def Apply(self):
from DockPrep import prep
if self.addHydVar.get():
import AddH
addHFunc = AddH.hbondAddHydrogens
else:
addHFunc = None
kw = self.applyKeywords
self.applyKeywords = {}
rotamerLib = rotamerPreserve = None
if self.incompleteVar.get():
incompleteVal = self.incompleteOpt.get()
if type(incompleteVal) != str:
rotamerLib = incompleteVal.importName
rotamerPreserve = True
incompleteVal = "rotamers"
prefs[INCOMPLETE_SC] = incompleteVal
else:
incompleteVal = None
prep(self.molListBox.getvalue(), addHFunc=addHFunc,
addCharges=self.addChargesVar.get(),
runSaveMol2Dialog=self.writeMol2Var.get(),
mutateMSE=self.mutMseVar.get(),
mutate5BU=self.mut5buVar.get(),
mutateUMS=self.mutUmsVar.get(),
mutateCSL=self.mutCslVar.get(),
delSolvent=self.delSolventVar.get(),
delIons=self.delIonsVar.get(),
delAltLocs=self.delAltLocsVar.get(),
incompleteSideChains=incompleteVal,
rotamerLib=rotamerLib,
rotamerPreserve=rotamerPreserve, **kw)
def main():
print sys.argv
if len(sys.argv) != 3: # if no input
print "ERROR: Wrong number of inputs"
print "syntax: chimera --nogui --script \"chimera_dockprep.py pdbinput output_prefix\""
print len(sys.argv)
return
#models = openModels.list(modelTypes=[chimera.Molecule])
input_pdb = sys.argv[1]
output_prefix = sys.argv[2]
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)
#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 DockPrep import prep
if self.addHydVar.get():
import AddH
addHFunc = AddH.hbondAddHydrogens
else:
addHFunc = None
kw = self.applyKeywords
self.applyKeywords = {}
rotamerLib = rotamerPreserve = None
if self.incompleteVar.get():
incompleteVal = self.incompleteOpt.get()
if type(incompleteVal) != str:
rotamerLib = incompleteVal.importName
rotamerPreserve = True
incompleteVal = "rotamers"
prefs[INCOMPLETE_SC] = incompleteVal
else:
incompleteVal = None
prep(self.molListBox.getvalue(),
addHFunc=addHFunc,
addCharges=self.addChargesVar.get(),
runSaveMol2Dialog=self.writeMol2Var.get(),
mutateMSE=self.mutMseVar.get(),
mutate5BU=self.mut5buVar.get(),
mutateUMS=self.mutUmsVar.get(),
mutateCSL=self.mutCslVar.get(),
delSolvent=self.delSolventVar.get(),
delIons=self.delIonsVar.get(),
delAltLocs=self.delAltLocsVar.get(),
incompleteSideChains=incompleteVal,
rotamerLib=rotamerLib,
rotamerPreserve=rotamerPreserve,
**kw)
def runDockPrep():
models = chimera.openModels.list(modelTypes=[chimera.Molecule])
prep(models)
#prep(models, hisScheme=None, mutateMSE=True, mutate5BU=True, mutateUMS=True,
# mutateUMS=True, mutateCSL=True, delSolvent=True, delIons=False,
# delLigands=False, delAltLocs=True, incompleteSideChains='rotamers',
# nongui=False, rotamerLib='Dunbrack', rotamerPreserve=True,
# memorize=False, memorizeName=None)
return
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 add_hydrogens_prep():
""" Performs DockPrep on the currently-loaded protein in Chimera
Arguments:
None
Requires:
A protein must be opened in Chimera (
e.g. 'runCommand("open " + file_name))' must have already run
It is also recommended that the loaded protein has already been
cleaned with clean_protein()
If surface computation is run after this function, the surface
computation may fail due to the added hydrogens
Returns:
Void
Effect:
Modifies the structure in the following ways:
1. Adds hydrogens
2. Mutates non-standard AAs to standard AAs
3. Modifies incomplete side chains
4. Deletes solven molecules
"""
