Otherwise, re-enumerate the atom serial numbers.

Returns

The converted entity.

Return type

str

get_entity_from_entry(entity, entry, model=0)[source]¶

Get a Chain or Residue instance based on the provided entry entry.

Parameters

entity (Entity) – The PDB object to recover the target entry from.
entry (Entry) – The target entry.
model (int) – The PDB model where the entry could be found. The default value is 0.

Returns

The target entry.

Return type

Entity

Raises

MoleculeNotFoundError – If the entry’s molecule was not found in entity.
ChainNotFoundError – If the entry’s chain was not found in entity.

get_residue_cov_bonds(residue, select=<Select all>)[source]¶

Get covalently bound atoms from residues or other molecules.

Parameters

residue (Residue) – The residue or other molecule from which covalently bound atoms will be recovered.
select (Select) – Decides which atoms will be consired. By default, all atoms are accepted.

Returns

List of pairs of covalently bound atoms.

Return type

list of tuple(Atom, Atom)

get_residue_neighbors(residue, select=<Select all>)[source]¶

Get all neighbors from a residue.

In the case of an amino acid that is part of a peptide bond, its neighbors are any predecessor or successor residues. The same idea applies to nucleic acids.

Parameters

residue (Residue) – The residue or other molecule from which covalently bound molecules will be recovered.
select (Select) – Decides which atoms will be consired. By default, all atoms are accepted.

Returns

neighbors – A dictionary containing the predecessor (previous) or successor (next) molecules.

Return type

dict of {str : Residue}

is_covalently_bound(atm1, atm2)[source]¶: Verifies if atoms atm1 and atm2 are covalently bound.

parse_from_file(pdb_id, file)[source]¶

Read a PDB file and return a Structure object.

Parameters

pdb_id (str) – The structure identifier.
file (str) – Pathname of the PDB file.

Returns

structure – The parsed PDB file as a Structure object.

Return type

Structure

Raises

PDBNotReadError – If the PDB file could not be parsed.

save_to_file(entity, output_file, select=<Select all>, write_conects=True, write_end=True, preserve_atom_numbering=True)[source]¶

Write a Structure object (or a subset of a Structure object) into a file.

Parameters

entity (Entity) – The PDB object to be saved.
output_file (str) – Save the selected atoms to this file.
select (Select) – Decide which atoms will be saved at the PDB output. By default, all atoms are accepted.
write_conects (bool) – If True, write CONECT records.
write_end (bool) – If True, write the END record.
preserve_atom_numbering (bool) – If True, preserve the atom numbering. Otherwise, re-enumerate the atom serial numbers.