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added Universe check and more tests
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@lilyminium
lilyminium committed Jan 20, 2020
1 parent 51176fa commit 0875ae0
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Showing 2 changed files with 283 additions and 228 deletions.
123 changes: 95 additions & 28 deletions package/MDAnalysis/core/universe.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1002,10 +1002,12 @@ def _add_topology_objects(self, object_type, values, types=None, guessed=False,
----------
object_type : {'bonds', 'angles', 'dihedrals', 'impropers'}
The type of TopologyObject to add.
values : iterable of tuples, AtomGroups, or TopologyObjects
values : TopologyGroup or iterable of tuples, AtomGroups, or TopologyObjects
An iterable of: tuples of atom indices, or AtomGroups,
or TopologyObjects. If every value is a TopologyObject, all
keywords are ignored.
If AtomGroups or TopologyObjects are passed, they *must* be from the same
Universe.
types : iterable (optional, default None)
None, or an iterable of hashable values with the same length as ``values``
guessed : bool or iterable (optional, default False)
Expand All @@ -1024,15 +1026,22 @@ def _add_topology_objects(self, object_type, values, types=None, guessed=False,
guessed = [t.is_guessed for t in values]
order = [t.order for t in values]

values = [x.indices if isinstance(x, (AtomGroup, TopologyObject))
else x for x in values]
indices = []
for x in values:
if isinstance(x, (AtomGroup, TopologyObject)):
if x.universe is not self:
err_msg = 'Cannot add {} from different Universes.'
raise ValueError(err_msg.format(object_type))
indices.append(x.indices)
else:
indices.append(x)

all_indices = set([i for obj in values for i in obj])
all_indices = set([i for obj in indices for i in obj])
nonexistent = all_indices - set(self.atoms.indices)
if nonexistent:
istr = ', '.join(map(str, nonexistent))
raise ValueError(('Cannot add {} for nonexistent'
' atom indices: {}').format(object_type, istr))
err_msg = 'Cannot add {} for nonexistent atom indices: {}'
raise ValueError(err_msg.format(object_type, istr))

try:
attr = getattr(self._topology, object_type)
Expand All @@ -1041,17 +1050,19 @@ def _add_topology_objects(self, object_type, values, types=None, guessed=False,
attr = getattr(self._topology, object_type)


attr._add_bonds(values, types=types, guessed=guessed, order=order)
attr._add_bonds(indices, types=types, guessed=guessed, order=order)

def add_bonds(self, values, types=None, guessed=False, order=None):
"""Add new Bonds to this Universe.
Parameters
----------
values : iterable of tuples, AtomGroups, or Bonds
values : iterable of tuples, AtomGroups, or Bonds; or TopologyGroup
An iterable of: tuples of 2 atom indices, or AtomGroups with 2 atoms,
or Bonds. If every value is a Bond, all
keywords are ignored.
If AtomGroups, Bonds, or a TopologyGroup are passed,
they *must* be from the same Universe.
types : iterable (optional, default None)
None, or an iterable of hashable values with the same length as ``values``
guessed : bool or iterable (optional, default False)
Expand All @@ -1063,16 +1074,26 @@ def add_bonds(self, values, types=None, guessed=False, order=None):
Example
-------
Adding TIP4P water bonds with a list of AtomGroups:
Adding TIP4P water bonds with a list of AtomGroups::
import MDAnalysis as mda
from MDAnalysis.tests.datafiles import GRO
u = mda.Universe(GRO)
sol = u.select_atoms('resname SOL')
ow_hw1 = sol.select_atoms('name OW or name HW1').split('residue')
ow_hw2 = sol.select_atoms('name OW or name HW2').split('residue')
ow_mw = sol.select_atoms('name OW or name MW').split('residue')
u.add_bonds(ow_hw1 + ow_hw2 + ow_mw)
>>> import MDAnalysis as mda
>>> from MDAnalysis.tests.datafiles import GRO
>>> u = mda.Universe(GRO)
>>> sol = u.select_atoms('resname SOL')
>>> ow_hw1 = sol.select_atoms('name OW or name HW1').split('residue')
>>> ow_hw2 = sol.select_atoms('name OW or name HW2').split('residue')
>>> ow_mw = sol.select_atoms('name OW or name MW').split('residue')
>>> u.add_bonds(ow_hw1 + ow_hw2 + ow_mw)
You can only add bonds from the same Universe. If you would like to add
AtomGroups, Bonds, or a TopologyGroup from a different Universe, convert
them to indices first. ::
from MDAnalysis.tests.datafiles import PSF
u2 = mda.Universe(PSF)
# assuming you have already added bonds to u
u2.add_bonds(u.bonds.to_indices())
.. versionadded:: 0.21.0
Expand All @@ -1086,10 +1107,12 @@ def add_angles(self, values, types=None, guessed=False):
Parameters
----------
values : iterable of tuples, AtomGroups, or Angles
values : iterable of tuples, AtomGroups, or Angles; or TopologyGroup
An iterable of: tuples of 3 atom indices, or AtomGroups with 3 atoms,
or Angles. If every value is a Angle, all
keywords are ignored.
If AtomGroups, Angles, or a TopologyGroup are passed,
they *must* be from the same Universe.
types : iterable (optional, default None)
None, or an iterable of hashable values with the same length as ``values``
guessed : bool or iterable (optional, default False)
Expand All @@ -1105,10 +1128,12 @@ def add_dihedrals(self, values, types=None, guessed=False):
Parameters
----------
values : iterable of tuples, AtomGroups, or Dihedrals
values : iterable of tuples, AtomGroups, or Dihedrals; or TopologyGroup
An iterable of: tuples of 4 atom indices, or AtomGroups with 4 atoms,
or Dihedrals. If every value is a Dihedral, all
keywords are ignored.
If AtomGroups, Dihedrals, or a TopologyGroup are passed,
they *must* be from the same Universe.
types : iterable (optional, default None)
None, or an iterable of hashable values with the same length as ``values``
guessed : bool or iterable (optional, default False)
Expand All @@ -1125,10 +1150,12 @@ def add_impropers(self, values, types=None, guessed=False):
Parameters
----------
values : iterable of tuples, AtomGroups, or Impropers
values : iterable of tuples, AtomGroups, or Impropers; or TopologyGroup
An iterable of: tuples of 4 atom indices, or AtomGroups with 4 atoms,
or Impropers. If every value is an Improper, all
keywords are ignored.
If AtomGroups, Impropers, or a TopologyGroup are passed,
they *must* be from the same Universe.
types : iterable (optional, default None)
None, or an iterable of hashable values with the same length as ``values``
guessed : bool or iterable (optional, default False)
Expand All @@ -1147,30 +1174,64 @@ def _delete_topology_objects(self, object_type, values):
----------
object_type : {'bonds', 'angles', 'dihedrals', 'impropers'}
The type of TopologyObject to add.
values : iterable of tuples, AtomGroups, or TopologyObjects
values : iterable of tuples, AtomGroups, or TopologyObjects; or TopologyGroup
An iterable of: tuples of atom indices, or AtomGroups,
or TopologyObjects.
If AtomGroups, TopologyObjects, or a TopologyGroup are passed,
they *must* be from the same Universe.
.. versionadded:: 0.21.0
"""
values = [x.indices if isinstance(x, (AtomGroup, TopologyObject))
else x for x in values]
indices = []
for x in values:
if isinstance(x, (AtomGroup, TopologyObject)):
if x.universe is not self:
err_msg = 'Cannot delete {} from different Universes.'
raise ValueError(err_msg.format(object_type))
indices.append(x.indices)
else:
indices.append(x)