# Add hydrogen atoms/charges, mutate MSE and other non-standard
# AAs to standard, and perform other basic DockPrep operations.
models = chimera.openModels.list(modelTypes=[chimera.Molecule])
# try:
prep(
models,
addHFunc=AddH.hbondAddHydrogens,
hisScheme=None,
mutateMSE=True,
mutate5BU=True,
mutateUMS=True,
mutateCSL=True,
delSolvent=True,
delIons=False,
delLigands=False,
delAltLocs=True,
incompleteSideChains="rotamers",
nogui=True,
rotamerLib=defaults[INCOMPLETE_SC],
rotamerPreserve=True,
memorize=False,
memorizeName=None,
)
resname_states_dict["GLU"] = ["GLU", "GLH1", "GLH2"]
resname_states_dict["ASP"] = ["ASP", "ASH1", "ASH2"]
rc("open %s" % args.RECEPTOR) # load the receptor
rc("open %s" % args.LIGAND) # load the ligand
if args.DOCKPREP:
import chimera
from Addions import initiateAddions
from DockPrep import prep
from AddCharge import estimateFormalCharge
models = chimera.openModels.list(modelTypes=[chimera.Molecule])
print(
"Preparing receptor for docking and calculating ligand AM1 charges (may be slow)."
)
prep(models, nogui=True, method='am1')
# Select the residues to be protonated
if args.RADIUS > 0:
rc("sel #1 z<%f & ~ #1" % args.RADIUS)
elif args.RADIUS == 0:
rc("sel #0")
residues = currentResidues() # get the residue of the pocket
residue_states = {}
protonatable_resids = []
protonatable_resnames = []
for r in residues:
if r.type in ["GLU", "GLH"]:
states = resname_states_dict["GLU"]
protonatable_resids.append(str(r.id))
protonatable_resnames.append(r.type)
#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")
import chimera from DockPrep import prep models = chimera.openModels.list(modelTypes=[chimera.Molecule]) prep(models) from WriteMol2 import writeMol2 writeMol2(models, "dp.mol2")
def makeAllMeshes(proID, jobID, peptideLen=40, pocketDist=5.0):
global curResID
global curProID
global meshDir
global pocketMap
global resCount
global curJobID
#Insure input is a 4 character protein ID
proID = proID[0:4]
#Create a new directory for the protein
meshDir = proID + 'Mesh'
curProID = proID
curJobID = jobID
# os.mkdir(meshDir)
# os.system("chmod 777 " + meshDir)
try:
#Fetch protein from the PDB
runCommand('open ' + proID)
#Initial prep for pocket search
runCommand('delete solvent')
runCommand('delete :HOH')
#Open protein model
model = openModels.list(modelTypes=[Molecule])[0]
RES_LIST = model.residues
resCount = len(RES_LIST)
#Pocket finding procedure
chains = []
counts = []
index = 0
print 'Counting Chain Lengths................'
for res in RES_LIST:
curChain = str(res.id.chainId)
if len(chains) == 0:
chains.append(curChain)
counts.append(1)
if curChain != chains[index]:
index = index + 1
chains.append(curChain)
counts.append(1)
else:
counts[index] = counts[index] + 1
print 'Finding Peptide Ligand Pockets................'
for i, chain in enumerate(chains):
if counts[i] < peptideLen: #Less than X amino acids = peptide
runCommand('~select')
runCommand('select ligand & :.' +
chain) #Check if actually ligand
runCommand('select selected zr<' +
str(pocketDist)) #Select pocket
runCommand('~select :/isHet zr<' +
str(pocketDist)) #De-select ligand
runCommand('~select ligand')
residues = selection.currentResidues() #Store pocket in memory
for res in residues:
if res in pocketMap:
pocketMap[res].append('|' + chain)
else:
pocketMap[res] = [chain]
print 'Finding non-Peptide Ligand Pockets................'
