Python EDrestraint.setPenalty方法代码示例

# 需要导入模块: from restraints import EDrestraint [as 别名]
# 或者: from restraints.EDrestraint import setPenalty [as 别名]
def main() :
    import optparse ; parser = optparse.OptionParser()
    parser.add_option("--scratchdir", action='store', type='string', dest='scratchdir', help='to create all the files during refinement. it shdnt be already present.')
    parser.add_option("--pdb", action='store', type='string', dest='pdbfile', help='starting pdb containing a model of pdb-ligand complex')
    parser.add_option("--offset", action='store', type='int', dest='offset', help='a +/- integer that describes the sequence shift to apply', default=0)
    parser.add_option("--truncateN", action='store', type='int', dest='truncateN', help='remove residues from Nterm', default=None)
    parser.add_option("--truncateC", action='store', type='int', dest='truncateC', help='remove residues from Cterm', default=None)
    parser.add_option("--delres", action='store', type='string', dest='delres', help='filename containing residues to be deleted. truncate and this option shdnt be used together', default=None)

    parser.add_option("--sf", action='store', type='string', dest='sf', help='structure factors file')
    parser.add_option("--a", action='store', type='float', dest='a', help='cell dimension a')
    parser.add_option("--b", action='store', type='float', dest='b', help='cell dimension b')
    parser.add_option("--c", action='store', type='float', dest='c', help='cell dimension c')
    parser.add_option("--alpha", action='store', type='float', dest='alpha', help='cell angle alpha')
    parser.add_option("--beta", action='store', type='float', dest='beta', help='cell angle beta')
    parser.add_option("--gamma", action='store', type='float', dest='gamma', help='cell angle gamma')
    parser.add_option("--sg", action='store', type='string', dest='sg', help='cell spacegroup, in CCP4 notation')
    parser.add_option("--resolution", action='store', type='float', dest='resolution', help='resolution of the data')
    parser.add_option("--extraTOP", action='store', type='string', dest='extraTOP', help='ligand CNS topology file')
    parser.add_option("--extraPAR", action='store', type='string', dest='extraPAR', help='ligand CNS params file')

    parser.add_option("--ca-restraint-radius", action='store', type='float', dest='caRad', help='radius of spherical restraint on CA position', default=1)
    parser.add_option("--sc-centroid-restraint-radius", action='store', type='float', dest='scRad', help='radius of spherical restraint on sidechain centroid', default=2)
    parser.add_option("--sidechain-vdw-reduction", action='store', type='float', dest='scReduction', help='factor to reduce effective vdw dist in case of sidechains', default=1)
    parser.add_option("--population-size", action='store', type='int', dest='popsize', help='population size for PopulationStrategy', default=100)
    parser.add_option("--verbose", action='store', type='int', dest='verbose', help='0 means least verbosity etc.', default=0)
    parser.add_option("--backtrack", action='store', type='string', dest='backtrack', help='use backtracking version of PopulationStrategy. eg 4X5 will set backtrack numsteps and stepsize to 4,5 respectively. not used by default.', default=None)
    parser.add_option("--noRTK", action='store', type='int', dest='noRTK', help='dont rebuild bad-fits with rtk', default=None)
    parser.add_option("--uselowres", action='store', type='int', dest='uselowres', help='lower the resolution artificially to have argument*numatoms reflections', default=None)
    parser.add_option("--randomize", action='store', type='int', dest='randomize', help='seed for randomizing', default=None)

    (options, args) = parser.parse_args()

    import misc
    misc.setVerbosity(options.verbose)
    from scplacement import SCplacement
    from loopbuild import Multiloop
    import prepareChain
    from restraints import EDrestraint ; EDrestraint.setPenalty(5.) ; EDrestraint.setScatRad(1.) ;
    esmin, esmax = 0.1, 1

    randomize(options.randomize)

    if options.delres != None :
        resdel = parseDelres(options.pdbfile, options.delres)
        print resdel

        ## amk sommmented 
        #for l in open(options.delres, 'r').readlines() :
        #    if l[0] == '#' : continue
        #    l = re.sub("\n", "", l)
        #    resdel.append( re.sub( "]", "", re.sub("\[", "", l) ) )

    #import sys; sys.exit(0)
    if not os.path.isdir(options.scratchdir) : os.mkdir(options.scratchdir)
    shutil.copyfile(options.sf, "%s/strfactors.mtz" % options.scratchdir)
    shutil.copyfile(options.pdbfile, "%s/%s" % (options.scratchdir,options.pdbfile))
    firstmodel = "%s/model0.pdb" % options.scratchdir
    if not os.path.isfile(firstmodel) :
        if options.caRad < 0.49 : shutil.copyfile(options.pdbfile, firstmodel)
        else :
            mlPrepC = prepareChain.PrepareChain("PRL")
            Multiloop(options.pdbfile, None, None, options.caRad, options.scRad, options.scReduction, None, options.popsize, options.backtrack, 1, firstmodel, None, mlPrepC).run()
        if options.delres != None :
            deleteResidues(firstmodel, resdel) #; sys.exit(0)

    os.chdir(options.scratchdir)

    shutil.copyfile("model0.pdb", "model0.AA.pdb")

    numRefCycles = 10
    cif2mtz("strfactors.mtz", "base.mtz", options.a, options.b, options.c, options.alpha, options.beta, options.gamma, options.sg)
    uniqueify("base.mtz", "rfree.mtz")

    if options.noRTK :
        removeRElines("model0.AA.pdb", ["^MODEL", "^ENDMDL"])
        copyNonprotein(options.pdbfile, "model0.AA.pdb")
        for cycle in range(numRefCycles) :
            modelIn = "model%d.AA.pdb" % cycle
            phasedmtz = "phased%d.mtz" % cycle # phase the str factors with current model
            sfall(modelIn, "rfree.mtz", phasedmtz)
            modelOut = "model%d.AA.pdb" % (cycle+1) # model to be generated in this cycle
            mtzout = "phased%d.mtz" % (cycle+1) # model to be generated in this cycle
            cnsRefinement(phasedmtz, modelIn, mtzout, modelOut,
                options.a, options.b, options.c, options.alpha, options.beta, options.gamma, options.sg, options.resolution,
                cnsArgs, cycle, options.extraTOP, options.extraPAR)
        sys.exit(0)

    keepMClinesOnly("model0.pdb")

    if options.offset != None : ## offset=0 by default, not None
        prot = protein("model0.pdb", read_hydrogens=0, read_waters=0, read_hets=0)
        res, resids, resnums, resns, chids, inscodes, pts = prot2res.readProtRes(prot)
        keys = list(resns.keys()) ; keys.sort()
        newresns = {}
        allAA = [ "GLY", "ALA", "VAL", "LEU", "ILE", "PRO", "PHE", "TYR", "TRP", "ASP", "GLU", "HIS", "LYS", "ARG", "CYS", "MET", "SER", "THR", "ASN", "GLN", ]
        if options.offset > 0 :
            for ki in range(options.offset, len(keys)) : newresns[ keys[ki] ] = resns[ keys[ki-options.offset] ]
            for ki in range(options.offset) : newresns[ keys[ki] ] = allAA[ int(len(allAA)*random.random()) ]
        elif options.offset < 0 :
#.........这里部分代码省略.........

