pkl = open(pklname, 'w')
pickle.dump(argdict, pkl)
pkl.close()
# a few things should be keep the same:
# the name of the pdb file (without .pdb extension)
# first column of the mutation file
# first column of the homologous file
# there should not be '_' in these
# read the input file and create a mutation list
pdbs = []
positions = []
with open(args.l) as mutf:
for l in mutf:
mut = Stability.getMutation(l.strip())
pdb, pos = mut.p, mut.dir
if not pdb in pdbs:
pdbs.append(pdb)
if not pos in positions:
positions.append(pos)
# run confind for all structures
for pdb in pdbs:
pdbf = args.i + '/' + pdb + '.pdb'
assert os.path.isfile(
pdbf), 'the pdb file ' + pdbf + ' does not exist; quit...'
confind_out = changeExt(pdbf, 'conf')
if os.path.isfile(confind_out):
continue
else: # run confind
def outputscore(mutlist, output, scan=0, bg=0):
if bg:
aafreq = np.array(PDB.aaFreq)
with open(mutlist) as mutf, open(output, 'w') as ofh:
for l in mutf:
l = l.strip()
mut = Stability.getMutation(l)
consf = mut.dir + '/' + mut.dir + '.conlist'
cons = []
with open(consf) as cf:
for cfl in cf:
cinfo = cfl.strip().split()
conname, conres, cond = cinfo[2], cinfo[-1], float(
cinfo[3])
if not os.path.isfile(mut.dir + '/' + mut.dir + '_' +
conname.replace(',', '') + '.pdb'):
continue
if cond >= 0.02:
cons.append([conname, conres, cond])
cons = sorted(cons, key=lambda x: x[0])
matf = mut.dir + '/' + mut.dir + '.' + args.ext + '.mat'
if not os.path.isfile(matf):
ofh.write(l + '\tNA\n')
continue
optparams = loadmat(matf)['optParams']
assert (optparams.shape[0] - 20) / 400 == len(cons), mut.dir
# if (optparams.shape[0] - 20) / 400 != len(cons):
# ofh.write(l + '\tNA\n')
# continue
selfdiff = optparams[PDB.aaindex[mut.m]] - optparams[PDB.aaindex[
mut.w]]
if bg:
selfdiff += np.log(aafreq[PDB.aaindex[mut.m]]) - np.log(
aafreq[PDB.aaindex[mut.w]])
pairdiff = []
if scan:
scanscore = optparams[0:20].T[0]
if bg:
scanscore += np.log(aafreq)
scanscore -= scanscore[PDB.aaindex[mut.w]]
for i in range(len(cons)):
paramsi = optparams[20 + 400 * i:20 + 400 * (i + 1)].reshape(
20, 20)
conind = PDB.aaindex[PDB.t2s(cons[i][1])]
pairdiff_i = paramsi[conind, PDB.aaindex[mut.m]] - paramsi[
conind, PDB.aaindex[mut.w]]
pairdiff.append(pairdiff_i)
# outstr = l + '\t' + cons[i][0] + '\t' + format(float(pairdiff_i), '.3f') # test
# ofh.write(outstr + '\n') # test
if scan:
scancon = np.array([paramsi[conind, x] for x in range(20)])
# use wt aa as the reference state
ref = paramsi[conind, PDB.aaindex[mut.w]]
scancon -= ref
scanscore += scancon
if not scan:
outstr = '\t'.join([
l,
format(float(selfdiff), '.3f'),
format(float(sum(pairdiff)), '.3f')
])
else:
outstr = '\t'.join([l] + [format(x, '.3f') for x in scanscore])
ofh.write(outstr + '\n')
# exit the program
exit(0)
