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 #seqToPSF('protG.seq') #protocol.initStruct("g_new.psf") # - or from file
simWorld.setRandomSeed( 785 ) import protocol backbone="name C or name CA or name N or name O or name HN" #Nilges topology/parameters xplor.command('evaluate ($par_nonbonded = "OPLSX")') protocol.parameters['protein']="waterRef/parallhdg5.3.pro.new" protocol.parameters['water'] ="waterRef/parallhdg5.3.sol" protocol.topology['protein'] ="waterRef/topallhdg5.3.pro.new" protocol.topology['water'] ="waterRef/topallhdg5.3.sol" waterResname="TIP3" protocol.initParams(("protein","ion.par")) #protocol.initStruct("zc2h2_waterref.psf") protocol.loadPDB(inputStructures[0],deleteUnknownAtoms=True) from potList import PotList from simulationTools import MultRamp, StaticRamp, FinalParams potList = PotList() rampedParams=[] # set up NOE potential noe=PotList('noe') potList.append(noe) from noePotTools import create_NOEPot for (name,scale,file) in [('all',1,"constraints/yourfolder/yourfoldernoe.tbl"),
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") # generate PSF data from sequence and initialize the correct parameters. # #from psfGen import seqToPSF #seqToPSF('protG.seq') #protocol.initStruct("g_new.psf") # - or from file # or read an existing model # from nefTools import readNEF nefData = readNEF(nefFile) from iupacNaming import toIUPAC, fromIUPAC toIUPAC()
seq = open(seqFilename).read() seqToPSF( seq, # Customize here for specific settings or get them from a dictionary with the project or so. startResid=1, deprotonateHIS=1, segName='', disulfide_bonds=[], disulfide_bridges=[], ) elif os.path.exists(pdbFilename): psfGen.pdbToPSF(pdbFilename) # protocol.initCoords(pdbFilename) elif os.path.exists(psfFilename): # read in the PSF file and initial structure command("structure @%s end" % psfFilename) protocol.initParams("protein.par", weak_omega=1) # command("coor @gb3_xray.pdb") else: print "ERROR: failed to find seq or psf file in %s" % os.getcwd() sys.exit(1) # end if # generate a random extended structure with correct covalent geometry protocol.genExtendedStructure(extFilename) # # a PotList conatins a list of potential terms. This is used to specify which # terms are active during refinement. # potList = PotList()
if os.path.exists( seqFilename ): seq = open(seqFilename).read() seqToPSF(seq, # Customize here for specific settings or get them from a dictionary with the project or so. startResid=1, deprotonateHIS=1, segName='', disulfide_bonds=[], disulfide_bridges=[], ) elif os.path.exists( pdbFilename ): psfGen.pdbToPSF(pdbFilename) # protocol.initCoords(pdbFilename) elif os.path.exists( psfFilename ): # read in the PSF file and initial structure command("structure @%s end" % psfFilename) protocol.initParams("protein.par", weak_omega=1) # command("coor @gb3_xray.pdb") else: print "ERROR: failed to find seq or psf file in %s" % os.getcwd() sys.exit(1) # end if # generate a random extended structure with correct covalent geometry protocol.genExtendedStructure(extFilename) # # a PotList conatins a list of potential terms. This is used to specify which # terms are active during refinement. # potList = PotList()
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") # generate PSF data from sequence and initialize the correct parameters. # #from psfGen import seqToPSF #seqToPSF('protG.seq') #protocol.initStruct("g_new.psf") # - or from file # or read an existing model # from nefTools import readNEF nefData = readNEF(nefFile) protocol.initStruct("ACD.psf", erase=False) protocol.initParams("ACD.par")