# 需要导入模块: from restraints import EDrestraint [as 别名]
# 或者: from restraints.EDrestraint import setPenalty [as 别名]

#.........这里部分代码省略.........
    l =  "--gamma = %s "%str(options.gamma) ;      print >> fp, l 
    l =  "--sg = %s "%str(options.sg) ;      print >> fp, l 
    l =  "--resolution = %s "%str(options.resolution) ;      print >> fp, l 
    l =  "--ca-restraint-radius = %s "%str(options.caRad) ;      print >> fp, l 
    l =  "--sc-centroid-restraint-radius = %s "%str(options.scRad) ;      print >> fp, l 
    l =  "--sidechain-vdw-reduction = %s "%str(options.scReduction) ;      print >> fp, l 
    l =  "--population-size = %s "%str(options.popsize) ;      print >> fp, l 
    l =  "--verbose = %s "%str(options.verbose) ;      print >> fp, l 
    l =  "--backtrack = %s "%str(options.backtrack) ;      print >> fp, l 
    l =  "--randomize = %s "%str(options.randomize) ;      print >> fp, l 
    l =  "--loopres = %s "%str(options.loopres) ;      print >> fp, l 
    l =  "--framework = %s "%str(options.framework) ;      print >> fp, l 
    l =  "--framework-ca-threshold = %s "%str(options.fcarad) ;      print >> fp, l 
    l =  "--framework-sc-threshold = %s "%str(options.fscrad) ;      print >> fp, l 
    l =  "--rebuild-poor-regions-only = %s "%str(options.poorOnly) ;      print >> fp, l 
    l =  "--poor-fit-threshold = %s "%str(options.poorThreshold) ;      print >> fp, l 
    l =  "--mconly = %s "%str(options.mconly) ;      print >> fp, l 
    l =  "--sconly = %s "%str(options.sconly) ;      print >> fp, l 
    l =  "--default-mainchain-b-factor = %s "%str(options.mcBfac) ;      print >> fp, l 
    l =  "--default-sidechain-b-factor = %s "%str(options.scBfac) ;      print >> fp, l 
    l =  "--models-get-native-bfactors = %s "%str(options.nativeBfac) ;      print >> fp, l 
    l =  "--dontusesc = %s "%str(options.dontusesc) ;      print >> fp, l 
    l =  "--num-models = %s "%str(options.nmodels) ;      print >> fp, l 
    l =  "--f1label = %s "%str(options.f1label) ;      print >> fp, l 
    l =  "--f2label = %s "%str(options.f2label) ;      print >> fp, l 
    l =  "--philabel = %s "%str(options.philabel) ;      print >> fp, l 
    l =  "--maptype = %s "%str(options.maptype) ;      print >> fp, l 
    l =  "--cacaCutoff = %s "%str(options.cacaCutoff) ;      print >> fp, l 
    l =  "--make-ed-optional = %s "%str(options.edOpt) ;      print >> fp, l
#    l =  "--chids = %s "%str(options.chids) ;      print >> fp, l 
    fp.close()
    
    guidedsampling = None
    from restraints import EDrestraint ; EDrestraint.setPenalty(2.) ; EDrestraint.setScatRad(1.) ;
    esmin, esmax, esmean, rcmult, xscoreCutoff = .000, 5., .0, 5, options.poorThreshold
    multiPrepC = prepareChain.PrepareChain("SCL1.0")
    xscorer = XrayScorer(None, xscoreCutoff)

    
    modelIn =  options.pdbfile
    rtkmodel = options.pdbout # rappertk model to be generated in this cycle


    if options.mapfn1 == None and options.mtzfn == None:
        print "Warning no mtz or map input, no electron density restraints will be used"
    
    if options.poorOnly == 1 :
        if  options.mtzfn == None and options.mapfn1 == None and options.mapfn2 == None:
            print "No mapfn1,mapfn2 or mtzfn  set"
            sys.exit()
        if options.mapfn2 == None and options.mapfn1 !=None and options.mtzfn == None:
            print "Both mapfn1 and mapfn2 need to be  set"
            sys.exit()            

        if options.mapfn1 == None and options.mapfn2 !=None and options.mtzfn == None :
            print "Both mapfn1 and mapfn2 need to be  set"
            sys.exit()            


        if options.mtzfn != None :
            badmcsc = xscorer.score(modelIn, options.mtzfn, options.f1label, options.f2label, options.philabel, options.maptype, "mcsc")
            badmc = xscorer.score(modelIn, options.mtzfn, options.f1label, options.f2label, options.philabel, options.maptype, "mc")
            badpept = xscorer.score(modelIn, options.mtzfn, options.f1label, options.f2label, options.philabel, options.maptype,"pept")
            badscs = xscorer.score(modelIn, options.mtzfn, options.f1label, options.f2label, options.philabel, options.maptype,"sc")
            
        elif options.mapfn1 !=None and options.mapfn2 != None  :

# 需要导入模块: from restraints import EDrestraint [as 别名]
# 或者: from restraints.EDrestraint import setPenalty [as 别名]
def main() :

    import optparse ; parser = optparse.OptionParser()
    parser.add_option("--scratchdir", action='store', type='string', dest='scratchdir', help='to create all the files during refinement. it shdnt be already present.')
    parser.add_option("--pdb", action='store', type='string', dest='pdbfile', help='starting pdb containing a model of pdb-ligand complex')

    parser.add_option("--sf", action='store', type='string', dest='sf', help='structure factors file')
    parser.add_option("--a", action='store', type='float', dest='a', help='cell dimension a')
    parser.add_option("--b", action='store', type='float', dest='b', help='cell dimension b')
    parser.add_option("--c", action='store', type='float', dest='c', help='cell dimension c')
    parser.add_option("--alpha", action='store', type='float', dest='alpha', help='cell angle alpha')
    parser.add_option("--beta", action='store', type='float', dest='beta', help='cell angle beta')
    parser.add_option("--gamma", action='store', type='float', dest='gamma', help='cell angle gamma')
    parser.add_option("--sg", action='store', type='string', dest='sg', help='cell spacegroup, in CCP4 notation')
    parser.add_option("--resolution", action='store', type='float', dest='resolution', help='resolution of the data')

    parser.add_option("--ca-restraint-radius", action='store', type='float', dest='caRad', help='radius of spherical restraint on CA position', default=1)
    parser.add_option("--sc-centroid-restraint-radius", action='store', type='float', dest='scRad', help='radius of spherical restraint on sidechain centroid', default=2)
    parser.add_option("--sidechain-vdw-reduction", action='store', type='float', dest='scReduction', help='factor to reduce effective vdw dist in case of sidechains', default=1)
    parser.add_option("--population-size", action='store', type='int', dest='popsize', help='population size for PopulationStrategy', default=100)
    parser.add_option("--verbose", action='store', type='int', dest='verbose', help='0 means least verbosity etc.', default=0)
    parser.add_option("--backtrack", action='store', type='string', dest='backtrack', help='use backtracking version of PopulationStrategy. eg 4X5 will set backtrack numsteps and stepsize to 4,5 respectively. not used by default.', default=None)
    parser.add_option("--noRTK", action='store', type='int', dest='noRTK', help='dont rebuild bad-fits with rtk', default=0)
    parser.add_option("--randomize", action='store', type='int', dest='randomize', help='seed for randomizing', default=None)
    parser.add_option("--loopres", action='store', type='string', dest='loopres', help='filename containing resids for starting perturbation', default=None)
    parser.add_option("--framework", action='store', type='int', dest='framework', help='to be used in conjunction with loopres. it puts a 1/3 ca/sc pos restr on non-loopres and perturbs them too', default=None)


