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pdb_neighbors_v1.py
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pdb_neighbors_v1.py
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import os
import sys
from collections import defaultdict
from Bio.PDB import NeighborSearch, PDBParser, Selection
import lt
BOND_CUTOFF = 3.5
def pdb_neighbors(pdb_f, pdb_id):
structure = PDBParser().get_structure(pdb_id, pdb_f)
atom_list = Selection.unfold_entities(structure, 'A')
ns = NeighborSearch(atom_list)
center = [(a, a.get_coord()) for a in structure.get_atoms() if a.get_parent().get_resname(
) in ['PTR', 'SEP', 'TPO'] and a.get_name() in ['O1P', 'O2P', 'O3P', 'OH', 'OG', 'OG1']]
# if there are no phos-atomes, return
if len(center) == 0:
return ''
neighbors = {}
for a, c in center:
# set neighbor distance cutoff
neighbor_list = ns.search(c, BOND_CUTOFF)
residue_list = list(set(Selection.unfold_entities(neighbor_list, 'R')))
try:
neighbors[Selection.unfold_entities(a, 'R')[0]] = [
x for x in residue_list if not x == Selection.unfold_entities(a, 'R')[0]]
except:
continue
# add residue id and chain id
neighbors_full = dict([('_'.join([k.get_resname(), str(k.get_id()[1]), str(k.get_parent().get_id())]),
['_'.join([vi.get_resname(), str(vi.get_id()[1]), str(vi.get_parent().get_id())]) for vi in v]) for k, v in neighbors.iteritems()])
return neighbors_full
@lt.run_time
def main():
phos_neighbors = {}
good_pdb = []
bad_pdb = []
for pdb_f in lt.files_in_dir(sys.argv[-1]):
f_path, f_name = os.path.split(pdb_f)
f_id, f_ex = os.path.splitext(f_name)
neighbors = pdb_neighbors(pdb_f, f_id)
print neighbors
if len(neighbors) > 0:
for k, v in neighbors.iteritems():
if len(v) > 0:
phos_neighbors[f_id] = neighbors
good_pdb.append(f_id)
else:
bad_pdb.append(f_id)
lt.write_list(good_pdb, 'good_pdb')
lt.write_list(bad_pdb, 'bad_pdb')
# delete res_id and clear empty
phos_neighbors_v1 = {}
for k, v in phos_neighbors.iteritems():
phos_neighbors_v1[k] = {}
for vk, vv in v.iteritems():
phos_neighbors_v1[k][vk] = []
vvn = []
if len(vv) > 0:
for vi in vv:
vvn.append(vi.split('_')[0])
vvn = sorted(vvn)
phos_neighbors_v1[k][vk] = vvn
# delete non-standard residues
stand_res = ['VAL', 'ILE', 'LEU', 'GLU', 'GLN', 'ASP', 'ASN', 'HIS', 'TRP', 'PHE', 'TYR', 'ARG',
'LYS', 'SER', 'THR', 'MET', 'ALA', 'GLY', 'PRO', 'CYS']
phos_neighbors_v2 = {}
for k, v in phos_neighbors_v1.iteritems():
phos_neighbors_v2[k] = {}
for vk, vv in v.iteritems():
vvn = []
for vi in vv:
if vi in stand_res:
vvn.append(vi)
if len(vvn) > 0:
vvn = sorted(vvn)
phos_neighbors_v2[k][vk] = vvn
# delete uncomplete patterns
phos_neighbors_v3 = {}
for k, v in phos_neighbors_v2.iteritems():
phos_neighbors_v3[k] = {}
for vk, vv in v.iteritems():
if len(vv) >= 3:
phos_neighbors_v3[k][vk] = vv
def write_phosneighbors(phos_neighbors, ofile):
keys = phos_neighbors.keys()
keys = sorted(keys)
for k in keys:
print >> ofile, k
print >> ofile, '*' * 80
for k in keys:
v = phos_neighbors[k]
print >> ofile, k
for vk, vv in v.iteritems():
print >> ofile, ' ', vk, '\t', ' '.join(vv)
print >> ofile, '*' * 80
phos_sta = {}
for k, v in phos_neighbors.iteritems():
for vk, vv in v.iteritems():
if not tuple(vv) in phos_sta.keys():
phos_sta[tuple(vv)] = [k]
else:
phos_sta[tuple(vv)].append(k)
phos_sta_list = []
for k, v in phos_sta.iteritems():
phos_sta_list.append((len(v), k, v))
phos_sta_list = sorted(phos_sta_list, reverse=True)
for len_v, k, v in phos_sta_list:
print >> ofile, '{0:150}{1:<8}{2}'.format(k, len_v, ','.join(v))
ofile = lt.open_file('phos_neighbors_original')
write_phosneighbors(phos_neighbors, ofile)
ofile = lt.open_file('phos_neighbors_sorted')
write_phosneighbors(phos_neighbors_v1, ofile)
ofile = lt.open_file('phos_neighbors_clear')
write_phosneighbors(phos_neighbors_v2, ofile)
ofile = lt.open_file('phos_neighbors_clean')
write_phosneighbors(phos_neighbors_v3, ofile)
main()