def start_universe(pdb_file):
"""
pdb_file: str, pdb file name
return MMTK.Universe
"""
universe = InfiniteUniverse()
molecules = _get_molecules(pdb_file)
universe.addObject(molecules)
return universe
def _makeUniverse(self):
import os.path
parmDir = os.path.dirname(__file__)
timestamp("_makeUniverse")
from MMTK import InfiniteUniverse
from MMTK.ForceFields.Amber import AmberData
from MMTK.ForceFields.Amber.AmberForceField import readAmber99
from MMTK.ForceFields.MMForceField import MMForceField
#
# GAFF uses lower case atom types to distinguish
# from Amber atom types. MMTK, however, normalizes
# all atom types to upper case. So we hack MMTK
# and temporarily replace _normalizeName function
# with ours while reading our parameter files.
# (We have to reread the parameter file each time
# because we potentially have different frcmod files
# for the different universes.)
#
saveNormalizeName = AmberData._normalizeName
AmberData._normalizeName = simpleNormalizeName
modFiles = [m.frcmod for m in self.molecules if m.frcmod is not None]
parameters = readAmber99(os.path.join(parmDir, "parm", "gaff.dat"),
modFiles)
self._mergeAmber99(parameters)
bondedScaleFactor = 1.0
ff = MMForceField("Amber99/GAFF", parameters, self.ljOptions,
self.esOptions, bondedScaleFactor)
AmberData._normalizeName = saveNormalizeName
timestamp("Made forcefield")
self.universe = InfiniteUniverse(ff)
timestamp("Made universe")
for mm in self.molecules:
self.universe.addObject(mm)
timestamp("Added model %s" % mm.name)
timestamp("end _makeUniverse")
def _makeUniverse(self):
import os.path
parmDir = os.path.dirname(__file__)
timestamp("_makeUniverse")
from MMTK import InfiniteUniverse
from MMTK.ForceFields.Amber import AmberData
from MMTK.ForceFields.Amber.AmberForceField import readAmber99
from MMTK.ForceFields.MMForceField import MMForceField
#
# GAFF uses lower case atom types to distinguish
# from Amber atom types. MMTK, however, normalizes
# all atom types to upper case. So we hack MMTK
# and temporarily replace _normalizeName function
# with ours while reading our parameter files.
# (We have to reread the parameter file each time
# because we potentially have different frcmod files
# for the different universes.)
#
saveNormalizeName = AmberData._normalizeName
AmberData._normalizeName = simpleNormalizeName
modFiles = [ m.frcmod for m in self.molecules
if m.frcmod is not None]
parameters = readAmber99(os.path.join(parmDir,
"parm", "gaff.dat"),
modFiles)
self._mergeAmber99(parameters)
bondedScaleFactor = 1.0
ff = MMForceField("Amber99/GAFF", parameters, self.ljOptions,
self.esOptions, bondedScaleFactor)
AmberData._normalizeName = saveNormalizeName
timestamp("Made forcefield")
self.universe = InfiniteUniverse(ff)
timestamp("Made universe")
for mm in self.molecules:
self.universe.addObject(mm)
timestamp("Added model %s" % mm.name)
timestamp("end _makeUniverse")
from MMTK import Database from MMTK import Molecule from MMTK.ParticleProperties import Configuration from MMTK.ForceFields import Amber12SBForceField from MMTK import Universe, InfiniteUniverse from MMTK import Units R = 8.3144621*Units.J/Units.mol/Units.K import CDHMC parm_dir = '/share/apps/amber/16/dat/leap/parm/' # Amber parameters directory newmol = Molecule(mol_FN) mol_frcmod = os.path.join(mol_dir, 'ligand.frcmod') gaff_FN = os.path.join(mol_dir,'gaff2.dat') universe = InfiniteUniverse(Amber12SBForceField(parameter_file=gaff_FN, mod_files=['frcmod.ff12SB', mol_frcmod])) universe.addObject(newmol) universe.configuration(); configuration = universe.configuration().array CDIntegrator = CDHMC.CDHMCIntegrator(universe, mol_dir, parm_dir) (confs, Es_MM, acc, ntrials, dt) = CDIntegrator.Call(10000, 10, 300, 0.0015, random.randint(1,300), 0, 1, 0.5) print "GC: ", Es_MM CDIntegrator.Clear()
