Add function to filter structure by stereochemistry issues: StereoCheck

Same logic as published for the lDDT paper but it also includes
nucleotides. If backbone atom is involved, full residue gets deleted,
only the sidechain otherwise. In case of nucleotides, the base is the
sidechain. Everything else is considered backbone.

modules/mol/alg/pymod/stereochemistry.py

@@ -259,7 +259,7 @@ def GetClashes(ent, vdw_radii = None, tolerance = 1.5, disulfid_dist = 2.03,
     :param disulfid_tolerance: The respective tolerance
     :type disulfid_dist: :class:`float`
     :returns: A :class:`list` of pairs. Each pair consists of two
-              :class:`ost.mol.AtomView` from *ent* that are clashing.
+              :class:`ost.mol.AtomHandle` from *ent* that are clashing.
     """
 
     if vdw_radii is None:
@@ -304,7 +304,7 @@ def GetClashes(ent, vdw_radii = None, tolerance = 1.5, disulfid_dist = 2.03,
                     hash_pair = (min(a_hash, ca_hash), max(a_hash, ca_hash))
                     if hash_pair not in done:
                         done.add(hash_pair)
-                        return_list.append((a, ca))
+                        return_list.append((a.handle, ca.handle))
     return return_list
 
 
@@ -360,3 +360,80 @@ def GetBadAngles(ent, stereo_data = None, tolerance=12):
             if diff > tolerance*std:
                 return_list.append(a)
     return return_list
+
+def StereoCheck(ent, stereo_data = None):
+    """ Remove atoms with stereochemical problems
+
+    Selects for peptide/nucleotides and calls :func:`GetClashes`,
+    :func:`GetBadBonds` and :func:`GetBadAngles` with default
+    parameters.
+
+    * Amino acids: Remove full residue if backbone atom is involved in
+      stereochemistry issue ("N", "CA", "C", "O"). Remove sidechain if any of
+      the sidechain atoms is involved in stereochemistry issues.
+    * Nucleotides: Remove full residue if backbone atom is involved in
+      stereochemistry issue ("P", "OP1", "OP2", "OP3", "O5'", "C5'", "C4'",
+      "C3'", "C2'", "C1'", "O4'", "O3'", "O2'"). Remove sidechain (base) if any
+      of the sidechain atoms is involved in stereochemistry issues.
+
+    :param ent: Entity to be stereochecked
+    :type ent: :class:`ost.mol.EntityHandle`/:class:`ost.mol.EntityView`
+    :param stereo_data: Stereochemistry data
+    :type stereo_data: :class:`dict`
+    :returns: Tuple with four elements: 1) :class:`ost.mol.EntityView` of
+              *ent* processed as described above 2) Return value of
+              :func:`GetClashes` 3) return value of :func:`GetBadBonds`
+              4) return value of :func:`GetBadAngles`
+    """
+    sel = ent.Select("peptide=true or nucleotide=true")
+    clashes = GetClashes(sel)
+    bad_bonds = GetBadBonds(sel, stereo_data = stereo_data)
+    bad_angles = GetBadAngles(sel, stereo_data = stereo_data)
+
+    # set stereo problems as properties on an atom level
+    for clash in clashes:
+        clash[0].SetIntProp("stereo_problem", 1)
+        clash[1].SetIntProp("stereo_problem", 1)
+
+    for bond in bad_bonds:
+        bond[0].SetIntProp("stereo_problem", 1)
+        bond[1].SetIntProp("stereo_problem", 1)
+
+    for angle in bad_angles:
+        angle[0].SetIntProp("stereo_problem", 1)
+        angle[1].SetIntProp("stereo_problem", 1)
+        angle[2].SetIntProp("stereo_problem", 1)
+
+    # set stereo problems as properties on a residue level
+    bad_ent = ent.Select("gastereo_problem:0=1")
+    if len(bad_ent.residues) > 0:
+        pep_bb = set(["N", "CA", "C", "O"])
+        nuc_bb = set(["P", "OP1", "OP2", "OP3", "O5'", "C5'", "C4'", "C3'",
+                      "C2'", "C1'", "O4'", "O3'", "O2'"])
+
+        for r in bad_ent.residues:
+            bad_atoms = set([a.GetName() for a in r.atoms])
+            r.SetIntProp("stereo_problem", 1)
+            if r.GetChemType() == mol.ChemType.NUCLEOTIDES:
+                if len(nuc_bb.intersection(bad_atoms)) > 0:
+                    r.SetIntProp("stereo_problem_bb", 1)
+            elif r.GetChemType() == mol.ChemType.AMINOACIDS:
+                if len(pep_bb.intersection(bad_atoms)) > 0:
+                    r.SetIntProp("stereo_problem_bb", 1)
+
+        # explicitely add " as OpenStructure query language would not
+        # understand ' otherwise
+        nuc_bb = [f"\"{name}\"" for name in nuc_bb]
+
+        pep_query = f"(peptide=true and grstereo_problem:0=0) or "
+        pep_query += f"(peptide=true and grstereo_problem_bb:0=0 and "
+        pep_query += f"aname={','.join(pep_bb)})"
+        nuc_query = f"(nucleotide=true and grstereo_problem:0=0) or "
+        nuc_query += f"(nucleotide=true and grstereo_problem_bb:0=0 and "
+        nuc_query += f"aname={','.join(nuc_bb)})"
+        query = pep_query + " or " + nuc_query
+        return_view = sel.Select(query)
+    else:
+        return_view = sel
+
+    return return_view, clashes, bad_bonds, bad_angles