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molecule.py
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molecule.py
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#!/usr/bin/env python
# encoding: utf-8
################################################################################
#
# RMG - Reaction Mechanism Generator
#
# Copyright (c) 2009-2011 by the RMG Team (rmg_dev@mit.edu)
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the 'Software'),
# to deal in the Software without restriction, including without limitation
# the rights to use, copy, modify, merge, publish, distribute, sublicense,
# and/or sell copies of the Software, and to permit persons to whom the
# Software is furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
# DEALINGS IN THE SOFTWARE.
#
################################################################################
"""
This module provides classes and methods for working with molecules and
molecular configurations. A molecule is represented internally using a graph
data type, where atoms correspond to vertices and bonds correspond to edges.
Both :class:`Atom` and :class:`Bond` objects store semantic information that
describe the corresponding atom or bond.
"""
import cython
import logging
import os
import re
import numpy
import urllib
from collections import OrderedDict
import element as elements
try:
import openbabel
except:
pass
from rdkit import Chem
from .graph import Vertex, Edge, Graph, getVertexConnectivityValue
import rmgpy.molecule.group as gr
from .atomtype import AtomType, atomTypes, getAtomType, AtomTypeError
import rmgpy.constants as constants
import rmgpy.molecule.parser as parser
import rmgpy.molecule.generator as generator
import rmgpy.molecule.resonance as resonance
################################################################################
bond_orders = {'S': 1, 'D': 2, 'T': 3}
globals().update({
'bond_orders': bond_orders,
})
class Atom(Vertex):
"""
An atom. The attributes are:
=================== =================== ====================================
Attribute Type Description
=================== =================== ====================================
`atomType` :class:`AtomType` The :ref:`atom type <atom-types>`
`element` :class:`Element` The chemical element the atom represents
`radicalElectrons` ``short`` The number of radical electrons
`charge` ``short`` The formal charge of the atom
`label` ``str`` A string label that can be used to tag individual atoms
`coords` ``numpy array`` The (x,y,z) coordinates in Angstrom
`lonePairs` ``short`` The number of lone electron pairs
=================== =================== ====================================
Additionally, the ``mass``, ``number``, and ``symbol`` attributes of the
atom's element can be read (but not written) directly from the atom object,
e.g. ``atom.symbol`` instead of ``atom.element.symbol``.
"""
def __init__(self, element=None, radicalElectrons=0, charge=0, label='', lonePairs=-100, coords=numpy.array([])):
Vertex.__init__(self)
if isinstance(element, str):
self.element = elements.__dict__[element]
else:
self.element = element
self.radicalElectrons = radicalElectrons
self.charge = charge
self.label = label
self.atomType = None
self.lonePairs = lonePairs
self.coords = coords
def __str__(self):
"""
Return a human-readable string representation of the object.
"""
return '{0}{1}{2}'.format(
str(self.element),
'.' * self.radicalElectrons,
'+' * self.charge if self.charge > 0 else '-' * -self.charge,
)
def __repr__(self):
"""
Return a representation that can be used to reconstruct the object.
"""
return "<Atom '{0}'>".format(str(self))
def __reduce__(self):
"""
A helper function used when pickling an object.
"""
d = {
'edges': self.edges,
'connectivity1': self.connectivity1,
'connectivity2': self.connectivity2,
'connectivity3': self.connectivity3,
'sortingLabel': self.sortingLabel,
'atomType': self.atomType.label if self.atomType else None,
'lonePairs': self.lonePairs,
}
return (Atom, (self.element.symbol, self.radicalElectrons, self.charge, self.label), d)
def __setstate__(self, d):
"""
A helper function used when unpickling an object.
"""
self.edges = d['edges']
self.connectivity1 = d['connectivity1']
self.connectivity2 = d['connectivity2']
self.connectivity3 = d['connectivity3']
self.sortingLabel = d['sortingLabel']
self.atomType = atomTypes[d['atomType']] if d['atomType'] else None
self.lonePairs = d['lonePairs']
@property
def mass(self): return self.element.mass
@property
def number(self): return self.element.number
@property
def symbol(self): return self.element.symbol
@property
def bonds(self): return self.edges
def equivalent(self, other):
"""
Return ``True`` if `other` is indistinguishable from this atom, or
``False`` otherwise. If `other` is an :class:`Atom` object, then all
attributes except `label` must match exactly. If `other` is an
:class:`GroupAtom` object, then the atom must match any of the
combinations in the atom pattern.
