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# coding: utf-8 

# Copyright (c) Pymatgen Development Team. 

# Distributed under the terms of the MIT License. 

 

from __future__ import unicode_literals 

 

""" 

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 

from six.moves import zip 

 

__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 

""" 

 

def __init__(self): 

pass 

 

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. 

 

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. 

""" 

 

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): 

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): 

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 = set([tuple(sorted(b)) 

for b in 

list(itertools.chain(*[list(itertools.combinations(p, 2)) 

for p in all_13_bond_atoms]))]) 

bonds_13 = all_2_and_13_bonds - set([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): 

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): 

return MoleculeStructureComparator( 

bond_length_cap=d["bond_length_cap"], 

covalent_radius=d["covalent_radius"], 

priority_bonds=d["priority_bonds"], 

priority_cap=d["priority_cap"])