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molecule_structure_comparator.py
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molecule_structure_comparator.py
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# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes to comparsion the structures of the two
molecule. As long as the two molecule have the same bond connection tables,
the molecules are deemed to be same. The atom in the two molecule must be
paired accordingly.
This module is supposed to perform rough comparisons with the atom order
correspondence prerequisite, while molecule_matcher is supposed to do exact
comparisons without the atom order correspondence prerequisite.
"""
import itertools
from monty.json import MSONable
__author__ = "Xiaohui Qu"
__copyright__ = "Copyright 2011, The Materials Project"
__version__ = "1.0"
__maintainer__ = "Xiaohui Qu"
__email__ = "xhqu1981@gmail.com"
__status__ = "Experimental"
__date__ = "Jan 22, 2014"
class CovalentRadius:
"""
Covalent Radius of the elements.
Beatriz C. et al. Dalton Trans. 2008, 2832-2838. DOI: 10.1039/b801115j
"""
radius = {
"H": 0.31,
"He": 0.28,
"Li": 1.28,
"Be": 0.96,
"B": 0.84,
"C": 0.73,
"N": 0.71,
"O": 0.66,
"F": 0.57,
"Ne": 0.58,
"Na": 1.66,
"Mg": 1.41,
"Al": 1.21,
"Si": 1.11,
"P": 1.07,
"S": 1.05,
"Cl": 1.02,
"Ar": 1.06,
"K": 2.03,
"Ca": 1.76,
"Sc": 1.70,
"Ti": 1.60,
"V": 1.53,
"Cr": 1.39,
"Mn": 1.50,
"Fe": 1.42,
"Co": 1.38,
"Ni": 1.24,
"Cu": 1.32,
"Zn": 1.22,
"Ga": 1.22,
"Ge": 1.20,
"As": 1.19,
"Se": 1.20,
"Br": 1.20,
"Kr": 1.16,
"Rb": 2.20,
"Sr": 1.95,
"Y": 1.90,
"Zr": 1.75,
"Nb": 1.64,
"Mo": 1.54,
"Tc": 1.47,
"Ru": 1.46,
"Rh": 1.42,
"Pd": 1.39,
"Ag": 1.45,
"Cd": 1.44,
"In": 1.42,
"Sn": 1.39,
"Sb": 1.39,
"Te": 1.38,
"I": 1.39,
"Xe": 1.40,
"Cs": 2.44,
"Ba": 2.15,
"La": 2.07,
"Ce": 2.04,
"Pr": 2.03,
"Nd": 2.01,
"Pm": 1.99,
"Sm": 1.98,
"Eu": 1.98,
"Gd": 1.96,
"Tb": 1.94,
"Dy": 1.92,
"Ho": 1.92,
"Er": 1.89,
"Tm": 1.90,
"Yb": 1.87,
"Lu": 1.87,
"Hf": 1.75,
"Ta": 1.70,
"W": 1.62,
"Re": 1.51,
"Os": 1.44,
"Ir": 1.41,
"Pt": 1.36,
"Au": 1.36,
"Hg": 1.32,
"Tl": 1.45,
"Pb": 1.46,
"Bi": 1.48,
"Po": 1.40,
"At": 1.50,
"Rn": 1.50,
"Fr": 2.60,
"Ra": 2.21,
"Ac": 2.15,
"Th": 2.06,
"Pa": 2.00,
"U": 1.96,
"Np": 1.90,
"Pu": 1.87,
"Am": 1.80,
"Cm": 1.69,
}
class MoleculeStructureComparator(MSONable):
"""
Class to check whether the connection tables of the two molecules are the
same. The atom in the two molecule must be paired accordingly.
"""
ionic_element_list = [
"Na",
"Mg",
"Al",
"Sc",
"V",
"Cr",
"Mn",
"Fe",
"Co",
"Ni",
"Cu",
"Zn",
"Ga",
"Rb",
"Sr",
]
halogen_list = ["F", "Cl", "Br", "I"]
def __init__(
self,
bond_length_cap=0.3,
covalent_radius=CovalentRadius.radius,
priority_bonds=(),
priority_cap=0.8,
ignore_ionic_bond=True,
bond_13_cap=0.05,
):
"""
Args:
bond_length_cap: The ratio of the elongation of the bond to be
acknowledged. If the distance between two atoms is less than (
empirical covalent bond length) X (1 + bond_length_cap), the bond
between the two atoms will be acknowledged.
covalent_radius: The covalent radius of the atoms.
dict (element symbol -> radius)
priority_bonds: The bonds that are known to be existed in the initial
molecule. Such bonds will be acknowledged in a loose criteria.