"""
cython.declare(atom=Atom, ap=gr.GroupAtom)
if isinstance(other, Atom):
atom = other
return (
self.element is atom.element and
self.radicalElectrons == atom.radicalElectrons and
self.lonePairs == atom.lonePairs and
self.charge == atom.charge
)
elif isinstance(other, gr.GroupAtom):
cython.declare(a=AtomType, radical=cython.short, lp=cython.short, charge=cython.short)
ap = other
for a in ap.atomType:
if self.atomType.equivalent(a): break
else:
return False
if ap.radicalElectrons:
for radical in ap.radicalElectrons:
if self.radicalElectrons == radical: break
else:
return False
if ap.lonePairs:
for lp in ap.lonePairs:
if self.lonePairs == lp: break
else:
return False
if ap.charge:
for charge in ap.charge:
if self.charge == charge: break
else:
return False
return True
def getDescriptor(self):
return (self.getAtomConnectivityValue(), self.number)
def getAtomConnectivityValue(self):
return -1*self.connectivity
def isSpecificCaseOf(self, other):
"""
Return ``True`` if `self` is a specific case of `other`, or ``False``
otherwise. If `other` is an :class:`Atom` object, then this is the same
as the :meth:`equivalent()` method. If `other` is an
:class:`GroupAtom` object, then the atom must match or be more
specific than any of the combinations in the atom pattern.
"""
if isinstance(other, Atom):
return self.equivalent(other)
elif isinstance(other, gr.GroupAtom):
cython.declare(atom=gr.GroupAtom, a=AtomType, radical=cython.short, lp = cython.short, charge=cython.short)
atom = other
if self.atomType is None:
return False
for a in atom.atomType:
if self.atomType.isSpecificCaseOf(a): break
else:
return False
if atom.radicalElectrons:
for radical in atom.radicalElectrons:
if self.radicalElectrons == radical: break
else:
return False
if atom.lonePairs:
for lp in atom.lonePairs:
if self.lonePairs == lp: break
else:
return False
if atom.charge:
for charge in atom.charge:
if self.charge == charge: break
else:
return False
return True
def copy(self):
"""
Generate a deep copy of the current atom. Modifying the
attributes of the copy will not affect the original.
"""
cython.declare(a=Atom)
#a = Atom(self.element, self.radicalElectrons, self.spinMultiplicity, self.charge, self.label)
a = Atom.__new__(Atom)
a.edges = {}
a.resetConnectivityValues()
a.element = self.element
a.radicalElectrons = self.radicalElectrons
a.charge = self.charge
a.label = self.label
a.atomType = self.atomType
a.lonePairs = self.lonePairs
a.coords = self.coords[:]
return a
def isHydrogen(self):
"""
Return ``True`` if the atom represents a hydrogen atom or ``False`` if
not.
"""
return self.element.number == 1
def isNonHydrogen(self):
"""
Return ``True`` if the atom does not represent a hydrogen atom or
``False`` if not.
"""
return self.element.number > 1
def isCarbon(self):
"""
Return ``True`` if the atom represents a carbon atom or ``False`` if
not.
"""
return self.element.number == 6
def isNitrogen(self):
"""
Return ``True`` if the atom represents a nitrogen atom or ``False`` if
not.
"""
return self.element.number == 7
def isOxygen(self):
"""
Return ``True`` if the atom represents an oxygen atom or ``False`` if
not.
"""
return self.element.number == 8
def isSilicon(self):
"""
Return ``True`` if the atom represents an silicon atom or ``False`` if
not.
"""
return self.element.number == 14
def isSulfur(self):
"""
Return ``True`` if the atom represents an sulfur atom or ``False`` if
not.
"""
return self.element.number == 16
def incrementRadical(self):
"""
Update the atom pattern as a result of applying a GAIN_RADICAL action,
where `radical` specifies the number of radical electrons to add.