for res in RES_LIST:
if res.isHet: #Check if "heterogenous residue" which includes ligands
curResID = str(res.id)
runCommand('~select')
runCommand('select :' + curResID +
' & ligand') #Check if actually ligand
runCommand('select selected zr<' +
str(pocketDist)) #Select pocket
runCommand('~select :' + curResID)
residues = selection.currentResidues() #Store pocket in memory
for pocketRes in residues:
if pocketRes in pocketMap:
pocketMap[pocketRes].append('|' + res.type + '-' +
curResID)
else:
pocketMap[pocketRes] = [res.type + '-' + curResID]
print 'Dock Prep................'
prep(openModels.list(modelTypes=[Molecule]))
runCommand('delete ligand')
print '\nRunning Delphi................'
runCommand('~select')
runCommand('write format pdb 0 ' + proID + curJobID +
'.pdb') #Write delphi-ready protein with hydrogens
#Create delphi parameter file
f = open('./param_' + curJobID, 'w')
f.write('in(pdb,file="' + proID + curJobID +
'.pdb")\n') #Input/Output files
f.write('in(siz,file="amber.siz")\n')
f.write('in(crg,file="amber.crg")\n')
f.write('out(phi,file="' + proID + curJobID + '.phi")\n')
f.write('indi=2\n') #Interior dielectric constant
f.write('exdi=80.0\n') #Exterior dielectric constant (water)
f.write('prbrad=1.4\n')
f.write('salt=0.15\n') #Salt concentration and radius
f.write('ionrad=2.0\n')
# f.write('nonit=20\n') #Non-linear iterations
f.close()
os.system("./DELPHI_2004_LINUX_v2/delphi_static param_" +
curJobID) #Run delphi
# print '\nExporting Mesh................'
runCommand('select #0')
runCommand('surface')
#runCommand('export format X3D ./' + proID + '.x3d') # Prints raw X3D file.
print '\nOpening Delphi Data................'
runCommand('open ' + proID + curJobID + '.phi')
runCommand('scolor #0 volume #1 cmap -1,red:0,white:1,blue;')
print '\nRemoving Temp Files................'
os.remove("./" + proID + curJobID + '.pdb')
os.remove("./" + proID + curJobID + '.phi')
os.remove('./param_' + curJobID)
print '\nDONE: ' + proID
except:
f = open("./" + 'ErrorLog' + curJobID + '.txt', 'w')
f.write(proID + ' error: ' + str(sys.exc_info()[0]) +
str(sys.exc_info()[1]) + '\n')
f.close()
raise
return
def makeAllMeshes(proID, jobID, peptideLen=40, pocketDist=5.0):
global curResID
global curProID
global meshDir
global pocketMap
global resCount
global curJobID
#Insure input is a 4 character protein ID
proID = proID[0:4]
#Create a new directory for the protein
meshDir = proID + 'Mesh'
curProID = proID
curJobID = jobID
# os.mkdir(meshDir)
# os.system("chmod 777 " + meshDir)
try:
#Fetch protein from the PDB
runCommand('open '+ proID)
#Initial prep for pocket search
runCommand('delete solvent')
runCommand('delete :HOH')
#Open protein model
model = openModels.list(modelTypes=[Molecule])[0]
RES_LIST = model.residues
resCount = len(RES_LIST)
#Pocket finding procedure
chains = []
counts = []
index = 0
print 'Counting Chain Lengths................'
for res in RES_LIST:
curChain = str(res.id.chainId)
if len(chains) == 0:
chains.append(curChain)
counts.append(1)
if curChain != chains[index]:
index = index + 1
chains.append(curChain)
counts.append(1)
else:
counts[index] = counts[index] + 1
print 'Finding Peptide Ligand Pockets................'
