def GetFinger(lig,pro,pts,pdbid):
mscore=0.0 #without volumn correction
mscorev=0.0 #with volumn correction
cutoff=12.0
Finger=[] #without volumn correction
Fingerv=[] #with volumn correction
#f1=open("%s_GlideAfinger.txt"%pdbid,'wb')
f2=open("%s.num"%pdbid,'wb')
#for i in range(len(dist.DC_TYPES)):
# Finger.append([0]*12)
#for i in range(len(dist.DC_TYPES)):
# Fingerv.append([0]*12)
for a1 in lig.atoms:
if a1.OBAtom.IsHydrogen():
continue
a1_type=pat.LigAtomTyper(a1.OBAtom)
if a1_type == '': continue
for a2 in pro.atoms:
if a2.OBAtom.IsHydrogen():
continue
a2_type=pat.ProAtomTyper(a2.OBAtom)
if a2_type in ('OW',''):continue
dis_type='%s-%s'%(a1_type,a2_type)
if dis_type not in dist.DC_TYPES:
print 'Atom pair type %s has not been defined, the following pair has been neglected.'%(dis_type)
print a1.OBAtom.GetType(),a1.OBAtom.GetIdx(),a2.OBAtom.GetType(),a2.OBAtom.GetIdx()
continue
j=dist.DC_TYPES.index(dis_type)
d=rpd.GetDistance(a1.OBAtom,a2.OBAtom)
if d>=cutoff:
continue
k=int((d-dist.D_MIN*0.1)/dist.D_DELT*10.0)
#print >>f2, "%s,%d,%.6f,%d"%(dis_type,j,d,k)
print >>f2, "%s,%d,%s,%d,%.6f"%(a1_type,a1.OBAtom.GetIdx(),a2_type,a2.OBAtom.GetIdx(),d)
mscorev += pts.vect[j][k][0]
mscore += pts.vect[j][k][1]
'''
ascore=pts.vect[j][k][0]
ascorev=pts.vect[j][k][1]
m=int(d/1.0)
Finger[j][m]+=ascore
Fingerv[j][m]+=ascorev
mscore+=ascore
mscorev+=ascorev
CFinger=CList(Finger)
CFingerv=CList(Fingerv)
print CFinger
for j in range(len(dist.DC_TYPES)):
dist_type=dist.DC_TYPES[j]
i=1
while i<12:
afinger=CFinger[j][i]
afingerv=CFingerv[j][i]
f1.write("%s-%d%10.2f\n"%(dist_type,i-1,afinger))
f2.write("%s-%d%10.2f\n"%(dist_type,i-1,afingerv))
i=i+1
f1.close()
'''
f2.close()
return mscore,mscorev
def dTypeGen(alist, blist, form):
sl, sr, dtlist = set(), set(), []
for a in alist:
for b in blist:
d, a1_type, a2_type = rpd.GetDistance(
a.OBAtom, b.OBAtom), pat.LigAtomTyper(
a.OBAtom), pat.ProAtomTyper(b.OBAtom)
if form(d, a1_type, a2_type):
sl.add(a)
sr.add(b)
dtlist.append((d, a1_type, a2_type))
return dtlist, len(sl), len(sr)
def GetFinger(lig,pro,pts,pdbid):
mscore=0.0 #with volumn correction
mscorev=0.0 #without volumn correction
cutoff=12.0
Finger=[]
Fingerv=[]
f1=open("%s_GlideCfinger.txt"%pdbid,'wb')
f2=open("%s_GlideCfingerv.txt"%pdbid,'wb')
for i in range(len(dist.DC_TYPES)):
Finger.append([0]*4)
for i in range(len(dist.DC_TYPES)):
Fingerv.append([0]*4)
for a1 in lig.atoms:
if a1.OBAtom.IsHydrogen():
continue
a1_type=pat.LigAtomTyper(a1.OBAtom)
for a2 in pro.atoms:
if a2.OBAtom.IsHydrogen():
continue
a2_type=pat.ProAtomTyper(a2.OBAtom)
if a2_type=='OW':continue
dis_type='%s-%s'%(a1_type,a2_type)
if dis_type not in dist.DC_TYPES:
print 'Atom pair type %s has not been defined, the following pair has been neglected.'%(dis_type)
print a1.OBAtom.GetType(),a1.OBAtom.GetIdx(),a2.OBAtom.GetType(),a2.OBAtom.GetIdx()
continue
j=dist.DC_TYPES.index(dis_type)
d=rpd.GetDistance(a1.OBAtom,a2.OBAtom)
if d>=cutoff:
continue
k=int((d-dist.D_MIN*0.1)/dist.D_DELT*10.0)
ascore=pts.vect[j][k][0]
ascorev=pts.vect[j][k][1]
m=int(d/3.0)
Finger[j][m]+=ascore
Fingerv[j][m]+=ascorev
mscore+=ascore
mscorev+=ascorev
CFinger=CList(Finger)
CFingerv=CList(Fingerv)
print CFinger
for j in range(len(dist.DC_TYPES)):
dist_type=dist.DC_TYPES[j]
for i in range(4):
afinger=CFinger[j][i]
afingerv=CFingerv[j][i]
f1.write("%s-%d%7.2f\n"%(dist_type,i,afinger))
f2.write("%s-%d%7.2f\n"%(dist_type,i,afingerv))
f1.close()
