py2sterimol.utils package
Submodules
py2sterimol.utils.functions module
- py2sterimol.utils.functions.smiles_and_pdb_to_verloop(smiles: str, pdb: str) str
Take a smiles string and pdb file and return the equivalent Verloop-encoded input card.
- Args:
smiles (str): SMILES string pdb (str): Filepath to pdb
- Returns:
str: Verloop-encoded string.
Example:
( “
- “
“1
- “
“HC(RC(H,H,H),RC(H,H,H),RC(H,H,H))
- “
“3
- “
“180.0 180.0 180.0
“)
py2sterimol.utils.lookuptables module
Usage: First key is the type of atom, second key is the bonds on the atom. Final resulting symbol is what sterimol uses to refer to that atom.
atom_and_bonds_to_symbol[“C”][(2, 1, 1)] -> “C2” - ethylene carbon
- py2sterimol.utils.lookuptables.atom_and_bonds_to_symbol = {'Br': {1: 'B1'}, 'C': {(1, 1, 1, 1): 'C', (2, 2, 1): 'C6', (2, 2, 1, 1): 'C8', (2, 2, 2): 'C66', (3, 1): 'C3', (3, 2, 1): 'C7', (3, 3, 1): 'C5', (4, 2, 1): 'C4'}, 'Cl': {1: 'C1'}, 'F': {1: 'F'}, 'H': {(1, 5): 'H'}, 'I': {1: 'I'}, 'N': {(1, 1, 1, 1): 'N', (2, 2, 1): 'N6', (3, 3, 1): 'N5', (5, 4, 1): 'N4'}, 'O': {(1, 1): 'O', 2: 'O2'}, 'P': {(1, 1, 1, 1): 'P'}, 'S': {(1, 1): 'S', (1, 1, 1, 1): 'S4', (1, 1, 1, 1, 1, 1): 'S1'}}
Usage: simple lookup for bond value to symbol for sterimol