from MMTK.ForceFields import Amber12SBForceField
from MMTK import Universe, InfiniteUniverse
from MMTK import Units
from VelocityVerlet import VelocityVerletIntegrator
import GCHMC
R = 8.3144621*Units.J/Units.mol/Units.K
mol_name = "ligand"
gaff_FN = 'gaff.dat'
parm_dir = './'
mol_dir = '2but'
newmol = Molecule('2but')
mol_frcmod = os.path.join(mol_dir, 'ligand.frcmod')
universe = InfiniteUniverse(Amber12SBForceField(parameter_file=gaff_FN, mod_files=['frcmod.ff12SB', mol_frcmod]))
universe.addObject(newmol)
universe.configuration();
configuration = universe.configuration().array
VVintegrator = VelocityVerletIntegrator(universe)
print "VV constructed"
GCintegrator = GCHMC.GCHMCIntegrator(universe, mol_dir, parm_dir + gaff_FN)
print "GCHMC constructed"
(confs, KEs_MM, Es_MM, acc, ntrials, dt) = VVintegrator(steps=200, steps_per_trial=50, T=300.0, delta_t=0.0015, \
normalize=False, adapt=False, random_seed=random.randint(1,300))
print "Velocity Verlet finished"
(confs, Es_MM, acc, ntrials, dt) = GCintegrator.Call(30, 10, 300, 0.0015, random.randint(1,300), 0, 1, 0.5)
def normalmodes_mmtk(selection,
cutoff=12.0,
ff='Deformation',
first=7,
last=10,
prefix='mmtk',
states=7,
factor=-1,
quiet=1):
'''
DESCRIPTION
Fast normal modes for large proteins using an elastic network model (CA only)
Based on:
http://dirac.cnrs-orleans.fr/MMTK/using-mmtk/mmtk-example-scripts/normal-modes/
'''
try:
import MMTK
except ImportError:
print('Failed to import MMTK, please add to PYTHONPATH')
raise CmdException
selection = selector.process(selection)
cutoff = float(cutoff)
first, last = int(first), int(last)
states, factor, quiet = int(states), float(factor), int(quiet)
from math import log
from chempy import cpv
from MMTK import InfiniteUniverse
from MMTK.PDB import PDBConfiguration
from MMTK.Proteins import Protein
from MMTK.NormalModes import NormalModes
from MMTK.ForceFields import DeformationForceField, CalphaForceField
from MMTK.FourierBasis import FourierBasis, estimateCutoff
from MMTK.NormalModes import NormalModes, SubspaceNormalModes
model = 'calpha'
ff = ff.lower()
if 'deformationforcefield'.startswith(ff):
forcefield = DeformationForceField(cutoff=cutoff / 10.)
elif 'calphaforcefield'.startswith(ff):
forcefield = CalphaForceField(cutoff=cutoff / 10.)
elif 'amber94forcefield'.startswith(ff):
from MMTK.ForceFields import Amber94ForceField
forcefield = Amber94ForceField()
model = 'all'
else:
raise NotImplementedError('unknown ff = ' + str(ff))
if not quiet:
print(' Forcefield:', forcefield.__class__.__name__)
if model == 'calpha':
selection = '(%s) and polymer and name CA' % (selection)
f = StringIO(cmd.get_pdbstr(selection))
conf = PDBConfiguration(f)
items = conf.createPeptideChains(model)
universe = InfiniteUniverse(forcefield)
universe.protein = Protein(*items)
nbasis = max(10, universe.numberOfAtoms() / 5)
cutoff, nbasis = estimateCutoff(universe, nbasis)
if not quiet:
print(" Calculating %d low-frequency modes." % nbasis)
if cutoff is None:
modes = NormalModes(universe)
else:
subspace = FourierBasis(universe, cutoff)
modes = SubspaceNormalModes(universe, subspace)
natoms = modes.array.shape[1]
frequencies = modes.frequencies
if factor < 0:
factor = log(natoms)
if not quiet:
print(' set factor to %.2f' % (factor))
if True: # cmd.count_atoms(selection) != natoms:
import tempfile, os
from MMTK import DCD
