def histogram(ifile, base, step):
res = {}
for line in ifile:
for word in line.split():
t = float(word)
t -= base
t = int(t//step)
if t not in res:
res[t] = 0
res[t] += 1
total = 0
for k, v in sorted(res.items()):
total += v
print base + step * k, '~', base + step * (k+1), v, total
def detailcmp():
from optparse import OptionParser
usage = '%prog [options] <xyzfname1> <xyzfname2>'
parser = OptionParser(usage=usage)
parser.add_option('-a', "--atoms", dest="atoms",
help="only compare selected atoms, 1-based",
metavar="STRING")
parser.add_option('-A', "--atomsfile", dest="atomsfile",
help="read the selected atoms from file",
metavar="FILE")
(options, args) = parser.parse_args()
if len(args) != 2:
parser.error("incorrect number of arguments")
if options.atoms and options.atomsfile:
parser.error("options conflict")
if options.atomsfile:
options.atoms = file(options.atomsfile).read()
atoms = None
if options.atoms:
atoms = [int(x)-1 for x in options.atoms.split()]
mol1 = read.readxyz(file(args[0]))
mol2 = read.readxyz(file(args[1]))
r1 = relalist.Relalist(mol1)
bonds_data = []
for i,j in r1.bonds:
if atoms is not None and (i not in atoms or j not in atoms): continue
l1 = mol1.calclen(i,j)
l2 = mol2.calclen(i,j)
bonds_data.append((abs(l1-l2), (i+1,j+1), l1, l2))
angles_data = []
for i,j,k in r1.angles:
if atoms is not None \
and (i not in atoms \
or j not in atoms \
or k not in atoms):
continue
a1 = math.degrees(mol1.calcang(i,j,k))
a2 = math.degrees(mol2.calcang(i,j,k))
angles_data.append((abs(a1-a2), (i+1,j+1,k+1), a1, a2))
torsions_data = []
for i,j,k,l in r1.torsions:
if atoms is not None \
and (i not in atoms \
or j not in atoms \
or k not in atoms
or l not in atoms):
continue
t1 = math.degrees(mol1.calctor(i,j,k,l))
t2 = math.degrees(mol2.calctor(i,j,k,l))
torsions_data.append((180-abs(abs(t1-t2)-180), (i+1,j+1,k+1,l+1), t1, t2))
print 'bonds:'
for x in sorted(bonds_data):
print x
print
print 'angles:'
for x in sorted(angles_data):
print x
print
print 'torsions:'
for x in sorted(torsions_data):
print x[1][0], x[1][1], x[1][2], x[1][3], x[2], x[3], x[0]