"""
# Set the new radical electron count
self.radicalElectrons += 1
if self.radicalElectrons <= 0:
raise gr.ActionError('Unable to update Atom due to GAIN_RADICAL action: Invalid radical electron set "{0}".'.format(self.radicalElectrons))
def decrementRadical(self):
"""
Update the atom pattern as a result of applying a LOSE_RADICAL action,
where `radical` specifies the number of radical electrons to remove.
"""
cython.declare(radicalElectrons=cython.short)
# Set the new radical electron count
radicalElectrons = self.radicalElectrons = self.radicalElectrons - 1
if radicalElectrons < 0:
raise gr.ActionError('Unable to update Atom due to LOSE_RADICAL action: Invalid radical electron set "{0}".'.format(self.radicalElectrons))
def setLonePairs(self,lonePairs):
"""
Set the number of lone electron pairs.
"""
# Set the number of electron pairs
self.lonePairs = lonePairs
if self.lonePairs < 0:
raise gr.ActionError('Unable to update Atom due to setLonePairs : Invalid lone electron pairs set "{0}".'.format(self.setLonePairs))
self.updateCharge()
def incrementLonePairs(self):
"""
Update the lone electron pairs pattern as a result of applying a GAIN_PAIR action.
"""
# Set the new lone electron pairs count
self.lonePairs += 1
if self.lonePairs <= 0:
raise gr.ActionError('Unable to update Atom due to GAIN_PAIR action: Invalid lone electron pairs set "{0}".'.format(self.lonePairs))
self.updateCharge()
def decrementLonePairs(self):
"""
Update the lone electron pairs pattern as a result of applying a LOSE_PAIR action.
"""
# Set the new lone electron pairs count
self.lonePairs -= 1
if self.lonePairs < 0:
raise gr.ActionError('Unable to update Atom due to LOSE_PAIR action: Invalid lone electron pairs set "{0}".'.format(self.lonePairs))
self.updateCharge()
def updateCharge(self):
"""
Update self.charge, according to the valence, and the
number and types of bonds, radicals, and lone pairs.
"""
valence_electron = elements.PeriodicSystem.valence_electrons[self.symbol]
order = self.getBondOrdersForAtom()
self.charge = valence_electron - order - self.radicalElectrons - 2*self.lonePairs
def applyAction(self, action):
"""
Update the atom pattern as a result of applying `action`, a tuple
containing the name of the reaction recipe action along with any
required parameters. The available actions can be found
:ref:`here <reaction-recipe-actions>`.
"""
# Invalidate current atom type
self.atomType = None
act = action[0].upper()
# Modify attributes if necessary
if act in ['CHANGE_BOND', 'FORM_BOND', 'BREAK_BOND']:
# Nothing else to do here
pass
elif act == 'GAIN_RADICAL':
for i in range(action[2]): self.incrementRadical()
elif act == 'LOSE_RADICAL':
for i in range(abs(action[2])): self.decrementRadical()
elif action[0].upper() == 'GAIN_PAIR':
for i in range(action[2]): self.incrementLonePairs()
elif action[0].upper() == 'LOSE_PAIR':
for i in range(abs(action[2])): self.decrementLonePairs()
else:
raise gr.ActionError('Unable to update Atom: Invalid action {0}".'.format(action))
def setSpinMultiplicity(self,spinMultiplicity):
"""
Set the spin multiplicity.
"""
raise NotImplementedError("I thought multiplicity was now a molecule attribute not atom?")
# Set the spin multiplicity
self.spinMultiplicity = spinMultiplicity
if self.spinMultiplicity < 0:
raise gr.ActionError('Unable to update Atom due to spin multiplicity : Invalid spin multiplicity set "{0}".'.format(self.spinMultiplicity))
self.updateCharge()
def getBondOrdersForAtom(self):
"""
This helper function is to help calculate total bond orders for an
input atom.