filename = tempfile.mktemp(suffix='.pdb')
sequence = DCD.writePDB(universe, None, filename)
z = [a.index for a in sequence]
selection = cmd.get_unused_name('_')
cmd.load(filename, selection, zoom=0)
os.remove(filename)
if cmd.count_atoms(selection) != natoms:
print('hmm... still wrong number of atoms')
def eigenfacs_iter(mode):
x = modes[mode - 1].array
return iter(x.take(z, 0))
for mode in range(first, min(last, len(modes)) + 1):
name = prefix + '%d' % mode
cmd.delete(name)
if not quiet:
print(' normalmodes: object "%s" for mode %d with freq. %.6f' % \
(name, mode, frequencies[mode-1]))
for state in range(1, states + 1):
cmd.create(name, selection, 1, state, zoom=0)
cmd.alter_state(
state,
name,
'(x,y,z) = cpv.add([x,y,z], cpv.scale(next(myit), myfac))',
space={
'cpv': cpv,
'myit': eigenfacs_iter(mode),
'next': next,
'myfac':
1e2 * factor * ((state - 1.0) / (states - 1.0) - 0.5)
})
cmd.delete(selection)
if model == 'calpha':
cmd.set('ribbon_trace_atoms', 1, prefix + '*')
cmd.show_as('ribbon', prefix + '*')
else:
cmd.show_as('lines', prefix + '*')
forcefield = Amber94ForceField()
model = 'all'
else:
raise NotImplementedError('unknown ff = ' + str(ff))
if not quiet:
print ' Forcefield:', forcefield.__class__.__name__
if model == 'calpha':
selection = '(%s) and polymer and name CA' % (selection)
from cStringIO import StringIO
f = StringIO(cmd.get_pdbstr(selection))
conf = PDBConfiguration(f)
items = conf.createPeptideChains(model)
universe = InfiniteUniverse(forcefield)
universe.protein = Protein(*items)
nbasis = max(10, universe.numberOfAtoms()/5)
cutoff, nbasis = estimateCutoff(universe, nbasis)
if not quiet:
print " Calculating %d low-frequency modes." % nbasis
if cutoff is None:
modes = NormalModes(universe)
else:
subspace = FourierBasis(universe, cutoff)
modes = SubspaceNormalModes(universe, subspace)
natoms = modes.array.shape[1]
frequencies = modes.frequencies
from MMTK.ForceFields import Amber94ForceField
forcefield = Amber94ForceField()
model = 'all'
else:
raise NotImplementedError('unknown ff = ' + str(ff))
if not quiet:
print(' Forcefield:', forcefield.__class__.__name__)
if model == 'calpha':
selection = '(%s) and polymer and name CA' % (selection)
f = StringIO(cmd.get_pdbstr(selection))
conf = PDBConfiguration(f)
items = conf.createPeptideChains(model)
universe = InfiniteUniverse(forcefield)
universe.protein = Protein(*items)
nbasis = max(10, universe.numberOfAtoms() / 5)
cutoff, nbasis = estimateCutoff(universe, nbasis)
if not quiet:
print(" Calculating %d low-frequency modes." % nbasis)
if cutoff is None:
modes = NormalModes(universe)
else:
subspace = FourierBasis(universe, cutoff)
modes = SubspaceNormalModes(universe, subspace)
natoms = modes.array.shape[1]
frequencies = modes.frequencies
class MMTKinter:
def __init__(self,
mols,
nogui=False,
addhyd=True,
ljOptions=None,
esOptions=None,
callback=None):
# MMTK lengths are in nm while Chimera ones are in Angstroms
# so we need a scale factor when converting
if not mols:
raise ValueError("No molecules specified")
self.tempDir = None
self.molId = 0
self.ljOptions = ljOptions
self.esOptions = esOptions
self.callback = callback
self.mols = mols
self._getParameters(mols, nogui, addhyd)
def _finishInit(self):
timestamp("_finishInit")
self.molecules = []
self.atomMap = {}
try:
for m in self.mols:
self.molecules.append(self._makeMolecule(m))
self._makeUniverse()
if self.callback:
self.callback(self)
del self.callback
finally:
self._removeTempDir()
def _makeUniverse(self):
import os.path
parmDir = os.path.dirname(__file__)
timestamp("_makeUniverse")
