本文整理汇总了Python中restraints.EDrestraint类的典型用法代码示例。如果您正苦于以下问题:Python EDrestraint类的具体用法?Python EDrestraint怎么用?Python EDrestraint使用的例子?那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。
在下文中一共展示了EDrestraint类的20个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于我们的系统推荐出更棒的Python代码示例。
示例1: calcCC
def calcCC(crdlist,pts,mapfile,esmin,esmax):
crdlist1 = VecVecFloat(crdlist)
pis = VecInt( range(crdlist1.size()) )
from restraints import EDrestraint
er = EDrestraint.makeEDrestraintFromMap(pis, "Xranker", mapfile, esmin, esmax, esmax)
xcorr = EDrestraint.findBadfit1(mtzfn, f1label, pts, ptinds)
print "xcor",xcorr,resids[ri]
return xcorr
开发者ID:swanandgore,项目名称:rappertk,代码行数:8,代码来源:emrefine.py
示例2: makeMaps
def makeMaps(mtzfile,pdbfile,sg):
a,b,c,alpha,beta,gamma = getCRYST(pdbfile)
cif2mtz(mtzfile, "base.mtz", a, b, c, alpha, beta, gamma, sg)
sfallA(pdbfile,"base.mtz" , "%s.phased.mtz" %pdbfile)
phasedmtz = "%s.phased.mtz"%pdbfile
## 0 : 2F1-F2 , 1: F1 , 2: F2
from restraints import EDrestraint
esmin, esmax, esmean, rcmult = 0.0001, 5.0, 0.05, 10
EDrestraint.makeMap(phasedmtz,"FP" ,"FC", "PHIC", 1 , esmin, esmax, esmax)
开发者ID:swanandgore,项目名称:rappertk,代码行数:11,代码来源:pdb2res.py
示例3: score
def score(s, pdbfile, mtzfn, f1label="FP", f2label="FC", philabel="PHIC", maptype="2F1-F2", aasc="mcsc") :
assert aasc in ["pept","mc","sc","mcsc"]
prot = protein(pdbfile, read_hydrogens=0, read_waters=1, read_hets=1)
res, resids, resnums, resns, chids, inscodes, pts = prot2res.readProtRes(prot)
pts = VecVecFloat(pts)
retkeys = []
badlines = []
allkeys = list(res.keys()) ; allkeys.sort()
for ai in range(len(allkeys)) :
ri = allkeys[ai]
key = resids[ri]
if not isAAres(resns[ri]) : continue
if aasc=="sc" and resns[ri] in ["GLY","ALA"] : continue
if aasc=="sc" and isAAres(resns[ri]) :
ptinds = []
for k,v in res[ri].items() :
if not k in [" N "," CA "," C "," O "," CB "] : ptinds.append(v)
ptinds = VecInt(ptinds)
elif aasc=="pept" and isAAres(resns[ri]) and ai+1 < len(allkeys) and isAAres(resns[allkeys[ai+1]]) :
ptinds = []
for k,v in res[ri].items() :
if k in [" C "," O "] : ptinds.append(v)
for k,v in res[ allkeys[ai+1] ].items() :
if k in [" N ",] : ptinds.append(v)
ptinds = VecInt(ptinds)
elif aasc=="mc" and isAAres(resns[ri]) :
ptinds = []
for k,v in res[ri].items() :
if k in [" N "," CA "," C "," O "," CB "] : ptinds.append(v)
ptinds = VecInt(ptinds)
elif aasc=="ca" and isAAres(resns[ri]) :
ptinds = []
for k,v in res[ri].items() :
if k in [" CA "] : ptinds.append(v)
ptinds = VecInt(ptinds)
else :
ptinds = VecInt( res[ri].values() )
if re.compile("\.map$").search(mtzfn) and re.compile("\.map$").search(f1label) :
xcorr = EDrestraint.findBadfit1(mtzfn, f1label, pts, ptinds)
print "xcor",xcorr,resids[ri]
else :
xcorr = EDrestraint.findBadfit(mtzfn, f1label, f2label, philabel, pts, ptinds)
#print "XcorrZ [%s]"%key, xcorr
if not s.scores.has_key(key) : s.scores[key] = [] ; s.keyorder.append(key)
s.scores[key].append(xcorr)
if xcorr < s.cutoff :
retkeys.append(key) ;
bl = "[%s]" % key
badlines.append(bl)
print len(badlines), "BADRESIDS", aasc, len(s.scores.values()[0]), s.cutoff, "------------------------------------" ;
for bl in badlines : print bl
s.gplot()
return retkeys
开发者ID:swanandgore,项目名称:rappertk,代码行数:54,代码来源:xcheck2.py
示例4: score
def score(s, crdlist, pis=None) :
crdlist1 = VecVecFloat(crdlist)
#print "-----------------------------------"
#for ci in range(crdlist1.size()) :
