def HBpairs(mols,com,thres,box):
pairs = []
for i,j in pairlist.pairlist(com,thres+1.1,box):
dmin = 999999.
dirmin = 0
mins = -1
for si in mols[i]:
if not si[0][0] in ("O","H"):
next
for sj in mols[j]:
if not sj[0][0] in ("O","H"):
next
dir = 0
if si[0][0] == "O" and sj[0][0] == "H":
dir = -1
if si[0][0] == "H" and sj[0][0] == "O":
dir = +1
if dir != 0:
d = si[1]-sj[1]
d = wrap(d,box)
d = numpy.linalg.norm(d)
if d < dmin:
dmin = d
dirmin = dir
if dmin < thres:
if dirmin > 0:
pairs.append((i,j))
else:
pairs.append((j,i))
return pairs
line = sys.stdin.readline()
r = map(float, line.split())
if tag == "@NX3A":
#xyz+euler angles
euler = numpy.array(r[3:6])
q = rotation_numpy.euler2quat(euler)
else:
#xyz + quaternion
q = r[3:7]
#store the rotation matrix and coordinate in arrays.
rotmats.append(rotation_numpy.quat2rotmat(q))
coms.append(numpy.array(r[0:3]))
#Fast pairlist maker
rc = 3.0
pairs = pairlist.pairlist(coms,rc,box)
# lookup HB pairs
print "@BMRK"
print nmol
for i,j in pairs:
d = wrap( coms[j] - coms[i], box )
ih1 = numpy.dot(rotmats[i], H1)
ih2 = numpy.dot(rotmats[i], H2)
di1 = numpy.linalg.norm( d - ih1 )
di2 = numpy.linalg.norm( d - ih2 )
di = min(di1,di2)
jh1 = numpy.dot(rotmats[j], H1)
jh2 = numpy.dot(rotmats[j], H2)
dj1 = numpy.linalg.norm( d + jh1 )
dj2 = numpy.linalg.norm( d + jh2 )
dj = min(dj1,dj2)