pass
if opt[0] == "nef": #specify -quick to just test that the script runs
nefFile = opt[1]
pass
if opt[0] == "cif": #specify -quick to just test that the script runs
cifFile = opt[1]
pass
pass
from os.path import splitext
id = splitext(nefFile)[0]
# protocol module has many high-level helper functions.
#
import protocol
protocol.initRandomSeed(3421) #explicitly set random seed
protocol.initParams("protein")
from glob import glob
for topFile in glob('*.top'):
protocol.initTopology(topFile)
pass
for parFile in glob('*.par'):
protocol.initParams(parFile)
pass
import psfGen
psfGen.addResidueName("ACD", "metal")
# generate PSF data from sequence and initialize the correct parameters.
#
#from psfGen import seqToPSF
# filename for output structures. This string must contain the STRUCTURE
# literal so that each calculated structure has a unique name. The SCRIPT
# literal is replaced by this filename (or stdin if redirected using <),
# but it is optional.
#
outFilename = "%s_SCRIPT_STRUCTURE_sa.pdb" % pname
numberOfStructures=20 #usually you want to create at least 20
if quick:
numberOfStructures=3
# end if
# protocol module has many high-level helper functions.
#
protocol.initRandomSeed() #set random seed - by time
command = xplor.command
# generate PSF data from sequence and initialize the correct parameters.
#
#seqToPSF('%s.seq'% pname)
#Simply read the psf already generated.
xplor.command("""struct @%s.psf end""" % pname)
# generate random extended initial structure with correct covalent geometry
#
protocol.genExtendedStructure()
#
# a PotList contains a list of potential terms. This is used to specify which
#
xplor.parseArguments()
# filename for output structures. This string must contain the STRUCTURE
# literal so that each calculated structure has a unique name. The SCRIPT
# literal is replaced by this filename (or stdin if redirected using <),
# but it is optional.
#
outFilename = "XPLOR_output/SCRIPT_STRUCTURE.pdb"
numberOfStructures = 100 #usually you want to create at least 20
# protocol module has many high-level helper functions.
#
import protocol
protocol.initRandomSeed(1603) #set random seed - by time
command = xplor.command
# generate PSF data from sequence and initialize the correct parameters.
#
from psfGen import seqToPSF
seqToPSF('protG.seq') ## modify ##
# generate random extended initial structure with correct covalent geometry
#
protocol.genExtendedStructure()
#
# a PotList contains a list of potential terms. This is used to specify which
# terms are active during refinement.
#
xplor.parseArguments()
# filename for output structures. This string must contain the STRUCTURE
# literal so that each calculated structure has a unique name. The SCRIPT
# literal is replaced by this filename (or stdin if redirected using <),
# but it is optional.
#
outFilename = "contacts55perfect_diheSSpsipred/SCRIPT_STRUCTURE.pdb"
numberOfStructures = 100 #usually you want to create at least 20
# protocol module has many high-level helper functions.
#
import protocol
protocol.initRandomSeed(1603) #explicitly set random seed
command = xplor.command
# read an existing model
#
protocol.loadPDB("contacts55perfect_diheSSpsipred/anneal_GB1_ave.pdb",
deleteUnknownAtoms=True)
protocol.fixupCovalentGeom(maxIters=100, useVDW=1)
#
# a PotList contains a list of potential terms. This is used to specify which
# terms are active during refinement.
#
from potList import PotList