def make_starshape():
u = make_Universe()
bonds = []
for seg in range(5):
segbase = seg * 25
for res in range(5):
# offset for atoms in this res
base = segbase + 5 * res
bonds.append((0 + base, 1 + base))
bonds.append((1 + base, 2 + base))
bonds.append((1 + base, 3 + base))
bonds.append((1 + base, 4 + base))
if not res == 4: # last res doesn't link onwards
bonds.append((4 + base, 5 + base))
u.add_TopologyAttr(Bonds(bonds))
return u
def universe(self):
universe = mda.Universe(Make_Whole)
bondlist = [(0, 1), (1, 2), (1, 3), (1, 4), (4, 5), (4, 6), (4, 7)]
universe.add_TopologyAttr(Bonds(bondlist))
return universe
def _load_bonds(self):
# Load some bonds into Universe, not required for all tests
bondlist = [(0, 1), (1, 2), (1, 3), (1, 4), (4, 5), (4, 6), (4, 7)]
self.u.add_TopologyAttr(Bonds(bondlist))
def parse(self):
"""
Access ESPResSo data and return the topology object.
Returns
-------
top : :class:`MDAnalysis.core.topology.Topology`
a topology object
"""
espresso = self.kwargs['espresso']
names = []
atomtypes = []
masses = []
charges = []
bonds = []
angles = []
dihedrals = []
for p in espresso.part:
names.append("A" + repr(p.type))
atomtypes.append("T" + repr(p.type))
masses.append(p.mass)
charges.append(p.q)
for bond in p.bonds:
partner_ids = bond[1:]
n_partner = len(partner_ids)
if n_partner == 1:
bonds.append((p.id, partner_ids[0]))
elif n_partner == 2:
angles.append((partner_ids[0], p.id, partner_ids[1]))
elif n_partner == 3:
dihedrals.append(
(partner_ids[0], p.id, partner_ids[1], partner_ids[2]))
else:
continue
natoms = len(espresso.part)
attrs = [
Atomnames(np.array(names, dtype=object)),
Atomids(np.arange(natoms) + 1),
Atomtypes(np.array(atomtypes, dtype=object)),
Masses(masses),
Resids(np.array([1])),
Resnums(np.array([1])),
Segids(np.array(['System'], dtype=object)),
AltLocs(np.array([' '] * natoms, dtype=object)),
Resnames(np.array(['R'], dtype=object)),
Occupancies(np.zeros(natoms)),
Tempfactors(np.zeros(natoms)),
ICodes(np.array([' '], dtype=object)),
Charges(np.array(charges)),
Bonds(bonds),
Angles(angles),
Dihedrals(dihedrals)
]
top = Topology(natoms, 1, 1, attrs=attrs)
return top