read _chem_comp_atom.alt_atom_id into ChemComp::Atom::old_id

in prepare_topology(), if old (alt) atom names are used,
print more informative warning message

Author: wojdyr

include/gemmi/chemcomp.hpp

@@ -341,6 +341,7 @@ struct ChemComp {
 
   struct Atom {
     std::string id;
+    std::string old_id;  // read from _chem_comp_atom.alt_atom_id
     Element el;
     // _chem_comp_atom.partial_charge can be non-integer,
     // _chem_comp_atom.charge is always integer (but sometimes has format
@@ -435,6 +436,14 @@ struct ChemComp {
     return find_atom(atom_id) != atoms.end();
   }
 
+  std::vector<Atom>::iterator find_atom_by_old_name(const std::string& old_id) {
+    return std::find_if(atoms.begin(), atoms.end(),
+                        [&](const Atom& a) { return a.old_id == old_id; });
+  }
+  std::vector<Atom>::const_iterator find_atom_by_old_name(const std::string& old_id) const {
+    return const_cast<ChemComp*>(this)->find_atom_by_old_name(old_id);
+  }
+
   int get_atom_index(const std::string& atom_id) const {
     auto it = find_atom(atom_id);
     if (it == atoms.end())
@@ -580,8 +589,10 @@ inline ChemComp make_chemcomp_from_block(const cif::Block& block_) {
     cc.type_or_group = type_col.str(0);
   for (auto row : block.find("_chem_comp_atom.",
                              {"atom_id", "type_symbol", "?type_energy",
-                             "?charge", "?partial_charge"}))
-    cc.atoms.push_back({row.str(0), Element(row.str(1)),
+                             "?charge", "?partial_charge", "?alt_atom_id"}))
+    cc.atoms.push_back({row.str(0),
+                        row.has(5) ? row.str(5) : "",
+                        Element(row.str(1)),
                         (float) cif::as_number(row.one_of(3, 4), 0.0),
                         row.has(2) ? row.str(2) : "",
                         Position()});

src/monlib.cpp

@@ -256,7 +256,7 @@ void ChemMod::apply_to(ChemComp& chemcomp, ChemComp::Group alias_group) const {
       if (mod.new_id.empty())
         fail("New atom id is not given");
       if (!chemcomp.has_atom(real(mod.new_id)))
-        chemcomp.atoms.push_back({mod.new_id, mod.el,
+        chemcomp.atoms.push_back({mod.new_id, "", mod.el,
                                   std::isnan(mod.charge) ? mod.charge : 0,
                                   mod.chem_type, Position()});
       continue;

src/topo.cpp

@@ -26,7 +26,7 @@ std::unique_ptr<ChemComp> make_chemcomp_with_restraints(const Residue& res) {
     if (el == El::D)
       el = El::H;
     const std::string& chem_type = el.uname();
-    cc->atoms.push_back(ChemComp::Atom{a.name, el, float(a.charge), chem_type, a.pos});
+    cc->atoms.push_back(ChemComp::Atom{a.name, "", el, float(a.charge), chem_type, a.pos});
   }
   // prepare pairs of atoms
   struct Pair {
@@ -929,8 +929,13 @@ prepare_topology(Structure& st, MonLib& monlib, size_t model_index,
         if (!cc.has_atom(atom.name)) {
           std::string msg = "definition not found for "
                           + atom_str(chain_info.chain_ref, *ri.res, atom);
-          if (ri.orig_chemcomp && ri.orig_chemcomp->has_atom(atom.name))
+          if (ri.orig_chemcomp && ri.orig_chemcomp->has_atom(atom.name)) {
             msg += " (linkage should remove this atom)";
+          } else {
+            auto it = cc.find_atom_by_old_name(atom.name);
+            if (it != cc.atoms.end())
+              cat_to(msg, " (replace ", atom.name, " with ", it->id, ')');
+          }
           topo->err(msg);
         }
       }