def main():
print sys.argv
if len(sys.argv) != 3 and len(sys.argv) != 4: # if no input
print "ERROR: Wrong number of inputs"
print "syntax: chimera --nogui --script \"chimera_dockprep.py pdbinput output_prefix keepH\""
print len(sys.argv)
return
#models = openModels.list(modelTypes=[chimera.Molecule])
input_pdb = sys.argv[1]
output_prefix = sys.argv[2]
if len(sys.argv) == 4:
if (sys.argv[3] == 'yes'):
keepH = True
elif (sys.argv[3] == 'no'):
keepH = False
else:
print("keepH must be yes or no, setting it to no.")
keepH = False
else:
keepH = False
print "pdb input = " + input_pdb
print "output prefix = " + output_prefix
#runCommand("open " + input_pdb)
#models = chimera.openModels.list(modelTypes=[chimera.Molecule])
#model = models
model = openModels.open(input_pdb)
if not (keepH):
runCommand("del @H,H?,H??,H???") # remove all hydrogens
writeMol2(model, output_prefix+"before_dockprep.mol2")
prep(model)
runCommand("write 0 "+output_prefix+".pdb")
writeMol2(model, output_prefix+".mol2")
runCommand("del HC") # remove all non-polar hydrogens
runCommand("write 0 "+output_prefix+"_polarH.pdb")
runCommand("del @H,H?,H??,H???") # remove all hydrogens
runCommand("write 0 "+output_prefix+"_noH.pdb")
def Apply(self):
from chimera import dialogs
kw = {'status': replyobj.status}
paths = self.getPaths()
if not paths:
replyobj.error('No save location chosen.\n')
return
path = paths[0]
models = self.modelList.getvalue()
if not models:
replyobj.error("No models chosen to save.\n")
return
if float(self.modelList.size()) > 1.5:
if self.saveRelativeVar.get():
kw['relModel'] = self.relModelMenu.getvalue()
else:
if self.saveUntransformedVar.get():
kw['relModel'] = models[0]
if self.writeGaffVar.get():
kw['gaffType'] = True
from chimera import UserError
kw['gaffFailError'] = UserError
if self.rigidVar.get():
sel = selection.copyCurrent()
sel.addImplied()
selAtoms = sel.atoms()
selBonds = sel.bonds()
if selAtoms and selBonds:
kw['anchor'] = sel
sybylHydNaming = self.sybylHydNamesVar.get()
if sybylHydNaming:
self.prefs["hydrogen naming"] = "sybyl"
else:
self.prefs["hydrogen naming"] = "pdb"
kw['hydNamingStyle'] = self.prefs["hydrogen naming"]
kw['resNum'] = self.resNumsVar.get()
from WriteMol2 import writeMol2
if len(models) < 2:
replyobj.status("Writing %s to %s\n" %
(models[0].name, path))
writeMol2(models, path, **kw)
replyobj.status("Wrote %s to %s\n" %
(models[0].name, path))
return
saveOpt = self.multiSaveMenu.getvalue()
for key, value in self.labelMap.items():
if saveOpt == value:
break
self.prefs["multiSaveMol2"] = key
# write multiple models to multiple files
if key == "multiple":
if path.endswith(".mol2"):
start, end = path[:-4], ".mol2"
else:
start, end = path, ""
for m in models:
modelPath = start + m.oslIdent()[1:] + end
replyobj.status("Writing %s (%s) to %s\n" %
(m.name, m.oslIdent(), modelPath))
writeMol2(m, modelPath, **kw)
replyobj.status("Wrote %s (%s) to %s\n" %
(m.name, m.oslIdent(), modelPath))
return
kw["multimodelHandling"] = key
# write multiple models to single file
replyobj.status("Writing multiple models to %s\n" % path)
writeMol2(models, path, **kw)
replyobj.status("Wrote multiple models to %s\n" % path)
#chdir("receptors") # change to the receptors file directory
for pdb in listdir("."):
if pdb.endswith("_aligned.pdb"):
continue
if pdb.endswith("_noH.pdb"):
continue
if not pdb.endswith("_mod2.pdb"): #originally was .pdb before pdb2pqr.py
continue
#if pdb == "1gzm.pdb": # don't need to do the pdb used for align
# continue
runCommand("open " + pdb)
runCommand("open 1gzm.pdb")
runCommand("mmaker #1 #0")
