def bond_length_types(self, a1, a2, lb, ub):
"""bond_length_types(a1, a2, lb, ub) --> get all a1-a2 distances.
a1 -- symbol of the first element in pair or "ALL"
a2 -- symbol of the second element in pair or "ALL"
lb -- lower bond length boundary
ub -- upper bond length boundary
Return a dictionary of distance data containing
dij : list of bond lenghts within given bounds
ddij : list of bond legnth standard deviations
ij0 : pairs of atom indices starting from 0
ij1 : pairs of atom indices starting from 1
Raises: ValueError if selected atom(s) does not exist
pdffit.unassignedError when no structure has been loaded.
"""
rv = pdffit2.bond_length_types(self._handle, a1, a2, lb, ub)
return rv
def bond_length_types(self, a1, a2, lb, ub):
"""bond_length_types(a1, a2, lb, ub) --> get all a1-a2 distances.
a1 -- symbol of the first element in pair or "ALL"
a2 -- symbol of the second element in pair or "ALL"
lb -- lower bond length boundary
ub -- upper bond length boundary
Return a dictionary of distance data containing
dij : list of bond lenghts within given bounds
ddij : list of bond legnth standard deviations
ij0 : pairs of atom indices starting from 0
ij1 : pairs of atom indices starting from 1
Raises: ValueError if selected atom(s) does not exist
pdffit.unassignedError when no structure has been loaded.
"""
rv = pdffit2.bond_length_types(self._handle, a1, a2, lb, ub)
return rv
def blen(self, *args):
"""blen(i, j) --> Show bond length defined by atoms i and j.
i -- index of the first atom starting at 1
j -- index of the second atom starting at 1
No return value. Use bond_length_atoms() to retrieve result.
Second form:
blen(a1, a2, lb, ub) --> Show sorted lengths of all a1-a2 bonds.
a1 -- symbol of the first element in pair or "ALL"
a2 -- symbol of the second element in pair or "ALL"
lb -- lower bond length boundary
ub -- upper bond length boundary
No return value. Use bond_length_types() to retrieve results.
Raises: ValueError if selected atom(s) does not exist
pdffit.unassignedError when no structure has been loaded
"""
# first form
if len(args)==2:
dij, ddij = self.bond_length_atoms(*args[0:2])
atom_symbols = self.get_atoms()
ij = (args[0], args[1])
# check ij
if min(ij) - 1 < 0 or max(ij) - 1 >= len(atom_symbols):
emsg = "Incorrect atom number(s): %i, %j" % ij
raise ValueError, emsg
symij = ( atom_symbols[ij[0] - 1].upper(),
atom_symbols[ij[1] - 1].upper() )
print >> output.stdout, _format_bond_length(dij, ddij, ij, symij)
# second form
elif len(args)==4:
a1, a2, lb, ub = args
try:
atom_types = self.get_atom_types()
if type(a1) is types.IntType: a1 = atom_types[a1 - 1]
if type(a2) is types.IntType: a2 = atom_types[a2 - 1]
except IndexError:
# index of non-existant atom type
return
# arguments are OK here, get bond length dictionary
bld = pdffit2.bond_length_types(self._handle, a1, a2, lb, ub)
s = "(%s,%s) bond lengths in [%gA,%gA] for current phase :" % \
(a1, a2, lb, ub)
print >> output.stdout, s
atom_symbols = self.get_atoms()
npts = len(bld['dij'])
for idx in range(npts):
dij = bld['dij'][idx]
ddij = bld['ddij'][idx]
ij0 = bld['ij0'][idx]
ij1 = bld['ij1'][idx]
symij = (atom_symbols[ij0[0]], atom_symbols[ij0[1]])
s = _format_bond_length(dij, ddij, ij1, symij)
print >> output.stdout, s
print >> output.stdout
if not bld['dij']:
print >> output.stdout, " *** No pairs found ***"
else:
emsg = "blen() takes 2 or 4 arguments (%i given)" % len(args)
raise TypeError, emsg
# done
return
def blen(self, *args):
"""blen(i, j) --> Show bond length defined by atoms i and j.
i -- index of the first atom starting at 1
j -- index of the second atom starting at 1
No return value. Use bond_length_atoms() to retrieve result.
Second form:
blen(a1, a2, lb, ub) --> Show sorted lengths of all a1-a2 bonds.
a1 -- symbol of the first element in pair or "ALL"
a2 -- symbol of the second element in pair or "ALL"
lb -- lower bond length boundary
ub -- upper bond length boundary
No return value. Use bond_length_types() to retrieve results.
Raises: ValueError if selected atom(s) does not exist
pdffit.unassignedError when no structure has been loaded
"""
# first form
if len(args)==2:
dij, ddij = self.bond_length_atoms(*args[0:2])
atom_symbols = self.get_atoms()
ij = (args[0], args[1])
# indices were already checked in bond_length_atoms call
assert (0 <= min(ij) - 1) and (max(ij) - 1 < len(atom_symbols))
symij = ( atom_symbols[ij[0] - 1].upper(),
atom_symbols[ij[1] - 1].upper() )
print(_format_bond_length(dij, ddij, ij, symij), file=output.stdout)
# second form
elif len(args)==4:
a1, a2, lb, ub = args
try:
atom_types = self.get_atom_types()
if isinstance(a1, numbers.Integral): a1 = atom_types[a1 - 1]
if isinstance(a2, numbers.Integral): a2 = atom_types[a2 - 1]
except IndexError:
# index of non-existant atom type
return
# arguments are OK here, get bond length dictionary
bld = pdffit2.bond_length_types(self._handle, a1, a2, lb, ub)
s = "(%s,%s) bond lengths in [%gA,%gA] for current phase :" % \
(a1, a2, lb, ub)
print(s, file=output.stdout)
atom_symbols = self.get_atoms()
npts = len(bld['dij'])
for idx in range(npts):
dij = bld['dij'][idx]
ddij = bld['ddij'][idx]
ij0 = bld['ij0'][idx]
ij1 = bld['ij1'][idx]
symij = (atom_symbols[ij0[0]], atom_symbols[ij0[1]])
s = _format_bond_length(dij, ddij, ij1, symij)
print(s, file=output.stdout)
print(file=output.stdout)
if not bld['dij']:
print(" *** No pairs found ***", file=output.stdout)
else:
emsg = "blen() takes 2 or 4 arguments (%i given)" % len(args)
raise TypeError(emsg)
# done
return
