add_entity_types(overwrite=True) now ignores old entity_type's

project-gemmi · Nov 16, 2023 · b9fc29c · b9fc29c
1 parent 195343c
commit b9fc29c
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Showing 2 changed files with 6 additions and 4 deletions.
diff --git a/include/gemmi/polyheur.hpp b/include/gemmi/polyheur.hpp
@@ -16,7 +16,8 @@ namespace gemmi {
 // A simplistic classification. It may change in the future.
 // It returns PolymerType which corresponds to _entity_poly.type,
 // but here we use only PeptideL, Rna, Dna, DnaRnaHybrid and Unknown.
-GEMMI_DLL PolymerType check_polymer_type(const ConstResidueSpan& span);
+GEMMI_DLL PolymerType check_polymer_type(const ConstResidueSpan& span,
+                                         bool ignore_entity_type=false);
 
 inline PolymerType get_or_check_polymer_type(const Entity* ent,
                                              const ConstResidueSpan& polymer) {

diff --git a/src/polyheur.cpp b/src/polyheur.cpp
@@ -4,7 +4,7 @@
 
 namespace gemmi {
 
-PolymerType check_polymer_type(const ConstResidueSpan& span) {
+PolymerType check_polymer_type(const ConstResidueSpan& span, bool ignore_entity_type) {
   if (span.empty())
     return PolymerType::Unknown;
   size_t counts[(int)ResidueKind::ELS+1] = {0};
@@ -13,7 +13,8 @@ PolymerType check_polymer_type(const ConstResidueSpan& span) {
   size_t total = 0;
   bool has_atom_record = false;
   for (const Residue& r : span)
-    if (r.entity_type == EntityType::Unknown ||
+    if (ignore_entity_type ||
+        r.entity_type == EntityType::Unknown ||
         r.entity_type == EntityType::Polymer) {
       if (r.het_flag == 'A')
         has_atom_record = true;
@@ -115,7 +116,7 @@ void add_entity_types(Chain& chain, bool overwrite) {
       std::all_of(chain.residues.begin(), chain.residues.end(),
                   [](const Residue& r) { return r.entity_type != EntityType::Unknown; }))
     return;
-  PolymerType ptype = check_polymer_type(chain.whole());
+  PolymerType ptype = check_polymer_type(chain.whole(), /*ignore_entity_type=*/overwrite);
   auto it = chain.residues.begin();
   if (ptype != PolymerType::Unknown) {
     auto polymer_end = infer_polymer_end(chain, ptype);