__author__ = 'fanzheng'
import sys
from General import *
import PDB
par = argparse.ArgumentParser()
par.add_argument('--p', nargs='+', help='input structures')
par.add_argument('--o', help='a file of mutation as output')
args = par.parse_args()
outf = open(args.o, 'w')
for p in args.p:
resi = PDB.ConRes(p)
renamep = getPath(p) + '/' + removePath(p).replace('_', '-')
if renamep != p:
os.system('cp ' + p + ' ' + renamep)
for r in resi:
chain, pos, wt = r.getChid(), r.getResnum(), r.getResname()
outstr = [
removePath(getBase(renamep)), chain,
PDB.t2s(wt),
str(pos), 'A', '0'
]
outstr = '\t'.join(outstr)
outf.write(outstr + '\n')
outf.close()
from General import *
import PDB
import scipy.io as sio
par =argparse.ArgumentParser()
par.add_argument('--p', required=True, help='input structure')
par.add_argument('--m', required = True, help = 'the output of matlab')
par.add_argument('--i', required = True, help = 'a residue file')
par.add_argument('--ii', required = True, help = 'a contact file')
par.add_argument('--o', required=True, help= 'output file')
args = par.parse_args()
vals = sio.loadmat(args.m)['currentParamsValues']
residueNames = {}
residues = PDB.ConRes(args.p)
for r in residues:
rid = r.getChid() + str(r.getResnum())
rname = r.getResname()
residueNames[rid] = rname
tscore = 0
with open(args.o, 'w') as of, open(args.i) as rf, open(args.ii) as cf:
rfl = rf.readlines()
cfl = cf.readlines()
for i in range(len(rfl)):
rid = rfl[i].strip()
rname = residueNames[rid]
rind = PDB.aaindex[PDB.t2s(rname)]
try:
score = vals[i][0].flatten()[rind]
