Changes in src/analysis_bonds.cpp [112b09:36166d]

File:

• src/analysis_bonds.cpp (modified) (6 diffs)

src/analysis_bonds.cpp

@@ -13 +13 @@
 #include "element.hpp"
 #include "info.hpp"
+#include "verbose.hpp"
 #include "log.hpp"
 #include "molecule.hpp"
@@ -121 +122 @@
  * \param *molecules molecules to count bonds
  * \param *InterfaceElement or NULL
- */
-int CountHydrogenBridgeBonds(MoleculeListClass *molecules, const element * InterfaceElement = NULL)
+ * \param *Interface2Element or NULL
+ */
+int CountHydrogenBridgeBonds(MoleculeListClass *molecules, const element * InterfaceElement = NULL, const element * Interface2Element = NULL)
 {
   int count = 0;
@@ -128 +130 @@
   double Otherangle = 0.;
   bool InterfaceFlag = false;
+  bool Interface2Flag = false;
   bool OtherHydrogenFlag = true;
   for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin();MolWalker != molecules->ListOfMolecules.end(); ++MolWalker) {
@@ -145 +148 @@
               OtherHydrogens = 0;
               InterfaceFlag = (InterfaceElement == NULL);
+              Interface2Flag = (Interface2Element == NULL);
               for (BondList::const_iterator BondRunner = (*Runner)->ListOfBonds.begin(); BondRunner != (*Runner)->ListOfBonds.end(); BondRunner++) {
                 atom * const OtherAtom = (*BondRunner)->GetOtherAtom(*Runner);
@@ -155 +159 @@
                 }
                 InterfaceFlag = InterfaceFlag || (OtherAtom->type == InterfaceElement);
+                Interface2Flag = Interface2Flag || (OtherAtom->type == Interface2Element);
               }
               DoLog(1) && (Log() << Verbose(1) << "Otherangle is " << Otherangle << " for " << OtherHydrogens << " hydrogens." << endl);
@@ -168 +173 @@
                   break;
               }
-              if (InterfaceFlag && OtherHydrogenFlag) {
+              if (InterfaceFlag && Interface2Flag && OtherHydrogenFlag) {
                 // on this element (Walker) we check for bond to hydrogen, i.e. part of water molecule
                 for (BondList::const_iterator BondRunner = (*Walker)->ListOfBonds.begin(); BondRunner != (*Walker)->ListOfBonds.end(); BondRunner++) {