# print crdlist1[ci][0] , crdlist1[ci][0] , crdlist1[ci][0]
if not pis : pis = VecInt( range(crdlist1.size()) )
else : pis = VecInt( range(pis) )
if re.compile("\.map$").search(s.phasedmtz) :
er = EDrestraint.makeEDrestraintFromMap(pis, "Xranker", s.phasedmtz, s.esmin, s.esmax, s.esmax)
else :
er = EDrestraint.makeEDrestraintFromMTZ(pis, "Xranker", s.phasedmtz, s.fplabel, s.fclabel, s.philabel, s.maptype, s.esmin, s.esmax, s.esmax)
return -1*er.scoreAround(crdlist1)
开发者ID:swanandgore,项目名称:rappertk,代码行数:12,代码来源:xcheck.py
示例5: main
def main(pdbfile, mtzfn, f1label, f2label, philabel, maptype, aasc=None) :
mt = {"2F1-F2":0, "F1":1}
prot = protein(pdbfile, read_hydrogens=0, read_waters=1, read_hets=1)
res, resids, resnums, resns, chids, inscodes, pts = prot2res.readProtRes(prot)
pts = VecVecFloat(pts)
Xcorrs = {}
# print len(res.keys()), len(set(res.keys()))
allkeys = list(res.keys()) ; allkeys.sort()
for ri in allkeys :
key = resids[ri]
if aasc and (not isAAres(resns[ri]) or resns[ri] in ["GLY","ALA"]) : continue
if aasc :
ptinds = []
for k,v in res[ri].items() :
if not k in [" N "," CA "," C "," O "," CB "] : ptinds.append(v)
ptinds = VecInt(ptinds)
else :
ptinds = VecInt( res[ri].values() )
xcorr = EDrestraint.findBadfit(mtzfn, f1label, f2label, philabel, pts, ptinds)
Xcorrs[ key ] = xcorr
# print ri, "RESID", key print "XcorrZ [%s]"%key, xcorr
#mean, stdev = findMeanStdev(Xcorrs.values())
#for key,val in Xcorrs.items() : print "XcorrZ", key, val, (val-mean) / stdev
return Xcorrs
开发者ID:swanandgore,项目名称:rappertk,代码行数:25,代码来源:xcheck.py
示例6: score_section
def score_section(s, pdbfile, mtzfn, f1label="FP", f2label="FC", philabel="PHIC", maptype="2F1-F2", aasc="mcsc",ptinds=[]) :
assert aasc in ["pept","mc","sc","mcsc"]
prot = protein(pdbfile, read_hydrogens=0, read_waters=1, read_hets=1)
res, resids, resnums, resns, chids, inscodes, pts = prot2res.readProtRes(prot)
pts = VecVecFloat(pts)
xcorr = EDrestraint.findBadfit1(mtzfn, f1label, pts, ptinds)
print "XcorrZ = ", xcorr
return []
开发者ID:swanandgore,项目名称:rappertk,代码行数:9,代码来源:xcheck2.py
示例7: getTime
def getTime(sf,pdb):
xrayRestGen = []
prot = protein(pdb, read_hydrogens=0, read_waters=0, read_hets=0)
res, resids, resnums, resns, chids, inscodes, pts = prot2res.readProtRes(prot)
esmin, esmax, esmean, rcmult, xscoreCutoff = .000, 5., .0, 5, 0.9
pis = VecInt(resids.keys())
er = EDrestraint.makeEDrestraintFromMap(pis, "Xranker", phasedmtz, esmin, esmax, smax)
score = er.scoreAll(VecVecFloat(pts))
print score
开发者ID:swanandgore,项目名称:rappertk,代码行数:9,代码来源:stumpTESTING.py
示例8: createXEnvelopeRestraints
def createXEnvelopeRestraints(blist, mapfile, aiSC) :
from restraints import EDrestraint
erlist = []
for b in blist :
bop = b.getOP()
edrIP = []
for i in range(bop.size()) :
if aiSC[bop[i]] != -1 : edrIP.append(bop[i])
rstr = "XEnvelopeRestraint on op of %s" % b.name()
esmin, esmax, esmean, rcmult = .000, 5., .0, 5
erlist.append( EDrestraint.makeEDrestraintFromMap(VecInt(edrIP), rstr, mapfile,esmin, esmax, esmean) )
return erlist
开发者ID:swanandgore,项目名称:rappertk,代码行数:12,代码来源:betaBuilderAK.py
示例9: generateMTZ
def generateMTZ(s, blist, aiSC) :
xrlist, optional = [], []
for b in blist :
bop = b.getOP()
edrIP = []
for i in range(bop.size()) :
if aiSC[bop[i]] != -1 : edrIP.append(bop[i])
if len(edrIP) > 0 :
xrlist.append( EDrestraint.makeEDrestraintFromMTZ(VecInt(edrIP), "EDrestraint on o/p of %s" % b.name(), \
s.mtzfn, s.folabel, s.fclabel, s.philabel, s.maptype, s.min, s.max, s.mean) )
