add intra stuff

package/CHANGELOG

@@ -22,7 +22,6 @@ The rules for this file:
   * 2.0.0
 
 Fixes
-<<<<<<< HEAD
   * A Universe created from an ROMol with no atoms returns now a Universe 
     with 0 atoms (Issue #3142)
   * ValueError raised when empty atomgroup is given to DensityAnalysis
@@ -39,55 +38,6 @@ Fixes
   * PDB writer now uses elements attribute instead of guessing elements from
     atom name (Issue #2423)
   * Cleanup and parametrization of test_atomgroup.py (Issue #2995)
-=======
-  * Removes use of absolute paths in setup.py to avoid Windows installation
-    failures (Issue #3129)
-  * Adds test for crashes caused by small box NSGrid searches (Issue #2670)
-  * Replaces decreated NumPy type aliases and fixes NEP 34 explicit ragged
-    array warnings (PR #3139, backports PRs #2845 and #2834)
-  * Fixed several issues with NSGrid and triclinic boxes not finding some pairs.
-    (Issues #2229 #2345 #2919, PR #2937).
-
-Changes
-  * Maximum pinned versions in setup.py removed for python 3.6+ (PR #3139)
-
-Deprecations
-  * ParmEdConverter no longer accepts Timestep objects at all
-    (Issue #3031, PR #3172)
-  * NCDFWriter `scale_factor` writing will change in version 2.0 to
-    better match AMBER outputs (Issue #2327)
-  * Deprecated using the last letter of the segid as the
-    chainID when writing PDB files (Issue #3144)
-  * Deprecated tempfactors and bfactors being separate
-    TopologyAttrs, with a warning (PR #3161)
-  * hbonds.WaterBridgeAnalysis will be removed in 2.0.0 and
-    replaced with hydrogenbonds.WaterBridgeAnalysis (#3111)
-  * TPRParser indexing resids from 0 by default is deprecated.
-    From 2.0 TPRParser will index resids from 1 by default.
-
-
-Enhancements
-  * Added `get_connections` method to get bonds, angles, dihedrals, etc.
-    with or without atoms outside the group (Issues #1264, #2821, PR #3160)
-  * Added `tpr_resid_from_one` keyword to select whether TPRParser
-    indexes resids from 0 or 1 (Issue #2364, PR #3153)
-
-
-01/17/21 richardjgowers, IAlibay, orbeckst, tylerjereddy, jbarnoud,
-         yuxuanzhuang, lilyminium, VOD555, p-j-smith, bieniekmateusz,
-         calcraven, ianmkenney, rcrehuet, manuel.nuno.melo, hanatok
-
-  * 1.0.1
-
-Fixes
-  * Due to issues with the reliability/accuracy of `nsgrid`, this method is
-    currently not recommended for use. It has also been removed as an option
-    from lib.capped_distance and lib.self_capped_distance. Please use PKDTree
-    instead (Issue #2930)
-  * Development status changed from beta to mature (Issue #2773)
-  * pip installation only requests Python 2.7-compatible packages (#2736)
-  * Testsuite does not use any more matplotlib.use('agg') (#2191)
->>>>>>> c58d2d370... undo half of PR 3160
   * The methods provided by topology attributes now appear in the
     documentation (Issue #1845)
   * AtomGroup.center now works correctly for compounds + unwrapping
@@ -137,6 +87,9 @@ Fixes
   * Fix syntax warning over comparison of literals using is (Issue #3066)
 
 Enhancements
+  * Added intra_bonds, intra_angles, intra_dihedrals etc. to return only
+    the connections involving atoms within the AtomGroup, instead of
+    including atoms outside the AtomGroup (Issue #1264, #2821, PR #3200)
   * Added a ValueError raised when not given a gridcenter while
     providing grid dimensions to DensityAnalysis, also added
     check for NaN in the input (Issue #3148, PR #3154)
@@ -191,9 +144,6 @@ Enhancements
 
 
 Changes
-  * AtomGroup.bonds, .angles, .dihedrals, .impropers etc. now return only
-    the connections involving atoms within the AtomGroup, instead of
-    including atoms outside the AtomGroup (Issue #1264, #2821, PR #3200)
   * TPRParser now loads TPR files with `tpr_resid_from_one=True` by default, 
     which starts TPR resid indexing from 1 (instead of 0 as in 1.x) (Issue #2364, PR #3152)
   * Introduces encore specific C compiler arguments to allow for lowering of

package/MDAnalysis/coordinates/MOL2.py

@@ -324,7 +324,7 @@ def encode_block(self, obj):
         if hasattr(obj, "bonds"):
             # Grab only bonds between atoms in the obj
             # ie none that extend out of it
-            bondgroup = obj.bonds
+            bondgroup = obj.intra_bonds
             bonds = sorted((b[0], b[1], b.order) for b in bondgroup)
             bond_lines = ["@<TRIPOS>BOND"]
             bls = ["{0:>5} {1:>5} {2:>5} {3:>2}".format(bid,

package/MDAnalysis/coordinates/ParmEd.py

@@ -272,7 +272,7 @@ def convert(self, obj):
 