    (options, args) = parser.parse_args()

    assert options.framework in [None, 1]

    import misc
    misc.setVerbosity(options.verbose)

    randomize(options.randomize)

    if options.loopres != None :
        ## expecting resids in [RSNcRESIa] format, one per line
        #shutil.copyfile(options.pdbfile, "temp.pdb" )
        #removeChainId("temp.pdb")
        loopresids = parseLoopres(options.pdbfile,options.loopres)
        ## amk commented 
        #for l in open(options.loopres, 'r').readlines() :
        #    if l[0] == "#" : continue
         #   lres = l[1:len(l)-2]
         #   loopresids.append(lres)
        options.loopres = loopresids #[ "VAL   47 ", "GLN   48 ", "GLY   49 ", "GLU   50 ", "GLU   51 ", "SER   52 ", "ASN   53 ", "ASP   54 ", "LYS   55 ", ]
        print "Do i come herer "

    print options.loopres


    #import sys ; sys.exit()
    if not os.path.isdir(options.scratchdir) : os.mkdir(options.scratchdir)
    shutil.copyfile(options.pdbfile, "%s/model0.pdb" % options.scratchdir)
    shutil.copyfile(options.sf, "%s/strfactors.mtz" % options.scratchdir)
    os.chdir(options.scratchdir)
    cif2mtz("strfactors.mtz", "base.mtz", options.a, options.b, options.c, options.alpha, options.beta, options.gamma, options.sg)
    uniqueify("base.mtz", "rfree.mtz")







    from scplacement import SCplacement
    from loopbuild import Multiloop
    import prepareChain

    from restraints import EDrestraint ; EDrestraint.setPenalty(2.) ; EDrestraint.setScatRad(1.) ;
    esmin, esmax, esmean, rcmult, xscoreCutoff = .000, 5., .0, 5, 0.9

    guidedsampling = None
    multiPrepC = prepareChain.PrepareChain("SCL1.0")

    xscorer = XrayScorer(None, xscoreCutoff)
    numRefCycles = 20 ; startCycle = 0
    for cycle in range(startCycle, numRefCycles) :
    
        print "***********************************************"
        print "********************CYCLE %d*******************" % cycle
        print "***********************************************"
        modelIn = "model%d.pdb" % cycle
        cnsout = "cns%d.pdb" % cycle
        rtkmodel = "model%d.pdb" % (cycle+1) # rappertk model to be generated in this cycle
        sfall(modelIn, "rfree.mtz", "phased.mtz")
        
        phasedmtz = "phased%d.mtz" % cycle # phase the str factors with current model

        if cycle > 3 : 

            toRemove = "phased%d.mtz" %(cycle-2) 
            if os.path.exists(toRemove) :
                os.remove(toRemove)

            
            toRemove = "phased%d.mtzfc.map"%(cycle-2)
            if os.path.exists(toRemove) :
#.........这里部分代码省略.........

# 需要导入模块: from restraints import EDrestraint [as 别名]
# 或者: from restraints.EDrestraint import setPenalty [as 别名]
def main() :
    import optparse ; parser = optparse.OptionParser()
    parser.add_option("--scratchdir", action='store', type='string', dest='scratchdir', help='to create all the files during refinement.')
    parser.add_option("--pdb", action='store', type='string', dest='pdbfile', help='starting pdb containing a model of pdb-ligand complex')
    parser.add_option("--sf", action='store', type='string', dest='sf', help='structure factors file')
    parser.add_option("--a", action='store', type='float', dest='a', help='cell dimension a')
    parser.add_option("--b", action='store', type='float', dest='b', help='cell dimension b')
    parser.add_option("--c", action='store', type='float', dest='c', help='cell dimension c')
    parser.add_option("--alpha", action='store', type='float', dest='alpha', help='cell angle alpha')
    parser.add_option("--beta", action='store', type='float', dest='beta', help='cell angle beta')
    parser.add_option("--gamma", action='store', type='float', dest='gamma', help='cell angle gamma')
    parser.add_option("--sg", action='store', type='string', dest='sg', help='cell spacegroup, in CCP4 notation')
    parser.add_option("--resolution", action='store', type='float', dest='resolution', help='resolution in angstroms')
    parser.add_option("--percent-r-free", action='store', type='string', dest='prfree', help='percentage R-free to take must be at least 500 reflections', default=0.05)
    parser.add_option("--n-models", action='store', type='int', dest='nmodel', help='the number of models required to make up the ensemble')
    parser.add_option("--restart-n", action='store', type='int', dest='restart', help='the CNS round to restart from', default=0)
    parser.add_option("--restart-n-mod", action='store', type='int', dest='restart_mod', help='the model round to restart from', default=0)
    parser.add_option("--refine-prog", action='store', type='string', dest='refinetype', help='Use CNS or PHENIX', default="CNS")
    parser.add_option("--multichain", action='store', type='int', dest='multichain', help='Does the target have more than one chain if so then use 1', default=0)
    parser.add_option("--ca-restraint-radius", action='store', type='float', dest='caRad', help='radius of spherical restraint on CA position', default=1)
    parser.add_option("--sc-centroid-restraint-radius", action='store', type='float', dest='scRad', help='radius of spherical restraint on sidechain centroid', default=2)
    parser.add_option("--sidechain-vdw-reduction", action='store', type='float', dest='scReduction', help='factor to reduce effective vdw dist in case of sidechains', default=1)
    parser.add_option("--population-size", action='store', type='int', dest='popsize', help='population size for PopulationStrategy', default=100)
    parser.add_option("--verbose", action='store', type='int', dest='verbose', help='0 means least verbosity etc.', default=0)
    parser.add_option("--ranseed", action='store', type='float', dest='ranseed', help='Explicitly set the random seed.', default=1)
    parser.add_option("--backtrack", action='store', type='string', dest='backtrack', help='use backtracking version of PopulationStrategy. eg 4X5 will set backtrack numsteps and stepsize to 4,5 respectively. not used by default.', default=None)
    parser.add_option("--noRTK", action='store', type='int', dest='noRTK',help='dont rebuild bad-fits with rtk', default=0)
    (options, args) = parser.parse_args()

    import misc
    misc.setVerbosity(options.verbose)
    misc.RanGen.instance().seedme( int(-1000 * options.ranseed) )
    
