Updating files that didn't merge correctly, so that they are identical

to the versions in devel
OpenBioSim · Oct 10, 2023 · b20865a · b20865a
1 parent 421a665
commit b20865a
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Showing 16 changed files with 775 additions and 8 deletions.
diff --git a/corelib/src/libs/SireSearch/ast.h b/corelib/src/libs/SireSearch/ast.h
@@ -190,6 +190,7 @@ namespace AST
     struct IDWith;
     struct IDWhere;
     struct IDCount;
+    struct IDClosest;
     struct IDNot;
     struct IDSubscript;
     struct IDWithin;
@@ -232,8 +233,8 @@ namespace AST
         boost::recursive_wrapper<IDProtein>, boost::recursive_wrapper<IDPerturbable>, boost::recursive_wrapper<IDMass>,
         boost::recursive_wrapper<IDCharge>, boost::recursive_wrapper<IDCmpMass>, boost::recursive_wrapper<IDCmpCharge>,
         boost::recursive_wrapper<IDObjMass>, boost::recursive_wrapper<IDObjCharge>, boost::recursive_wrapper<IDObjCmpMass>,
-        boost::recursive_wrapper<IDObjCmpCharge>, boost::recursive_wrapper<IDSmarts>, boost::recursive_wrapper<ExpressionPart>,
-        boost::recursive_wrapper<Expression>>;
+        boost::recursive_wrapper<IDObjCmpCharge>, boost::recursive_wrapper<IDSmarts>, boost::recursive_wrapper<IDClosest>,
+        boost::recursive_wrapper<ExpressionPart>, boost::recursive_wrapper<Expression>>;
 
     QString expression_to_string(const ExpressionVariant &expression);
 
@@ -303,6 +304,11 @@ namespace AST
         double value;
         SireUnits::Dimension::Length unit;
 
+        SireUnits::Dimension::Length toLength() const
+        {
+            return value * unit;
+        }
+
         QString toString() const;
     };
 
@@ -343,6 +349,13 @@ namespace AST
             return *this;
         }
 
+        SireMaths::Vector toVector() const
+        {
+            return SireMaths::Vector(x.toLength().to(SireUnits::angstrom),
+                                     y.toLength().to(SireUnits::angstrom),
+                                     z.toLength().to(SireUnits::angstrom));
+        }
+
         QString toString() const;
 
     private:
@@ -460,6 +473,11 @@ namespace AST
 
         QString toString() const;
 
+        bool isNull() const
+        {
+            return this->toEngine() == SelectEnginePtr();
+        }
+
         SelectEnginePtr toEngine() const;
     };
 
@@ -871,6 +889,52 @@ namespace AST
         SelectEnginePtr toEngine() const;
     };
 
+    /** Struct that holds "closest N X to Y" and "further N X from Y"
+     *  expressions
+     */
+    struct IDClosest
+    {
+        Expression search_set;
+        bool is_closest;
+        int n;
+        Expression reference_set;
+        SireMaths::Vector point;
+
+        IDClosest &operator+=(const Expression &s)
+        {
+            search_set = s;
+            return *this;
+        }
+
+        IDClosest &operator+=(int number)
+        {
+            n = number;
+            return *this;
+        }
+
+        IDClosest &operator*=(const Expression &r)
+        {
+            reference_set = r;
+            return *this;
+        }
+
+        IDClosest &operator*=(const VectorValue &v)
+        {
+            point = v.toVector();
+            return *this;
+        }
+
+        IDClosest &operator-=(bool c)
+        {
+            is_closest = c;
+            return *this;
+        }
+
+        QString toString() const;
+
+        SelectEnginePtr toEngine() const;
+    };
+
     /** Struct that holds a "where within"
         expression, e.g. residues where center is within 5 A of resname /lig/i */
     struct IDWhereWithin

diff --git a/corelib/src/libs/SireSearch/grammar.h b/corelib/src/libs/SireSearch/grammar.h
@@ -270,7 +270,7 @@ class Grammar : public qi::grammar<IteratorT, AST::Node(), SkipperT>
         expressionPartRule = idNameRule | idNumberRule | idElementRule | propertyRule | bondRule | water_token |
                              pert_token | protein_token | notRule | joinRule | massRule | massCmpRule | chargeRule |
                              chargeCmpRule | massObjRule | massObjCmpRule | chargeObjRule | chargeObjCmpRule |
-                             all_token | countRule | smartsRule | user_token;
+                             all_token | countRule | closestRule | smartsRule | user_token;
 
