def __init__(self, file):
MoleculeFactory.__init__(self)
for event, element in iterparse(file):
tag = element.tag
ob_id = element.attrib.get('id', None)
if tag == 'molecule' and ob_id is not None:
self.makeGroup(element)
element.clear()
elif tag == 'templates':
element.clear()
elif tag == 'universe':
self.makeUniverse(element)
def __init__(self, file):
MoleculeFactory.__init__(self)
for event, element in iterparse(file):
tag = element.tag
ob_id = element.attrib.get('id', None)
if tag == 'molecule' and ob_id is not None:
self.makeGroup(element)
element.clear()
elif tag == 'templates':
element.clear()
elif tag == 'universe':
self.makeUniverse(element)
def __init__(self, pdb_conf, residue_filter=None, atom_filter=None):
"""
@param pdb_conf: a PDBConfiguration
@type pdb_conf: L{MMTK.PDB.PDBConfiguration}
@param residue_filter: a function taking a residue object
(as defined in Scientific.IO.PDB)
and returning True if that residue is
to be kept in the molecule factory
@type residue_filter: callable
@param atom_filter: a function taking a residue object and an
atom object (as defined in Scientific.IO.PDB)
and returning True if that atom is
to be kept in the molecule factory
@type atom_filter: callable
"""
MoleculeFactory.__init__(self)
if residue_filter is None and atom_filter is None:
self.pdb_conf = pdb_conf
else:
self.pdb_conf = copy.deepcopy(pdb_conf)
for residue in self.pdb_conf.residues:
delete = []
for atom in residue:
if atom_filter is not None \
and not atom_filter(residue, atom):
delete.append(atom)
for atom in delete:
residue.deleteAtom(atom)
delete = []
for residue in self.pdb_conf.residues:
if len(residue) == 0 or \
(residue_filter is not None
and not residue_filter(residue)):
delete.append(residue)
for residue in delete:
self.pdb_conf.deleteResidue(residue)
self.peptide_chains = []
self.nucleotide_chains = []
self.molecules = {}
self.makeAll()
def __init__(self, pdb_conf, residue_filter=None, atom_filter=None):
"""
:param pdb_conf: a PDBConfiguration
:type pdb_conf: :class:`~MMTK.PDB.PDBConfiguration`
:param residue_filter: a function taking a residue object
(as defined in Scientific.IO.PDB)
and returning True if that residue is
to be kept in the molecule factory
:type residue_filter: callable
:param atom_filter: a function taking a residue object and an
atom object (as defined in Scientific.IO.PDB)
and returning True if that atom is
to be kept in the molecule factory
:type atom_filter: callable
"""
MoleculeFactory.__init__(self)
if residue_filter is None and atom_filter is None:
self.pdb_conf = pdb_conf
else:
self.pdb_conf = copy.deepcopy(pdb_conf)
if atom_filter is not None:
for residue in self.pdb_conf.residues:
delete = [atom for atom in residue
if not atom_filter(residue, atom)]
for atom in delete:
residue.deleteAtom(atom)
if residue_filter is not None:
delete = [residue for residue in self.pdb_conf.residues
if len(residue) == 0 or not residue_filter(residue)]
for residue in delete:
self.pdb_conf.deleteResidue(residue)
self.peptide_chains = []
self.nucleotide_chains = []
self.molecules = {}
self.makeAll()
def __init__(self, mol_system):
MoleculeFactory.__init__(self)
self.mol_system = mol_system
self.group_name_mapping = {}
self.peptide_chains = {}
self.makeAllGroups()
import unittest
from subsets import SubsetTest
from MMTK import *
from MMTK.MoleculeFactory import MoleculeFactory
from MMTK.ForceFields import Amber99ForceField, LennardJonesForceField
from MMTK_forcefield import NonbondedList
from MMTK.Random import randomPointInBox
from MMTK.Geometry import SCLattice
from MMTK.Utility import pairs
from Scientific.Geometry import ex, ey, ez
from Scientific import N
from cStringIO import StringIO
import itertools
factory = MoleculeFactory()
factory.createGroup('dihedral_test')
factory.addAtom('dihedral_test', 'C1', 'C')
factory.addAtom('dihedral_test', 'C2', 'C')
factory.addAtom('dihedral_test', 'C3', 'C')
factory.addAtom('dihedral_test', 'C4', 'C')
factory.addBond('dihedral_test', 'C1', 'C2')
factory.addBond('dihedral_test', 'C2', 'C3')
factory.addBond('dihedral_test', 'C3', 'C4')
factory.setAttribute('dihedral_test', 'C1.amber_atom_type', 'D1')
factory.setAttribute('dihedral_test', 'C2.amber_atom_type', 'D2')
factory.setAttribute('dihedral_test', 'C3.amber_atom_type', 'D3')
factory.setAttribute('dihedral_test', 'C4.amber_atom_type', 'D4')