for i, chain in enumerate(chains):
if counts[i] < peptideLen: #Less than X amino acids = peptide
runCommand('~select')
runCommand('select ligand & :.' + chain) #Check if actually ligand
runCommand('select selected zr<' + str(pocketDist)) #Select pocket
runCommand('~select :/isHet zr<' + str(pocketDist)) #De-select ligand
runCommand('~select ligand')
residues = selection.currentResidues() #Store pocket in memory
for res in residues:
if res in pocketMap:
pocketMap[res].append('|' + chain)
else:
pocketMap[res] = [chain]
print 'Finding non-Peptide Ligand Pockets................'
for res in RES_LIST:
if res.isHet: #Check if "heterogenous residue" which includes ligands
curResID = str(res.id)
runCommand('~select')
runCommand('select :' + curResID + ' & ligand') #Check if actually ligand
runCommand('select selected zr<' + str(pocketDist)) #Select pocket
runCommand('~select :' + curResID)
residues = selection.currentResidues() #Store pocket in memory
for pocketRes in residues:
if pocketRes in pocketMap:
pocketMap[pocketRes].append('|' + res.type + '-' + curResID)
else:
pocketMap[pocketRes] = [res.type + '-' + curResID]
print 'Dock Prep................'
prep(openModels.list(modelTypes=[Molecule]))
runCommand('delete ligand')
print '\nRunning Delphi................'
runCommand('~select')
runCommand('write format pdb 0 '+ proID + curJobID + '.pdb') #Write delphi-ready protein with hydrogens
#Create delphi parameter file
f = open('./param_' + curJobID, 'w')
f.write('in(pdb,file="'+ proID + curJobID + '.pdb")\n') #Input/Output files
f.write('in(siz,file="amber.siz")\n')
f.write('in(crg,file="amber.crg")\n')
f.write('out(phi,file="'+ proID + curJobID + '.phi")\n')
f.write('indi=2\n') #Interior dielectric constant
f.write('exdi=80.0\n') #Exterior dielectric constant (water)
f.write('prbrad=1.4\n')
f.write('salt=0.15\n') #Salt concentration and radius
f.write('ionrad=2.0\n')
# f.write('nonit=20\n') #Non-linear iterations
f.close()
os.system("./DELPHI_2004_LINUX_v2/delphi_static param_" + curJobID) #Run delphi
# print '\nExporting Mesh................'
runCommand('select #0')
runCommand('surface')
#runCommand('export format X3D ./' + proID + '.x3d') # Prints raw X3D file.
print '\nOpening Delphi Data................'
runCommand('open '+ proID + curJobID + '.phi')
runCommand('scolor #0 volume #1 cmap -1,red:0,white:1,blue;')
print '\nRemoving Temp Files................'
os.remove("./" + proID + curJobID + '.pdb')
os.remove("./" + proID + curJobID + '.phi')
os.remove('./param_' + curJobID)
print '\nDONE: ' + proID
except:
f = open("./" + 'ErrorLog' + curJobID + '.txt', 'w')
f.write(proID + ' error: ' + str(sys.exc_info()[0]) + str(sys.exc_info()[1]) + '\n')
f.close()
raise
import chimera
import sys
import re
from DockPrep import prep
from DockPrep import AddH
from WriteMol2 import writeMol2
# ref: http://mailman.docking.org/pipermail/dock-fans/2007-May/001043.html
models = chimera.openModels.list(modelTypes=[chimera.Molecule])
prep(models, addHFunc=AddH.hbondAddHydrogens)
root = models[0].name.replace(".pdb", "")
if len(sys.argv) == 2:
d = re.sub("/$", "", sys.argv[1]) + "/"
else:
d = ""
writeMol2(models, d + root + "_prepped.mol2")
# ref: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-March/006134.html
chimera.runCommand("surf")
surf = chimera.openModels.list(modelTypes=[chimera.MSMSModel])[0]
from WriteDMS import writeDMS
writeDMS(surf, d + root + ".dms")
rc("sel #0.2") # select the ligand
ligres = currentResidues()[0]
ligres.type = 'LIG' # change the resname of the ligand to 'LIG'
rc("combine #0.1 modelId 1"
) # create a new molecule containing just the receptor
rc("combine #0.2 modelId 2"
) # create a new molecule containing just the ligand
rc("del #0")
if args.REC_NET_CHARGE != None:
rec_charge = args.REC_NET_CHARGE
else:
