def optimize(self):
"""Run the optimization with MMTK"""
print '\n-------------------------------------------------------------------------------'
print '\n MMTK Optimization starts...'
print '\t.. building universe'
configuration = PDBConfiguration(self.temp_pdb_file)
# Construct the nucleotide chain object. This also constructs positions
# for the missing hydrogens, using geometrical criteria.
chain = configuration.createNucleotideChains()[0]
universe = InfiniteUniverse()
universe.addObject(chain)
restraints = self.create_restraints(chain)
# define force field
print '\t.. setting up force field'
if restraints:
ff = Amber94ForceField() + restraints
else:
ff = Amber94ForceField()
universe.setForceField(ff)
# do the minimization
print '\t.. starting minimization with %i cycles'%self.cycles
minimizer = ConjugateGradientMinimizer(universe)
minimizer(steps = self.cycles)
# write the intermediate output
print '\t.. writing MMTK output to %s'% self.temp_pdb_file
if self.model_passive:
print '\t (please note that MMTK applies a different numeration of residues.\n\t The original one will be restored in the final output).'
universe.writeToFile(self.mmtk_output_file)
open(self.temp_pdb_file, 'w').write(open(self.mmtk_output_file).read())
print '\n-------------------------------------------------------------------------------'
continue
if not done.has_key((index1, index2)):
clist.append(Contact(a1, a2, dist))
done[(index1, index2)] = 1
return clist
if __name__ == '__main__':
from MMTK.PDB import PDBConfiguration
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]),
""" nucleotide_construction.py creates a nucleotide chain with a ligand from PDB file """
from MMTK import *
from MMTK.PDB import PDBConfiguration
from MMTK.NucleicAcids import NucleotideChain
from MMTK.Visualization import view
""" Load PDB entry 110d. It contains a single DNA strand with a ligand daunomycin """
configuration = PDBConfiguration('110d.pdb')
""" Construct nucleotide chain object. This also constructs positions for missing hydrogens, using geometrical criteria. """
chain = configuration.createNucleotideChains()[0]
""" Construct the ligand. There is no definition of it in the database, so it can only be constructed as a collection of atoms. The second argument of createMolecules() is set to one in order to allow this use of an unknown residue. """
ligand = configuration.createMolecules(['DM1'], 1)
# Put everything in a universe and show it graphically
universe = InfiniteUniverse()
universe.addObject(chain)
universe.addObject(ligand)
view(universe)
if not done.has_key((index1, index2)):
clist.append(Contact(a1, a2, dist))
done[(index1, index2)] = 1
return clist
if __name__ == '__main__':
from MMTK.PDB import PDBConfiguration
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]),
# Create a nucleotide chain with a ligand from a PDB file.
#
from MMTK import *
from MMTK.PDB import PDBConfiguration
from MMTK.NucleicAcids import NucleotideChain
from MMTK.Visualization import view
# Load the PDB entry 110d. It contains a single DNA strand with a
# ligand (daunomycin).
configuration = PDBConfiguration('110d.pdb')
# Construct the nucleotide chain object. This also constructs positions
# for the missing hydrogens, using geometrical criteria.
chain = configuration.createNucleotideChains()[0]
# Construct the ligand. There is no definition of it in the database,
# so it can only be constructed as a collection of atoms. The second
# argument of createMolecules() is set to one in order to allow
# this use of an unknown residue.
ligand = configuration.createMolecules(['DM1'], 1)
# Put everyting in a universe and show it graphically.
universe = InfiniteUniverse()
universe.addObject(chain)
universe.addObject(ligand)
view(universe)
