added cname.rnum.aname shortcut to query language

The shortcut doesn't work when

 - cname is an empty string, numeric or any special character not
   allow in identifiers
 - the aname starts with a number. This is due to the fact, that the
   "." is both used as a decimal point in floating point numbers and
   as a separator between chain, residue number and atom name. When
   parsing a numerical token, we have deal with trailing "."
   appropriately and stop parsing when the next character is not
   numeric. However, when the character following the "." is numeric,
   we also treat it as part of the numeric value.

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

@@ -107,19 +107,24 @@ QueryToken QueryLexer::LexQuotedStringLiteral()
 QueryToken QueryLexer::LexNumericToken() {
   Range range(current_, 0);
   static String allowed_chars("_");  
-  bool dot_present=false, is_string=false;
+  bool dot_present=false, is_string=false, last_was_dot=false;
   //TODO Better checking for duplicate -
   while(current_<query_string_.size()){
     if (isdigit(query_string_[current_]) || query_string_[current_]=='-') {
       current_++;
+      last_was_dot=false;
     } else if (query_string_[current_]=='.') {
       if (dot_present) {
         is_string=true;
         break;
       }
       dot_present = true;
+      last_was_dot=true;
       current_++;
     } else {
+      if (last_was_dot) {
+        break;
+      }
       is_string=isalnum(query_string_[current_]) || 
                 allowed_chars.find_first_of(query_string_[current_])!=String::npos;
       break;
@@ -128,6 +133,11 @@ QueryToken QueryLexer::LexNumericToken() {
   range.Length=current_-range.Loc;
   if (!is_string) {
     if (dot_present) {
+      if (last_was_dot) {
+        current_--;
+        return QueryToken(Range(range.Loc, range.Length-1), 
+                          tok::IntegralValue);
+      }
       return QueryToken(range, tok::FloatingValue);      
     } else {
       return QueryToken(range, tok::IntegralValue);      
@@ -173,7 +183,10 @@ QueryToken QueryLexer::LexToken() {
         return QueryToken(Range(current_-1, 1), tok::Coma);
       case ':':
         current_++;
-        return QueryToken(Range(current_-1, 1), tok::Colon);        
+        return QueryToken(Range(current_-1, 1), tok::Colon);
+      case '.':
+        current_++;
+        return QueryToken(Range(current_-1, 1), tok::Dot);           
       case '{':
         current_++;
         return QueryToken(Range(current_-1, 1), tok::LeftCurlyBrace);
@@ -605,6 +618,44 @@ Node* QueryImpl::ParsePropValueExpr(QueryLexer& lexer) {
   String s=query_string_.substr(sname.GetRange().Loc,sname.GetRange().Length);
   Prop property=PropertyFromString(s);
   QueryToken op=lexer.NextToken();
+  
+  // this block deals with the cname.rnum.aname shortcut.
+  if (op.GetType()==tok::Dot) {
+    QueryToken cname=sname;
+    QueryToken rnum=lexer.NextToken();
+    if (!this->Expect(tok::IntegralValue, "residue number", rnum)) {
+      return NULL;
+    }
+    if (!this->Expect(tok::Dot, "'.'", lexer.NextToken())) {
+      return NULL;
+    }
+    QueryToken aname=lexer.NextToken();
+    if (!this->Expect(tok::Identifier, "atom name", aname)) {
+      return NULL;
+    }
+    LogicOP lop=inversion_stack_.back() ? LOP_OR : LOP_AND;
+    CompOP cop=inversion_stack_.back() ? COP_NEQ : COP_EQ;
+    ParamType cname_val(query_string_.substr(cname.GetValueRange().Loc,
+                        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(query_string_.substr(aname.GetValueRange().Loc,
+                        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()));
+    Prop rnum_prop(Prop::RNUM, Prop::INT, Prop::RESIDUE);                            
+    SelNode* rnum_node=new SelNode(rnum_prop, cop, rnum_val);
+    LogicOPNode* and_one=new LogicOPNode(lop);
+    LogicOPNode* and_two=new LogicOPNode(lop);  
+    and_one->SetLHS(and_two);
+    and_one->SetRHS(cname_node);
+    and_two->SetLHS(rnum_node);
+    and_two->SetRHS(aname_node);
+    lexer.NextToken();
+    return and_one;
+  }
   if (property.id>=Prop::CUSTOM) {
     property.id=(Prop::ID)(Prop::CUSTOM+num_gen_prop_++);
     EntityPropertyMapper epm=EntityPropertyMapper(s.substr(2), property.level);

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

@@ -45,7 +45,8 @@ namespace tok {
     IntegralValue,
     FloatingValue,
     Colon,
-    Coma, 
+    Coma,
+    Dot, 
     And,
     Or, 
     Not,