Advanced topology concepts
Adding a Residue or Segment to a Universe
To add a Residue or Segment to a topology, use the Universe.add_Residue or Universe.add_Segment methods.
>>> u = mda.Universe(PSF, DCD)
>>> u.segments
<SegmentGroup with 1 segment>
>>> u.segments.segids
array(['4AKE'], dtype=object)
>>> newseg = u.add_Segment(segid='X')
>>> u.segments.segids
array(['4AKE', 'X'], dtype=object)
>>> newseg.atoms
<AtomGroup with 0 atoms>
To assign the last 100 residues from the Universe to this new Segment:
>>> u.residues[-100:].segments = newseg
>>> newseg.atoms
<AtomGroup with 1600 atoms>
Another example is creating custom segments for protein domains.
Molecules
In MDAnalysis, a molecule is a GROMACS-only concept that is relevant in some analysis methods. A group of atoms is considered a “molecule” if it is defined by the [ moleculetype ] section in a GROMACS topology. Molecules are only defined if a Universe is created from a GROMACS topology file (i.e. with a .tpr extension). Unlike fragments, they are not accessible directly from atoms.
>>> tpr = mda.Universe(TPR)
>>> tpr.atoms.molecules
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "MDAnalysis/core/groups.py", line 2278, in __getattr__
cls=self.__class__.__name__, attr=attr))
AttributeError: AtomGroup has no attribute molecules
However, the order (molnum) and name (moltype) of each molecule is accessible as topology attributes:
>>> tpr.atoms.molnums
array([ 0, 0, 0, ..., 11086, 11087, 11088])
>>> tpr.atoms.moltypes
array(['AKeco', 'AKeco', 'AKeco', ..., 'NA+', 'NA+', 'NA+'], dtype=object)