runCommand("write relative #1 #0 " + pdb[:-4] + "_aligned.pdb")
runCommand("close all")
pdb = pdb[:-4] + "_aligned.pdb"
runCommand("open " + pdb)
from DockPrep import prep
models = chimera.openModels.list(modelTypes=[chimera.Molecule])
prep(models)
from WriteMol2 import writeMol2
writeMol2(models, pdb[:-4]+ "_charged.mol2")
runCommand("select H")
runCommand("del sel")
runCommand("write format pdb 0 " + pdb[:-4] + "_noH.pdb")
runCommand("close all")
from chimera import runCommand
from chimera import openModels, Molecule
from os import chdir, listdir
import chimera
from WriteMol2 import writeMol2
import sys
file = open("com.txt")
for line in file:
if line.find("centroid has center") != -1:
#print "OPENED:%s" % line
word = line.split()
#print word
x = float(word[3])
y = float(word[4])
z = float(word[5]) + 16
center = Point(x, y, z)
runCommand("open " + sys.argv[1])
model0 = openModels.list(id=0, modelTypes=[Molecule])[0]
c = BuildStructure.placeHelium('com', model=model0, position=center)
runCommand("select He")
runCommand("namesel helium")
runCommand("select helium za>10")
runCommand("del sel")
runCommand("del helium")
writeMol2(chimera.openModels.list(modelTypes=[chimera.Molecule]), sys.argv[1][:-4] + ".mol2")
runCommand("close all")
def initiateSolvate(models, method, solvent, extent, center, status):
import os
import chimera
from chimera import replyobj
from chimera.molEdit import addAtom
from WriteMol2 import writeMol2
from tempfile import mkdtemp
for m in models:
tempDir = mkdtemp()
print 'tempDir: ', tempDir
def _clean():
for fn in os.listdir(tempDir):
os.unlink(os.path.join(tempDir, fn))
os.rmdir(tempDir)
sleapIn = os.path.join(tempDir, "sleap.in.mol2")
sleapOut= os.path.join(tempDir, "sleap.out.mol2")
writeMol2([m], sleapIn, status=status)
leaprc = os.path.join(tempDir, "solvate.cmd")
writeLeaprc(tempDir, method, solvent, extent, center, leaprc)
chimeraRoot = os.environ["CHIMERA"]
amberHome = os.path.join(chimeraRoot, "bin", "amber10")
command = [os.path.join(amberHome, "exe", "sleap"), "-f", leaprc]
print 'command: ', command
if status:
status("Running sleap" )
from subprocess import Popen, STDOUT, PIPE
# For some reason on Windows, if shell==False then antechamber
# cannot run bondtype via system().
import sys
if sys.platform == "win32":
shell = True
else:
shell = False
replyobj.info("Running sleap command: %s\n" % " ".join(command))
import os
os.environ["AMBERHOME"]=amberHome
sleapMessages = Popen(command, stdin=PIPE, stdout=PIPE, stderr=STDOUT,
cwd=tempDir, shell=shell, bufsize=1).stdout
while True:
line = sleapMessages.readline()
if not line:
break
replyobj.status("(solvate) %s" % line, log=True)
if not os.path.exists(sleapOut):
_clean()
from chimera import NonChimeraError
raise NonChimeraError("Failure running sleap \n"
"Check reply log for details\n")
if status:
status("Reading sleap output\n")
from chimera import Mol2io, defaultMol2ioHelper
mol2io = Mol2io(defaultMol2ioHelper)
mols = mol2io.readMol2file(sleapOut)
if not mol2io.ok():
_clean()
raise IOError(mol2io.error())
if not mols:
_clean()
raise RuntimeError("No molecules in sleap output")
assert len(mols)==1
outm = mols[0]
natom = len(m.atoms)
nresd = len(m.residues)
inAtoms = m.atoms
outAtoms = outm.atoms
# sort in coordIndex (i.e. input) order
# (due to deletions, coordIndex values need _not_ be consecutive)
serialSort = lambda a1, a2: cmp(a1.coordIndex, a2.coordIndex)
inAtoms.sort(serialSort)
outAtoms.sort(serialSort)
if status:
status("Translating %d atoms" % len(inAtoms))
for inA, outA in zip(inAtoms, outAtoms[:len(inAtoms)]):
inA.setCoord(outA.coord())