if not "LigandBuilder" in b.name() : optional.append(len(xrlist)-1)
return xrlist, optional
开发者ID:swanandgore,项目名称:rappertk,代码行数:12,代码来源:prepareChain.py
示例10: generateMAP
def generateMAP(s, blist, aiSC) :
print s.mapfn, s.min, s.max, s.mean
erlist = []
for b in blist :
bop = b.getOP()
edrIP = []
for i in range(bop.size()) :
if aiSC[bop[i]] != -1 : edrIP.append(bop[i])
rstr = "XEnvelopeRestraint on op of %s" % b.name()
print s.mapfn, s.min, s.max, s.mean
erlist.append( EDrestraint.makeEDrestraintFromMap(VecInt(edrIP), rstr, s.mapfn, s.min, s.max, s.mean) )
return erlist
开发者ID:swanandgore,项目名称:rappertk,代码行数:12,代码来源:prepareChain.py
示例11: createXEnvelopeRestraintsCA
def createXEnvelopeRestraintsCA(blist, mapfile, aiSC) :
from restraints import EDrestraint
erlist = []
for b in blist :
bop = b.getOP()
edrIP = []
if "Pept" in b.name() or "anchor" in b.name():
for i in range(bop.size()) :
print bop[i]
#if aiSC[bop[i]] != -1 :
edrIP.append(bop[i])
rstr = "XEnvelopeRestraint on op of %s" % b.name()
esmin, esmax, esmean, rcmult = .000, 5., .0, 5
erlist.append( EDrestraint.makeEDrestraintFromMap(VecInt(edrIP), rstr, mapfile,esmin, esmax, esmean) )
else :
print "DDD", b.name()
continue
return erlist
开发者ID:swanandgore,项目名称:rappertk,代码行数:19,代码来源:betaBuilderAK.py
示例12: createXEnvelopeRestraints2
def createXEnvelopeRestraints2(blist, mapfile, aiSC,ncDummies) :
from restraints import EDrestraint
erlist = []
print "aiSC",aiSC
print "NCD",ncDummies
for b in blist :
bop = b.getOP()
edrIP = []
rstr = "XEnvelopeRestraint on op of %s" % b.name()
print rstr
for i in range(bop.size()) :
print i , bop[i]
if aiSC[bop[i]] != -1 :
edrIP.append(bop[i])
esmin, esmax, esmean, rcmult = .000, 5., .0, 5
erlist.append( EDrestraint.makeEDrestraintFromMap(VecInt(edrIP), rstr, mapfile,esmin, esmax, esmean) )
return erlist
开发者ID:swanandgore,项目名称:rappertk,代码行数:20,代码来源:betaBuilderAK.py
示例13: getTime
def getTime(sf,pdb,sg):
a,b,c,alpha,beta,gamma = getCRYST(pdb)
cif2mtz(sf, "base.mtz", a, b, c, alpha, beta, gamma, sg)
uniqueify("base.mtz", "rfree.mtz")
sfall(pdb, "rfree.mtz", "phased.mtz")
xrayRestGen = []
prot = protein(pdb, read_hydrogens=0, read_waters=0, read_hets=0)
res, resids, resnums, resns, chids, inscodes, pts = prot2res.readProtRes(prot)
esmin, esmax, esmean, rcmult, xscoreCutoff = .000, 5., .0, 5, 0.9
pis = VecInt(resids.keys())
folabel="FP"
fclabel="FC"
philabel="PHIC"
maptype="2F1-F2"
if maptype == '2F1-F2' : maptype = 0
elif maptype == 'F1' : maptype = 1
else : print "unknown maptype ", maptype ; sys.exit(1)
er = EDrestraint.makeEDrestraintFromMTZ(pis, "EDrestraint", "phased.mtz", folabel, fclabel, philabel, maptype, esmin, esmax, esmean)
score = er.scoreAll(VecVecFloat(pts))
print score
sys.exit()
开发者ID:swanandgore,项目名称:rappertk,代码行数:22,代码来源:pdb2res.py
示例14: main
#.........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 :
开发者ID:swanandgore,项目名称:rappertk,代码行数:67,代码来源:prefRapper.bu1.py
示例15: main
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.........
开发者ID:swanandgore,项目名称:rappertk,代码行数:101,代码来源:prefRapperV9CNS.py
示例16: main
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.........
开发者ID:swanandgore,项目名称:rappertk,代码行数:101,代码来源:emrefine.py
示例17: main
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")
开发者ID:swanandgore,项目名称:rappertk,代码行数:87,代码来源:multProtref.py
示例18: main
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", a
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