def initialize(self):
"""
Initialize the input parameters and analysis self variables
"""
self.configuration["dcd_file"]["instance"] = DCDFile(self.configuration["dcd_file"]['filename'])
# The number of steps of the analysis.
self.numberOfSteps = self.configuration['dcd_file']['instance']['n_frames']
# Create all objects from the PDB file.
conf = PDBConfiguration(self.configuration['pdb_file']['filename'])
# Creates a collection of all the chemical objects stored in the PDB file
molecules = conf.createAll()
# If the input trajectory has PBC create a periodic universe.
if self.configuration['dcd_file']['instance']['has_pbc_data']:
self._universe = ParallelepipedicPeriodicUniverse()
# Otherwise create an infinite universe.
else:
self._universe = InfiniteUniverse()
# The chemical objects found in the PDB file introduced into the universe.
self._universe.addObject(molecules)
resolve_undefined_molecules_name(self._universe)
# A MMTK trajectory is opened for writing.
self._trajectory = Trajectory(self._universe, self.configuration['output_file']['files'][0], mode='w')
# A frame generator is created.
self._snapshot = SnapshotGenerator(self._universe, actions=[TrajectoryOutput(self._trajectory, ["all"], 0, None, 1)])
from MMTK import Units
import sys
target_filename = sys.argv[2]
pdb_conf1 = PDBConfiguration(target_filename)
if sys.argv[1][:2] == '-f':
chains = pdb_conf1.createNucleotideChains()
molecule_names = []
if len(chains) >= 2:
clist = findContacts(chains[0], chains[1])
else:
molecule_names = []
for (key, mol) in pdb_conf1.molecules.items():
for o in mol:
molecule_names.append(o.name)
targets = pdb_conf1.createAll(molecule_names = molecule_names)
if len(molecule_names) > 1:
clist = findContacts(targets[0], targets[1])
else:
atoms = targets.atomList()
mid = len(atoms)/2
clist = findContacts(Collection(atoms[:mid]),
Collection(atoms[mid:]))
print len(clist), 'contacts'
for c in clist[:8]:
print '%-64s %6.2f' % (c, c.dist/Units.Ang)
else:
target = pdb_conf1.createAll()
if sys.argv[1][:2] == '-v':
(a, v) = target.surfaceAndVolume()
print 'surface area %.2f volume %.2f' \
# This example shows how a universe can be built from a PDB file in such
# a way that all objects in the PDB file are represented as well as
# possible, using AtomCluster objects when nothing more specific can
# be constructed.
#
# This procedure is the only way to construct a universe that uses the
# same internal atom order as the PDB file, which is important for
# data exchange with other programs.
from MMTK import *
from MMTK.PDB import PDBConfiguration
configuration = PDBConfiguration('some_file.pdb')
universe = InfiniteUniverse()
universe.addObject(configuration.createAll(None, 1))
from MMTK import Units
import sys
target_filename = sys.argv[2]
pdb_conf1 = PDBConfiguration(target_filename)
if sys.argv[1][:2] == '-f':
chains = pdb_conf1.createNucleotideChains()
molecule_names = []
if len(chains) >= 2:
clist = findContacts(chains[0], chains[1])
else:
molecule_names = []
for (key, mol) in pdb_conf1.molecules.items():
for o in mol:
molecule_names.append(o.name)
targets = pdb_conf1.createAll(molecule_names=molecule_names)
if len(molecule_names) > 1:
clist = findContacts(targets[0], targets[1])
else:
atoms = targets.atomList()
mid = len(atoms) / 2
clist = findContacts(Collection(atoms[:mid]),
Collection(atoms[mid:]))
print len(clist), 'contacts'
for c in clist[:8]:
print '%-64s %6.2f' % (c, c.dist / Units.Ang)
else:
target = pdb_conf1.createAll()
if sys.argv[1][:2] == '-v':
(a, v) = target.surfaceAndVolume()
print 'surface area %.2f volume %.2f' \
def _get_molecules(pdb_file):
configuration = PDBConfiguration(pdb_file)
molecules = configuration.createAll()
return molecules