    #import sys; sys.exit(0)
    if not os.path.isdir(options.scratchdir) :
        os.mkdir(options.scratchdir)
        shutil.copyfile(options.pdbfile, "%s/PDB.pdb" % options.scratchdir)
        shutil.copyfile(options.sf, "%s/strfactors.mtz" % options.scratchdir)
    os.chdir(options.scratchdir)

    from xcheck import main as xcheckMain
    from loopbuild import Multiloop
    from scplacement import SCplacement
    import prepareChain
    from restraints import EDrestraint ; EDrestraint.setPenalty(5.) ; EDrestraint.setScatRad(1.) ;
    esmin, esmax, esmean, rcmult = 0.0001, 5.0, .1, 10
    EDrestraint.setScatRad(.5) ;
    multiPrepC = prepareChain.PrepareChain("PRL1.0") ##here we can pass sc lib option

    if options.restart == 0 and options.restart_mod == 0:
        Multiloop("PDB.pdb", None, None, options.caRad, options.scRad, options.scReduction, None , options.popsize, options.backtrack, options.nmodel, "model.pdb", None, multiPrepC).run()
        ## change to remove n models requested NDF 15/01/07 ###
        for mod_num in range(options.nmodel):
            print "Model file manipulation on %d .pdb" %mod_num 
            removeMODEL_multi("model", mod_num)
            mod_file_num = mod_num + 1
            mfn_st = "%d" % mod_file_num
            copyNonprotein("PDB.pdb", "model"+mfn_st+".pdb")

    cif2mtz("strfactors.mtz", "base.mtz", options.a, options.b, options.c, options.alpha, options.beta, options.gamma, options.sg)
    uniqueify("base.mtz", "rfree.mtz", options.prfree) ## add here the percentage need to generate r-free - note for low res need to be 10% otherwise 5%

    
    ## for each model generate a subdir and copy in model then run script in each sub file NDF 15/01/07 ##
    for mod_dir in range(options.restart_mod, options.nmodel):
        mod_num_st = "%d" % (mod_dir + 1)
        if not os.path.isdir("model_"+mod_num_st+"_refine"): 
            os.mkdir("model_"+mod_num_st+"_refine")
            shutil.copyfile("model"+mod_num_st+".pdb", "model_"+mod_num_st+"_refine/model"+mod_num_st+"_0.pdb")
            shutil.copyfile("../"+options.sf, "model_"+mod_num_st+"_refine/strfactors.mtz")
            shutil.copyfile("rfree.mtz", "model_"+mod_num_st+"_refine/rfree.mtz")
            shutil.copyfile("base.mtz", "model_"+mod_num_st+"_refine/base.mtz")
        ##if we get a cluster working here we want to paralalise the job NDF 17/01/2007 ##
        
        os.chdir("model_"+mod_num_st+"_refine")
        print "HAVE MOVED TO model_"+mod_num_st+"_refine" 
            
        justcns = None
        numRefCycles = 10
        
        for cycle in range(options.restart, numRefCycles):
            print "***********************************************"
            print "**************** CNS CYCLE %d*******************" % cycle
            print "***********************************************"
            
            xscorer = XrayScorer(None, 0.90)

            model_stem = "model"+mod_num_st+"_%d" % cycle
            modelIn = "model"+mod_num_st+"_%d.pdb" % cycle
            cnsout = "ref%d.pdb" % cycle
            rtkmodel = "model"+mod_num_st+"_%d.pdb" % (cycle+1) # rappertk model to be generated in this cycle
            cnsdiffmap = "cns%ddiff.map" % cycle
            
            if cycle >= 8:
                multiPrepC = prepareChain.PrepareChain("SCL0.5") 
            else:
                multiPrepC = prepareChain.PrepareChain("PRL1.0") 

            
            sfall(modelIn, "rfree.mtz", "phased.mtz")
#.........这里部分代码省略.........

# 需要导入模块: from restraints import EDrestraint [as 别名]
# 或者: from restraints.EDrestraint import setPenalty [as 别名]
def main():
    import optparse ; parser = optparse.OptionParser()
    parser.add_option("--scratchdir", action='store', type='string', dest='scratchdir', help='to create all the files during refinement. it shdnt be already present.')
    parser.add_option("--pdb", action='store', type='string', dest='pdbfile', help='starting pdb containing a mainchain-only fragment')

    parser.add_option("--mtz", action='store', type='string', dest='mtz', help='str factors as mtz file')
    parser.add_option("--a", action='store', type='float', dest='a', help='cell dimension a')
    parser.add_option("--b", action='store', type='float', dest='b', help='cell dimension b')
    parser.add_option("--c", action='store', type='float', dest='c', help='cell dimension c')
    parser.add_option("--alpha", action='store', type='float', dest='alpha', help='cell angle alpha')
    parser.add_option("--beta", action='store', type='float', dest='beta', help='cell angle beta')
    parser.add_option("--gamma", action='store', type='float', dest='gamma', help='cell angle gamma')
    parser.add_option("--sg", action='store', type='string', dest='sg', help='cell spacegroup, in CCP4 notation')
    parser.add_option("--resolution", action='store', type='float', dest='resolution', help='resolution of the data')

    parser.add_option("--ca-restraint-radius", action='store', type='float', dest='caRad', help='radius of spherical restraint on CA position', default=1)
    parser.add_option("--sc-centroid-restraint-radius", action='store', type='float', dest='scRad', help='radius of spherical restraint on sidechain centroid', default=2)
    parser.add_option("--sidechain-vdw-reduction", action='store', type='float', dest='scReduction', help='factor to reduce effective vdw dist in case of sidechains', default=1)
    parser.add_option("--population-size", action='store', type='int', dest='popsize', help='population size for PopulationStrategy', default=100)
    parser.add_option("--backtrack", action='store', type='string', dest='backtrack', help='use backtracking version of PopulationStrategy. eg 4X5 will set backtrack numsteps and stepsize to 4,5 respectively. not used by default.', default=None)
    parser.add_option("--verbose", action='store', type='int', dest='verbose', help='0 means least verbosity etc.', default=0)
    parser.add_option("--randomize", action='store', type='int', dest='randomize', help='seed for randomizing', default=None)

    parser.add_option("--sequence", action='store', type='string', dest='sequence', help='seq to slide over the given fragment', default=None)
    parser.add_option("--slideres", action='store', type='string', dest='slideres', help='file containing resids over which sequence is to be slided', default=None)

    (options, args) = parser.parse_args()

    if not os.path.isdir(options.scratchdir) : os.mkdir(options.scratchdir)
    os.chdir(options.scratchdir)

    misc.setVerbosity(options.verbose)

    randomize(options.randomize)

    slideres = []
    for l in open(options.slideres, 'r').readlines() :
        l = re.sub("\n", "", re.sub("#.*", "", l))
        if len(l) == 0 : continue
        if not l[0] == "#" : slideres.append( l[1:len(l)-1] )
    print "SLIDERES", slideres
    options.slideres = slideres

    refprot = protein(options.pdbfile, read_hydrogens=0, read_waters=0, read_hets=0)
    refres, refresids, refresnums, refresns, refchids, refinscodes, refpts = prot2res.readProtRes(refprot)
    for ri in range(len(refres)) :
        assert refresns[ri] == "GLY"
        for an in refres[ri].keys() : assert an in [" N  "," CA "," C  "," O  "]

    from restraints import EDrestraint ; EDrestraint.setPenalty(0.) ; EDrestraint.setScatRad(1.) ;
    esmin, esmax, esmean, rcmult, xscoreCutoff = .000, 5., .0, 5, 0.9