Some special consideration for the order `B` bond. For atoms having
three `B` bonds, the order for each is 4/3.0, while for atoms having other
than three `B` bonds, the order for each is 3/2.0
"""
num_B_bond = 0
order = 0
for _, bond in self.bonds.iteritems():
if bond.order == 'B':
num_B_bond += 1
else:
order += bond_orders[bond.order]
if num_B_bond == 3:
order += num_B_bond * 4/3.0
else:
order += num_B_bond * 3/2.0
return order
################################################################################
class Bond(Edge):
"""
A chemical bond. The attributes are:
=================== =================== ====================================
Attribute Type Description
=================== =================== ====================================
`order` ``str`` The :ref:`bond type <bond-types>`
=================== =================== ====================================
"""
def __init__(self, atom1, atom2, order='S'):
Edge.__init__(self, atom1, atom2)
self.order = order
def __str__(self):
"""
Return a human-readable string representation of the object.
"""
return self.order
def __repr__(self):
"""
Return a representation that can be used to reconstruct the object.
"""
return '<Bond "{0}">'.format(self.order)
def __reduce__(self):
"""
A helper function used when pickling an object.
"""
return (Bond, (self.vertex1, self.vertex2, self.order))
@property
def atom1(self):
return self.vertex1
@property
def atom2(self):
return self.vertex2
def equivalent(self, other):
"""
Return ``True`` if `other` is indistinguishable from this bond, or
``False`` otherwise. `other` can be either a :class:`Bond` or a
:class:`GroupBond` object.
"""
cython.declare(bond=Bond, bp=gr.GroupBond)
if isinstance(other, Bond):
bond = other
return (self.order == bond.order)
elif isinstance(other, gr.GroupBond):
bp = other
return (self.order in bp.order)
def isSpecificCaseOf(self, other):
"""
Return ``True`` if `self` is a specific case of `other`, or ``False``
otherwise. `other` can be either a :class:`Bond` or a
:class:`GroupBond` object.
"""
# There are no generic bond types, so isSpecificCaseOf is the same as equivalent
return self.equivalent(other)
def copy(self):
"""
Generate a deep copy of the current bond. Modifying the
attributes of the copy will not affect the original.
"""
#return Bond(self.vertex1, self.vertex2, self.order)
cython.declare(b=Bond)
b = Bond.__new__(Bond)
b.vertex1 = self.vertex1
b.vertex2 = self.vertex2
b.order = self.order
return b
def isSingle(self):
"""
Return ``True`` if the bond represents a single bond or ``False`` if
not.
"""
return self.order == 'S'
def isDouble(self):
"""
Return ``True`` if the bond represents a double bond or ``False`` if
not.
"""
return self.order == 'D'
def isTriple(self):
"""
Return ``True`` if the bond represents a triple bond or ``False`` if
not.
"""
return self.order == 'T'
def isBenzene(self):
"""
Return ``True`` if the bond represents a benzene bond or ``False`` if
not.
"""
return self.order == 'B'
def incrementOrder(self):
"""
Update the bond as a result of applying a CHANGE_BOND action to
increase the order by one.
"""
if self.order == 'S': self.order = 'D'
elif self.order == 'D': self.order = 'T'
else:
raise gr.ActionError('Unable to update Bond due to CHANGE_BOND action: Invalid bond order "{0}".'.format(self.order))
def decrementOrder(self):
"""
Update the bond as a result of applying a CHANGE_BOND action to
decrease the order by one.
"""
if self.order == 'D': self.order = 'S'
elif self.order == 'T': self.order = 'D'
else:
raise gr.ActionError('Unable to update Bond due to CHANGE_BOND action: Invalid bond order "{0}".'.format(self.order))
def __changeBond(self, order):
"""
Update the bond as a result of applying a CHANGE_BOND action,
where `order` specifies whether the bond is incremented or decremented
in bond order, and should be 1 or -1.
"""
if order == 1:
if self.order == 'S': self.order = 'D'
elif self.order == 'D': self.order = 'T'
else:
raise gr.ActionError('Unable to update Bond due to CHANGE_BOND action: Invalid bond order "{0}".'.format(self.order))
elif order == -1:
if self.order == 'D': self.order = 'S'
elif self.order == 'T': self.order = 'D'
else:
raise gr.ActionError('Unable to update Bond due to CHANGE_BOND action: Invalid bond order "{0}".'.format(self.order))
else:
raise gr.ActionError('Unable to update Bond due to CHANGE_BOND action: Invalid order "{0}".'.format(order))
def applyAction(self, action):
"""
Update the bond as a result of applying `action`, a tuple
containing the name of the reaction recipe action along with any
required parameters. The available actions can be found
:ref:`here <reaction-recipe-actions>`.