try:
attr = getattr(self._topology, object_type)
except AttributeError:
raise ValueError('There are no {} to delete'.format(object_type))

attr._delete_bonds(values)
attr._delete_bonds(indices)

def delete_bonds(self, values):
"""Delete Bonds from this Universe.
Parameters
----------
values : iterable of tuples, AtomGroups, or Bonds
values : iterable of tuples, AtomGroups, or Bonds; or TopologyGroup
An iterable of: tuples of 2 atom indices, or AtomGroups with 2 atoms,
or Bonds.
If AtomGroups, Bonds, or a TopologyGroup are passed,
they *must* be from the same Universe.
Example
-------
Deleting bonds from a Universe::
import MDAnalysis as mda
from MDAnalysis.tests.datafiles import PSF
u = mda.Universe(PSF)
# delete first 5 bonds
u.delete_bonds(u.bonds[:5])
If you are deleting bonds in the form of AtomGroups, Bonds, or a
TopologyGroup, they must come from the same Universe. If you want to
delete bonds from another Universe, convert them to indices first. ::
from MDAnalysis.tests.datafiles import PDB
u2 = mda.Universe(PDB)
u.delete_bonds(u2.bonds.to_indices())
.. versionadded:: 0.21.0
Expand All @@ -1183,9 +1244,11 @@ def delete_angles(self, values):
Parameters
----------
values : iterable of tuples, AtomGroups, or Angles
values : iterable of tuples, AtomGroups, or Angles; or TopologyGroup
An iterable of: tuples of 3 atom indices, or AtomGroups with 3 atoms,
or Angles.
If AtomGroups, Angles, or a TopologyGroup are passed,
they *must* be from the same Universe.
.. versionadded:: 0.21.0
Expand All @@ -1197,9 +1260,11 @@ def delete_dihedrals(self, values):
Parameters
----------
values : iterable of tuples, AtomGroups, or Dihedrals
values : iterable of tuples, AtomGroups, or Dihedrals; or TopologyGroup
An iterable of: tuples of 4 atom indices, or AtomGroups with 4 atoms,
or Dihedrals.
If AtomGroups, Dihedrals, or a TopologyGroup are passed,
they *must* be from the same Universe.
.. versionadded:: 0.21.0
Expand All @@ -1211,9 +1276,11 @@ def delete_impropers(self, values):
Parameters
----------
values : iterable of tuples, AtomGroups, or Impropers
values : iterable of tuples, AtomGroups, or Impropers; or TopologyGroup
An iterable of: tuples of 4 atom indices, or AtomGroups with 4 atoms,
or Impropers.
If AtomGroups, Angles, or a TopologyGroup are passed,
they *must* be from the same Universe.
.. versionadded:: 0.21.0
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