MolecularDiffusion.utils.xyz2mol.converter¶

Attributes¶

`atomic_valence`
`atomic_valence_electrons`
`av`
`elemdatabase`
`rdEHTTools`
`valence_electrons`

Functions¶

`AC2BO`(AC, atoms, charge[, allow_charged_fragments, ...])	implemenation of algorithm shown in Figure 2
`AC2mol`(mol, AC, atoms, charge[, ...])
`BO2mol`(mol, BO_matrix, atoms, ...[, ...])	based on code written by Paolo Toscani
`BO_is_OK`(BO, AC, charge, DU, atomic_valence_electrons, ...)	Sanity of bond-orders
`charge_is_OK`(BO, AC, charge, DU, ...[, ...])
`chiral_stereo_check`(mol)	Find and embed chiral information into the model based on the coordinates
`clean_charges`(mol)	This hack should not be needed anymore, but is kept just in case
`get_BO`(AC, UA, DU, valences, UA_pairs[, use_graph])
`get_UA`(maxValence_list, valence_list)
`get_UA_pairs`(UA, AC[, use_graph])
`get_atomic_charge`(atom, atomic_valence_electrons, ...)
`get_atomic_valences`(k)
`get_bonds`(UA, AC)
`get_proto_mol`(atoms)
`int_atom`(atom)	convert str atom to integer atom
`read_xyz_file`(filename[, look_for_charge])
`set_atomic_charges`(mol, atoms, ...)
`set_atomic_radicals`(mol, atoms, ...)	The number of radical electrons = absolute atomic charge
`str_atom`(atom)	convert integer atom to string atom
`valences_not_too_large`(BO, valences)
`xyz2mol`(atoms, coordinates, AC, covalent_factor[, ...])	Generate a rdkit molobj from atoms, coordinates and a total_charge.

Module Contents¶

MolecularDiffusion.utils.xyz2mol.converter.AC2BO(AC, atoms, charge, allow_charged_fragments=True, use_graph=True)¶: implemenation of algorithm shown in Figure 2 UA: unsaturated atoms DU: degree of unsaturation (u matrix in Figure) best_BO: Bcurr in Figure

MolecularDiffusion.utils.xyz2mol.converter.AC2mol(mol, AC, atoms, charge, allow_charged_fragments=True, use_graph=True)¶

MolecularDiffusion.utils.xyz2mol.converter.BO2mol(mol, BO_matrix, atoms, atomic_valence_electrons, mol_charge, allow_charged_fragments=True)¶

based on code written by Paolo Toscani

From bond order, atoms, valence structure and total charge, generate an rdkit molecule.

Parameters:

molecule (mol_charge - total charge of)
molecule
symbols (atoms - list of integer atomic)
- (atomic_valence_electrons)
molecule

optional:: allow_charged_fragments - bool - allow charged fragments
returns: mol - updated rdkit molecule with bond connectivity

MolecularDiffusion.utils.xyz2mol.converter.BO_is_OK(BO, AC, charge, DU, atomic_valence_electrons, atoms, valences, allow_charged_fragments=True)¶

Sanity of bond-orders

Parameters:

- (DU)
-
-
-

optional: allow_charges_fragments -

Returns:: boolean - true of molecule is OK, false if not

MolecularDiffusion.utils.xyz2mol.converter.charge_is_OK(BO, AC, charge, DU, atomic_valence_electrons, atoms, valences, allow_charged_fragments=True)¶

MolecularDiffusion.utils.xyz2mol.converter.chiral_stereo_check(mol)¶

Find and embed chiral information into the model based on the coordinates

Parameters:

molecule (mol - rdkit)
conformer (with embeded)

MolecularDiffusion.utils.xyz2mol.converter.clean_charges(mol)¶: This hack should not be needed anymore, but is kept just in case

MolecularDiffusion.utils.xyz2mol.converter.get_BO(AC, UA, DU, valences, UA_pairs, use_graph=True)¶

MolecularDiffusion.utils.xyz2mol.converter.get_UA(maxValence_list, valence_list)¶

MolecularDiffusion.utils.xyz2mol.converter.get_UA_pairs(UA, AC, use_graph=True)¶

MolecularDiffusion.utils.xyz2mol.converter.get_atomic_charge(atom, atomic_valence_electrons, BO_valence)¶

MolecularDiffusion.utils.xyz2mol.converter.get_atomic_valences(k)¶

MolecularDiffusion.utils.xyz2mol.converter.get_bonds(UA, AC)¶

MolecularDiffusion.utils.xyz2mol.converter.get_proto_mol(atoms)¶

MolecularDiffusion.utils.xyz2mol.converter.int_atom(atom)¶: convert str atom to integer atom

MolecularDiffusion.utils.xyz2mol.converter.read_xyz_file(filename, look_for_charge=True)¶

MolecularDiffusion.utils.xyz2mol.converter.set_atomic_charges(mol, atoms, atomic_valence_electrons, BO_valences, BO_matrix, mol_charge)¶

MolecularDiffusion.utils.xyz2mol.converter.set_atomic_radicals(mol, atoms, atomic_valence_electrons, BO_valences)¶: The number of radical electrons = absolute atomic charge

MolecularDiffusion.utils.xyz2mol.converter.str_atom(atom)¶: convert integer atom to string atom

MolecularDiffusion.utils.xyz2mol.converter.valences_not_too_large(BO, valences)¶

MolecularDiffusion.utils.xyz2mol.converter.xyz2mol(atoms, coordinates, AC, covalent_factor, charge=0, allow_charged_fragments=True, use_graph=True, use_huckel=False, embed_chiral=True, exportBO=False)¶

Generate a rdkit molobj from atoms, coordinates and a total_charge.

Parameters:

types (atoms - list of atom)
coordinates (coordinates - 3xN Cartesian)
(default (charge - total charge of the system) –

optional:: allow_charged_fragments - alternatively radicals are made use_graph - use graph (networkx) use_huckel - Use Huckel method for atom connectivity prediction embed_chiral - embed chiral information to the molecule

Returns:: mols - list of rdkit molobjects

MolecularDiffusion.utils.xyz2mol.converter.atomic_valence¶

MolecularDiffusion.utils.xyz2mol.converter.atomic_valence_electrons¶

MolecularDiffusion.utils.xyz2mol.converter.av = [3, 4]¶

MolecularDiffusion.utils.xyz2mol.converter.elemdatabase¶

MolecularDiffusion.utils.xyz2mol.converter.rdEHTTools = None¶

MolecularDiffusion.utils.xyz2mol.converter.valence_electrons = []¶