fixed missing aindex selection property

modules/mol/base/src/impl/atom_impl.cc

@@ -316,6 +316,10 @@ void AtomImpl::DeleteConnector(const ConnectorImplP& conn,
 
 int AtomImpl::GetIntProperty(Prop::ID prop_id) const
 {
+  switch (prop_id) {
+  case Prop::AINDEX:
+    return index_;
+  }
   throw PropertyError(prop_id);
 }
 

modules/mol/base/src/impl/query_impl.cc

@@ -650,12 +650,12 @@ Node* QueryImpl::ParsePropValueExpr(QueryLexer& lexer) {
     LogicOP lop=inversion_stack_.back() ? LOP_OR : LOP_AND;
     CompOP cop=inversion_stack_.back() ? COP_NEQ : COP_EQ;
     ParamType cname_val(StringOrRegexParam(query_string_.substr(cname.GetValueRange().Loc,
-								cname.GetValueRange().Length).c_str()));
+                                                                cname.GetValueRange().Length).c_str()));
     Prop cname_prop(Prop::CNAME, Prop::STRING, Prop::CHAIN);
     SelNode* cname_node=new SelNode(cname_prop, cop, cname_val);
     ParamType aname_val(StringOrRegexParam(query_string_.substr(aname.GetValueRange().Loc,
-								aname.GetValueRange().Length).c_str()));
-   Prop aname_prop(Prop::ANAME, Prop::STRING, Prop::ATOM);
+                                                                aname.GetValueRange().Length).c_str()));
+    Prop aname_prop(Prop::ANAME, Prop::STRING, Prop::ATOM);
     SelNode* aname_node=new SelNode(aname_prop, cop, aname_val);
     ParamType rnum_val(atoi(query_string_.substr(rnum.GetValueRange().Loc,
                             rnum.GetValueRange().Length).c_str()));

modules/mol/base/src/property_id.cc

@@ -39,6 +39,7 @@ struct Properties : public boost::spirit::symbols<Prop> {
       ("rtype", Prop(Prop::RTYPE, Prop::STRING, Prop::RESIDUE))        
       ("ele", Prop(Prop::ELE, Prop::STRING, Prop::ATOM))
       ("anum", Prop(Prop::ANUM, Prop::INT, Prop::ATOM))
+      ("aindex", Prop(Prop::AINDEX, Prop::INT, Prop::ATOM))
       ("x",Prop(Prop::AX, Prop::FLOAT, Prop::ATOM))
       ("y",Prop(Prop::AY, Prop::FLOAT, Prop::ATOM))
       ("z",Prop(Prop::AZ, Prop::FLOAT, Prop::ATOM))

modules/mol/base/src/property_id.hh

@@ -39,7 +39,7 @@ public:
   /// the GenericProp 'propname' at the atom, residue and chain level
   /// respectively.
   typedef enum {
-    RNAME, ANAME, CNAME, ELE, RNUM, ANUM, AX, AY, AZ, OCC, RTYPE, ISHETATM,
+    RNAME, ANAME, CNAME, ELE, RNUM, ANUM, AX, AY, AZ, OCC, AINDEX, RTYPE, ISHETATM,
     RBFAC, ABFAC, PEPTIDE, ACHARGE, RINDEX, PROTEIN, LIGAND, WATER, WITHIN, 
     UNDEF, CUSTOM
   } ID;

modules/mol/base/src/query_state.cc

@@ -323,6 +323,10 @@ boost::logic::tribool QueryState::EvalAtom(const AtomImplPtr& a) {
         s_[*i] = cmp_string(ss.comp_op,str_value,
 			    boost::get<StringOrRegexParam>(ss.param));                  
         break;
+      case Prop::AINDEX:
+        int_value=(a->GetIndex());
+        s_[*i]=cmp_num<int>(ss.comp_op, int_value,boost::get<int>(ss.param));
+        break;
       case Prop::AX:
         float_value=(a->GetPos())[0];
         s_[*i]=cmp_num<Real>(ss.comp_op, float_value, 

modules/mol/base/tests/test_query.cc

@@ -116,6 +116,7 @@ BOOST_AUTO_TEST_CASE(test_query_parse_properties)
   BOOST_CHECK(Query("x=3").IsValid());
   BOOST_CHECK(Query("y=4").IsValid());
   BOOST_CHECK(Query("z=6").IsValid());
+  BOOST_CHECK(Query("aindex=1").IsValid());
   BOOST_CHECK(Query("gatest=7").IsValid());
   BOOST_CHECK(Query("grtest=8").IsValid());
   BOOST_CHECK(Query("gctest=9").IsValid());
@@ -151,6 +152,10 @@ BOOST_AUTO_TEST_CASE(test_query_parse_value_type)
   BOOST_CHECK(Query("rnum=WTF").IsValid()==false);
   BOOST_CHECK(Query("rnum=3.0").IsValid()==false);
   BOOST_CHECK(Query("ele>=XXX").IsValid()==false);
+
+  BOOST_CHECK(Query("aindex=1,2").IsValid());
+  BOOST_CHECK(Query("aindex=1:10,12:20").IsValid());
+  BOOST_CHECK(Query("aindex>7").IsValid());
 }
 
 BOOST_AUTO_TEST_CASE(test_query_parse_logical_op) 
@@ -198,6 +203,7 @@ BOOST_AUTO_TEST_CASE(test_query_eval)
   ensure_counts(e, "cname=A", 1, 3, 27);
   ensure_counts(e, "aname=CA", 1, 3, 3);
   ensure_counts(e, "aname=SD", 1, 1, 1);
+  ensure_counts(e, "aindex=1,3,99", 1, 1, 2);
   ensure_counts(e, "rnum=1:2", 1, 2, 19);
   ensure_counts(e, "rnum=1,2", 1, 2, 19);
   ensure_counts(e, "rnum>3", 0, 0, 0);