Changeset 794482 for molecuilder/src/bondgraph.cpp

Timestamp:

Apr 1, 2010, 1:49:25 PM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

6250e5

Parents:

768125

git-author:

Frederik Heber <heber@…> (04/01/10 12:42:07)

git-committer:

Frederik Heber <heber@…> (04/01/10 13:49:25)

Message:

Moved functions CountBondsOfTwo(), CountBondsOfThree() and CountHydrogenBridgeBonds() from bondgraph.cpp to analysis_bonds.cpp

Signed-off-by: Frederik Heber <heber@…>

File:

• molecuilder/src/bondgraph.cpp (modified) (1 diff)

molecuilder/src/bondgraph.cpp

@@ -171 +171 @@
   }
 };
-
-/** Counts the number of hydrogen bridge bonds.
- * With \a *InterfaceElement an extra element can be specified that identifies some boundary.
- * Then, counting is for the h-bridges that connect to interface only.
- * \param *molecules molecules to count bonds
- * \param *InterfaceElement or NULL
- */
-int CountHydrogenBridgeBonds(MoleculeListClass *molecules, element * InterfaceElement = NULL)
-{
-  Info FunctionInfo(__func__);
-  atom *Walker = NULL;
-  atom *Runner = NULL;
-  Vector OHBond;
-  Vector OOBond;
-  int count = 0;
-  bool InterfaceFlag = false;
-  for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin();MolWalker != molecules->ListOfMolecules.end(); MolWalker++) {
-    Walker = (*MolWalker)->start;
-    while (Walker->next != (*MolWalker)->end) {
-      Walker = Walker->next;
-      for (MoleculeList::const_iterator MolRunner = molecules->ListOfMolecules.begin();MolRunner != molecules->ListOfMolecules.end(); MolRunner++) {
-        Runner = (*MolRunner)->start;
-        while (Runner->next != (*MolRunner)->end) {
-          Runner = Runner->next;
-          if ((Runner != Walker) && (Walker->type->Z  == 8) && (Runner->type->Z  == 8)) {
-            // check distance
-            const double distance = Runner->x.DistanceSquared(&Walker->x);
-            if ((distance > MYEPSILON) && (distance < HBRIDGEDISTANCE*HBRIDGEDISTANCE)) { // distance >0 means  different atoms
-              InterfaceFlag = (InterfaceElement == NULL);
-              // on other atom(Runner) we check for bond to interface element
-              for (BondList::const_iterator BondRunner = Runner->ListOfBonds.begin(); ((!InterfaceFlag) && (BondRunner != Runner->ListOfBonds.end())); BondRunner++) {
-                atom * const OtherAtom = (*BondRunner)->GetOtherAtom(Runner);
-                InterfaceFlag = InterfaceFlag || (OtherAtom->type == InterfaceElement);
-              }
-              if (InterfaceFlag) {
-                // 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++) {
-                  atom * const OtherAtom = (*BondRunner)->GetOtherAtom(Walker);
-                  if (OtherAtom->type->Z == 1) {
-                    // check angle
-                    OHBond.CopyVector(&OtherAtom->x);
-                    OHBond.SubtractVector(&Walker->x);
-                    OOBond.CopyVector(&Runner->x);
-                    OOBond.SubtractVector(&Walker->x);
-                    const double angle = OHBond.Angle(&OOBond);
-                    if (angle < M_PI*(30./180.)) {
-                      DoLog(1) && (Log() << Verbose(1) << Walker->Name << ", " << OtherAtom->Name << " and " << Runner->Name << " have a hydrogen bridge bond with " << sqrt(distance) << " and at angle " << (180./M_PI)*angle << " degrees." << endl);
-                      count++;
-                      break;
-                    }
-                  }
-                }
-              }
-            }
-          }
-        }
-      }
-    }
-  }
-  return count;
-}
-
-/** Counts the number of bonds between two given elements.
- * \param *molecules list of molecules with all atoms
- * \param *first pointer to first element
- * \param *second pointer to second element
- * \return number of found bonds (\a *first-\a *second)
- */
-int CountBondsOfTwo(MoleculeListClass * const molecules, const element * const first, const element * const second)
-{
-  atom *Walker = NULL;
-  int count = 0;
-
-  for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin();MolWalker != molecules->ListOfMolecules.end(); MolWalker++) {
-    Walker = (*MolWalker)->start;
-    while (Walker->next != (*MolWalker)->end) {
-      Walker = Walker->next;
-      if ((Walker->type == first) || (Walker->type == second)) {  // first element matches
-        for (BondList::const_iterator BondRunner = Walker->ListOfBonds.begin(); BondRunner != Walker->ListOfBonds.end(); BondRunner++) {
-          atom * const OtherAtom = (*BondRunner)->GetOtherAtom(Walker);
-          if (((OtherAtom->type == first) || (OtherAtom->type == second)) && (Walker->nr < OtherAtom->nr)) {
-            count++;
-            DoLog(1) && (Log() << Verbose(1) << first->name << "-" << second->name << " bond found between " << *Walker << " and " << *OtherAtom << "." << endl);
-          }
-        }
-      }
-    }
-  }
-  return count;
-};
-
-/** Counts the number of bonds between three given elements.
- * Note that we do not look for arbitrary sequence of given bonds, but \a *second will be the central atom and we check
- * whether it has bonds to both \a *first and \a *third.
- * \param *molecules list of molecules with all atoms
- * \param *first pointer to first element
- * \param *second pointer to second element
- * \param *third pointer to third element
- * \return number of found bonds (\a *first-\a *second-\a *third, \a *third-\a *second-\a *first, respectively)
- */
-int CountBondsOfThree(MoleculeListClass * const molecules, const element * const first, const element * const second, const element * const third)
-{
-  int count = 0;
-  bool MatchFlag[2];
-  bool result = false;
-  atom *Walker = NULL;
-  const element * ElementArray[2];
-  ElementArray[0] = first;
-  ElementArray[1] = third;
-
-  for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin();MolWalker != molecules->ListOfMolecules.end(); MolWalker++) {
-    Walker = (*MolWalker)->start;
-    while (Walker->next != (*MolWalker)->end) {
-      Walker = Walker->next;
-      if (Walker->type == second) {  // first element matches
-        for (int i=0;i<2;i++)
-          MatchFlag[i] = false;
-        for (BondList::const_iterator BondRunner = Walker->ListOfBonds.begin(); BondRunner != Walker->ListOfBonds.end(); BondRunner++) {
-          atom * const OtherAtom = (*BondRunner)->GetOtherAtom(Walker);
-          for (int i=0;i<2;i++)
-            if ((!MatchFlag[i]) && (OtherAtom->type == ElementArray[i])) {
-              MatchFlag[i] = true;
-              break;  // each bonding atom can match at most one element we are looking for
-            }
-        }
-        result = true;
-        for (int i=0;i<2;i++) // gather results
-          result = result && MatchFlag[i];
-        if (result) { // check results
-          count++;
-          DoLog(1) && (Log() << Verbose(1) << first->name << "-" << second->name << "-" << third->name << " bond found at " << *Walker << "." << endl);
-        }
-      }
-    }
-  }
-  return count;
-};