f2.close()
return mscore,mscorev
def RawDisPrint(lig, pro):
v = []
for a1 in lig.atoms:
atom1 = a1.OBAtom
## if a1.OBAtom.IsHydrogen():
## continue
a1_type = pat.LigAtomTyper(atom1)
a1_idx = -1
if a1_type in pat.LIG_TYPES:
a1_idx = pat.LIG_TYPES.index(a1_type)
for a2 in pro.atoms:
atom2 = a2.OBAtom
## if a2.OBAtom.IsHydrogen():
## continue
distance = GetDistance(atom1, atom2)
if distance >= 12.0: continue
a2_type = pat.ProAtomTyper(atom2)
a2_idx = -1
if a2_type in pat.PRO_TYPES:
a2_idx = pat.PRO_TYPES.index(a2_type)
dis_type = '%s-%s' % (a1_type, a2_type)
info = FormatedOutput(atom1, atom2)
line = '%s,%d,%d,%s,%.4fA\n' % (dis_type, a1_idx, a2_idx, info,
distance)
v.append(line)
for a2 in lig.atoms:
atom2 = a2.OBAtom
## if a2.OBAtom.IsHydrogen():
## continue
if atom1.GetIdx() == atom2.GetIdx():
continue
distance = GetDistance(atom1, atom2)
if distance >= 12.0: continue
a2_type = pat.LigAtomTyper(atom2)
a2_idx = -1
if a2_type in pat.LIG_TYPES:
a2_idx = pat.LIG_TYPES.index(a2_type)
dis_type = '#%s-%s' % (a1_type, a2_type)
info = FormatedOutput(atom1, atom2)
line = '%s,%d,%d,%s,%.4fA\n' % (dis_type, a1_idx, a2_idx, info,
distance)
v.append(line)
return v
def run(self):
global mutex, ligand, protein, outf, ap_iter
while True:
mutex.acquire()
try:
i, j = ap_iter.next()
except StopIteration:
break
mutex.release()
dist = protein.atoms[j].OBAtom.GetDistance(ligand.atoms[i].OBAtom)
if dist >= 12.0:
continue
ltype = pmf_atom_typer.LigAtomTyper(ligand.atoms[i].OBAtom)
if ltype == "":
continue
ptype = pmf_atom_typer.ProAtomTyper(protein.atoms[j].OBAtom)
if ptype in ("", "HD"):
continue
mutex.acquire()
print >> outf, "%s,%d,%s,%d,%.6f" % (ltype, i + 1, ptype, j + 1,
dist)
#outf.flush()
mutex.release()
def do_for_each(name):
_format = name[name.rfind(".") + 1:]
basename = name[:name.rfind(".")]
out_name = basename + ".num"
pdb_id = basename.split("_")[-1]
#if len(pro_atom[pdb_id]) == 0:
# print "to do atom typing for %s..."%pdb_id,
# sys.stdout.flush()
# calc_pro_types(pdb_id)
# print " Done"
# sys.stdout.flush()
pdb_name = "/home/xmluo/jlpeng/cMet/pdb_protein/%s_protein.pdb" % pdb_id
lig = pybel.readfile(_format, name).next()
pro = pybel.readfile("pdb", pdb_name).next()
outf = open(out_name, "w")
for al in lig.atoms:
if al.OBAtom.IsHydrogen():
continue
ltype = pmf_atom_typer.LigAtomTyper(al.OBAtom)
lidx = al.OBAtom.GetIdx()
if ltype == "":
continue
for j in xrange(len(pro.atoms)):
ap = pro.atoms[j]
if ap.OBAtom.IsHydrogen():
continue
dist = ap.OBAtom.GetDistance(al.OBAtom)
if dist >= cutoff:
continue
#ptype = pro_atom[pdb_id][j]
ptype = pmf_atom_typer.ProAtomTyper(ap.OBAtom)
pidx = ap.OBAtom.GetIdx()
if ptype in ('', 'OW'):
continue
print >> outf, "%s,%d,%s,%d,%.6f" % (ltype, lidx, ptype, pidx,
dist)
outf.close()
def calc_pro_types(pdb_id):
name = "/home/xmluo/jlpeng/cMet/pdb_protein/%s_protein.pdb" % pdb_id
pro = pybel.readfile("pdb", name).next()
pro_atom[pdb_id] = [None] * len(pro.atoms)
for i in xrange(len(pro.atoms)):
pro_atom[pdb_id][i] = pmf_atom_typer.ProAtomTyper(pro.atoms[i].OBAtom)
def dTypeGen_old(alist, blist):
for a in alist:
for b in blist:
yield rpd.GetDistance(a.OBAtom, b.OBAtom), pat.LigAtomTyper(
a.OBAtom), pat.ProAtomTyper(b.OBAtom)
def GetDscrptor(lig, pro, pts):
dscrptorDict1 = dict(zip(DESCRIPTOR, [0.0] * len(DESCRIPTOR)))
cutoff = 12.0
polar_type = ['CP','AP','CW','CO','CN','NC','NP','NA','ND','NR','N0',\
'NS','OC','OA','OE','OS','OD','SO','P','SA','SD','CL',\