from MMTK import InfiniteUniverse
from MMTK.ForceFields.Amber import AmberData
from MMTK.ForceFields.Amber.AmberForceField import readAmber99
from MMTK.ForceFields.MMForceField import MMForceField
#
# GAFF uses lower case atom types to distinguish
# from Amber atom types. MMTK, however, normalizes
# all atom types to upper case. So we hack MMTK
# and temporarily replace _normalizeName function
# with ours while reading our parameter files.
# (We have to reread the parameter file each time
# because we potentially have different frcmod files
# for the different universes.)
#
saveNormalizeName = AmberData._normalizeName
AmberData._normalizeName = simpleNormalizeName
modFiles = [m.frcmod for m in self.molecules if m.frcmod is not None]
parameters = readAmber99(os.path.join(parmDir, "parm", "gaff.dat"),
modFiles)
self._mergeAmber99(parameters)
bondedScaleFactor = 1.0
ff = MMForceField("Amber99/GAFF", parameters, self.ljOptions,
self.esOptions, bondedScaleFactor)
AmberData._normalizeName = saveNormalizeName
timestamp("Made forcefield")
self.universe = InfiniteUniverse(ff)
timestamp("Made universe")
for mm in self.molecules:
self.universe.addObject(mm)
timestamp("Added model %s" % mm.name)
timestamp("end _makeUniverse")
def _getParameters(self, mols, nogui, addhyd):
timestamp("_getParameters")
import DockPrep
import chimera
self.originalAtoms = set([])
for m in mols:
self.originalAtoms.update(m.atoms)
from AddCharge import AMBER99SB
kw = {
"doneCB": self._finishDockPrep,
"gaffType": True,
"chargeModel": AMBER99SB
}
if nogui or chimera.nogui:
if not addhyd:
kw["addHFunc"] = None
DockPrep.prep(mols, nogui=nogui, **kw)
else:
from DockPrep.gui import DockPrepDialog
from chimera import dialogs
d = dialogs.display(DockPrepDialog.name, wait=True)
d.addHydVar.set(addhyd)
d.applyKeywords = kw
d.molListBox.setvalue(mols)
d.writeMol2Var.set(False)
"""
d = DockPrep.memoryPrep("Minimize", "use", mols, nogui=nogui, **kw)
if d:
d.addHydVar.set(addhyd)
d.writeMol2Var.set(False)
"""
def _finishDockPrep(self):
timestamp("end _getParameters")
from chimera import selection
selectedAtoms = set(selection.currentAtoms())
addSelected = []
numAdded = 0
for m in self.mols:
for a in m.atoms:
if a in self.originalAtoms:
continue
numAdded += 1
# This atom was added. If it was added to
# a selected atom, then we add this atom
# into the current selection as well.
for b in a.bonds:
oa = a.bonds[0].otherAtom(a)
if oa in selectedAtoms:
addSelected.append(a)
break
del self.originalAtoms
if addSelected:
selection.addCurrent(addSelected)
#from chimera import replyobj
#replyobj.info("%d atoms added, %d selected\n"
# % (numAdded, len(addSelected)))
self._finishInit()
def _mergeAmber99(self, parm):
"Merge MMTK Amber99 parameters into our parameters"
from MMTK.ForceFields.Amber.AmberForceField import readAmber99
parm99 = readAmber99()
parm.atom_types.update(parm99.atom_types)
parm.bonds.update(parm99.bonds)
parm.bond_angles.update(parm99.bond_angles)
parm.dihedrals.update(parm99.dihedrals)
parm.dihedrals_2.update(parm99.dihedrals_2)
parm.impropers.update(parm99.impropers)
parm.impropers_1.update(parm99.impropers_1)
parm.impropers_2.update(parm99.impropers_2)
parm.hbonds.update(parm99.hbonds)
parm.lj_equivalent.update(parm99.lj_equivalent)
for name, ljpar_set99 in parm99.ljpar_sets.iteritems():
try:
ljpar_set = parm.ljpar_sets[name]
except KeyError:
parm.ljpar_sets[name] = ljpar_set99
else:
if ljpar_set.type != ljpar_set99.type:
print "incompatible ljpar_set"
print " GAFF type:", ljpar_set.type
print " AMBER99 type:", ljpar_set99.type
ljpar_set.entries.update(ljpar_set99.entries)
def _makeMolecule(self, m):
timestamp("_makeMolecule %s" % m.name)
mm = MMTKChimeraModel(m, self.molId, self)
self.molId += 1
timestamp("end _makeMolecule")
return mm
def setFixed(self, which):
from chimera import selection
if which == "none" or selection.currentEmpty():
