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
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 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)
print "GC: ", Es_MM
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
