def test_copy(self):
sub = Substituent("COCH3")
sub = sub.copy(name="COCH3")
self.is_COCH3(sub)
return
def substitute(
session,
selection=None,
substituents=None,
newName=None,
guessAttachment=True,
modify=True,
minimize=False,
useRemoteness=False,
available=False,
newResidue=False,
):
if available:
substitute_list(session)
return
if not selection:
selection = selected_atoms(session)
if not substituents:
session.logger.error("missing required \"substituents\" argument")
return
attached = {}
if newName is None:
newName = [None for s in substituents]
elif any(len(name.strip()) > 4 for name in newName):
raise RuntimeError("residue names must be 4 characters or less")
elif not all(name.isalnum() for name in newName):
raise RuntimeError("invalid residue name: %s" % " ".join(newName))
elif len(substituents) != len(newName):
raise RuntimeError(
"number of substituents is not the same as the number of new names"
)
if not guessAttachment:
models, attached = avoidTargets(selection)
else:
models, attached = guessAttachmentTargets(selection, session)
first_pass = True
new_structures = []
for ndx, subname in enumerate(substituents):
subname = subname.strip()
sub = Substituent(subname)
# when minimizing, we only want to deal with residues that are close to the substituent
# determine the size of the new substituent to limit this
if minimize:
size = 5
for atom in sub.atoms:
d = np.linalg.norm(atom.coords)
if d > size:
size = d
for model in models:
if modify and first_pass:
conv_res = []
for res in models[model]:
if res not in conv_res:
conv_res.append(res)
if minimize:
for chix_res in model.residues:
if chix_res in conv_res:
continue
added_res = False
for atom in chix_res.atoms:
for target in models[model][res]:
d = np.linalg.norm(atom.coord -
target.coord)
if d < (size + 3):
conv_res.append(chix_res)
added_res = True
break
if added_res:
break
rescol = ResidueCollection(model, convert_residues=conv_res)
for res in models[model]:
for target in models[model][res]:
if attached is not None:
end = AtomSpec(attached[target].atomspec)
else:
end = None
# call substitute on the ResidueCollection b/c we need to see
# the other residues if minimize=True
rescol.substitute(
sub.copy(),
AtomSpec(target.atomspec),
attached_to=end,
minimize=minimize,
use_greek=useRemoteness,
new_residue=newResidue,
new_name=newName[ndx],
)
rescol.update_chix(model)
elif modify and not first_pass:
raise RuntimeError("only the first model can be replaced")
else:
model_copy = model.copy()
conv_res = [
model_copy.residues[i] for i in
[model.residues.index(res) for res in models[model]]
]
# modifying_residues = [model_copy.residues[i] for i in [model.residues.index(res) for res in models[model]]]
modifying_residues = [r for r in conv_res]
if minimize:
for chix_res in model_copy.residues:
if chix_res in conv_res:
continue
added_res = False
for res in models[model]:
for target in models[model][res]:
for atom in chix_res.atoms:
d = np.linalg.norm(atom.coord -
target.coord)
if d < (size + 3):
conv_res.append(chix_res)
added_res = True
break
if added_res:
break
if added_res:
break
rescol = ResidueCollection(model_copy,
convert_residues=conv_res)
for residue, res in zip(modifying_residues, models[model]):
for target in models[model][res]:
if attached is not None:
end = AtomSpec(model_copy.atoms[model.atoms.index(
attached[target])].atomspec)
else:
end = None
rescol.substitute(
sub.copy(),
AtomSpec(model_copy.atoms[model.atoms.index(
target)].atomspec),
attached_to=end,
minimize=minimize,
use_greek=useRemoteness,
new_residue=newResidue,
new_name=newName[ndx],
)
rescol.update_chix(model_copy)
new_structures.append(model_copy)
first_pass = False
if not modify:
session.models.add(new_structures)
