def max_cover_pdb(protein, pdbch, top=-1):
""" Input a list of PDB chain pair for a protein
Return a sorted list with the same coverage but less members
"""
pdbch = sorted(list(pdbch))
from map_pdb_res import pdblist_to_uniprot
pdbmap = pdblist_to_uniprot([pdb for pdb, ch in pdbch])
newlist = []
covres = set()
while len(pdbch) > 0: ## all checked
best_cov = covres
best_pdbch = None
for pdb, ch in pdbch:
newres = set()
for pdbres in pdbmap:
if pdbres.startswith(pdb + ":" + ch + ":"):
prores = pdbmap[pdbres]
if prores.startswith(protein): ## same protein
newres.add(prores)
if len(covres | newres) > len(best_cov):
best_cov = covres | newres
best_pdbch = pdb, ch
if best_pdbch == None: ## maximum coverage
break
pdbch.remove(best_pdbch)
if len(best_cov) > len(covres): ## improved
newlist.append(best_pdbch)
if len(newlist) == top:
break
covres = best_cov
return newlist
def max_cover_pdb(protein, pdbch, top=-1):
''' Input a list of PDB chain pair for a protein
Return a sorted list with the same coverage but less members
'''
pdbch = sorted(list(pdbch))
from map_pdb_res import pdblist_to_uniprot
pdbmap = pdblist_to_uniprot([pdb for pdb, ch in pdbch])
newlist = []
covres = set()
while len(pdbch) > 0: ## all checked
best_cov = covres
best_pdbch = None
for pdb, ch in pdbch:
newres = set()
for pdbres in pdbmap:
if pdbres.startswith(pdb + ':' + ch + ':'):
prores = pdbmap[pdbres]
if prores.startswith(protein): ## same protein
newres.add(prores)
if len(covres | newres) > len(best_cov):
best_cov = covres | newres
best_pdbch = pdb, ch
if best_pdbch == None: ## maximum coverage
break
pdbch.remove(best_pdbch)
if len(best_cov) > len(covres): ## improved
newlist.append(best_pdbch)
if len(newlist) == top:
break
covres = best_cov
return newlist
def combine_pdb_residue(filename, listname=None, outname=None):
''' Combine the features vectors from prepare_feature functions
by taking the maximum values for PDB residues mapped to the same
resiude in a protein pair.
Output is a file with the same format
'''
if listname == None:
listname = filename.replace('.fea','.map')
if outname == None:
outname = filename + '.max'
data = []
pdblist = set()
with open(filename, 'r') as tempfile:
for line in tempfile:
ele = line.split('\t')
info = ele[0]
pp, idx, res = info.split(',')
pdblist.add(res.split(':')[0])
vals = [float(val) for val in ele[1:]]
data.append([pp, res, vals])
from map_pdb_res import pdblist_to_uniprot
res_map = pdblist_to_uniprot(pdblist)
sup_map = {} ## supplimentary residue map from the input list
with open(listname, 'r') as tempfile:
for line in tempfile:
p,s,c = line.split('\t')
sup_map[s] = p
comb = {}
for pp, res, vals in data:
if res in res_map:
res = res_map[res]
if res.count(':') == 2:
pdb, ch, pos = res.split(':')
if pdb in sup_map:
res = sup_map[pdb]+':'+pos
if (pp,res) in comb:
maxv = []
for i,j in zip(comb[(pp,res)], vals):
if i == float('nan'):
maxv.append(j)
elif j == float('nan'):
maxv.append(i)
else:
maxv.append(max(i,j))
comb[(pp,res)] = maxv
else:
comb[(pp,res)] = vals
with open(outname, 'w') as tempfile:
for pp,res in sorted(comb.keys()):
tempfile.write('%s,0,%s'%(pp,res))
for val in comb[(pp,res)]:
tempfile.write('\t%s'%val)
tempfile.write('\n')
return outname
def map_pdb_residue(filename, listname, useidx=1):
''' Input file format:
for each line:
p1=p2,index,pdb:chain:pos value others
Output format:
a list:
p1=p2, residue, max(value)
'''
data = []
pdblist = set()
infile = open(filename, 'r')
for line in infile:
ele = line.split('\t')
g1g2, pdbidx, pdbres = ele[0].split(',')
has_na = False
for v in ele:
if v.lower().startswith('na'):
has_na = True
if has_na:
continue
value = ele[useidx].strip()
data.append((g1g2, pdbres, float(value)))
pdblist.add(pdbres.split(':')[0])
infile.close()
from map_pdb_res import pdblist_to_uniprot
res_map = pdblist_to_uniprot(pdblist)
sup_map = {} ## supplimentary residue map from the input list
with open(listname, 'r') as tempfile:
for line in tempfile:
p,s,c = line.split('\t')
sup_map[s] = p
comb = {}
for pp, res, val in data:
if res in res_map:
res = res_map[res]
elif res.count(':') == 2:
pdb, ch, pos = res.split(':')
if pdb in sup_map:
res = sup_map[pdb]+':'+pos
if (pp, res) in comb and comb[(pp, res)] > val:
continue ## no need to update if having a larger value
comb[(pp, res)] = val
output = []
for pp, res in comb:
output.append((pp, res, comb[(pp, res)]))
output.sort()
return output