for ma in self.universe.atomList():
ma.fixed = False
elif which == "selected":
import chimera
for ma in self.universe.atomList():
ma.fixed = False
for a in selection.currentAtoms():
if a.molecule in self.mols:
ma = self.atomMap[a]
ma.fixed = True
else:
import chimera
for ma in self.universe.atomList():
ma.fixed = True
for a in selection.currentAtoms():
if a.molecule in self.mols:
ma = self.atomMap[a]
ma.fixed = False
def loadMMTKCoordinates(self):
"Load MMTK coordinates from Chimera models"
import chimera
from Scientific.Geometry import Vector
from MMTK import Units
s = Units.Ang
for ma in self.universe.atomList():
try:
ca = ma.getAtomProperty(ma, "chimera_atom")
except AttributeError:
pass
else:
c = ca.coord()
p = Vector(c[0] * s, c[1] * s, c[2] * s)
ma.setPosition(p)
def saveMMTKCoordinates(self):
"Save MMTK coordinates into Chimera models"
import chimera
from chimera import Coord
from MMTK import Units
s = Units.Ang
sum = 0.0
count = 0
for ma in self.universe.atomList():
if ma.fixed:
continue
ca = ma.getAtomProperty(ma, "chimera_atom")
p = ma.position()
c = Coord(p[0] / s, p[1] / s, p[2] / s)
dsq = (c - ca.coord()).sqlength()
ca.setCoord(c)
#print "%.6f" % dsq
sum += dsq
count += 1
import math
if count > 0:
print "Updated", count, "atoms. RMSD: %.6f" \
% math.sqrt(sum / count)
else:
print "No atoms updated."
def minimize(self,
nsteps,
stepsize=0.02,
interval=None,
action=None,
**kw):
from chimera import replyobj
timestamp("_minimize")
from MMTK import Units
from MMTK.ForceFields.Amber import AmberData
from MMTK.Minimization import SteepestDescentMinimizer
from MMTK.Trajectory import LogOutput
import sys
if not interval:
actions = []
else:
actions = [
LogOutput(sys.stdout, ["energy"], interval, None, interval)
]
kw["step_size"] = stepsize * Units.Ang
minimizer = SteepestDescentMinimizer(self.universe,
actions=actions,
**kw)
if action is None or not interval:
interval = None
msg = "Initial energy: %f" % self.universe.energy()
replyobj.status(msg)
replyobj.info(msg)
saveNormalizeName = AmberData._normalizeName
AmberData._normalizeName = simpleNormalizeName
remaining = nsteps
while remaining > 0:
timestamp(" minimize interval")
if interval is None:
realSteps = remaining
else:
realSteps = min(remaining, interval)
minimizer(steps=realSteps)
remaining -= realSteps
if action is not None:
action(self)
timestamp(" finished %d steps" % realSteps)
msg = "Finished %d of %d minimization steps" % (nsteps - remaining,
nsteps)
replyobj.status(msg)
replyobj.info(msg)
replyobj.info("\n")
AmberData._normalizeName = saveNormalizeName
timestamp("end _minimize")
def getTempDir(self):
if self.tempDir:
return self.tempDir
from tempfile import mkdtemp
self.tempDir = mkdtemp()
#self.tempDir = "."
return self.tempDir
def _removeTempDir(self):
if not self.tempDir:
return
if True:
import os, os.path
for filename in os.listdir(self.tempDir):
os.remove(os.path.join(self.tempDir, filename))
os.rmdir(self.tempDir)
else:
print "Did not clean up temp dir", self.tempDir
self.tempDir = None
class MMTKinter:
def __init__(self, mols, nogui=False, addhyd=True,
ljOptions=None, esOptions=None, callback=None):
# MMTK lengths are in nm while Chimera ones are in Angstroms
# so we need a scale factor when converting
if not mols:
raise ValueError("No molecules specified")
self.tempDir = None
self.molId = 0
self.ljOptions = ljOptions
self.esOptions = esOptions
self.callback = callback
self.mols = mols
self._getParameters(mols, nogui, addhyd)
def _finishInit(self):
timestamp("_finishInit")
self.molecules = []
self.atomMap = {}
try:
for m in self.mols:
self.molecules.append(self._makeMolecule(m))
self._makeUniverse()
if self.callback:
self.callback(self)
del self.callback
finally:
self._removeTempDir()
def _makeUniverse(self):
import os.path
parmDir = os.path.dirname(__file__)
timestamp("_makeUniverse")
