def FromAtomPaths(selfClass, atomPaths, atoms=None):
"""Create a sequence from a list of atom paths."""
# . Argument check.
if (atoms is not None) and (len(atoms) != len(atomPaths)):
raise ValueError(
"The \"atomPaths\" and \"atoms\" arguments are incompatible.")
createAtoms = (atoms is None)
# . Initialization.
self = selfClass()
# . Process the paths.
duplicateAtoms = 0
index = 0
for atomPath in atomPaths:
(entityLabel, componentLabel, atomLabel) = self.ParsePath(atomPath,
labels=3)
(entity, component,
atom) = self.GetDescendantsFromLabels(entityLabel, componentLabel,
atomLabel)
if entity is None:
entity = SequenceEntity(label=entityLabel)
self.AddChild(entity)
if component is None:
genericLabel = self.ParseLabel(componentLabel, fields=1)[0]
component = SequenceComponent(genericLabel=genericLabel,
label=componentLabel)
entity.AddChild(component)
if atom is None:
if createAtoms:
atom = Atom(index=index, label=atomLabel)
else:
atom = atoms[index]
atom.index = index
atom.label = atomLabel
index += 1
component.AddChild(atom)
else:
duplicateAtoms += 1
if duplicateAtoms > 0:
raise ValueError(
"There were {:d} duplicate atom paths in the sequence.".format(
duplicateAtoms))
# . Finish up.
return self