# Create molecules from scratch
#
# This example shows how a molecular system (SPCE water) can be set up using
# molecule factories instead of the molecular database.
#
from MMTK import *
from MMTK.MoleculeFactory import MoleculeFactory
from MMTK.ForceFields import SPCEForceField
# Create a new molecule factory.
factory = MoleculeFactory()
# Create the empty molecule. There is no distinction between groups
# and molecules at this level. Everything is a building block.
factory.createGroup('water')
# Add the atoms.
factory.addAtom('water', 'O', 'O')
factory.addAtom('water', 'H1', 'H')
factory.addAtom('water', 'H2', 'H')
# Add the bonds.
factory.addBond('water', 'O', 'H1')
factory.addBond('water', 'O', 'H2')
# Define the atom positions
factory.setPosition('water', 'O', Vector(0., 0., 0.00655616814675))
factory.setPosition('water', 'H1',
Vector(-0.0756950327264, 0., -0.0520320595151))
factory.setPosition('water', 'H2',
import unittest
from subsets import SubsetTest
from MMTK import *
from MMTK.MoleculeFactory import MoleculeFactory
from MMTK.ForceFields import Amber99ForceField, LennardJonesForceField
from MMTK_forcefield import NonbondedList
from MMTK.Random import randomPointInBox
from MMTK.Geometry import SCLattice
from MMTK.Utility import pairs
from Scientific.Geometry import ex, ey, ez
from Scientific import N
from cStringIO import StringIO
import itertools
factory = MoleculeFactory()
factory.createGroup('dihedral_test')
factory.addAtom('dihedral_test', 'C1', 'C')
factory.addAtom('dihedral_test', 'C2', 'C')
factory.addAtom('dihedral_test', 'C3', 'C')
factory.addAtom('dihedral_test', 'C4', 'C')
factory.addBond('dihedral_test', 'C1', 'C2')
factory.addBond('dihedral_test', 'C2', 'C3')
factory.addBond('dihedral_test', 'C3', 'C4')
factory.setAttribute('dihedral_test', 'C1.amber_atom_type', 'D1')
factory.setAttribute('dihedral_test', 'C2.amber_atom_type', 'D2')
factory.setAttribute('dihedral_test', 'C3.amber_atom_type', 'D3')
factory.setAttribute('dihedral_test', 'C4.amber_atom_type', 'D4')
def __init__(self, mol_system):
MoleculeFactory.__init__(self)
self.mol_system = mol_system
self.group_name_mapping = {}
self.peptide_chains = {}
self.makeAllGroups()
# Create molecules from scratch
#
# This example shows how a molecular system (SPCE water) can be set up using
# molecule factories instead of the molecular database.
#
from MMTK import *
from MMTK.MoleculeFactory import MoleculeFactory
from MMTK.ForceFields import SPCEForceField
# Create a new molecule factory.
factory = MoleculeFactory()
# Create the empty molecule. There is no distinction between groups
# and molecules at this level. Everything is a building block.
factory.createGroup('water')
# Add the atoms.
factory.addAtom('water', 'O', 'O')
factory.addAtom('water', 'H1', 'H')
factory.addAtom('water', 'H2', 'H')
# Add the bonds.
factory.addBond('water', 'O', 'H1')
factory.addBond('water', 'O', 'H2')
# Define the atom positions
factory.setPosition('water', 'O', Vector(0., 0., 0.00655616814675))
factory.setPosition('water', 'H1',
Vector(-0.0756950327264, 0., -0.0520320595151))
factory.setPosition('water', 'H2',