def Apply(self):
path = self.getPaths()[0]
surf = self.surfList.getvalue()
if not surf:
replyobj.error("No surface chosen to save.\n")
return
from WriteDMS import writeDMS
replyobj.status("Writing DMS surface to %s\n" % path)
writeDMS(surf, path, writeNormals=self.saveNormalsVar.get(),
displayedOnly=self.displayedOnlyVar.get())
replyobj.status("Wrote DMS surface to %s\n" % path)
def Apply(self):
path = self.getPaths()[0]
surf = self.surfList.getvalue()
if not surf:
replyobj.error("No surface chosen to save.\n")
return
from WriteDMS import writeDMS
replyobj.status("Writing DMS surface to %s\n" % path)
writeDMS(surf,
path,
writeNormals=self.saveNormalsVar.get(),
displayedOnly=self.displayedOnlyVar.get())
replyobj.status("Wrote DMS surface to %s\n" % path)
def main():
if len(sys.argv) != 3: # if no input
print "ERORR"
return
input_mol2 = sys.argv[1]
output_dms = sys.argv[2]
runCommand("open " + input_mol2)
# generate surface using 'surf' command
runCommand("surf")
# get the surf object
surf = openModels.list(modelTypes=[MSMSModel])[0]
# write DMS
writeDMS(surf, output_dms)
return
import optparse
parser = optparse.OptionParser()
parser.add_option('--pdb_in', default=None, help='Input PDB file')
parser.add_option('--dms_out', default=None, help='Output dms file')
(args, options) = parser.parse_args()
import os
if not os.path.exists(args.pdb_in):
raise Exception(args.pdb_in+' does not exist')
print 'Processing '+args.pdb_in
import chimera
chimera.openModels.open(args.pdb_in)
# Molecular surface
from chimera import runCommand, openModels, MSMSModel
chimera.runCommand("surf") # generate surface using 'surf' command
surf = openModels.list(modelTypes=[MSMSModel])[0] # get the surf object
from WriteDMS import writeDMS
writeDMS(surf, args.dms_out) # write DMS
# run with
## chimera --nogui olfr1392_1u19_noH.pdb writedms.py
## chimera --nogui pdb:3D7F_withoutLigand writedms.py
# chimera --nogui Q9I8C1_27_noH.pdb writedms.py
# where this py file is named writedms.py
# it would run chimera without gui on the file 3D7F_withoutLigand.pdb
# and it would output to a file called 3D7F_without_ligand.dms
from chimera import runCommand, openModels, MSMSModel
# generate surface using 'surf' command
runCommand("surf")
# get the surf object
surf = openModels.list(modelTypes=[MSMSModel])[0]
# write DMS
from WriteDMS import writeDMS
#writeDMS(surf, "3D7F_rec_noH.dms")
#writeDMS(surf, "olfr1392_1u19_noH.dms")
#writeDMS(surf, "Q9I8C1_27_aligned_noH.dms")
writeDMS(surf, "rec.dms")
# run with
## chimera --nogui olfr1392_1u19_noH.pdb writedms.py
## chimera --nogui pdb:3D7F_withoutLigand writedms.py
# chimera --nogui Q9I8C1_27_noH.pdb writedms.py
# where this py file is named writedms.py
# it would run chimera without gui on the file 3D7F_withoutLigand.pdb
# and it would output to a file called 3D7F_without_ligand.dms
from chimera import runCommand, openModels, MSMSModel
# generate surface using 'surf' command
runCommand("surf")
# get the surf object
surf = openModels.list(modelTypes=[MSMSModel])[0]
# write DMS
from WriteDMS import writeDMS
#writeDMS(surf, "3D7F_rec_noH.dms")
#writeDMS(surf, "olfr1392_1u19_noH.dms")
#writeDMS(surf, "Q9I8C1_27_aligned_noH.dms")
writeDMS(surf, "rec.dms")
import optparse
parser = optparse.OptionParser()
parser.add_option('--pdb_in', default=None, help='Input PDB file')
parser.add_option('--dms_out', default=None, help='Output dms file')
(args, options) = parser.parse_args()
import os
if not os.path.exists(args.pdb_in):
raise Exception(args.pdb_in + ' does not exist')
print 'Processing ' + args.pdb_in
import chimera
chimera.openModels.open(args.pdb_in)
# Molecular surface
from chimera import runCommand, openModels, MSMSModel
chimera.runCommand("surf") # generate surface using 'surf' command
surf = openModels.list(modelTypes=[MSMSModel])[0] # get the surf object
from WriteDMS import writeDMS
writeDMS(surf, args.dms_out) # write DMS
import sys
from chimera import runCommand, openModels, MSMSModel
infile = sys.argv[1]
probe_radius = sys.argv[2]
dms_filename = sys.argv[3]
runCommand("open %s" % infile)
runCommand("surface probeRadius %s" % probe_radius)
surf = openModels.list(modelTypes=[MSMSModel])[0]
from WriteDMS import writeDMS
writeDMS(surf, dms_filename)
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")
#!/usr/bin/env python
"""
use chimera to generate a receptor surface file
example usage:
>> chimera --nogui --script "/home/kmckiern/scripts/clc/dock/gen_surf.py \
receptor.pdb"
"""
import os
from chimera import runCommand as rc
from chimera import openModels, MSMSModel
from WriteDMS import writeDMS
import sys
fn = sys.argv[1]
pref = fn.split('.')[0]
rc('open ' + fn)
rc("surf")
surf = openModels.list(modelTypes=[MSMSModel])[0]
writeDMS(surf, pref + '.dms')
rc('close all')
rc('stop now')