         # bonds
         try:
-            params = ag_or_ts.bonds
+            params = ag_or_ts.intra_bonds
         except AttributeError:
             pass
         else:

package/MDAnalysis/core/selection.py

@@ -525,15 +525,14 @@ def __init__(self, parser, tokens):
     def apply(self, group):
         grp = self.sel.apply(group)
         # Check if we have bonds
-        bonds = group.get_connections("bonds", outside=True)
-        if not bonds:
+        if not group.bonds:
             warnings.warn("Bonded selection has 0 bonds")
             return group[[]]
 
         grpidx = grp.indices
 
         # (n, 2) array of bond indices
-        bix = np.array(bonds.to_indices())
+        bix = np.array(group.bonds.to_indices())
 
         idx = []
         # left side

package/MDAnalysis/core/topologyattrs.py

@@ -32,17 +32,19 @@
 These are usually read by the TopologyParser.
 """
 
-import Bio.Seq
-import Bio.SeqRecord
 from collections import defaultdict
 import copy
 import functools
 import itertools
 import numbers
-import numpy as np
+from inspect import signature as inspect_signature
 import warnings
 import textwrap
-from inspect import signature as inspect_signature
+from types import MethodType
+
+import Bio.Seq
+import Bio.SeqRecord
+import numpy as np
 
 from ..lib.util import (cached, convert_aa_code, iterable, warn_if_not_unique,
                         unique_int_1d)
@@ -263,6 +265,11 @@ def _attach_transplant_stubs(attribute_name, topology_attribute_class):
                 setattr(dest_class, method_name, stub)
 
 
+def intra_connection(self, ag):
+    """Get connections only within this AtomGroup
+    """
+    return ag.get_connections(self.attrname, outside=False)
+
 class _TopologyAttrMeta(type):
     r"""Register TopologyAttrs on class creation
 
@@ -291,6 +298,12 @@ def __init__(cls, name, bases, classdict):
         if attrname is None:
             attrname = singular
 
+        # add intra connections
+        if any("Connection" in x.__name__ for x in cls.__bases__):
+            method = MethodType(intra_connection, cls)
+            prop = property(method, None, None, method.__doc__)
+            cls.transplants[AtomGroup].append((f"intra_{attrname}", prop))
+
         if singular:
             _TOPOLOGY_ATTRS[singular] = _TOPOLOGY_ATTRS[attrname] = cls
             _singular = singular.lower().replace('_', '')
@@ -2310,7 +2323,6 @@ def get_atoms(self, ag):
         except TypeError:
             # maybe we got passed an Atom
             unique_bonds = self._bondDict[ag.ix]
-            outside = True
         unique_bonds = np.array(sorted(unique_bonds), dtype=object)
         bond_idx, types, guessed, order = np.hsplit(unique_bonds, 4)
         bond_idx = np.array(bond_idx.ravel().tolist(), dtype=np.int32)

testsuite/MDAnalysisTests/core/test_groups.py

@@ -1585,3 +1585,25 @@ def test_get_empty_group(self, tpr, outside):
         cxns = ag.get_connections("impropers", outside=outside)
         assert len(imp) == 0
         assert len(cxns) == 0
+
+@pytest.mark.parametrize("typename, n_inside", [
+    ("intra_bonds", 9),
+    ("intra_angles", 15),
+    ("intra_dihedrals", 12),
+])
+def test_topologygroup_gets_connections_inside(tpr, typename, n_inside):
+    ag = tpr.atoms[:10]
+    cxns = getattr(ag, typename)
+    assert len(cxns) == n_inside
+    indices = np.ravel(cxns.to_indices())
+    assert np.all(np.in1d(indices, ag.indices))
+
+@pytest.mark.parametrize("typename, n_outside", [
+    ("bonds", 13),
+    ("angles", 27),
+    ("dihedrals", 38),
+])
+def test_topologygroup_gets_connections_outside(tpr, typename, n_outside):
+    ag = tpr.atoms[:10]
+    cxns = getattr(ag, typename)
+    assert len(cxns) == n_outside

