def populate_clash_table_from_geometry(self, model):
'''
If no simulation is running, use ChimeraX's built-in clash toolset to find
and list geometric clashes in decreasing order of overlap severity.
'''
atoms = model.atoms
from chimerax.clashes import clashes
clash_dict = clashes.find_clashes(self.session,
atoms,
inter_model=False)
t = self._geom_clash_table
t.setRowCount(0)
if not clash_dict:
return
from functools import reduce
# Clash dict is bi-directional, so number of clashes is half the total count
clash_count = 1 / 2 * reduce(lambda x, y: x + y,
(len(d.keys())
for d in clash_dict.values()))
t.setRowCount(clash_count)
seen = set()
from chimerax.atomic import Atoms
# Make list of unique clashing atom pairs and their distances
clash_list = []
for a1, clashes in clash_dict.items():
seen.add(a1)
for a2, dist in clashes.items():
if a2 in seen:
continue
clash_list.append((Atoms([a1, a2]), dist))
# Sort clashes in decreasing order of overlap
clash_list = sorted(clash_list, key=lambda x: x[1], reverse=True)
from Qt.QtWidgets import QTableWidgetItem
for i, (catoms, overlap) in enumerate(clash_list):
a1, a2 = catoms
r1, r2 = catoms.residues
data = ("{} {}{}: {}".format(r1.name, r1.chain_id, r1.number,
a1.name),
"{} {}{}: {}".format(r2.name, r2.chain_id, r2.number,
a2.name), "{:0.2f}".format(overlap))
for j, d in enumerate(data):
item = QTableWidgetItem(d)
item.data = catoms
t.setItem(i, j, item)
t.resizeColumnsToContents()
def populate_clash_table_from_energies(self, atoms, clashing_indices,
forces):
'''
When running a simulation, list atoms that are experiencing extreme forces.
This is preferable, since clashes in a static molecule can lead to
extremely stretched bonds on energy minimization, with no van der Waals
overlap to detect.
Args:
* atoms:
- All currently-simulated atoms, in the order they were added to
the simulation
* clashing_indices:
- Indices of atoms experiencing excessive forces, sorted in
decreasing order of force magnitude
* forces:
- The forces on the clashing atoms, in decreasing order
* clash_table:
- The table to populate with details of the clashing atoms
'''
catoms = atoms[clashing_indices]
t = self._energy_clash_table
t.setRowCount(0)
if not len(catoms):
return
forces /= 10 # kJ mol-1 nm-1 to kJ mol-1 A-1
residues = catoms.residues
chain_ids = residues.chain_ids
resnames = residues.names
resnums = residues.numbers
anames = catoms.names
from Qt.QtWidgets import QTableWidgetItem
from chimerax.atomic import Atoms
t.setRowCount(len(catoms))
for i, (a, cid, rname, rnum, aname, force) in enumerate(
zip(catoms, chain_ids, resnames, resnums, anames, forces)):
data = (cid, "{}-{}".format(rname,
rnum), aname, "{:0.3g}".format(force))
aa = Atoms([a])
for j, d in enumerate(data):
item = QTableWidgetItem(d)
item.data = aa
t.setItem(i, j, item)
t.resizeColumnsToContents()