"""
if action[0].upper() == 'CHANGE_BOND':
if action[2] == 1:
self.incrementOrder()
elif action[2] == -1:
self.decrementOrder()
elif action[2] == 'B':
self.order = 'B'
else:
raise gr.ActionError('Unable to update Bond due to CHANGE_BOND action: Invalid order "{0}".'.format(action[2]))
else:
raise gr.ActionError('Unable to update GroupBond: Invalid action {0}.'.format(action))
#################################################################################
class Molecule(Graph):
"""
A representation of a molecular structure using a graph data type, extending
the :class:`Graph` class. The `atoms` and `bonds` attributes are aliases
for the `vertices` and `edges` attributes. Other attributes are:
======================= =========== ========================================
Attribute Type Description
======================= =========== ========================================
`symmetryNumber` ``int`` The (estimated) external + internal symmetry number of the molecule
`multiplicity` ``int`` The multiplicity of this species, multiplicity = 2*total_spin+1
======================= =========== ========================================
A new molecule object can be easily instantiated by passing the `SMILES` or
`InChI` string representing the molecular structure.
"""
def __init__(self, atoms=None, symmetry=-1, multiplicity=-187, props=None, SMILES=''):
Graph.__init__(self, atoms)
self.symmetryNumber = symmetry
self.multiplicity = multiplicity
self._fingerprint = None
self.InChI = ''
if SMILES != '': self.fromSMILES(SMILES)
self.props = props or {}
if multiplicity != -187: # it was set explicitly, so re-set it (fromSMILES etc may have changed it)
self.multiplicity = multiplicity
def __hash__(self):
return hash((self.getFingerprint()))
def __richcmp__(x, y, op):
if op == 2:#Py_EQ
return x.is_equal(y)
if op == 3:#Py_NE
return not x.is_equal(y)
else:
raise NotImplementedError("Can only check equality of molecules, not > or <")
def is_equal(self,other):
"""Method to test equality of two Molecule objects."""
if not isinstance(other, Molecule): return False #different type
elif self is other: return True #same reference in memory
elif self.getFingerprint() != other.getFingerprint(): return False
else:
return self.isIsomorphic(other)
def __str__(self):
"""
Return a human-readable string representation of the object.
"""
return '<Molecule "{0}">'.format(self.toSMILES())
def __repr__(self):
"""
Return a representation that can be used to reconstruct the object.
"""
cython.declare(multiplicity=cython.int)
multiplicity = self.multiplicity
if multiplicity != self.getRadicalCount() + 1:
return 'Molecule(SMILES="{0}", multiplicity={1:d})'.format(self.toSMILES(), multiplicity)
return 'Molecule(SMILES="{0}")'.format(self.toSMILES())
def __reduce__(self):
"""
A helper function used when pickling an object.
"""
return (Molecule, (self.vertices, self.symmetryNumber, self.multiplicity, self.props))
def __getAtoms(self): return self.vertices
def __setAtoms(self, atoms): self.vertices = atoms
atoms = property(__getAtoms, __setAtoms)
def addAtom(self, atom):
"""
Add an `atom` to the graph. The atom is initialized with no bonds.
"""
self._fingerprint = None
return self.addVertex(atom)
def addBond(self, bond):
"""
Add a `bond` to the graph as an edge connecting the two atoms `atom1`
and `atom2`.
"""
self._fingerprint = None
return self.addEdge(bond)
def getBonds(self, atom):
"""
Return a list of the bonds involving the specified `atom`.
"""
return self.getEdges(atom)
def getBond(self, atom1, atom2):
"""
Returns the bond connecting atoms `atom1` and `atom2`.
"""
return self.getEdge(atom1, atom2)
def hasAtom(self, atom):
"""
Returns ``True`` if `atom` is an atom in the graph, or ``False`` if
not.
"""
return self.hasVertex(atom)
def hasBond(self, atom1, atom2):
"""
Returns ``True`` if atoms `atom1` and `atom2` are connected
by an bond, or ``False`` if not.