# added solvent hydrogens may not have been categorized yet, so use
# this less obvious way of gathering solvent atoms...
existingSolvent = set()
from chimera.elements import metals, alkaliMetals
nonAlkaliMetals = metals - alkaliMetals
for r in m.residues:
if len(r.atoms) == 1 and r.atoms[0].element in nonAlkaliMetals:
continue
for a in r.atoms:
if a.surfaceCategory in ["solvent", "ions"]:
existingSolvent.update(r.atoms)
break
# copy mol2 comment which contain the info of the solvent: shape, size, etc
if hasattr( outm, "mol2comments" ) and len(outm.mol2comments) > 0:
m.solventInfo = outm.mol2comments[0]
print "solvent info: ", m.solventInfo
if existingSolvent:
solventCharges = {}
for r in outm.residues[nresd:]:
solventNum = r.id.position - nresd
if status:
status("Creating solvent residue %d " % solventNum )
atomMap = {}
nr = m.newResidue(r.type, ' ', solventNum, ' ')
# mark residue for exclusion by AddCharge...
nr._solvateCharged = True
for a in r.atoms:
na = addAtom(a.name, a.element, nr, a.coord(),
serialNumber=a.serialNumber)
na.charge = a.charge
na.gaffType = a.mol2type
atomMap[a] = na
if a.name[0]=="H": na.element = 1
if a.name[0]=="C": na.element = 6
if a.name[0]=="N": na.element = 7
if a.name[0]=="O": na.element = 8
if a.name[0]=="P": na.element = 15
if a.name[0]=="S": na.element = 16
if a.name[0:2]=="Cl": na.element = 17
if existingSolvent:
solventCharges[(r.type, a.name)] = a.charge
if r.type == "WAT":
solventCharges[
("HOH", a.name)] = a.charge
for a in r.atoms:
na = atomMap[a]
for n in a.neighbors:
assert n.residue == r
nn = atomMap[n]
if nn in na.bondsMap:
continue
m.newBond(na, nn)
if existingSolvent:
unknowns = set()
for sa in existingSolvent:
key = (sa.residue.type, sa.name)
try:
sa.charge = solventCharges[key]
except KeyError:
unknowns.add(key)
sa.residue._solvateCharged = True
if unknowns:
replyobj.warning("Could not determine charges for"
" pre-existing solvent/ions from added solvent"
"/ions for: " + ", ".join([" ".join(x)
for x in unknowns]))
_clean()
from Midas import window
window(models)
def initiateAddions(models, iontype, numion, status):
import os
import chimera
from chimera import replyobj
from chimera.molEdit import addAtom
from WriteMol2 import writeMol2
from tempfile import mkdtemp
for m in models:
tempDir = mkdtemp()
def _clean():
for fn in os.listdir(tempDir):
os.unlink(os.path.join(tempDir, fn))
os.rmdir(tempDir)
sleapIn = os.path.join(tempDir, "sleap.in.mol2")
sleapOut= os.path.join(tempDir, "sleap.out.mol2")
writeMol2([m], sleapIn, status=status, gaffType=True)
leaprc = os.path.join(tempDir, "solvate.cmd")
writeLeaprc(tempDir, iontype, numion, leaprc)
chimeraRoot = os.environ["CHIMERA"]
amberHome = os.path.join(chimeraRoot, "bin", "amber10")
command = [os.path.join(amberHome, "exe", "sleap"), "-f", leaprc]
if status:
status("Running sleap" )
