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updated so that bonding to dummy atoms are removed in the 3D viewer #349

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merged 1 commit into from
Mar 12, 2024
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updated so that bonding to dummy atoms are removed in the 3D viewer #349

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35 changes: 23 additions & 12 deletions MDANSE_GUI/Src/MDANSE_GUI/MolecularViewer/MolecularViewer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -594,12 +594,6 @@ def set_coordinates(self, frame: int, tolerance=0.04):

# update the atoms
coords = self._reader.read_frame(self._current_frame)
cov_radii = np.array(
[
CHEMICAL_ELEMENTS.get_atom_property(at, "covalent_radius")
for at in self._reader.atom_types
]
)

atoms = vtk.vtkPoints()
atoms.SetNumberOfPoints(self._n_atoms)
Expand All @@ -610,20 +604,37 @@ def set_coordinates(self, frame: int, tolerance=0.04):
self._polydata.SetPoints(atoms)

if self._bonds_visible:

# do not bond atoms to dummy atoms
not_du = np.array(
[
i
for i, at in enumerate(self._reader.atom_types)
if CHEMICAL_ELEMENTS.get_atom_property(at, "element") != "dummy"
]
)
rs = coords[not_du]
covs = np.array(
[
CHEMICAL_ELEMENTS.get_atom_property(at, "covalent_radius")
for at in self._reader.atom_types
]
)[not_du]

# determine and set bonds without PBC applied
tree = KDTree(coords)
tree = KDTree(rs)
bonds = vtk.vtkCellArray()
contacts = tree.query_ball_tree(tree, 2 * np.max(cov_radii) + tolerance)
contacts = tree.query_ball_tree(tree, 2 * np.max(covs) + tolerance)
for i, idxs in enumerate(contacts):
if len(idxs) == 0:
continue
diff = coords[i] - coords[idxs]
diff = rs[i] - rs[idxs]
dist = np.sum(diff * diff, axis=1)
sum_radii = (cov_radii[i] + cov_radii[idxs] + tolerance) ** 2
sum_radii = (covs[i] + covs[idxs] + tolerance) ** 2
js = np.array(idxs)[(0 < dist) & (dist < sum_radii)]
for j in js[i < js]:
for j in not_du[js[i < js]]:
line = vtk.vtkLine()
line.GetPointIds().SetId(0, i)
line.GetPointIds().SetId(0, not_du[i])
line.GetPointIds().SetId(1, j)
bonds.InsertNextCell(line)

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