testsuite/MDAnalysisTests/core/test_topologyobjects.py

@@ -278,8 +278,7 @@ def test_td_universe(self, b_td, PSFDCD):
     def test_bonds_types(self, PSFDCD, res1):
         """Tests TopologyDict for bonds"""
         assert len(PSFDCD.atoms.bonds.types()) == 57
-        assert len(res1.atoms.get_connections("bonds").types()) == 12
-        assert len(res1.atoms.bonds.types()) == 11
+        assert len(res1.atoms.bonds.types()) == 12
 
     def test_bonds_contains(self, b_td):
         assert ('57', '2') in b_td
@@ -426,8 +425,8 @@ def test_TG_loose_intersection(self, PSFDCD, attr):
         """Pull bonds from a TG which are at least partially in an AG"""
         ag = PSFDCD.atoms[10:60]
 
-        TG = PSFDCD.atoms.get_connections(attr, outside=True)
-        ref = ag.get_connections(attr, outside=True)
+        TG = getattr(PSFDCD.atoms, attr)
+        ref = getattr(ag, attr)
         newTG = TG.atomgroup_intersection(ag)
 
         assert newTG == ref
@@ -613,22 +612,22 @@ class TestTopologyGroup_Cython(object):
     @staticmethod
     @pytest.fixture
     def bgroup(PSFDCD):
-        return PSFDCD.atoms[:5].get_connections("bonds", outside=True)
+        return PSFDCD.atoms[:5].bonds
 
     @staticmethod
     @pytest.fixture
     def agroup(PSFDCD):
-        return PSFDCD.atoms[:5].get_connections("angles", outside=True)
+        return PSFDCD.atoms[:5].angles
 
     @staticmethod
     @pytest.fixture
     def dgroup(PSFDCD):
-        return PSFDCD.atoms[:5].get_connections("dihedrals", outside=True)
+        return PSFDCD.atoms[:5].dihedrals
 
     @staticmethod
     @pytest.fixture
     def igroup(PSFDCD):
-        return PSFDCD.atoms[:5].get_connections("impropers", outside=True)
+        return PSFDCD.atoms[:5].impropers
 
     # bonds
     def test_wrong_type_bonds(self, agroup, dgroup, igroup):

testsuite/MDAnalysisTests/topology/test_itp.py

@@ -87,8 +87,8 @@ class TestITP(BaseITP):
 
 
     def test_bonds_atom_counts(self, universe):
-        assert len(universe.atoms[0].bonds) == 3
-        assert len(universe.atoms[42].bonds) == 1
+        assert len(universe.atoms[[0]].bonds) == 3
+        assert len(universe.atoms[[42]].bonds) == 1
 
     def test_bonds_values(self, top):
         vals = top.bonds.values
@@ -99,8 +99,8 @@ def test_bonds_type(self, universe):
         assert universe.bonds[0].type == 2
 
     def test_angles_atom_counts(self, universe):
-        assert len(universe.atoms[0].angles) == 5
-        assert len(universe.atoms[42].angles) == 2
+        assert len(universe.atoms[[0]].angles) == 5
+        assert len(universe.atoms[[42]].angles) == 2
 
     def test_angles_values(self, top):
         vals = top.angles.values
@@ -111,7 +111,7 @@ def test_angles_type(self, universe):
         assert universe.angles[0].type == 2
 
     def test_dihedrals_atom_counts(self, universe):
-        assert len(universe.atoms[0].dihedrals) == 2
+        assert len(universe.atoms[[0]].dihedrals) == 2
 
     def test_dihedrals_multiple_types(self, universe):
         ag = universe.atoms[[0, 3, 5, 7]]
@@ -128,7 +128,7 @@ def test_dihedrals_type(self, universe):
 
 
     def test_impropers_atom_counts(self, universe):
-        assert len(universe.atoms[0].impropers) == 1
+        assert len(universe.atoms[[0]].impropers) == 1
 
     def test_impropers_values(self, top):
         vals = top.impropers.values
@@ -174,11 +174,11 @@ def test_no_extra_angles(self, top):
             assert a not in top.angles.values
 
     def test_bonds_atom_counts(self, universe):
-        assert len(universe.atoms[0].bonds) == 5
-        assert len(universe.atoms[42].bonds) == 5
+        assert len(universe.atoms[[0]].bonds) == 5
+        assert len(universe.atoms[[42]].bonds) == 5
 
