def do_maplig(self):
lignames = self.ligname.text()
selection = selected_atoms(self.session)
if len(selection) < 1:
raise RuntimeWarning("nothing selected")
models = {}
for atom in selection:
if atom.structure not in models:
models[atom.structure] = [AtomSpec(atom.atomspec)]
else:
models[atom.structure].append(AtomSpec(atom.atomspec))
first_pass = True
new_structures = []
for ligname in lignames.split(','):
ligname = ligname.strip()
lig = Component(ligname)
for model in models:
if self.close_previous_bool and first_pass:
rescol = ResidueCollection(model)
elif self.close_previous_bool and not first_pass:
raise RuntimeError("only the first model can be replaced")
else:
model_copy = model.copy()
rescol = ResidueCollection(model_copy)
for i, atom in enumerate(model.atoms):
rescol.atoms[i].atomspec = atom.atomspec
rescol.atoms[i].add_tag(atom.atomspec)
rescol.atoms[i].chix_atom = atom
target = rescol.find(models[model])
if len(target) % len(lig.key_atoms) == 0:
k = 0
ligands = []
while k != len(target):
res_lig = ResidueCollection(lig.copy(), comment=lig.comment)
res_lig.parse_comment()
res_lig = Component(res_lig, key_atoms = ",".join([str(k + 1) for k in res_lig.other["key_atoms"]]))
ligands.append(res_lig)
k += len(lig.key_atoms)
else:
raise RuntimeError("number of key atoms no not match: %i now, new ligand has %i" % (len(target), len(lig.key_atoms)))
rescol.map_ligand(ligands, target)
for center_atom in rescol.center:
center_atom.connected = set([])
for atom in rescol.atoms:
if atom not in rescol.center:
if center_atom.is_connected(atom):
atom.connected.add(center_atom)
center_atom.connected.add(atom)
if self.close_previous_bool:
rescol.update_chix(model)
else:
struc = rescol.get_chimera(self.session)
new_structures.append(struc)
first_pass = False
if not self.close_previous_bool:
self.session.models.add(new_structures)
def test_map_ligand(self):
monodentate = Component(TestGeometry.monodentate)
tridentate = Component(TestGeometry.tridentate)
debug = False
# import cProfile
#
# profile = cProfile.Profile()
# profile.enable()
"""
#TODO: get a reference file for this
# two monodentate -> bidentate
ptco4 = TestGeometry.ptco4.copy()
ptco4.map_ligand('EDA', ["3", "5"])
"""
# bidentate -> monodentate, none
ref = Geometry(os.path.join(prefix, "ref_files", "lig_map_1.xyz"))
tm_simple = Geometry(TestGeometry.tm_simple)
tm_simple.map_ligand(monodentate.copy(), ["35"])
self.assertTrue(
validate(tm_simple,
ref,
heavy_only=True,
thresh="loose",
debug=debug))
# bidentate -> two monodentate
ref = Geometry(os.path.join(prefix, "ref_files", "lig_map_2.xyz"))
tm_simple = Geometry(TestGeometry.tm_simple)
tm_simple.map_ligand([monodentate.copy(), "ACN"], ["35", "36"])
self.assertTrue(
validate(tm_simple,
ref,
thresh="loose",
heavy_only=True,
debug=debug))
# bidentate -> bidentate
ref = Geometry(os.path.join(prefix, "ref_files", "lig_map_3.xyz"))
tm_simple = Geometry(TestGeometry.tm_simple)
tm_simple.map_ligand("S-tBu-BOX", ["35", "36"])
self.assertTrue(
validate(tm_simple,
ref,
thresh="loose",
heavy_only=True,
debug=debug))
# tridentate -> tridentate
ref = Geometry(os.path.join(prefix, "ref_files", "lig_map_4.xyz"))
org_tri = Geometry(TestGeometry.org_tri)
org_tri.map_ligand(tridentate, ["30", "28", "58"])
self.assertTrue(
validate(org_tri,
ref,
thresh="loose",
heavy_only=True,
debug=debug))
# tridentate -> monodentate + bidentate -> tridentate
ref = Geometry(os.path.join(prefix, "ref_files", "lig_map_6.xyz"))
org_tri = Geometry(TestGeometry.org_tri)
org_tri.map_ligand(["EDA", "ACN"], ["30", "28", "58"])
self.assertTrue(
validate(org_tri,
ref,
thresh="loose",
heavy_only=True,
debug=debug))
ref = Geometry(os.path.join(prefix, "ref_files", "lig_map_7.xyz"))
org_tri = Geometry(os.path.join(prefix, "ref_files", "lig_map_6.xyz"))
org_tri.map_ligand(tridentate, ["10", "11", "2"])
self.assertTrue(
validate(org_tri,
ref,
thresh="loose",
heavy_only=True,
debug=debug))
# bidentate -> two bulky monodentate
ref = Geometry(os.path.join(prefix, "ref_files", "lig_map_5.xyz"))
tm_simple = Geometry(TestGeometry.tm_simple)
tm_simple.map_ligand(["iPr-NC3C"] * 2, ["35", "36"])
self.assertTrue(
validate(tm_simple,
ref,
thresh="loose",
heavy_only=True,
debug=debug))
