def detect_donor(mol):
'''detect_donor(mol) -> yield (H-idx, H's neighbour's idx)
'''
for idx, atom in enumerate(mol.atoms):
if atom.no != 1:
continue
neighbours = tools.neighbours(mol, idx)
neighbour = neighbours[0]
if mol.atoms[neighbour].no in [7, 8, 16]:
yield (idx, neighbour)
def sub_pyramid_check(fname, atoms):
mol = read.readxyz(file(fname))
if atoms is None:
atoms = range(len(mol))
res = []
for atom in atoms:
neis = neighbours(mol, atom)
if len(neis) != 4:
continue
if is_pyramid(mol.coords[atom],
mol.coords[neis[0]],
mol.coords[neis[1]],
mol.coords[neis[2]],
mol.coords[neis[3]]):
res.append(atom)
return res
def write(mol, ofile=sys.stdout, comment = None):
if comment is None:
comment = 'generated by itcc'
if comment:
ofile.write('HEADER %s\n' % comment)
for i in range(len(mol)):
atom, coord = mol[i]
ofile.write('%-6s%5i %-3s %3s %4i %8.3f%8.3f%8.3f%6.2f%6.2f\n' %
('HETATM', i+1, atom.symbol, 'UNK', 1,
coord[0], coord[1], coord[2], 1.0, 0.0))
for i in range(len(mol)):
ns = tools.neighbours(mol, i)
if not ns: continue
ofile.write('CONNECT %4i' % (i+1))
for x in ns:
ofile.write(' %4i' % (x+1))
ofile.write('\n')
ofile.write('END\n')
def test_1(self):
mol = read.readxyz(StringIO.StringIO(test_methane_in))
neighbours = tools.neighbours(mol, 0)
neighbours.sort()
neighbours = tuple(neighbours)
self.assertEqual(neighbours, (1,2,3,4))