'F','Br','I','ME','OW','Se']
np_type = ['CF', 'AF', 'C3']
chg_type = ['NC', 'OC']
def getScore(d, a1_type, a2_type):
k = int((d - dist.D_MIN * 0.1) / dist.D_DELT * 10.0)
dis_type = '%s-%s' % (a1_type, a2_type)
if dis_type not in dist.DC_TYPES: return 0.0
j = dist.DC_TYPES.index(dis_type)
nj_bulk = pts.vect[j][0][3]
if nj_bulk < 1000: return 0.0
return pts.vect[j][k][0]
def form_hbond(d, a1_type, a2_type):
if d > 3.2: return False
hb_a = [
'OA', 'OW', 'OE', 'OS', 'OC', 'NA', 'N0', 'NR', 'NP', 'SA', 'SO',
'F'
]
hb_d = ['OD', 'OW', 'NS', 'ND', 'NC', 'SD']
if a1_type in hb_a and a2_type in hb_d: return True
elif a1_type in hb_d and a2_type in hb_a: return True
return False
def form_electro(d, a1_type, a2_type):
if d > 12.0: return False
if a1_type in chg_type and a2_type in chg_type: return True
return False
def form_polar(d, a1_type, a2_type):
if form_hbond(d, a1_type, a2_type): return False
if form_electro(d, a1_type, a2_type): return False
if d > 9.0: return False
if a1_type in polar_type and a2_type in polar_type: return True
return False
def form_np(d, a1_type, a2_type):
return all([d < 6.0, a1_type in np_type, a2_type in np_type])
def dTypeGen_old(alist, blist):
for a in alist:
for b in blist:
yield rpd.GetDistance(a.OBAtom, b.OBAtom), pat.LigAtomTyper(
a.OBAtom), pat.ProAtomTyper(b.OBAtom)
def dTypeGen(alist, blist, form):
sl, sr, dtlist = set(), set(), []
for a in alist:
for b in blist:
d, a1_type, a2_type = rpd.GetDistance(
a.OBAtom, b.OBAtom), pat.LigAtomTyper(
a.OBAtom), pat.ProAtomTyper(b.OBAtom)
if form(d, a1_type, a2_type):
sl.add(a)
sr.add(b)
dtlist.append((d, a1_type, a2_type))
return dtlist, len(sl), len(sr)
def keyResi(num):
return [
a2 for a2 in heavyProAtoms
if a2.OBAtom.GetResidue().GetNum() == num
]
# Functional programming: more independent energy decomposition
heavyLigAtoms = [a1 for a1 in lig.atoms if not a1.OBAtom.IsHydrogen()]
heavyProAtoms = [a2 for a2 in pro.atoms if not a2.OBAtom.IsHydrogen()]
waterOs = [
a2 for a2 in heavyProAtoms if pat.ProAtomTyper(a2.OBAtom) == 'OW'
]
# Water interactions
dist_type_list_whb, w_hbNl, w_hbNr = dTypeGen(heavyLigAtoms, waterOs,
form_hbond)
if w_hbNl != 0.0 and w_hbNr != 0.0:
score_list_whb = [getScore(*dt) for dt in dist_type_list_whb]
dscrptorDict1['w_hb'] += sum(score_list_whb) / w_hbNl
# 140 H-bond interactions
dist_type_list_140hb, hb140Nl, hb140Nr = dTypeGen(heavyLigAtoms,
keyResi(140), form_hbond)
if hb140Nl != 0.0 and hb140Nr != 0.0:
score_list_140hb = [getScore(*dt) for dt in dist_type_list_140hb]
dscrptorDict1['140_hb'] += sum(score_list_140hb) / hb140Nl
# Electro interactions
dist_type_list_e, eNl, eNr = dTypeGen(heavyLigAtoms, heavyProAtoms,
form_electro)
if eNl != 0.0 and eNr != 0.0:
dscrptorDict1['electro'] += sum(
[getScore(*dt) for dt in dist_type_list_e]) / eNl
# Others: polar or non-polar interactions
for des in DESCRIPTOR[:-3]:
num = int(des.split('_')[0])
if des.endswith('np'):
dist_type_list_np, npNl, npNr = dTypeGen(heavyLigAtoms,
keyResi(num), form_np)
if npNl != 0.0 and npNr != 0.0:
score_list_np = [getScore(*dt) for dt in dist_type_list_np]
dscrptorDict1[des] += sum(score_list_np) / npNl
elif des.endswith('polar'):
dist_type_list_polar, polarNl, polarNr = dTypeGen(
heavyLigAtoms, keyResi(num), form_polar)
if polarNl != 0.0 and polarNr != 0.0:
score_list_polar = [
getScore(*dt) for dt in dist_type_list_polar
]
dscrptorDict1[des] += sum(score_list_polar) / polarNl
return dscrptorDict1