"""
return self.hasEdge(atom1, atom2)
def removeAtom(self, atom):
"""
Remove `atom` and all bonds associated with it from the graph. Does
not remove atoms that no longer have any bonds as a result of this
removal.
"""
self._fingerprint = None
return self.removeVertex(atom)
def removeBond(self, bond):
"""
Remove the bond between atoms `atom1` and `atom2` from the graph.
Does not remove atoms that no longer have any bonds as a result of
this removal.
"""
self._fingerprint = None
return self.removeEdge(bond)
def sortAtoms(self):
"""
Sort the atoms in the graph. This can make certain operations, e.g.
the isomorphism functions, much more efficient.
"""
return self.sortVertices()
def update(self):
"""
Update connectivity values, atom types of atoms.
Update multiplicity, and sort atoms using the new
connectivity values.
"""
self.updateAtomTypes()
self.updateMultiplicity()
self.sortVertices()
def getFormula(self):
"""
Return the molecular formula for the molecule.
"""
cython.declare(atom=Atom, symbol=str, elements=dict, keys=list, formula=str)
cython.declare(hasCarbon=cython.bint, hasHydrogen=cython.bint)
# Count the number of each element in the molecule
hasCarbon = False; hasHydrogen = False
elements = {}
for atom in self.vertices:
symbol = atom.element.symbol
elements[symbol] = elements.get(symbol, 0) + 1
# Use the Hill system to generate the formula
formula = ''
# Carbon and hydrogen always come first if carbon is present
if hasCarbon:
count = elements['C']
formula += 'C{0:d}'.format(count) if count > 1 else 'C'
del elements['C']
if hasHydrogen:
count = elements['H']
formula += 'H{0:d}'.format(count) if count > 1 else 'H'
del elements['H']
# Other atoms are in alphabetical order
# (This includes hydrogen if carbon is not present)
keys = elements.keys()
keys.sort()
for key in keys:
count = elements[key]
formula += '{0}{1:d}'.format(key, count) if count > 1 else key
return formula
def getMolecularWeight(self):
"""
Return the molecular weight of the molecule in kg/mol.
"""
cython.declare(atom=Atom, mass=cython.double)
mass = 0
for atom in self.vertices:
mass += atom.element.mass
return mass
def getRadicalCount(self):
"""
Return the number of unpaired electrons.
"""
cython.declare(atom=Atom, radicals=cython.short)
radicals = 0
for atom in self.vertices:
radicals += atom.radicalElectrons
return radicals
def getNumAtoms(self, element = None):
"""
Return the number of atoms in molecule. If element is given, ie. "H" or "C",
the number of atoms of that element is returned.
"""
cython.declare(numAtoms=cython.int, atom=Atom)
if element == None:
return len(self.vertices)
else:
numAtoms = 0
for atom in self.vertices:
if atom.element.symbol == element:
numAtoms += 1
return numAtoms
def getNumberOfRadicalElectrons(self):
"""
Return the total number of radical electrons on all atoms in the
molecule. In this function, monoradical atoms count as one, biradicals
count as two, etc.
"""
cython.declare(numRadicals=cython.int, atom=Atom)
numRadicals = 0
for atom in self.vertices:
numRadicals += atom.radicalElectrons
return numRadicals
def copy(self, deep=False):
"""
Create a copy of the current graph. If `deep` is ``True``, a deep copy
is made: copies of the vertices and edges are used in the new graph.
If `deep` is ``False`` or not specified, a shallow copy is made: the
original vertices and edges are used in the new graph.
"""
other = cython.declare(Molecule)
g = Graph.copy(self, deep)
other = Molecule(g.vertices)
other.multiplicity = self.multiplicity
return other
def merge(self, other):
"""
Merge two molecules so as to store them in a single :class:`Molecule`
object. The merged :class:`Molecule` object is returned.
"""
g = Graph.merge(self, other)
molecule = Molecule(atoms=g.vertices)
return molecule
def split(self):
"""
Convert a single :class:`Molecule` object containing two or more
unconnected molecules into separate class:`Molecule` objects.
"""
graphs = Graph.split(self)
molecules = []
for g in graphs:
molecule = Molecule(atoms=g.vertices)
molecules.append(molecule)
return molecules
def deleteHydrogens(self):
"""
Irreversibly delete all non-labeled hydrogens without updating
connectivity values. If there's nothing but hydrogens, it does nothing.
