def connection_analysis(path,ma=3.0,mi=2.0):
all_res={}
res,d=pre_data(path,ma,mi)
for a,li in res:
for b in li:
con=hb.connections('.'.join(path.split('.')[:-1])+'.xyz')
lis = con.bfs(a-1,b-1)
if len(lis)==4:
dih=con.dihedral(lis)
li=[a,b]
li.sort()
#print li
all_res[tuple(li)]=[dih,distance(d[a][1:],d[b][1:]),d[a][0]+'-'+d[b][0],lis]
return all_res
def connection_analysis(path,ma=4.0,mi=1.8):
all_res={}
res,d=pre_data(path,ma,mi)
for n,a,li in res:
#print a,h,li
for b in li:
con=hb.connections('.'.join(path.split('.')[:-1])+'.xyz')
lis = con.bfs(a-1,b-1)
if len(lis)==5 and distance(d[a][1:],d[b][1:]) < 2.50:
li=[n,a,b]
#print n,a,b
all_res[tuple(li)]=[lis,d[n][0]+d[a][0]+'-'+d[b][0]]
return all_res
def job(path):
dic=get_ids(path,suffix='_ah')
p_id={}
con=hb.connections(path[:-4]+'.xyz')
for i in dic:
a,b,c=dic[i]
#print a,b,c
refe_lis=con.bfs(int(a)-1,int(c)-1)
if len(refe_lis)==0:
p_id[i]='None'
elif 0 and len(refe_lis)==4:
# for writing dihedral in bracket for 5 memberd rings
p_id[i]='I('+str(len(refe_lis)+1)+')'+'('+str(con.dihedral(refe_lis))+')'
else:
p_id[i]='I('+str(len(refe_lis)+1)+')'
return addRing(path,p_id)
def test(path):
def lmode_id(path):
f=open(path,'r')
lines=f.readlines()
f.close()
i=-1
i2=0
ref=0
lm={}
length=0
kr_st=None
for line in lines:
i+=1
if ref==5:
break
if ref==1 and not kr_st:
kr=line.strip().split()
if kr[0]!='DonarSymbol':
kr_st=(43,67)
else:
kr_st=(11,36)
if 'File format' in line:
ref+=1
if len(line.strip().split())==0 and ref>0:
ref+=1
if ref==2:
lines[i-1]=' '.join(lines[i-1].strip().split())+', IntramolecularRing(size)(dihedral for C5 type) \n'
if ref==2 or ref==3:
ref+=1
if ref==4:
s,e=kr_st
#print line[s:e]
l=line.strip().split()
st=l[-3]
lm[str(i2+1)+'.']=st
#lines[i]=lines[i].strip()+' '+lmodes[i2]+'\n'
i2+=1
return lm
dic=get_ids(path,suffix='_ah')
l_d=lmode_id(path)
#print l_d
p_id={}
con=hb.connections(path[:-4]+'.xyz')
st_d = {}
count = 0
for i in dic:
a,b,c=dic[i]
#print a,b,c
a,b,c = list(map(int,[a,b,c]))
refe_lis=con.bfs(int(a)-1,int(c)-1)
dist=con.distance(int(a),int(c))
hbl = con.distance(int(b),int(c))
if len(refe_lis)==0:
p_id[i]='None'
elif len(refe_lis)==4:
make_input_pucker(refe_lis+[b],con.d,count)
count+=1
p_id[i]='I('+str(len(refe_lis)+1)+')'+'('+str(con.dihedral(refe_lis))+')'
bond = con.atom_name(int(a))+'-'+con.atom_name(int(c))
if bond in st_d:
st_d[bond]+=bond+' '+str(dist)+' '+str(con.dihedral(refe_lis))+' '+l_d[i]+' '+str(hbl)+' '+str(a)+' '+str(b)+' '+str(c)+'\n'
else:
st_d[bond] = bond+' '+str(dist)+' '+str(con.dihedral(refe_lis))+' '+l_d[i]+' '+str(hbl)+' '+str(a)+' '+str(b)+' '+str(c)+'\n'
else:
p_id[i]='I('+str(len(refe_lis)+1)+')'
return st_d
f.write(' '.join(map(str,con.d[i]))+'\n')
f.write('\n\n')
f.close()
return
if __name__=='__main__':
ref = 1
name = sys.argv[1].split('.')[0]
ids = aR.get_ids(name+'.txt')
con=hb.connections(name+'.xyz')
xyz_d = {}
for i in ids:
a,b,c = map(int,ids[i])
lis = con.bfs(b-1,c-1)
if len(lis) == 5:
ns1 = map(lambda x: x+1,con.next_state(lis[0],3.5))
ns2 = map(lambda x: x+1,con.next_state(lis[-1],3.5))
#print con.d[a][0]
write_o(list(set(lis+ns1+ns2)),ref,con,con.d[a][0]+con.d[b][0]+con.d[c][0])
#vs = set()
#count = 0
#xyz_d[i] = xyz(lis,con,ref)
ref+=1