group_decomposition.utils

utils.py

Various utilities used in fragmenting molecules - retrieving information from molecules Identifying small parts of molecules, and tools for minor manipulations of SMILES or molecules

Functions

add_cml_atoms_bonds(el_list, bond_list)	create a molecule from cml file, building it one atom at a time then adding in bond orders.
all_data_from_cml(data)	Gets symbols, xyz coords, bonds and charge of a mol from cml file
data_from_cml(cml_file[, bonds])	Gets symbols, xyz coords, bonds and charge of a mol from cml file
get_canonical_molecule(smile)	Ensures that molecule numbering is consistent with creating molecule from canonical SMILES for consistency.
get_cml_atom_types(cml_file)	Extract atom types from cml file
get_molecules_atomicnum(molecule)	Given molecule object, get list of atomic numbers.
get_molecules_atomsinrings(molecule)	Given molecule object, get Boolean list of if atoms are in a ring.
link_molecules(mol_1, mol_2, dl_1, dl_2)	Given two mols, each with dummy atoms that have dummyAtomLabels, link the molecules between the dummy atoms specified by labels dl_1 and dl_2
list_to_str(lst)	Convert a list to string.
mol_from_cml(cml_file[, input_type])	Creates a molecule from a cml file and returns atoms, xyz and types
mol_from_molfile(mol_file)	takes mol_file and returns mol wth atom numbers the same
mol_from_xyzfile(xyz_file, cml_file)	Attempt to create a molecule from an xyz file by automatically determining bond orders
mol_with_atom_index(mol)	Label a molecule with map numbers for order atoms are in molecule.
smiles_from_cml(cml_file[, smile_tag])	Finds the Retreivium SMILES in a cml file with a given label
trim_placeholders(rwmol)	Given Chem.RWmol, remove atoms with atomic number 0.
xyz_from_cml(cml_file)	Extract xyz coordinates from cml file
xyz_list_to_str(xyz_list)	Convert 2d array to string [[a,b,c],[d,e,f]] -> a, b, c d, e, f