     def test_dihedrals_atom_counts(self, universe):
-        assert len(universe.atoms[0].dihedrals) == 1
+        assert len(universe.atoms[[0]].dihedrals) == 1
 
     def test_dihedrals_identity(self, universe):
         assert universe.dihedrals[0].type == (1, 1)

testsuite/MDAnalysisTests/topology/test_parmed.py

@@ -124,8 +124,8 @@ class TestParmedParserPSF(BaseTestParmedParser):
     expected_elems = (np.array(['' for i in range(3341)], dtype=object),)
 
     def test_bonds_atom_counts(self, universe):
-        assert len(universe.atoms[0].bonds) == 4
-        assert len(universe.atoms[42].bonds) == 1
+        assert len(universe.atoms[[0]].bonds) == 4
+        assert len(universe.atoms[[42]].bonds) == 1
 
     @pytest.mark.parametrize('value', (
         (0, 1),
@@ -145,8 +145,8 @@ def test_bond_types(self, universe):
         assert b1.type.type is None
 
     def test_angles_atom_counts(self, universe):
-        assert len(universe.atoms[0].angles), 9
-        assert len(universe.atoms[42].angles), 2
+        assert len(universe.atoms[[0]].angles), 9
+        assert len(universe.atoms[[42]].angles), 2
 
     @pytest.mark.parametrize('value', (
         (1, 0, 2),
@@ -158,7 +158,7 @@ def test_angles_identity(self, top, value):
         assert value in vals or value[::-1] in vals
 
     def test_dihedrals_atom_counts(self, universe):
-        assert len(universe.atoms[0].dihedrals) == 14
+        assert len(universe.atoms[[0]].dihedrals) == 14
 
     @pytest.mark.parametrize('value', (
         (0, 4, 6, 7),
@@ -195,8 +195,8 @@ class TestParmedParserPRM(BaseTestParmedParser):
                                dtype=object))
 
     def test_bonds_atom_counts(self, universe):
-        assert len(universe.atoms[0].bonds) == 4
-        assert len(universe.atoms[42].bonds) == 1
+        assert len(universe.atoms[[0]].bonds) == 4
+        assert len(universe.atoms[[42]].bonds) == 1
 
     @pytest.mark.parametrize('value', (
         (10, 11),
@@ -217,8 +217,8 @@ def test_bond_types(self, universe):
         assert b1.type.type.req == 1.010
 
     def test_angles_atom_counts(self, universe):
-        assert len(universe.atoms[0].angles), 9
-        assert len(universe.atoms[42].angles), 2
+        assert len(universe.atoms[[0]].angles), 9
+        assert len(universe.atoms[[42]].angles), 2
 
     @pytest.mark.parametrize('value', (
         (11, 10, 12),
@@ -231,7 +231,7 @@ def test_angles_identity(self, top, value):
         assert value in vals or value[::-1] in vals
 
     def test_dihedrals_atom_counts(self, universe):
-        assert len(universe.atoms[0].dihedrals) == 14
+        assert len(universe.atoms[[0]].dihedrals) == 14
 
     @pytest.mark.parametrize('value', (
         (11, 10, 12, 14),

testsuite/MDAnalysisTests/topology/test_psf.py

@@ -72,8 +72,8 @@ def test_bonds_total_counts(self, top):
 
     def test_bonds_atom_counts(self, filename):
         u = mda.Universe(filename)
-        assert len(u.atoms[0].bonds) == 4
-        assert len(u.atoms[42].bonds) == 1
+        assert len(u.atoms[[0]].bonds) == 4
+        assert len(u.atoms[[42]].bonds) == 1
 
     def test_bonds_identity(self, top):
         vals = top.bonds.values
@@ -85,8 +85,8 @@ def test_angles_total_counts(self, top):
 
     def test_angles_atom_counts(self, filename):
         u = mda.Universe(filename)
-        assert len(u.atoms[0].angles), 9
-        assert len(u.atoms[42].angles), 2
+        assert len(u.atoms[[0]].angles), 9
+        assert len(u.atoms[[42]].angles), 2
 
     def test_angles_identity(self, top):
         vals = top.angles.values
@@ -98,7 +98,7 @@ def test_dihedrals_total_counts(self, top):
 
     def test_dihedrals_atom_counts(self, filename):
         u = mda.Universe(filename)
-        assert len(u.atoms[0].dihedrals) == 14
+        assert len(u.atoms[[0]].dihedrals) == 14
 
     def test_dihedrals_identity(self, top):
         vals = top.dihedrals.values