from MMTK import InfiniteUniverse
from MMTK.ForceFields.Amber import AmberData
from MMTK.ForceFields.Amber.AmberForceField import readAmber99
from MMTK.ForceFields.MMForceField import MMForceField
#
# GAFF uses lower case atom types to distinguish
# from Amber atom types. MMTK, however, normalizes
# all atom types to upper case. So we hack MMTK
# and temporarily replace _normalizeName function
# with ours while reading our parameter files.
# (We have to reread the parameter file each time
# because we potentially have different frcmod files
# for the different universes.)
#
saveNormalizeName = AmberData._normalizeName
AmberData._normalizeName = simpleNormalizeName
modFiles = [ m.frcmod for m in self.molecules
if m.frcmod is not None]
parameters = readAmber99(os.path.join(parmDir,
"parm", "gaff.dat"),
modFiles)
self._mergeAmber99(parameters)
bondedScaleFactor = 1.0
ff = MMForceField("Amber99/GAFF", parameters, self.ljOptions,
self.esOptions, bondedScaleFactor)
AmberData._normalizeName = saveNormalizeName
timestamp("Made forcefield")
self.universe = InfiniteUniverse(ff)
timestamp("Made universe")
for mm in self.molecules:
self.universe.addObject(mm)
timestamp("Added model %s" % mm.name)
timestamp("end _makeUniverse")
def _getParameters(self, mols, nogui, addhyd):
timestamp("_getParameters")
import DockPrep
import chimera
self.originalAtoms = set([])
for m in mols:
self.originalAtoms.update(m.atoms)
from AddCharge import AMBER99SB
kw = { "doneCB": self._finishDockPrep, "gaffType": True,
"chargeModel": AMBER99SB }
if nogui or chimera.nogui:
if not addhyd:
kw["addHFunc"] = None
DockPrep.prep(mols, nogui=nogui, **kw)
else:
from DockPrep.gui import DockPrepDialog
from chimera import dialogs
d = dialogs.display(DockPrepDialog.name, wait=True)
d.addHydVar.set(addhyd)
d.applyKeywords = kw
d.molListBox.setvalue(mols)
d.writeMol2Var.set(False)
"""
d = DockPrep.memoryPrep("Minimize", "use", mols, nogui=nogui, **kw)
if d:
d.addHydVar.set(addhyd)
d.writeMol2Var.set(False)
"""
def _finishDockPrep(self):
timestamp("end _getParameters")
from chimera import selection
selectedAtoms = set(selection.currentAtoms())
addSelected = []
numAdded = 0
for m in self.mols:
for a in m.atoms:
if a in self.originalAtoms:
