def _postAddPrep(mols, addCharges=False, gaffType=True, nogui=False, chargeModel=None, method=None, **kw): if addCharges: from AddCharge import initiateAddCharges initiateAddCharges(models=mols, status=replyobj.status, gaffType=gaffType, chargeModel=chargeModel, nogui=nogui, method=method, cb=lambda ur, uc, m=mols, kw=kw: _chargeCB(ur, uc, m, **kw)) else: _postAddCharge(mols, **kw)
def addcharge(molecule):
AMBER99SB = "AMBER ff99SB"
AMBER99bsc0 = "AMBER ff99bsc0"
AMBER02pol_r1 = "AMBER ff02pol.r1"
AMBER03ua = "AMBER ff03ua"
AMBER03_r1 = "AMBER ff03.r1"
AMBER12SB = "AMBER ff12SB"
try:
initiateAddCharges(models=molecule,
method='am1-bcc',
nogui=True,
chargeModel=AMBER12SB)
return molecule
except KeyboardInterrupt:
print 'Stop by user'
sys.exit()
except:
return None
def _postAddPrep(mols,
addCharges=False,
gaffType=True,
nogui=False,
chargeModel=None,
method=None,
**kw):
if addCharges:
from AddCharge import initiateAddCharges
initiateAddCharges(
models=mols,
status=replyobj.status,
gaffType=gaffType,
chargeModel=chargeModel,
nogui=nogui,
method=method,
cb=lambda ur, uc, m=mols, kw=kw: _chargeCB(ur, uc, m, **kw))
else:
_postAddCharge(mols, **kw)
def Apply(self): from AddCharge import initiateAddCharges from AddH.gui import checkNoHyds mols = self.molList.getvalue() chargeModel = self.chargeModel.getvalue() chargeMethod = self.chargeMethod.getvalue() checkNoHyds(mols, lambda mols=mols: initiateAddCharges( cb=self.cb, models=mols, chargeModel=chargeModel, method=chargeMethod, status=chimera.replyobj.status, labelStandard=self.labelStandardVar.get(), labelNonstandard=self.labelNonstandardVar.get()), self.process)
def Apply(self):
from AddCharge import initiateAddCharges
from AddH.gui import checkNoHyds
mols = self.molList.getvalue()
chargeModel = self.chargeModel.getvalue()
chargeMethod = self.chargeMethod.getvalue()
checkNoHyds(mols,
lambda mols=mols: initiateAddCharges(
cb=self.cb,
models=mols,
chargeModel=chargeModel,
method=chargeMethod,
status=chimera.replyobj.status,
labelStandard=self.labelStandardVar.get(),
labelNonstandard=self.labelNonstandardVar.get()),
self.process)
#!/usr/bin/env python
import sys
import os
import chimera
from chimera import runCommand
from AddCharge import initiateAddCharges
initiateAddCharges(method='am1-bcc', nogui=True)
#use: chimera --nogui --script drreposer_run_vina.py OR open with UCSF Chimera
#Have to install Chimera first
#prepare ligand molecule for docking - ligand derived from complexes
#e.g. 1sn0 - protein-drug complex
#e.g. 602.B - drug molecule
runCommand(
'open 1sn0; sel :602.B; sel invert; del sel; del solvent; del ions; wait')
runCommand(
'swapaa same sel preserve true ignoreOtherModels true; addh; addcharge s; wait'
)
#save files to current directory
runCommand('write format mol2 0 predictedbs.ligand.mol2; wait')
#prepare receptor structure for docking - give a pdb id and only select the first model in the case of nmr structure
#e.g 2k0z - protein to be search for its potential of binding to ligand
runCommand(
'open 2k0z; del #1.2-100; sel protein; sel invert sel; del sel; del solvent; del ions; wait'
)
runCommand(
'swapaa same sel preserve true ignoreOtherModels true; addh; addcharge s; wait'
)
#save files to current directory
runCommand('write format mol2 1 predictedbs.receptor.mol2; wait')
for fn in file_names:
#Open the file and extract the first line which contains the name of the molecule
with open(fn) as myfile:
head = [next(myfile) for x in xrange(1)]
#------------------------------------------------------------------
# Processing the molecule using Chimera
#------------------------------------------------------------------
#Open the file in Chimera
rc("open " + fn)
#Add Gasteiger charges
initiateAddCharges(method='gasteiger', nogui=True)
rc('surface vertexDensity 2') # Add surface to molecule
rc('coulombic -10 red 0 white 10 blue'
) # Colr surface by coulombic charge
rc(
'select'
) # Select the molecule from the model panel, also selects the surface for processing
#------------------------------------------------------------------
# Surface processing
#------------------------------------------------------------------
#Surface processing section
slist = [m for m in selection.currentGraphs() if isinstance(m, MSMSModel)
] # initiates selected surface to object
vertices = [] # empty list to populate with vertices
s = slist[0] # takes the surface from the surface object