    ## make a SA-weighted 2FoFc map based on given given mconly fragment
    cnsArgs = {}
    for cycle in range(20) : cnsArgs[cycle] = {} ; cnsArgs[cycle]["num_cycles"] = 1 ; cnsArgs[cycle]["temperature"] = 50 ; cnsArgs[cycle]["harmCA"] = 1
    cnsArgs[1]["num_cycles"] = 2 ; cnsArgs[1]["temperature"] = 3000
    sfall(options.pdbfile, options.mtz, "rfree.mtz")
    cnsRefinement("rfree.mtz", options.pdbfile, "phased0.mtz", "dontcare.pdb",
                options.a, options.b, options.c, options.alpha, options.beta, options.gamma, options.sg, options.resolution,
                cnsArgs, 0)
    restoreChainids("dontcare.pdb", options.pdbfile)

    #refprot = protein("dontcare.pdb", read_hydrogens=0, read_waters=0, read_hets=0)
    #refres, refresids, refresnums, refresns, refchids, refinscodes, refpts = prot2res.readProtRes(refprot)
        #res, resids, resnums, resns, chids, inscodes, pts = makeFrag( options.sequence[si:si+len(refres)] )

    for si in range( len(options.sequence)-len(options.slideres)+1 ) :
        prot = protein("dontcare.pdb", read_hydrogens=0, read_waters=0, read_hets=0)
        res, resids, resnums, resns, chids, inscodes, pts = prot2res.readProtRes(prot)
        mutmap = {}
        for resid in options.slideres :
            for k,v in resids.items() :
                if v == resid : mutmap[k] = options.sequence[ si + options.slideres.index(resid) ]
        from data import resAtoms
        from pdbr import makeResid
        from protinfo import AA13
        for ri,aa1 in mutmap.items() :
            print "mutate %5d [%s] -> %s" % (k, resids[ri], aa1)
            for an in resAtoms[ AA13[aa1] ] :
                if an in [" N  "," CA "," C  "," O  "] : continue
                assert not an in res[ri].keys()
                res[ri][an] = len(pts)
                pts.append( [-999., -999., -999.] )
            resns[ri] = AA13[aa1]
            resids[ri] = makeResid( resns[ri], chids[ri], resnums[ri], inscodes[ri] )
        badresids = []
        for ri,aa1 in mutmap.items() : badresids.append( resids[ri] )
        print "badresids", badresids

        ModelRenderer(res, resns, chids, resnums, inscodes, [], "start.pdb").render(pts)

        multiPrepC = prepareChain.PrepareChain("SCL1.0")
        xrayRestGen = [ prepareChain.XrayRestraintsGenerator("phased0.mtz2fofc.map", "map", "FC", "PHIC", "2F1-F2", esmin, esmax, esmean, ["SCLbuilder","ChiBuilder","CBbuilder"], ) ]
        ml = Multiloop("start.pdb", badresids, None, options.caRad, options.scRad, options.scReduction, None, options.popsize,
            options.backtrack, 1, "end.pdb", xrayRestGen, multiPrepC)
        ml.ranker = XrayRanker("phased0.mtz2fofc.map", "map", "FC", "PHIC", "2F1-F2", esmin, esmax)
        ml.ranker.rankChildren = rcmult ; ml.ranker.rankRecurse = 1
        ml.ranker.rankLeaderBuilderOnly = None ; ml.ranker.rankGivenEnsemble = None
        ml.cellsym = [ options.a, options.b, options.c, options.alpha, options.beta, options.gamma, sgtable[options.sg][0] ]
        ml.run()
#.........这里部分代码省略.........

# 需要导入模块: from restraints import EDrestraint [as 别名]
# 或者: from restraints.EDrestraint import setPenalty [as 别名]
def main() :

    import optparse ; parser = optparse.OptionParser()
    parser.add_option("--scratchdir", action='store', type='string', dest='scratchdir', help='to create all the files during refinement. it shdnt be already present.')
    parser.add_option("--pdb", action='store', type='string', dest='pdbfile', help='starting pdb containing a model of pdb-ligand complex')
    parser.add_option("--outpdb", action='store', type='string', dest='outpdb', help='starting pdb containing a model of pdb-ligand complex')
    parser.add_option("--ca-restraint-radius", action='store', type='float', dest='caRad', help='radius of spherical restraint on CA position', default=1)
    parser.add_option("--sc-centroid-restraint-radius", action='store', type='float', dest='scRad', help='radius of spherical restraint on sidechain centroid', default=2)
    parser.add_option("--sidechain-vdw-reduction", action='store', type='float', dest='scReduction', help='factor to reduce effective vdw dist in case of sidechains', default=1)
    parser.add_option("--population-size", action='store', type='int', dest='popsize', help='population size for PopulationStrategy', default=100)
    parser.add_option("--verbose", action='store', type='int', dest='verbose', help='0 means least verbosity etc.', default=0)
    parser.add_option("--backtrack", action='store', type='string', dest='backtrack', help='use backtracking version of PopulationStrategy. eg 4X5 will set backtrack numsteps and stepsize to 4,5 respectively. not used by default.', default=None)
    parser.add_option("--noRTK", action='store', type='int', dest='noRTK', help='dont rebuild bad-fits with rtk', default=0)
    parser.add_option("--randomize", action='store', type='int', dest='randomize', help='seed for randomizing', default=None)
    parser.add_option("--num-models-wanted", action='store', type='int', dest='nmodels', help='seed for randomizing', default=None)
    parser.add_option("--loopres", action='store', type='string', dest='loopres', help='filename containing resids for starting perturbation', default=None)
    parser.add_option("--framework", action='store', type='int', dest='framework', help='to be used in conjunction with loopres. it puts a 1/3 ca/sc pos restr on non-loopres and perturbs them too', default=None)


    (options, args) = parser.parse_args()

    assert options.framework in [None, 1]

    import misc
    misc.setVerbosity(options.verbose)

    randomize(options.randomize)

    if options.loopres != None :
        ## expecting resids in [RSNcRESIa] format, one per line

        #removeChainId("temp.pdb")
        loopresids = parseLoopres(options.pdbfile,options.loopres)
        ## amk commented 
        #for l in open(options.loopres, 'r').readlines() :
        #    if l[0] == "#" : continue
         #   lres = l[1:len(l)-2]
         #   loopresids.append(lres)
        options.loopres = loopresids #[ "VAL   47 ", "GLN   48 ", "GLY   49 ", "GLU   50 ", "GLU   51 ", "SER   52 ", "ASN   53 ", "ASP   54 ", "LYS   55 ", ]
        print "Do i come herer "

    print options.loopres


    #import sys ; sys.exit()
    if not os.path.isdir(options.scratchdir) : os.mkdir(options.scratchdir)
    shutil.copyfile(options.pdbfile, "%s/%s" % (options.scratchdir,options.pdbfile))
    os.chdir(options.scratchdir)
    

    from scplacement import SCplacement
    from loopbuild import Multiloop
    import prepareChain

    from restraints import EDrestraint ; EDrestraint.setPenalty(2.) ; EDrestraint.setScatRad(1.) ;
    esmin, esmax, esmean, rcmult, xscoreCutoff = .000, 5., .0, 5, 0.9

    guidedsampling = None
    multiPrepC = prepareChain.PrepareChain("SCL1.0")

    badresids   = None
    badresids = options.loopres


    scvdwr = options.scReduction ;
    popsize = options.popsize
    xrayRestGen = None

    ml = Multiloop(options.pdbfile, badresids, None, options.caRad, options.scRad, scvdwr, guidedsampling, popsize,
                   options.backtrack, options.nmodels, options.outpdb, xrayRestGen, multiPrepC)

    
    nb = ml.run()

