def test_guess_bonds_withlist(self):
bondlist = (
(0, 1), (0, 2), (0, 3), (0, 4), (0, 5), (1, 2), (1, 3),
(1, 4), (2, 3), (2, 4), (2, 8), (3, 4), (4, 5), (4, 6),
(6, 7), (6, 8), (6, 9), (7, 8))
user_vdw = {'56': 1.5, '2': 1.5, '22': 1.5, '6': 1.5, '23': 1.5, '3': 1.5}
assert_equal(guess_bonds(list(self.u.atoms[:10]),
self.u.atoms.positions[:10],
vdwradii=user_vdw),
bondlist)
def test_guess_bonds_withag(self):
# here's one I prepared earlier
bondlist = (
(0, 1), (0, 2), (0, 3), (0, 4), (0, 5), (1, 2), (1, 3),
(1, 4), (2, 3), (2, 4), (2, 8), (3, 4), (4, 5), (4, 6),
(6, 7), (6, 8), (6, 9), (7, 8))
user_vdw = {'56': 1.5, '2': 1.5, '22': 1.5, '6': 1.5, '23': 1.5, '3': 1.5}
assert_equal(guess_bonds(self.u.atoms[:10],
self.u.atoms.positions[:10],
vdwradii=user_vdw),
bondlist)
def test_guess_bonds_withlist(self):
bondlist = ((0, 1), (0, 2), (0, 3), (0, 4), (0, 5), (1, 2), (1, 3),
(1, 4), (2, 3), (2, 4), (2, 8), (3, 4), (4, 5), (4, 6),
(6, 7), (6, 8), (6, 9), (7, 8))
user_vdw = {
'56': 1.5,
'2': 1.5,
'22': 1.5,
'6': 1.5,
'23': 1.5,
'3': 1.5
}
assert_equal(
guess_bonds(list(self.u.atoms[:10]),
self.u.atoms.positions[:10],
vdwradii=user_vdw), bondlist)
def test_guess_bonds_withag(self):
# here's one I prepared earlier
bondlist = ((0, 1), (0, 2), (0, 3), (0, 4), (0, 5), (1, 2), (1, 3),
(1, 4), (2, 3), (2, 4), (2, 8), (3, 4), (4, 5), (4, 6),
(6, 7), (6, 8), (6, 9), (7, 8))
user_vdw = {
'56': 1.5,
'2': 1.5,
'22': 1.5,
'6': 1.5,
'23': 1.5,
'3': 1.5
}
assert_equal(
guess_bonds(self.u.atoms[:10],
self.u.atoms.positions[:10],
vdwradii=user_vdw), bondlist)
def _parsebonds(self, primitive_pdb_reader):
if self.guess_bonds_mode:
guessed_bonds = guess_bonds(self.structure["_atoms"],
np.array(primitive_pdb_reader.ts))
self.structure["_guessed_bonds"] = guessed_bonds
# Mapping between the atom array indicies a.number and atom ids
# (serial) in the original PDB file
mapping = dict((a.serial, a.number) for a in self.structure["_atoms"])
bonds = set()
with openany(self.filename, "r") as fname:
lines = ((num, line[6:].split()) for num, line in enumerate(fname)
if line[:6] == "CONECT")
for num, bond in lines:
atom, atoms = int(bond[0]), map(int, bond[1:])
for a in atoms:
bond = tuple([mapping[atom], mapping[a]])
bonds.add(bond)
self.structure["_bonds"] = tuple(bonds)
def _parsebonds(self, primitive_pdb_reader):
if self.guess_bonds_mode:
guessed_bonds = guess_bonds(self.structure["_atoms"],
np.array(primitive_pdb_reader.ts))
self.structure["_guessed_bonds"] = guessed_bonds
# Mapping between the atom array indicies a.number and atom ids
# (serial) in the original PDB file
mapping = dict((a.serial, a.number) for a in self.structure["_atoms"])
bonds = set()
with openany(self.filename, "r") as fname:
lines = ((num, line[6:].split()) for num, line in enumerate(fname)
if line[:6] == "CONECT")
for num, bond in lines:
atom, atoms = int(bond[0]), map(int, bond[1:])
for a in atoms:
bond = tuple([mapping[atom], mapping[a]])
bonds.add(bond)
self.structure["_bonds"] = tuple(bonds)