from subprocess import Popen, STDOUT, PIPE
# For some reason on Windows, if shell==False then antechamber
# cannot run bondtype via system().
import sys
if sys.platform == "win32":
shell = True
else:
shell = False
replyobj.info("Running sleap command: %s\n" % " ".join(command))
import os
os.environ["AMBERHOME"]=amberHome
sleapMessages = Popen(command, stdin=PIPE, stdout=PIPE, stderr=STDOUT,
cwd=tempDir, shell=shell, bufsize=1).stdout
while True:
line = sleapMessages.readline()
if not line:
break
replyobj.status("(addions) %s" % line, log=True)
if not os.path.exists(sleapOut):
_clean()
from chimera import NonChimeraError
raise NonChimeraError("Failure running sleap \n"
"Check reply log for details\n")
if status:
status("Reading sleap output\n")
from chimera import Mol2io, defaultMol2ioHelper
mol2io = Mol2io(defaultMol2ioHelper)
mols = mol2io.readMol2file(sleapOut)
if not mol2io.ok():
_clean()
raise IOError(mol2io.error())
if not mols:
_clean()
raise RuntimeError("No molecules in sleap output")
assert len(mols)==1
outm = mols[0]
solute_nresd = get_solute_nresd(m)
print "total, solute, solvent: ", len(m.residues), solute_nresd, len(m.residues)-solute_nresd
if status:
status( "Deleting old solvents" )
while len(m.residues) > solute_nresd:
m.deleteResidue( m.residues[solute_nresd] )
inAtoms = m.atoms
outAtoms = outm.atoms
# sort in coordIndex (i.e. input) order
# (due to deletions, coordIndex values need _not_ be consecutive)
serialSort = lambda a1, a2: cmp(a1.coordIndex, a2.coordIndex)
inAtoms.sort(serialSort)
outAtoms.sort(serialSort)
# sleap repositions solute...
if status:
status("Translating %d atoms" % len(inAtoms))
for inA, outA in zip(inAtoms, outAtoms[:len(inAtoms)]):
inA.setCoord(outA.coord())
for r in outm.residues[solute_nresd:]:
if status:
status("Creating ions/solvent residue %d " % (r.id.position-solute_nresd) )
atomMap = {}
nr = m.newResidue(r.type, ' ', 1, ' ')
for a in r.atoms:
na = addAtom(a.name, a.element, nr, a.coord(),
serialNumber=a.serialNumber)
na.charge = a.charge
na.gaffType = a.mol2type
if len(a.neighbors)==0:
na.drawMode = chimera.Atom.Sphere
atomMap[a] = na
if a.name[0:2]=="Br": na.element = 35
elif a.name[0:2]=="Cl": na.element = 17
elif a.name[0:2]=="Cs": na.element = 47
elif a.name[0:2]=="Mg": na.element = 12
elif a.name[0:2]=="Na": na.element = 11
elif a.name[0:2]=="Rb": na.element = 48
elif a.name[0]=='F': na.element = 9
elif a.name[0]=='I': na.element = 53
elif a.name[0]=='K': na.element = 19
elif a.name[0]=="H": na.element = 1
elif a.name[0]=="C": na.element = 6
elif a.name[0]=="N": na.element = 7
elif a.name[0]=="O": na.element = 8
elif a.name[0]=="P": na.element = 15
elif a.name[0]=="S": na.element = 16
for a in r.atoms:
na = atomMap[a]
for n in a.neighbors:
assert n.residue == r
nn = atomMap[n]
if nn in na.bondsMap:
continue
m.newBond(na, nn)
_clean()
def writePrmtop(m, topfile, parmset, unchargedAtoms=None):
import os
import chimera
from chimera import replyobj
from WriteMol2 import writeMol2
from tempfile import mkdtemp
status = replyobj.status
if unchargedAtoms and parmset.lower().endswith("ua"):
# united atom
replyobj.warning("Some uncharged/untyped protons expected due"
" to use of united-atom force field.\n")
unchargedHeavy = []
skip = []
for uncharged in unchargedAtoms.values():
for uc in uncharged:
if uc.element.number == 1:
skip.append(uc)
else:
unchargedHeavy.append(uc)
unchargedAtoms = unchargedHeavy
else:
skip = []
if unchargedAtoms:
if chimera.nogui:
raise ValueError("Some atoms don't have charges/types")
from chimera.baseDialog import AskYesNoDialog
d = AskYesNoDialog("Some atoms don't have charges/types"
" assigned. Write prmtop anyway?")