# 需要导入模块: from restraints import EDrestraint [as 别名]
# 或者: from restraints.EDrestraint import setPenalty [as 别名]
def main() :
    import optparse ; parser = optparse.OptionParser()
    parser.add_option("--scratchdir", action='store', type='string', dest='scratchdir', help='to create all the files during refinement. it shdnt be already present.')
    parser.add_option("--pdb", action='store', type='string', dest='pdbfile', help='starting pdb')
    parser.add_option("--ensembleSize", action='store', type='int', dest='esize', help='number of conformers in a multiconformer model', default=1)

    parser.add_option("--sf", action='store', type='string', dest='sf', help='structure factors file')
    parser.add_option("--a", action='store', type='float', dest='a', help='cell dimension a')
    parser.add_option("--b", action='store', type='float', dest='b', help='cell dimension b')
    parser.add_option("--c", action='store', type='float', dest='c', help='cell dimension c')
    parser.add_option("--alpha", action='store', type='float', dest='alpha', help='cell angle alpha')
    parser.add_option("--beta", action='store', type='float', dest='beta', help='cell angle beta')
    parser.add_option("--gamma", action='store', type='float', dest='gamma', help='cell angle gamma')
    parser.add_option("--sg", action='store', type='string', dest='sg', help='cell spacegroup, in CCP4 notation')
    parser.add_option("--resolution", action='store', type='float', dest='resolution', help='resolution of the data')

    parser.add_option("--ca-restraint-radius", action='store', type='float', dest='caRad', help='radius of spherical restraint on CA position', default=1)
    parser.add_option("--sc-centroid-restraint-radius", action='store', type='float', dest='scRad', help='radius of spherical restraint on sidechain centroid', default=2)
    parser.add_option("--sidechain-vdw-reduction", action='store', type='float', dest='scReduction', help='factor to reduce effective vdw dist in case of sidechains', default=1)
    parser.add_option("--population-size", action='store', type='int', dest='popsize', help='population size for PopulationStrategy', default=100)
    parser.add_option("--verbose", action='store', type='int', dest='verbose', help='0 means least verbosity etc.', default=0)
    parser.add_option("--backtrack", action='store', type='string', dest='backtrack', help='use backtracking version of PopulationStrategy. eg 4X5 will set backtrack numsteps and stepsize to 4,5 respectively. not used by default.', default=None)
    parser.add_option("--randomize", action='store', type='int', dest='randomize', help='randomize will produce a different refinement trajectory by seeding rtk randomly', default=None)
    
    (options, args) = parser.parse_args()

    from loopbuild import Multiloop
    from scplacement import SCplacement
    import prepareChain
    import misc
    misc.setVerbosity(options.verbose)

    pref.randomize(options.randomize)

    if not os.path.isdir(options.scratchdir) : os.mkdir(options.scratchdir)
    for mi in range(options.esize) :
        shutil.copyfile(options.pdbfile, "%s/c0m%d.pdb" % (options.scratchdir,mi))
    shutil.copyfile(options.sf, "%s/strfactors.mtz" % options.scratchdir)
    os.chdir(options.scratchdir)
    cif2mtz("strfactors.mtz", "base.mtz", options.a, options.b, options.c, options.alpha, options.beta, options.gamma, options.sg)
    uniqueify("base.mtz", "rfree.mtz")

    from restraints import EDrestraint ; EDrestraint.setPenalty(5.) ; EDrestraint.setScatRad(1.) ;
    esmin, esmax, esmean, rcmult = 0.0001, 5.0, 0.05, 10
    from builders import PeptideBridgeBuilder ; PeptideBridgeBuilder.setCTtrials(25); PeptideBridgeBuilder.setThetastep(5);
    from data import consts ; consts.set("TAU_QUALITY", 40.)

    mconly, guidedsampling = None, None

    xscorer = XrayScorer(None, 0.9)
    startcycle, endcycle = 0, 10
    for cycle in range(startcycle, endcycle) :
        badresids, xrayRestGen, xranker = None, None, None
        multiPrepC = prepareChain.PrepareChain("PRL")
        rtkmodel, joinpdbs = "r%d.pdb"%(cycle), []
        for mi in range(options.esize) :
            cnsin = "c%dm%d.pdb" % (cycle,mi) ; rtkout = "r%dm%d.pdb" % (cycle,mi)
            if cycle > 0 :
                badresids = xscorer.score(cnsin, phasedmtz, "FP", "FC", "PHIC", "2F1-F2") ## assess bad fit
                #xrayRestGen = [ prepareChain.XrayRestraintsGenerator(phasedmtz, "FP", "FC", "PHIC", "2F1-F2", esmin, esmax, esmean ) ]
                xranker = XrayRanker(phasedmtz, "FP", "FC", "PHIC", "2F1-F2", esmin, esmax)
                xranker.rankChildren = 10 ; xranker.rankRecurse = 1 ; xranker.rankGivenEnsemble = None
            ml = Multiloop(cnsin, badresids, mconly, options.caRad, options.scRad, options.scReduction, guidedsampling, options.popsize,
                options.backtrack, 1, "pre."+rtkout, xrayRestGen, multiPrepC)
            ml.ranker = xranker
            nb = ml.run()
            print mi, "multiloop built", nb, "model/s" ; assert nb > 0
            if cycle == 0 : os.rename("pre."+rtkout, rtkout)
            else :
                badresids = findChangedSC(cnsin, "pre."+rtkout)
                scPrepC = prepareChain.PrepareChain("PRL")
                SCplacement("pre."+rtkout, options.scReduction, rtkout, "dotfile", None, phasedmtz, "FP", "FC", "PHIC", "2F1-F2", esmin, esmax, None, 1, badresids, scPrepC).run()
                adjustBfac(rtkout, cnsin)
            removeRElines(rtkout, ["^MODEL", "^ENDMDL",])
            copyNonprotein(cnsin, rtkout)
            joinpdbs.append(rtkout)
        joinPDBs(rtkmodel, joinpdbs) ## all models pasted together, with occupancy fractionalized, extra ENDs removed, segids corrected
        sfall(rtkmodel, "rfree.mtz", "phased.mtz")

        phasedmtz, cnsout = "phased%d.mtz"%(cycle+1), "c%d.pdb"%(cycle+1),
        cnsRefinement("phased.mtz", rtkmodel, phasedmtz, cnsout,
            options.a, options.b, options.c, options.alpha, options.beta, options.gamma, options.sg, options.resolution, None,cycle)

        newpdbs = []
        for mi in range(options.esize) : newpdbs.append("c%dm%d.pdb" % (cycle+1,mi))
        splitPDBs(cnsout, newpdbs)
        for newpdb in newpdbs : restoreChainids(newpdb, "c0m0.pdb")