         // grammar that specifies a list of names (comma-separated)
         nameValuesRule = (nameValueRule % qi::lit(','));
@@ -356,6 +356,46 @@ class Grammar : public qi::grammar<IteratorT, AST::Node(), SkipperT>
         countRule = eps[_val = AST::IDCount()] >> (qi::lit("count(") >> expressionRule[_val += _1] >> qi::lit(")") >>
                                                    cmp_token[_val += _1] >> qi::int_[_val += _1]);
 
+        // grammar for a closest or furthest expression, e.g.
+        // closest 5 waters to ligand, furthest 10 ions from protein
+        closestRule = eps[_val = AST::IDClosest()] >>
+                          (qi::lit("closest")[_val -= true] >>
+                           qi::int_[_val += _1] >>
+                           expressionRule[_val += _1] >>
+                           qi::lit("to") >>
+                           expressionRule[_val *= _1]) |
+                      (qi::lit("closest")[_val -= true] >>
+                       expressionRule[_val += _1] >>
+                       qi::lit("to")[_val += 1] >>
+                       expressionRule[_val *= _1]) |
+                      (qi::lit("furthest")[_val -= false] >>
+                       qi::int_[_val += _1] >>
+                       expressionRule[_val += _1] >>
+                       qi::lit("from") >>
+                       expressionRule[_val *= _1]) |
+                      (qi::lit("furthest")[_val -= false] >>
+                       expressionRule[_val += _1] >>
+                       qi::lit("from")[_val += 1] >>
+                       expressionRule[_val *= _1]) |
+                      (qi::lit("closest")[_val -= true] >>
+                       qi::int_[_val += _1] >>
+                       expressionRule[_val += _1] >>
+                       qi::lit("to") >>
+                       vectorValueRule[_val *= _1]) |
+                      (qi::lit("closest")[_val -= true] >>
+                       expressionRule[_val += _1] >>
+                       qi::lit("to")[_val += 1] >>
+                       vectorValueRule[_val *= _1]) |
+                      (qi::lit("furthest")[_val -= false] >>
+                       qi::int_[_val += _1] >>
+                       expressionRule[_val += _1] >>
+                       qi::lit("from") >>
+                       vectorValueRule[_val *= _1]) |
+                      (qi::lit("furthest")[_val -= false] >>
+                       expressionRule[_val += _1] >>
+                       qi::lit("from")[_val += 1] >>
+                       vectorValueRule[_val *= _1]);
+
         /////
         ///// name all of the rules to simplify error messages
         /////
@@ -374,6 +414,7 @@ class Grammar : public qi::grammar<IteratorT, AST::Node(), SkipperT>
         whereWithinRule.name("Where Within");
         whereCompareRule.name("Where Compare");
         countRule.name("Count Rule");
+        closestRule.name("Closest Rule");
         lhsRule.name("LHS");
         rhsRule.name("RHS");
         expressionRule.name("Expression");
@@ -435,6 +476,7 @@ class Grammar : public qi::grammar<IteratorT, AST::Node(), SkipperT>
     qi::rule<IteratorT, AST::IDWhereWithin(), SkipperT> whereWithinRule;
     qi::rule<IteratorT, AST::IDWhereCompare(), SkipperT> whereCompareRule;
     qi::rule<IteratorT, AST::IDCount(), SkipperT> countRule;
+    qi::rule<IteratorT, AST::IDClosest(), SkipperT> closestRule;
 
     qi::rule<IteratorT, AST::Expression(), SkipperT> lhsRule;
     qi::rule<IteratorT, AST::Expression(), SkipperT> rhsRule;