The index should start from 0.
priority_cap: The ratio of the elongation of the bond to be
acknowledged for the priority bonds.
"""
self.bond_length_cap = bond_length_cap
self.covalent_radius = covalent_radius
self.priority_bonds = [tuple(sorted(b)) for b in priority_bonds]
self.priority_cap = priority_cap
self.ignore_ionic_bond = ignore_ionic_bond
self.ignore_halogen_self_bond = True
self.bond_13_cap = bond_13_cap
def are_equal(self, mol1, mol2):
"""
Compare the bond table of the two molecules.
Args:
mol1: first molecule. pymatgen Molecule object.
mol2: second moleculs. pymatgen Molecule objec.
"""
b1 = set(self._get_bonds(mol1))
b2 = set(self._get_bonds(mol2))
return b1 == b2
@staticmethod
def get_13_bonds(priority_bonds):
"""
Args:
priority_bonds ():
Returns:
"""
all_bond_pairs = list(itertools.combinations(priority_bonds, r=2))
all_2_bond_atoms = [set(b1 + b2) for b1, b2 in all_bond_pairs]
all_13_bond_atoms = [a for a in all_2_bond_atoms if len(a) == 3]
all_2_and_13_bonds = {
tuple(sorted(b)) for b in itertools.chain(*[itertools.combinations(p, 2) for p in all_13_bond_atoms])
}
bonds_13 = all_2_and_13_bonds - {tuple(b) for b in priority_bonds}
return tuple(sorted(bonds_13))
def _get_bonds(self, mol):
"""
Find all the bond in a molcule
Args:
mol: the molecule. pymatgen Molecule object
Returns:
List of tuple. Each tuple correspond to a bond represented by the
id of the two end atoms.
"""
num_atoms = len(mol)
# index starting from 0
if self.ignore_ionic_bond:
covalent_atoms = [i for i in range(num_atoms) if mol.species[i].symbol not in self.ionic_element_list]
else:
covalent_atoms = list(range(num_atoms))
all_pairs = list(itertools.combinations(covalent_atoms, 2))
pair_dists = [mol.get_distance(*p) for p in all_pairs]
elements = mol.composition.as_dict().keys()
unavailable_elements = list(set(elements) - set(self.covalent_radius.keys()))
if len(unavailable_elements) > 0:
raise ValueError("The covalent radius for element {} is not " "available".format(unavailable_elements))
bond_13 = self.get_13_bonds(self.priority_bonds)
max_length = [
(self.covalent_radius[mol.sites[p[0]].specie.symbol] + self.covalent_radius[mol.sites[p[1]].specie.symbol])
* (
1
+ (
self.priority_cap
if p in self.priority_bonds
else (self.bond_length_cap if p not in bond_13 else self.bond_13_cap)
)
)
* (
0.1
if (
self.ignore_halogen_self_bond
and p not in self.priority_bonds
and mol.sites[p[0]].specie.symbol in self.halogen_list
and mol.sites[p[1]].specie.symbol in self.halogen_list
)
else 1.0
)
for p in all_pairs
]
bonds = [bond for bond, dist, cap in zip(all_pairs, pair_dists, max_length) if dist <= cap]
return bonds
def as_dict(self):
"""
Returns: MSONable dict
"""
return {
"version": __version__,
"@module": self.__class__.__module__,
"@class": self.__class__.__name__,
"bond_length_cap": self.bond_length_cap,
"covalent_radius": self.covalent_radius,
"priority_bonds": self.priority_bonds,
"priority_cap": self.priority_cap,
}
@classmethod
def from_dict(cls, d):
"""
Args:
d (dict): Dict representation
Returns:
MoleculeStructureComparator
"""
return MoleculeStructureComparator(
bond_length_cap=d["bond_length_cap"],
covalent_radius=d["covalent_radius"],
priority_bonds=d["priority_bonds"],
priority_cap=d["priority_cap"],
)