# 需要导入模块: from restraints import EDrestraint [as 别名]
# 或者: from restraints.EDrestraint import setPenalty [as 别名]
def main() :

    import optparse ; parser = optparse.OptionParser()

    parser.add_option("--scratchdir", action='store', type='string', dest='scratchdir', help='to create all the files during refinement. it shdnt be already present.')
    parser.add_option("--pdb", action='store', type='string', dest='pdbfile', help='starting pdb containing a model of pdb-ligand complex')

    parser.add_option("--debug", action='store', type='int', dest='debug', help='starting pdb containing a model of pdb-ligand complex')
    parser.add_option("--hbdfile", action='store', type='string', dest='hbdfile', help='Hbond restraints to enfirce SS structure')
    parser.add_option("--buildN2C", action='store', type='int', dest='buildN2C', help='by default, build from N to C terminal. build C->N if 0.', default=1)
    parser.add_option("--map", action='store', type='string', dest='map', help='structure factors file')
    parser.add_option("--init-map", action='store', type='string', dest='inimap', help='structure factors file',default=None)
    parser.add_option("--resolution", action='store', type='float', dest='resolution', help='resolution of the data')
    parser.add_option("--test", action='store', type='float', dest='test', help='resolution of the data',default =1.)
    parser.add_option("--startcycle", action='store', type='int', dest='startcycle', help='Total number of RTK cycles',default=1)
    parser.add_option("--stopcycle", action='store', type='int', dest='stopcycle', help='Total number of RTK cycles',default=50)
    parser.add_option("--num-models-wanted", action='store', type='int', dest='nmodels', help='number of models desired, 100 attempts per model. DEFAULT 100', default=100)

    parser.add_option("--sidechain-vdw-reduction", action='store', type='float', dest='scReduction', help='factor to reduce effective vdw dist in case of sidechains', default=1)
    parser.add_option("--optional", action='store', type='int', dest='opt', help='Optional:0 , Not optional:1',default=0)
    parser.add_option("--population-size", action='store', type='int', dest='popsize', help='population size for PopulationStrategy', default=100)
    parser.add_option("--verbose", action='store', type='int', dest='verbose', help='0 means least verbosity etc.', default=0)
    parser.add_option("--backtrack", action='store', type='string', dest='backtrack', help='use backtracking version of PopulationStrategy. eg 4X5 will set backtrack numsteps and stepsize to 4,5 respectively. not used by default.', default=None)
    parser.add_option("--ca-restraint-radius", action='store', type='float', dest='caRad', help='radius of spherical restraint on CA position', default=1)
    parser.add_option("--sc-centroid-restraint-radius", action='store', type='float', dest='scRad', help='radius of spherical restraint on sidechain centroid', default=2)
    parser.add_option("--randomize", action='store', type='int', dest='randomize', help='seed for randomizing', default=None)

    parser.add_option("--start", action='store', type='int', dest='start', help='start', default=None)
    parser.add_option("--stop", action='store', type='int', dest='stop', help='stop', default=None)
    parser.add_option("--mconly", action='store', type='int', dest='mconly', help='mconly:1', default=None)
    parser.add_option("--ssfile", action='store', type='string', dest='ssfile', help='list of secondary structures, see applications/ssfile for example')
    parser.add_option("--modelAll", action='store', type='int', dest='modelAll', help='Rebuiild only loop,set tp 1',default=0)
    parser.add_option("--cutoff", action='store', type='float', dest='cutoff', help='CC cut off for flagginf mis-fit regions',default=None)
    parser.add_option("--loopOnly", action='store', type='int', dest='loopOnly', help='Rebuiild only loop,set tp 1',default=0)
    parser.add_option("--helicesOnly", action='store', type='int', dest='helicesOnly', help='Rebuiild only helices',default=0)
    parser.add_option("--pre-process", action='store', type='int', dest='preProcess', help='Preprocessing bad regions to overcome possible local minima True:1 , False:0',default=0)
    parser.add_option("--restoreSS", action='store', type='int', dest='restoreSS', help='Restore SS ? ',default=0)
    parser.add_option("--use-midloop", action='store', type='int', dest='midloop', help='Use bridge building, True:1 , False:0',default=1)


    parser.add_option("--rank", action='store', type='int', dest='ranker', help='Rank, True:1 , False:0',default=1)

### Additional homo infor

    parser.add_option("--pir", action='store', type='string', dest='pirfile', help='pir file')
    parser.add_option("--ensemble", action='store', type='string', dest='ensemble', help='make Ensemble',default=1)
    parser.add_option("--clr", action='store', type='string', dest='clrfile', help='clr file')
    parser.add_option("--use-choral", action='store', type='int', dest='choral', help='use choral',default=0)
    parser.add_option("--pdbext", action='store', type='str', dest='pdbext', help='extension of template files [atm/ brk / pdb ] ?? ',default="pdb")
    parser.add_option("--pdb-path", action='store', type='str', dest='pdbpath', help='directory containning the pdb files ',default='/home/anjum/')
    parser.add_option("--band", action='store', type='int', dest='band', help='band ss elements ? ? ', default=None)
    parser.add_option("--short_sidechain_restraint_threshold", action='store', type='float', dest='ssc_threshold', help='Restraint radii on short side chain atoms', default=1.5)
    parser.add_option("--mainchain_restraint_threshold", action='store', type='float', dest='mc_threshold', help='Restraint radii on MC atoms', default=1.5)

    parser.add_option("--params", action='store', type='string', dest='paramfile', help='parameter file')
    parser.add_option("--modelfrag", action='store', type='string', dest='modelfrag', help='modelfrag?')

    (options, args) = parser.parse_args()
    import misc
    misc.setVerbosity(options.verbose)
    randomize(options.randomize)
    if not os.path.isdir(options.scratchdir) : os.mkdir(options.scratchdir)
    if options.ssfile !=None:
        shutil.copyfile(options.ssfile,"%s/ssfile" % (options.scratchdir))
    if options.hbdfile !=None:
        shutil.copyfile(options.hbdfile,"%s/%s" % (options.scratchdir,options.hbdfile))



    shutil.copyfile(options.pdbfile, "%s/model%d.pdb" % (options.scratchdir,options.startcycle-1))

    ssList = []  ; resList  = [] 
    if options.clrfile !=None or options.pirfile !=None :
        from homologyEM import main as homologymain
        print options.clrfile
        res, resids, resnums, resns, chids, inscodes, pts , resList ,start ,stop, params , msa  = homologymain(options.scratchdir, options.pirfile , options.clrfile, options.paramfile, None, None , options.choral, None, None , options.verbose , options.mconly , options.pdbext , options.pdbpath , None , None , None , None , None , options.mc_threshold,options.ssc_threshold,None, 1)

