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(c) 2016 Thomas Holder, Schrodinger Inc.
License: BSD-2-Clause
from pymol import cmd, CmdException
def mcsalign(mobile, target,
mobile_state=-1, target_state=-1,
cycles=5, timeout=10, method='', exact=0, quiet=1,
object=None, _self=cmd):
Align two (ligand) selections based on Maximum-Common-Substructure.
Requires: (rdkit | indigo), csb
mobile = str: atom selection of mobile object
target = str: atom selection of target object
mobile_state = int: object state of mobile selection
{default: -1 = current state}
target_state = int: object state of target selection
{default: -1 = current state}
cycles = int: number of weight-refinement iterations for
weighted RMS fitting {default: 5}
timeout = int: MCS search timeout {default: 10}
method = indigo or rdkit {default: check availability}
exact = 0/1: match elements and bond orders {default: 0}
object = str: create an aligment object (requires PyMOL 2.3)
fetch 3zcf 4n8t, async=0
mcsalign /3zcf//A/HEC, /4n8t//A/HEM
zoom /4n8t//A/HEM, animate=2, buffer=3
from numpy import identity, dot, take
from import distance_sq, wfit, fit
# moving object
m_objects = _self.get_object_list(mobile)
if len(m_objects) != 1:
# If selection covers multiple objects, call "mcsalign" for every object
for m_object in m_objects:
mcsalign('(%s) & model %s' % (mobile, m_object), target,
mobile_state, target_state, cycles, timeout, method, quiet)
# get molecules from selections
m_sdf = get_molstr(mobile, mobile_state, _self=_self)
t_sdf = get_molstr(target, target_state, _self=_self)
# find maximum common substructure
m_indices, t_indices = get_mcs_indices(method, quiet, m_sdf, t_sdf, timeout, int(exact))
if len(m_indices) < 3:
raise CmdException('not enough atoms in MCS')
if not int(quiet):
print(' MCS-Align: found MCS with %d atoms (%s)' % (len(m_indices), m_objects[0]))
# coordinates
Y = take(_self.get_coords(mobile, mobile_state), m_indices, 0)
X = take(_self.get_coords(target, target_state), t_indices, 0)
# weighted RMS fitting
R, t = fit(X, Y)
for _ in range(int(cycles)):
data = distance_sq(Y, dot(X - t, R))
scales = 1.0 / data.clip(1e-3)
R, t = wfit(X, Y, scales)
# superpose
m = identity(4)
m[0:3,0:3] = R
m[0:3,3] = t
_self.transform_object(m_objects[0], list(m.flat), mobile_state)
if object:
t_idx_list = iterate_state_to_list(target_state, target, 'model, index')
m_idx_list = iterate_state_to_list(mobile_state, mobile, 'model, index')
raw = [[t_idx_list[i], m_idx_list[j]] for (i, j) in zip(t_indices, m_indices)]
_self.set_raw_alignment(object, raw, guide=t_idx_list[0][0])
except AttributeError:
raise CmdException('Creating an alignment object requires PyMOL 2.3')
def iterate_state_to_list(state, selection, expression, space=None, _self=cmd):
'''Like cmd.iterate_state, but collect the results in a list
@rtype list
space = dict(space or ())
space['_result_list'] = []
_self.iterate_state(state, selection,
'_result_list.append((' + expression + '))',
return space['_result_list']
def get_molstr(sele, state, *, _self=cmd):
'''Export the given selection to a molfile string'''
# new in PyMOL 1.8.4
return _self.get_str('mol', sele, state)
except Exception as e:
from chempy import io
model = _self.get_model(sele, state)
for a in model.atom:
a.symbol = a.symbol.capitalize()
return ''.join(io.mol.toList(model))
def get_mcs_indices(method, quiet, *args, **kwargs):
'''Find the MCS between two molecules and return the substructure
atom indices for both molecules.
@param method: empty string, rdkit, or indigo
@param quiet: 0 or 1 (verbosity flag)
@param m_sdf: mobile molecule as MOL string
@param t_sdf: target molecule as MOL string
@param timeout: timeout in seconds (only used with rdkit)
@return: two sequences of integers with atom indices
@rtype: tuple
methods = {
'rdkit': get_mcs_indices_rdkit,
'indigo': get_mcs_indices_indigo,
if not method:
for method in methods:
except ImportError:
raise CmdException('neither "rdkit" nor "indigo" available')
if not int(quiet):
print(" Note: using method '%s'" % (method,))
return methods[method](*args, **kwargs)
def get_mcs_indices_rdkit(m_sdf, t_sdf, timeout, exact=False):
from rdkit.Chem.rdFMCS import FindMCS
except ImportError:
# backwards compatibility
from rdkit.Chem.MCS import FindMCS
kwargs = {'bondCompare': 'any', 'atomCompare': 'any'}
from rdkit.Chem import rdFMCS
kwargs = {'bondCompare': rdFMCS.BondCompare.CompareAny,
'atomCompare': rdFMCS.AtomCompare.CompareAny}
if exact:
from rdkit import Chem
m_mol = Chem.MolFromMolBlock(m_sdf, False, False)
t_mol = Chem.MolFromMolBlock(t_sdf, False, False)
# find maximum common substructure
timeout = int(timeout) if timeout else None
mcs = FindMCS([m_mol, t_mol], timeout=timeout, **kwargs)
# backwards compatibility
if hasattr(mcs, 'completed'):
mcs.canceled = not mcs.completed
mcs.smartsString = mcs.smarts
if mcs.canceled:
raise CmdException('MCS search has timed out')
# atom indices of match
patt = Chem.MolFromSmarts(mcs.smartsString)
m_indices = m_mol.GetSubstructMatch(patt)
t_indices = t_mol.GetSubstructMatch(patt)
return m_indices, t_indices
def get_mcs_indices_indigo(m_sdf, t_sdf, timeout=None, exact=False):
import indigo
indigo = indigo.Indigo()
m_mol = indigo.loadMolecule(m_sdf)
t_mol = indigo.loadMolecule(t_sdf)
# find common substructure
arr = indigo.createArray()
mcs = indigo.extractCommonScaffold(arr, 'exact' if exact else 'approx')
# match to scaffold
query = indigo.loadQueryMolecule(mcs.smiles())
m_match = indigo.substructureMatcher(m_mol).match(query)
t_match = indigo.substructureMatcher(t_mol).match(query)
# atom indices of match
m_atoms = [m_match.mapAtom(a) for a in query.iterateAtoms()]
t_atoms = [t_match.mapAtom(a) for a in query.iterateAtoms()]
m_indices = [a.index() for a in m_atoms if a is not None]
t_indices = [a.index() for a in t_atoms if a is not None]
return m_indices, t_indices
# pymol commands
cmd.extend('mcsalign', mcsalign)
# auto-completion
cmd.auto_arg[0]['mcsalign'] = cmd.auto_arg[0]['align']
cmd.auto_arg[1]['mcsalign'] = cmd.auto_arg[1]['align']
# vi: ts=4:sw=4:smarttab:expandtab