if d.run(chimera.tkgui.app) == "no":
return
tempDir = mkdtemp()
def _clean():
for fn in os.listdir(tempDir):
os.unlink(os.path.join(tempDir, fn))
os.rmdir(tempDir)
sleapIn = os.path.join(tempDir, "sleap.in.mol2")
writeMol2([m], sleapIn, status=status, gaffType=True, skip=skip)
leaprc = os.path.join(tempDir, "solvate.cmd")
writeLeaprc(tempDir, topfile, parmset, leaprc)
chimeraRoot = os.environ["CHIMERA"]
amberHome = os.path.join(chimeraRoot, "bin", "amber10")
acHome = os.path.join(chimeraRoot, "bin", "antechamber")
command = [os.path.join(amberHome, "exe", "sleap"), "-f", leaprc]
print 'command: ', command
if status:
status("Running sleap" )
from subprocess import Popen, STDOUT, PIPE
# For some reason on Windows, if shell==False then antechamber
# cannot run bondtype via system().
import sys
if sys.platform == "win32":
shell = True
else:
shell = False
replyobj.info("Running sleap command: %s\n" % " ".join(command))
import os
os.environ["AMBERHOME"]=amberHome
os.environ["ACHOME"]=acHome
sleapMessages = Popen(command, stdin=PIPE, stdout=PIPE, stderr=STDOUT,
cwd=tempDir, shell=shell, bufsize=1).stdout
while True:
line = sleapMessages.readline()
if not line:
break
replyobj.status("(writeprmtop) %s" % line, log=True)
if not os.path.exists(topfile):
_clean()
from chimera import NonChimeraError
raise NonChimeraError("Failure running sleap \n"
"Check reply log for details\n")
else:
replyobj.status("Wrote parmtop file %s\n" % topfile, log=True)
def _nonStdCharge(residues, netCharge, method, gaffType, status, showCharges):
r = residues[0]
if status:
status("Copying residue %s\n" % r.type)
# create a fake Molecule that we can write to a Mol2 file
nm = chimera.Molecule()
nm.name = r.type
# write out the residue's atoms first, since those are the
# ones we will be caring about
nr = nm.newResidue(r.type, ' ', 1, ' ')
from chimera.molEdit import addAtom
atomMap = {}
atomNames = set()
ratoms = r.atoms
# use same ordering of atoms as they had in input, to improve
# consistency of antechamber charges
ratoms.sort(lambda a1, a2: cmp(a1.coordIndex, a2.coordIndex))
for a in ratoms:
atomMap[a] = addAtom(a.name, a.element, nr, a.coord())
atomNames.add(a.name)
# add the intraresidue bonds and remember the interresidue ones
nearby = set()
for a in ratoms:
na = atomMap[a]
for n in a.neighbors:
if n.residue != r:
nearby.add(n)
continue
nn = atomMap[n]
if nn in na.bondsMap:
continue
nm.newBond(na, nn)
from chimera.idatm import typeInfo
extras = set()
while nearby:
nb = nearby.pop()
aname = _getAName(str(nb.element), atomNames)
na = addAtom(aname, nb.element, nr, nb.coord())
atomMap[nb] = na
extras.add(na)
for nbn in nb.neighbors:
if nbn in atomMap:
nm.newBond(na, atomMap[nbn])
else:
try:
ti = typeInfo[nbn.idatmType]
except KeyError:
fc = 0
geom = 4
else:
fc = estimateNetCharge([nbn])
geom = ti.geometry
if fc or geom != 4:
nearby.add(nbn)
else:
extras.update(
_methylate(na, nbn, atomNames))
totalNetCharge = netCharge + estimateNetCharge(extras)
from tempfile import mkdtemp
import os, os.path
tempDir = mkdtemp()
def _clean():
for fn in os.listdir(tempDir):
os.unlink(os.path.join(tempDir, fn))
os.rmdir(tempDir)
from WriteMol2 import writeMol2
anteIn = os.path.join(tempDir, "ante.in.mol2")
writeMol2([nm], anteIn, status=status)
chimeraRoot = os.environ["CHIMERA"]
anteHome = os.path.join(chimeraRoot, 'bin', 'antechamber')
anteOut = os.path.join(tempDir, "ante.out.mol2")
if method.lower().startswith("am1"):
mth = "bcc"
elif method.lower().startswith("gas"):
mth = "gas"
else:
_clean()
raise ValueError("Unknown charge method: %s" % method)
command = [os.path.join(anteHome, "exe", "antechamber"),
"-i", anteIn,
"-fi", "mol2",
"-o", anteOut,
"-fo", "mol2",
"-c", mth,
"-nc", str(totalNetCharge),
"-df", "0",
"-j", "5",
"-s", "2"]
if status:
status("Running ANTECHAMBER for residue %s\n" % r.type)
