Python create_atom_types Examples

Example #1

from nose.tools import assert_equal, assert_true, assert_false
import logging
from rmgpy.molecule.element import PeriodicSystem
from rmgpy.molecule.atomtype import atomTypes
from rmgpy.molecule.atomtypedatabase import create_atom_types

import itertools
import unittest
from external.wip import work_in_progress
from rmgpy.molecule.molecule import Molecule
from rmgpy.molecule.group import Group

molecule_atom_types = ['C', 'O', 'N', 'S', 'Si', 'Cl', 'I', 'F']
group_atomtypes = {}

for item in create_atom_types():
    group_atomtypes[item.label] = item


def get_multiplicity(unpaired_electrons):
    '''
    2*s + 1, with s = 1/2
    
    = unpaired electrons + 1 
    '''
    return unpaired_electrons + 1


def get_lone_pairs(atom_type):
    if atom_type in group_atomtypes:
        return group_atomtypes[atom_type].lp  #

Example #2

File: isomorphismTest.py Project: ReactionMechanismGenerator/RMG-Py

from nose.tools import assert_equal, assert_true, assert_false
import logging
from rmgpy.molecule.element import PeriodicSystem
from rmgpy.molecule.atomtype import atomTypes
from rmgpy.molecule.atomtypedatabase import create_atom_types 
  
import itertools
import unittest
from external.wip import work_in_progress
from rmgpy.molecule.molecule import Molecule
from rmgpy.molecule.group import Group

molecule_atom_types           = [ 'C', 'O', 'N', 'S', 'Si', 'Cl', 'I', 'F']
group_atomtypes = {}

for item in create_atom_types() :
    group_atomtypes[item.label] = item
    
def get_multiplicity(unpaired_electrons):
    '''
    2*s + 1, with s = 1/2
    
    = unpaired electrons + 1 
    '''
    return unpaired_electrons+1

def get_lone_pairs(atom_type):
    if atom_type in group_atomtypes:
        return group_atomtypes[atom_type].lp#
    return PeriodicSystem.lone_pairs[atom_type]