continue
numAdded += 1
# This atom was added. If it was added to
# a selected atom, then we add this atom
# into the current selection as well.
for b in a.bonds:
oa = a.bonds[0].otherAtom(a)
if oa in selectedAtoms:
addSelected.append(a)
break
del self.originalAtoms
if addSelected:
selection.addCurrent(addSelected)
#from chimera import replyobj
#replyobj.info("%d atoms added, %d selected\n"
# % (numAdded, len(addSelected)))
self._finishInit()
def _mergeAmber99(self, parm):
"Merge MMTK Amber99 parameters into our parameters"
from MMTK.ForceFields.Amber.AmberForceField import readAmber99
parm99 = readAmber99()
parm.atom_types.update(parm99.atom_types)
parm.bonds.update(parm99.bonds)
parm.bond_angles.update(parm99.bond_angles)
parm.dihedrals.update(parm99.dihedrals)
parm.dihedrals_2.update(parm99.dihedrals_2)
parm.impropers.update(parm99.impropers)
parm.impropers_1.update(parm99.impropers_1)
parm.impropers_2.update(parm99.impropers_2)
parm.hbonds.update(parm99.hbonds)
parm.lj_equivalent.update(parm99.lj_equivalent)
for name, ljpar_set99 in parm99.ljpar_sets.iteritems():
try:
ljpar_set = parm.ljpar_sets[name]
except KeyError:
parm.ljpar_sets[name] = ljpar_set99
else:
if ljpar_set.type != ljpar_set99.type:
print "incompatible ljpar_set"
print " GAFF type:", ljpar_set.type
print " AMBER99 type:", ljpar_set99.type
ljpar_set.entries.update(ljpar_set99.entries)
def _makeMolecule(self, m):
timestamp("_makeMolecule %s" % m.name)
mm = MMTKChimeraModel(m, self.molId, self)
self.molId += 1
timestamp("end _makeMolecule")
return mm
def setFixed(self, which):
from chimera import selection
if which == "none" or selection.currentEmpty():
for ma in self.universe.atomList():
ma.fixed = False
elif which == "selected":
import chimera
for ma in self.universe.atomList():
ma.fixed = False
for a in selection.currentAtoms():
if a.molecule in self.mols:
ma = self.atomMap[a]
ma.fixed = True
else:
import chimera
for ma in self.universe.atomList():
ma.fixed = True
for a in selection.currentAtoms():
if a.molecule in self.mols:
ma = self.atomMap[a]
ma.fixed = False
def loadMMTKCoordinates(self):
"Load MMTK coordinates from Chimera models"
import chimera
from Scientific.Geometry import Vector
from MMTK import Units
s = Units.Ang
for ma in self.universe.atomList():
try:
ca = ma.getAtomProperty(ma, "chimera_atom")
except AttributeError:
pass
else:
c = ca.coord()
p = Vector(c[0] * s, c[1] * s, c[2] * s)
ma.setPosition(p)
def saveMMTKCoordinates(self):
"Save MMTK coordinates into Chimera models"
import chimera
from chimera import Coord
from MMTK import Units
s = Units.Ang
sum = 0.0
count = 0
for ma in self.universe.atomList():
if ma.fixed:
continue
ca = ma.getAtomProperty(ma, "chimera_atom")
p = ma.position()
c = Coord(p[0] / s, p[1] / s, p[2] / s)
dsq = (c - ca.coord()).sqlength()
ca.setCoord(c)
#print "%.6f" % dsq
sum += dsq
count += 1
import math
if count > 0:
print "Updated", count, "atoms. RMSD: %.6f" \
% math.sqrt(sum / count)
else:
print "No atoms updated."
def minimize(self, nsteps, stepsize=0.02,
interval=None, action=None, **kw):
from chimera import replyobj
timestamp("_minimize")
from MMTK import Units
from MMTK.ForceFields.Amber import AmberData
from MMTK.Minimization import SteepestDescentMinimizer
from MMTK.Trajectory import LogOutput
import sys
if not interval:
actions = []
else:
actions = [ LogOutput(sys.stdout, ["energy"],
interval, None, interval) ]
kw["step_size"] = stepsize * Units.Ang
minimizer = SteepestDescentMinimizer(self.universe,
actions=actions, **kw)
if action is None or not interval:
interval = None
msg = "Initial energy: %f" % self.universe.energy()
replyobj.status(msg)
replyobj.info(msg)
saveNormalizeName = AmberData._normalizeName
AmberData._normalizeName = simpleNormalizeName
remaining = nsteps
while remaining > 0:
timestamp(" minimize interval")
if interval is None:
realSteps = remaining
else:
realSteps = min(remaining, interval)
minimizer(steps=realSteps)
remaining -= realSteps
if action is not None:
action(self)
timestamp(" finished %d steps" % realSteps)
msg = "Finished %d of %d minimization steps" % (
nsteps - remaining, nsteps)
replyobj.status(msg)
replyobj.info(msg)
replyobj.info("\n")
AmberData._normalizeName = saveNormalizeName
timestamp("end _minimize")
def getTempDir(self):
if self.tempDir:
return self.tempDir
from tempfile import mkdtemp
self.tempDir = mkdtemp()
#self.tempDir = "."
return self.tempDir
def _removeTempDir(self):
if not self.tempDir:
return
if True:
import os, os.path
for filename in os.listdir(self.tempDir):
os.remove(os.path.join(self.tempDir, filename))
os.rmdir(self.tempDir)
else:
print "Did not clean up temp dir", self.tempDir
self.tempDir = None