from subprocess import Popen, STDOUT, PIPE
# For some reason on Windows, if shell==False then antechamber
# cannot run bondtype via system().
import sys
if sys.platform == "win32":
shell = True
else:
shell = False
replyobj.info("Running ANTECHAMBER command: %s\n" % " ".join(command))
import os
os.environ['ACHOME'] = anteHome
anteMessages = Popen(command, stdin=PIPE, stdout=PIPE, stderr=STDOUT,
cwd=tempDir, shell=shell, bufsize=1).stdout
while True:
line = anteMessages.readline()
if not line:
break
replyobj.status("(%s) %s" % (r.type, line), log=True)
if not os.path.exists(anteOut):
_clean()
raise ChargeError("Failure running ANTECHAMBER for residue %s\n"
"Check reply log for details\n" % r.type)
if status:
status("Reading ANTECHAMBER output for residue %s\n" % r.type)
from chimera import Mol2io, defaultMol2ioHelper
mol2io = Mol2io(defaultMol2ioHelper)
mols = mol2io.readMol2file(anteOut)
if not mol2io.ok():
_clean()
raise IOError(mol2io.error())
if not mols:
_clean()
raise RuntimeError("No molecules in ANTECHAMBER output for"
" residue %s" % r.type)
chargedAtoms = mols[0].atoms
if len(chargedAtoms) != len(nm.atoms):
_clean()
raise RuntimeError("Wrong number of atoms (%d, should be %d)"
" in ANTECHAMBER output for residue %s"
% (r.type, len(chargedAtoms), len(nm.atoms)))
if status:
status("Assigning charges for residue %s\n" % r.type)
# put charges in template
templateAtoms = nm.atoms
# can't rely on order...
templateAtoms.sort(lambda a1, a2: cmp(a1.serialNumber, a2.serialNumber))
nonZero = False
addedChargeSum = 0.0
_totalCharge = 0.0
for ta, ca in zip(templateAtoms, chargedAtoms):
_totalCharge += ca.charge
if ta in extras:
addedChargeSum += ca.charge
continue
if ca.charge:
nonZero = True
if not nonZero:
_clean()
raise ChargeError("Failure running ANTECHAMBER for residue %s\n"
"Check reply log for details\n" % r.type)
# adjust charges to compensate for added atoms...
adjustment = (addedChargeSum - (totalNetCharge - netCharge)) / (
len(templateAtoms) - len(extras))
for ta, ca in zip(templateAtoms, chargedAtoms):
if ta in extras:
continue
ta.charge = ca.charge + adjustment
if gaffType:
ta.gaffType = ca.mol2type
# map template charges onto first residue
track = chimera.TrackChanges.get()
for fa, ta in atomMap.items():
if ta in extras:
continue
fa.charge = ta.charge
if showCharges:
fa.label = "%+g" % fa.charge
track.addModified(fa, ATTR_SET)
if gaffType:
fa.gaffType = ta.gaffType
# map charges onto remaining residues
for rr in residues[1:]:
for fa, ra in zip(r.oslChildren(), rr.oslChildren()):
ra.charge = fa.charge
if showCharges:
ra.label = "%+g" % ra.charge
track.addModified(ra, ATTR_SET)
if gaffType:
ra.gaffType = fa.gaffType
_clean()
if status:
status("Charges for residue %s determined\n" % r.type)
replyobj.info("Charges for residue %s determined\n" % r.type)
return True