def test_constructors(self):
qlist = []
for i in range(10):
atom = self.molecule.addAtom()
self.list.append(atom)
qlist.append(atom)
self.assertEqual(self.list.size, 10)
list2 = Avogadro.PrimitiveList(self.list)
self.assertEqual(list2.size, 10)
list3 = Avogadro.PrimitiveList(qlist)
self.assertEqual(list3.size, 10)
def selectBackbone(self, glwidget):
mol = glwidget.molecule
# create a PrimitiveList to call GLWidget.setSelected(PrimitiveList, bool)
primitiveList = Avogadro.PrimitiveList()
# find the backbone atoms
for atom in mol.atoms:
# get the atomId and strip of white spaces
atomId = atom.residue.atomId(atom.id).strip()
print atomId
# add the atom to the list if the atomId matches N, CA, C, O or H
if atomId == "N":
primitiveList.append(atom)
elif atomId == "CA":
primitiveList.append(atom)
elif atomId == "C":
primitiveList.append(atom)
elif atomId == "O":
primitiveList.append(atom)
elif atomId == "H":
primitiveList.append(atom)
# find all bonds between backbone atoms
for bond in mol.bonds:
beginAtom = bond.beginAtom
endAtom = bond.endAtom
if primitiveList.contains(beginAtom) and primitiveList.contains(
endAtom):
primitiveList.append(bond)
# clear the current selection
glwidget.clearSelected()
# select the backbone atom
glwidget.setSelected(primitiveList, True)
def test_primitives(self):
molecule = Avogadro.molecules.addMolecule()
for i in range(10):
molecule.addAtom()
list = Avogadro.PrimitiveList(molecule.atoms)
for engine in self.engines:
self.assertEqual(engine.primitives.size, 0)
engine.primitives = list
self.assertNotEqual(engine.primitives.size, 0)
engine.clearPrimitives()
self.assertEqual(engine.primitives.size, 0)
def selectBindingSite(self, glwidget):
# returns (double, bool ok) as tuple
result = QInputDialog.getDouble(
None, "Create Binding Site Around Selection", "radius", 5.0, 2.0,
20.0, 1)
if not result[1]:
return
r = result[0]
r2 = r * r
selectedAtoms = glwidget.selectedPrimitives.subList(
Avogadro.PrimitiveType.AtomType)
newSelection = Avogadro.PrimitiveList()
atomIds = []
for residue in glwidget.molecule.residues:
keepResidue = False
# compute distance between residue atoms and selected atoms
for atomId in residue.atoms:
atom = glwidget.molecule.atomById(atomId)
if not atom:
continue
for selectedAtom in selectedAtoms:
ab = selectedAtom.pos - atom.pos
dist2 = dot(ab, ab)
if dist2 < r2:
keepResidue = True
break
if keepResidue:
break
if keepResidue:
for atomId in residue.atoms:
atom = glwidget.molecule.atomById(atomId)
newSelection.append(atom)
atomIds.append(atom.id)
# find all bonds between the atoms
for bond in glwidget.molecule.bonds:
beginAtom = bond.beginAtom
endAtom = bond.endAtom
if atomIds.count(beginAtom.id) and atomIds.count(endAtom.id):
newSelection.append(bond)
glwidget.setSelected(newSelection, True)
def test_namedSelections(self):
l = Avogadro.PrimitiveList([self.molecule.atom(0)])
self.glwidget.addNamedSelection("test", l)
self.assertNotEqual(len(self.glwidget.namedSelections), 0)
self.assertEqual(self.glwidget.namedSelections[0], "test")
self.glwidget.removeNamedSelection("test")
self.assertEqual(len(self.glwidget.namedSelections), 0)
self.glwidget.addNamedSelection("test", l)
self.glwidget.removeNamedSelection(0)
self.assertEqual(len(self.glwidget.namedSelections), 0)
self.glwidget.addNamedSelection("test", l)
self.glwidget.renameNamedSelection(0, "test2")
self.assertEqual(self.glwidget.namedSelections[0], "test2")
self.assertNotEqual(self.glwidget.namedSelectionPrimitives("test2"),
None)
self.assertNotEqual(self.glwidget.namedSelectionPrimitives(0), None)
def setUp(self):
self.molecule = Avogadro.molecules.addMolecule()
self.list = Avogadro.PrimitiveList()