It destroys information; be careful with it.
"""
cython.declare(atom=Atom, hydrogens=list)
# Check that the structure contains at least one heavy atom
for atom in self.vertices:
if not atom.isHydrogen():
break
else:
# No heavy atoms, so leave explicit
return
hydrogens = []
for atom in self.vertices:
if atom.isHydrogen() and atom.label == '':
hydrogens.append(atom)
# Remove the hydrogen atoms from the structure
for atom in hydrogens:
self.removeAtom(atom)
def connectTheDots(self):
"""
Delete all bonds, and set them again based on the Atoms' coords.
Does not detect bond type.
"""
cython.declare(criticalDistance=float, i=int, atom1=Atom, atom2=Atom,
bond=Bond, atoms=list, zBoundary=float)
# groupBond=GroupBond,
self._fingerprint = None
atoms = self.vertices
# Ensure there are coordinates to work with
for atom in atoms:
assert len(atom.coords) != 0
# If there are any bonds, remove them
for atom1 in atoms:
for bond in self.getBonds(atom1):
self.removeEdge(bond)
# Sort atoms by distance on the z-axis
sortedAtoms = sorted(atoms, key=lambda x: x.coords[2])
for i, atom1 in enumerate(sortedAtoms):
for atom2 in sortedAtoms[i+1:]:
# Set upper limit for bond distance
criticalDistance = (atom1.element.covRadius + atom2.element.covRadius + 0.45)**2
# First atom that is more than 4.0 Anstroms away in the z-axis, break the loop
# Atoms are sorted along the z-axis, so all following atoms should be even further
zBoundary = (atom1.coords[2] - atom2.coords[2])**2
if zBoundary > 16.0:
break
distanceSquared = sum((atom1.coords - atom2.coords)**2)
if distanceSquared > criticalDistance or distanceSquared < 0.40:
continue
else:
# groupBond = GroupBond(atom1, atom2, ['S','D','T','B'])
bond = Bond(atom1, atom2, 'S')
self.addBond(bond)
self.updateAtomTypes()
def updateAtomTypes(self, logSpecies=True):
"""
Iterate through the atoms in the structure, checking their atom types
to ensure they are correct (i.e. accurately describe their local bond
environment) and complete (i.e. are as detailed as possible).
"""
for atom in self.vertices:
try:
atom.atomType = getAtomType(atom, atom.edges)
except AtomTypeError:
if logSpecies:
logging.error("Could not update atomtypes for {0}.\n{1}".format(self, self.toAdjacencyList()))
raise
def updateMultiplicity(self):
"""
Update the multiplicity of a newly formed molecule.
"""
# Assume this is always true
# There are cases where 2 radicalElectrons is a singlet, but
# the triplet is often more stable,
self.multiplicity = self.getRadicalCount() + 1
def clearLabeledAtoms(self):
"""
Remove the labels from all atoms in the molecule.
"""
for atom in self.vertices:
atom.label = ''
def containsLabeledAtom(self, label):
"""
Return :data:`True` if the molecule contains an atom with the label
`label` and :data:`False` otherwise.
"""
for atom in self.vertices:
if atom.label == label: return True
return False
def getLabeledAtom(self, label):
"""
Return the atoms in the molecule that are labeled.
"""
for atom in self.vertices:
if atom.label == label: return atom
raise ValueError('No atom in the molecule has the label "{0}".'.format(label))
def getLabeledAtoms(self):
"""
Return the labeled atoms as a ``dict`` with the keys being the labels
and the values the atoms themselves. If two or more atoms have the
same label, the value is converted to a list of these atoms.
"""
labeled = {}
for atom in self.vertices:
if atom.label != '':
if atom.label in labeled:
if isinstance(labeled[atom.label],list):
labeled[atom.label].append(atom)
else:
labeled[atom.label] = [labeled[atom.label]]
labeled[atom.label].append(atom)
else:
labeled[atom.label] = atom
return labeled
def getFingerprint(self):
"""
Return a string containing the "fingerprint" used to accelerate graph
isomorphism comparisons with other molecules. The fingerprint is a