def refTop():
return topology.Topology(
3, 2, 2,
attrs = [
ta.Atomnames(TA_FILLER[object]),
ta.Masses(TA_FILLER[float]),
ta.Resids(TA_FILLER[int]),
ta.Bonds(TA_FILLER['bond']),
],
atom_resindex=np.array([0, 0, 1]),
residue_segindex=np.array([0, 1])
)
def setUp(self):
names = self.names = ta.Atomnames(
np.array(['A', 'B', 'C'], dtype=object))
types = self.types = ta.Atomtypes(np.array(['X', 'Y', 'Z'],
dtype=object),
guessed=True)
resids = self.resids = ta.Resids(np.array([1]))
resnames = self.resnames = ta.Resnames(np.array(['ABC'], dtype=object),
guessed=True)
self.top = Topology(n_atoms=3,
n_res=1,
attrs=[names, types, resids, resnames])
def make_resids(size):
"""Resids 1 and upwards"""
import MDAnalysis.core.topologyattrs as ta
na, nr, ns = size
return ta.Resids(np.arange(nr, dtype=np.int64) + 1)
def _apply_map(self, mapping):
"""Apply the mapping scheme to the beads.
Parameters
----------
mapping : dict
Mapping definitions per bead/
Returns
-------
:class:`~MDAnalysis.core.topology.Topology` defining the new universe.
"""
# Allocate arrays
_beads = []
atomnames = []
atomids = []
resids = []
resnames = []
segids = []
charges = []
masses = []
residues = self.atu.atoms.split("residue")
select_residues = enumerate(
itertools.product(residues, viewitems(mapping)))
for i, (res, (name, selection)) in select_residues:
if name != "CB":
bead = res.select_atoms(selection)
else:
bead = res.select_atoms(
selection.get(res.resname[0],
"hsidechain and not name H*"))
if bead:
_beads.append(bead)
atomnames.append(name)
atomids.append(i)
resids.append(bead.resids[0])
resnames.append(bead.resnames[0])
segids.append(bead.segids[0].split("_")[-1])
try:
charges.append(bead.total_charge())
except AttributeError:
charges.append(0.)
masses.append(bead.total_mass())
_beads = np.array(_beads)
n_atoms = len(_beads)
# Atom
# _beads = topattrs._Beads(_beads)
vdwradii = np.zeros_like(atomids)
vdwradii = topologyattrs.Radii(vdwradii)
atomids = topologyattrs.Atomids(np.asarray(atomids))
atomnames = topologyattrs.Atomnames(
np.asarray(atomnames, dtype=np.object))
atomtypes = topologyattrs.Atomtypes(
np.asarray(np.arange(n_atoms) + 100))
charges = topologyattrs.Charges(np.asarray(charges))
masses = topologyattrs.Masses(np.asarray(masses))
# Residue
# resids, resnames
segids = np.asarray(segids, dtype=np.object)
resids = np.asarray(resids)
resnames = np.asarray(resnames, dtype=np.object)
residx, (new_resids, new_resnames, new_segids) = topbase.change_squash(
(resids, ), (resids, resnames, segids))
# transform from atom:Rid to atom:Rix
residueids = topologyattrs.Resids(new_resids)
residuenums = topologyattrs.Resnums(new_resids.copy())
residuenames = topologyattrs.Resnames(new_resnames)
# Segment
segidx, (perseg_segids, ) = topbase.change_squash((new_segids, ),
(new_segids, ))
segids = topologyattrs.Segids(perseg_segids)
# Setup topology
top = topology.Topology(len(atomids),
len(new_resids),
len(segids),
attrs=[
atomids, atomnames, atomtypes, charges,
masses, vdwradii, residueids, residuenums,
residuenames, segids
],
atom_resindex=residx,
residue_segindex=segidx)
return top
def resids(self):
return ta.Resids(np.array([1]))