trim_to_alanine(): update het_flag if needed

and also move the definition from header to cpp

include/gemmi/polyheur.hpp

@@ -180,21 +180,7 @@ template<> inline void remove_ligands_and_waters(Chain& ch) {
 }
 
 // Trim to alanine. Returns true if trimmed, false if it's (likely) not AA.
-inline bool trim_to_alanine(Residue& res) {
-  static const std::pair<std::string, El> ala_atoms[6] = {
-    {"N", El::N}, {"CA", El::C}, {"C", El::C}, {"O", El::O}, {"CB", El::C},
-    {"OXT", El::O}
-  };
-  if (res.get_ca() == nullptr)
-    return false;
-  vector_remove_if(res.atoms, [](const Atom& a) {
-      for (const auto& name_el : ala_atoms)
-        if (a.name == name_el.first && a.element == name_el.second)
-          return false;
-      return true;
-  });
-  return true;
-}
+GEMMI_DLL bool trim_to_alanine(Residue& res);
 
 inline void trim_to_alanine(Chain& chain) {
   for (Residue& res : chain.residues)

src/polyheur.cpp

@@ -309,6 +309,25 @@ char recommended_het_flag(const Residue& res) {
     return 'H';
 }
 
+bool trim_to_alanine(Residue& res) {
+  static const std::pair<std::string, El> ala_atoms[6] = {
+    {"N", El::N}, {"CA", El::C}, {"C", El::C}, {"O", El::O}, {"CB", El::C},
+    {"OXT", El::O}
+  };
+  if (res.get_ca() == nullptr)
+    return false;
+  vector_remove_if(res.atoms, [](const Atom& a) {
+      for (const auto& name_el : ala_atoms)
+        if (a.name == name_el.first && a.element == name_el.second)
+          return false;
+      return true;
+  });
+  // if non-standard polymer residue was mutated, update het_flag
+  if (res.entity_type == EntityType::Polymer && res.het_flag == 'H')
+    res.het_flag = 'A';
+  return true;
+}
+
 void change_ccd_code(Structure& st, const std::string& old, const std::string& new_) {
   auto process = [&](ResidueId& rid) {
     if (rid.name == old)