add ignore_same_residue kwarg to InterRDF

package/CHANGELOG

@@ -13,13 +13,14 @@ The rules for this file:
   * release numbers follow "Semantic Versioning" http://semver.org
 
 ------------------------------------------------------------------------------
-??/??/?? IAlibay
+??/??/?? IAlibay, orionarcher
 
  * 2.6.0
 
 Fixes
 
 Enhancements
+  * Added a ignore_same_residue kwarg to InterRDF (PR #4161)
 
 Changes
 

package/MDAnalysis/analysis/rdf.py

@@ -125,6 +125,8 @@ class InterRDF(AnalysisBase):
 
     exclusion_block : tuple
         A tuple representing the tile to exclude from the distance array.
+    ignore_same_residue : bool
+        If `True`, ignore distances between atoms in the same residue.
     verbose : bool
         Show detailed progress of the calculation if set to `True`
 
@@ -220,6 +222,7 @@ def __init__(self,
                  range=(0.0, 15.0),
                  norm="rdf",
                  exclusion_block=None,
+                 ignore_same_residue=False,
                  **kwargs):
         super(InterRDF, self).__init__(g1.universe.trajectory, **kwargs)
         self.g1 = g1
@@ -229,6 +232,7 @@ def __init__(self,
         self.rdf_settings = {'bins': nbins,
                              'range': range}
         self._exclusion_block = exclusion_block
+        self.ignore_same_residue = ignore_same_residue
 
         if self.norm not in ['rdf', 'density', 'none']:
             raise ValueError(f"'{self.norm}' is an invalid norm. "
@@ -261,6 +265,13 @@ def _single_frame(self):
             mask = np.where(idxA != idxB)[0]
             dist = dist[mask]
 
+        if self.ignore_same_residue:
+            # Ignore distances between atoms in the same residue
+            resixA = self.g1.resindices[pairs[:, 0]]
+            resixB = self.g2.resindices[pairs[:, 1]]
+            mask = np.where(resixA != resixB)[0]
+            dist = dist[mask]
+
         count, _ = np.histogram(dist, **self.rdf_settings)
         self.results.count += count
 

testsuite/MDAnalysisTests/analysis/test_rdf.py

@@ -93,6 +93,12 @@ def test_exclusion(sels):
     rdf = InterRDF(s1, s2, exclusion_block=(1, 2)).run()
     assert rdf.results.count.sum() == 4
 
+def test_ignore_same_residues(sels):
+    # should see two distances with 4 counts each
+    s1, s2 = sels
+    rdf = InterRDF(s2, s2, ignore_same_residue=True).run()
+    assert rdf.rdf[0] == 0
+    assert rdf.results.count.sum() == 8
 
 @pytest.mark.parametrize("attr", ("rdf", "bins", "edges", "count"))
 def test_rdf_attr_warning(sels, attr):