def alternativeAbundance(matchf, pds, topn = 50):
MASTER = '/home/anthill/fzheng/home/scripts/termanal_updating'
# generate the original structures of topn hits
# pds = General.changeExt(pdb, 'pds')
# cmd = [MASTER + '/createPDS', '--type', 'query', '--pdb', pdb, '--pds', pds]
# cmd = ' '.join(cmd)
# os.system(cmd)
cmd = [MASTER + '/master', '--query', pds, '--matchIn', matchf, '--structOut', General.getBase(pds) + 'tmp', '--outType', 'match', '--bbRMSD', '--topN', str(topn)]
cmd = ' '.join(cmd)
os.system(cmd)
# for these N structures, calculate RMSD between any two. should be O(N^2)
odir = os.getcwd()
ndir = General.getBase(pds) + 'tmp'
os.chdir(ndir)
mpdbs = glob.glob('*.pdb')
mpdbs.sort()
RMSDs = []
print 'calculating pairwise RMSD'
for i in range(len(mpdbs)-1):
for j in range(i+1, len(mpdbs)):
mol1, mol2 = parsePDB(mpdbs[i]), parsePDB(mpdbs[j])
bbAtoms1, bbAtoms2 = mol1.select('backbone').copy(), mol2.select('backbone').copy()
trans = calcTransformation(bbAtoms2, bbAtoms1)
bbAtoms2_t = applyTransformation(trans, bbAtoms2)
rmsd = calcRMSD(bbAtoms1, bbAtoms2_t)
RMSDs.append(round(rmsd, 3))
print 'finish calculating RMSD'
os.chdir(odir)
# now calculate the average Z-score of all the rmsds of the query
RMSDs = np.array(RMSDs)
qRMSD = Analyze.readColumn(matchf, 0, top = topn)
qRMSD = np.array([float(x) for x in qRMSD])
meanRMSD, stdRMSD = np.mean(RMSDs), np.std(RMSDs)
Z_qRMSD = (qRMSD - meanRMSD) / stdRMSD
return round(np.median(Z_qRMSD), 3)
for seqf in seqfs:
pdbf = General.changeExt( seqf.replace(args.head + '_', ''), 'pdb')
if not os.path.isfile(pdbf):
print(pdbf + ' doesn\'t exist!')
continue
outf = General.changeExt(pdbf, args.o)
if args.wgap != None: # specific to gap
assert args.conR == False, 'wgap and conR cannot be specified simultaneously'
dirname = General.getBase(pdbf)
pdbf = args.wgap + '/' + dirname + '/'+ pdbf
index = PDB.findPositionInPDB(pdbf, resnum, cid)
aacol = Analyze.readColumn(seqf, index, top = args.uplimit)
if args.conR: # should contacting residue be constrained?
conid = General.getBase(seqf).split('_')[-1]
ccid, cresnum = conid[0], conid[1:]
cindex = PDB.findPositionInPDB(pdbf, cresnum, ccid)
cres = PDB.getResByInd(pdbf, ccid, cresnum).getResname()
cres = PDB.t2s(cres)
caacol = Analyze.readColumn(seqf, cindex, top = args.uplimit)
if args.env != None: # environment corrected counts
envf = General.getBase(seqf.replace(args.head, args.envhead)) + '.' + args.env
if not os.path.isfile(envf):
print(envf + ' doesn\'t exist!')
continue
import glob
import Analyze
dscdat = glob.glob('*.dsc50.TR*.dat')
dscdat.sort()
oldpath = '/home/anthill/fzheng/home/designScore/allfeatures_individual/'
for d in dscdat:
modelname = d.split('.')[-2]
oldfile = oldpath + 'allfeatures.' + modelname + '.dat'
newdsc = Analyze.readColumn(d, -1)
ad = d.replace('dsc', 'abd')
sd = d.replace('dsc', 'ssc')
newabd = Analyze.readColumn(ad, -1)
newssc = Analyze.readColumn(sd, -1)
newdsc.insert(0, 'new_designscore')
newabd.insert(0, 'new_abundance')
newssc.insert(0, 'new_structurescore')
newfile = modelname + '.dat'
newfh = open(newfile, 'w')
array = open(oldfile).readlines()
for i in range(len(array)):
outstr = '\t'.join(array[i].split()[0:3] + [newdsc[i], newabd[i], newssc[i]])
# outstr = '\t'.join(array[i].split()[0:3] + [newdsc[i]])
newfh.write(outstr + '\n')