# We will estimate the receptor's net charge. For this we need to DockPrep the receptor (is fast).
models = chimera.openModels.list(modelTypes=[chimera.Molecule])
# For a full list of DockPrep options, look into file Chimera-alpha_py2.7/share/DockPrep/__init__.py
prep([models[0]],
nogui=True,
method=args.CHARGE_METHOD,
addHFunc=addHFunc)
rec_charge = estimateFormalCharge(
models[0].atoms
) # DockPred does not assign charges to receptor atoms, only to ligand atoms
print("Receptor's net charge =", rec_charge)
# Now that we calculated the charges of the protein and the ligand, we just need the complex
rc("combine #1,2 modelId 3"
) # create a new molecule containing the protein-ligand complex
rc("del #1-2")
pdb = args.COMPLEX.replace(".pdb", "_prep.pdb")
elif args.RECEPTOR and args.LIGAND:
rc("open %s" % args.RECEPTOR) # load the receptor
if args.REC_NET_CHARGE == None:
standardize_terminal_protein_residues(
args.RECEPTOR, "#0"
import chimera
from DockPrep import prep
import Midas
import sys
import os
PDB_file = sys.argv[1]
lig_name = sys.argv[2]
num = sys.argv[3]
ligand = chimera.openModels.open("%s_%s_CH%s.pdb" % (PDB_file, lig_name, num))
prep(ligand, addCharges=False)
#prep(ligand,addCharges=True)
Midas.write(ligand, None,
PDB_file + "_" + lig_name + "_ADDH_CH" + num + ".pdb")
print("success!")
ligres = currentResidues()[0]
ligres.type = 'LIG' # change the resname of the ligand to 'LIG'
rc("combine #0,1 modelId 2"
) # create a new molecule containing the protein-ligand complex
rc("combine #2 modelId 3"
) # create a new molecule containing the protein-ligand complex
rc("del #0-2")
pdb = os.path.splitext(os.path.basename(
args.RECEPTOR))[0] + "_" + os.path.splitext(
os.path.basename(args.LIGAND))[0] + "_prep.pdb"
print(
"Preparing receptor for docking and calculating ligand '%s' charges (may be slow)."
% args.CHARGE_METHOD)
models = chimera.openModels.list(modelTypes=[chimera.Molecule])
prep(models, nogui=True, method=args.CHARGE_METHOD)
net_charge = estimateFormalCharge(models[0].atoms)
# Neutralize system
if args.NEUTRALIZE:
if net_charge < 0:
initiateAddions(models, "Na+", "neutralize",
chimera.replyobj.status)
elif net_charge > 0:
initiateAddions(models, "Cl-", "neutralize",
chimera.replyobj.status)
if net_charge != 0:
# change the resids of the ions, which by default they are all 1
rc("sel ~ions")
existing_resids = [
int(str(r.id).split('.')[0]) for r in currentResidues()
]
## PDB_FILE SHOULD THE COMPLETE PATH OF THE FILE
## REPLACE BNZ with LIGAND resname
## USAGE: Chimera --nogui --script "prep_prot_lig.py 4w52.pdb BNZ"
import chimera
from DockPrep import prep
import Midas
import sys
import os
PDB_file = sys.argv[1]
lig_name = sys.argv[2]
os.system('grep ATOM %s > %s_clean.pdb'%(PDB_file,PDB_file[:-4]))
os.system('grep %s %s > %s.pdb'%(lig_name,PDB_file,lig_name))
protein=chimera.openModels.open('%s_clean.pdb'%PDB_file[:-4])
ligand=chimera.openModels.open('%s.pdb'%lig_name)
prep(protein,addHFunc=None,addCharges=False)
prep(ligand)
Midas.write(protein,None,"protein_clean.pdb")
Midas.write(ligand,None,"ligand_wH.pdb")