    else:
        os.chdir(options.scratchdir)
    ### Values of params and i/o file names 
    guidedsampling = None
    multiPrepC = prepareChain.PrepareChain("PRL")
    popsize = options.popsize
    #totcycles = options.totcycles
    if options.cutoff == None:
        if options.resolution == 10.0:
            options.cutoff = 0.98
        if options.resolution == 6.0:
            options.cutoff = 0.97
            

    from restraints import EDrestraint ; EDrestraint.setPenalty(5.) ; EDrestraint.setScatRad(1.) ;
    esmin, esmax, esmean, rcmult, xscoreCutoff = .000, 5., .0, 1, options.cutoff
    
    ranker = XrayRanker(options.map, "map", "FC", "PHIC", "F1", esmin, esmax)
    xrayRestGen = []
    #xrayRestGen.append( prepareChain.XrayRestraintsGenerator(options.map, "map", "FC", "PHIC", "F1", esmin, esmax, esmean, ["SCLbuilder","ChiBuilder","CBbuilder"], ) )
    xrayRestGen.append( prepareChain.XrayRestraintsGenerator(options.map, "map", "FC", "PHIC", "F1", esmin, esmax, esmean, [], ) )
    
    ## make working directory and copy files over
#.........这里部分代码省略.........

# 需要导入模块: from restraints import EDrestraint [as 别名]
# 或者: from restraints.EDrestraint import setPenalty [as 别名]
def main() :

    import optparse ; parser = optparse.OptionParser()
    parser.add_option("--scratchdir", action='store', type='string', dest='scratchdir', help='to create all the files during refinement. it shdnt be already present.')
    parser.add_option("--pdb", action='store', type='string', dest='pdbfile', help='starting pdb containing a model of pdb-ligand complex')

    parser.add_option("--sf", action='store', type='string', dest='sf', help='structure factors file')
    parser.add_option("--a", action='store', type='float', dest='a', help='cell dimension a')
    parser.add_option("--b", action='store', type='float', dest='b', help='cell dimension b')
    parser.add_option("--c", action='store', type='float', dest='c', help='cell dimension c')
    parser.add_option("--alpha", action='store', type='float', dest='alpha', help='cell angle alpha')
    parser.add_option("--beta", action='store', type='float', dest='beta', help='cell angle beta')
    parser.add_option("--gamma", action='store', type='float', dest='gamma', help='cell angle gamma')
    parser.add_option("--sg", action='store', type='string', dest='sg', help='cell spacegroup, in CCP4 notation')
    parser.add_option("--resolution", action='store', type='float', dest='resolution', help='resolution of the data')

    parser.add_option("--ca-restraint-radius", action='store', type='float', dest='caRad', help='radius of spherical restraint on CA position', default=1)
    parser.add_option("--sc-centroid-restraint-radius", action='store', type='float', dest='scRad', help='radius of spherical restraint on sidechain centroid', default=2)
    parser.add_option("--sidechain-vdw-reduction", action='store', type='float', dest='scReduction', help='factor to reduce effective vdw dist in case of sidechains', default=1)
    parser.add_option("--population-size", action='store', type='int', dest='popsize', help='population size for PopulationStrategy', default=100)
    parser.add_option("--verbose", action='store', type='int', dest='verbose', help='0 means least verbosity etc.', default=0)
    parser.add_option("--backtrack", action='store', type='string', dest='backtrack', help='use backtracking version of PopulationStrategy. eg 4X5 will set backtrack numsteps and stepsize to 4,5 respectively. not used by default.', default=None)
    parser.add_option("--noRTK", action='store', type='int', dest='noRTK', help='dont rebuild bad-fits with rtk', default=0)
    parser.add_option("--randomize", action='store', type='int', dest='randomize', help='seed for randomizing', default=None)
    parser.add_option("--loopres", action='store', type='string', dest='loopres', help='filename containing resids for starting perturbation', default=None)
    parser.add_option("--framework", action='store', type='int', dest='framework', help='to be used in conjunction with loopres. it puts a 1/3 ca/sc pos restr on non-loopres and perturbs them too', default=None)


    (options, args) = parser.parse_args()



    import misc; misc.setVerbosity(options.verbose)
    randomize(options.randomize)
    if not os.path.isdir(options.scratchdir) : os.mkdir(options.scratchdir)
    shutil.copyfile(options.pdbfile, "%s/model0.pdb" % options.scratchdir)
    shutil.copyfile(options.sf, "%s/rfree.mtz" % options.scratchdir)
    os.chdir(options.scratchdir)

    #cif2mtz("strfactors.mtz", "base.mtz", options.a, options.b, options.c, options.alpha, options.beta, options.gamma, options.sg)
    #uniqueify("base.mtz", "rfree.mtz")


    esmin, esmax, esmean, rcmult, xscoreCutoff = .000, 5., .0, 5, 0.9
    guidedsampling = None
    multiPrepC = prepareChain.PrepareChain("SCL1.0")
    numRefCycles = 10 ; startCycle = 0

    from stump import getCRYST , getRESO
    if (options.a == None or options.b == None or options.c == None or options.alpha == None or options.beta == None or options.gamma == None) :
        
        print "Getting cell paramters from coordinate file....."
        options.a,options.b,options.c,options.alpha , options.beta , options.gamma,d1  = getCRYST(options.pdbfile)
        
        if (options.a == None or options.b == None or options.c == None or options.alpha== None or options.beta==None or options.gamma == None ):
            print "CRYST card cannot be read from coordinate file. Please input cell paramater a, b , c , alpha, beta , gamma = ",options.a , options.b , options.c , options.alpha , options.beta  , options.gamma 
            import sys ; sys.exit()

        print "Found a b c alpha beta gamma  ", options.a , options.b , options.c , options.alpha , options.beta  , options.gamma 
            
    if options.sg == None : 
        print "Getting space group from coordinate file....."
        d1,d2,d3,d4 , d5 , d6, options.sg  = getCRYST(options.pdbfile)
        if options.sg == None : 
            print "Please input space group " , options.sg ; import sys ; sys.exit()
        ss = ""
        for sg1 in options.sg:
            if sg1 in ["\n","\t","\s"]:
                continue
            else :
                ss = ss+sg1
        options.sg = ss
        print "Space Group ",options.sg

    if options.sg  in long2shortHM.keys():
        shortsg = long2shortHM[options.sg]
        options.sg = shortsg
    if options.sg not in sgtable.keys():
        print "Check --sg , Not recognised [%s][%d]"%( options.sg, len(options.sg))
        import sys ; sys.exit()

    if options.resolution == None : 
        print "Getting resolution limit from coordinate file........"
        options.resolution = getRESO(options.pdbfile)
        if (options.resolution == None):
            print "Please input resolution " , options.resolution
            import sys ; sys.exit()
                
        print "Resolution = [ " , options.resolution, " ] "


    from restraints import EDrestraint ; EDrestraint.setPenalty(2.) ; EDrestraint.setScatRad(1.) ;
    for cycle in range(startCycle, numRefCycles) :

        if cycle < 10 :
            xscoreCutoff = 0.8
        else :
            xscoreCutoff = 0.9

        xscorer = XrayScorer(None, xscoreCutoff) ; xrayRestGen = []
#.........这里部分代码省略.........