Changes in src/analysis_bonds.cpp [fe238c:220cf37]

File:

• src/analysis_bonds.cpp (modified) (3 diffs)

src/analysis_bonds.cpp

@@ -9 +9 @@
 #include "atom.hpp"
 #include "bond.hpp"
-#include "element.hpp"
-#include "info.hpp"
 #include "log.hpp"
 #include "molecule.hpp"
@@ -39 +37 @@
   }
   if (((int)Mean % 2) != 0)
-    DoeLog(1) && (eLog()<< Verbose(1) << "Something is wrong with the bond structure, the number of bonds is not even!" << endl);
+    eLog() << Verbose(1) << "Something is wrong with the bond structure, the number of bonds is not even!" << endl;
   Mean /= (double)AtomCount;
 };
@@ -81 +79 @@
   }
 };
-
-/** Calculate the angle between \a *first and \a *origin and \a *second and \a *origin.
- * \param *first first Vector
- * \param *origin origin of angle taking
- * \param *second second Vector
- * \return angle between \a *first and \a *second, both relative to origin at \a *origin.
- */
-double CalculateAngle(Vector *first, Vector *central, Vector *second)
-{
-  Vector OHBond;
-  Vector OOBond;
-
-  OHBond.CopyVector(first);
-  OHBond.SubtractVector(central);
-  OOBond.CopyVector(second);
-  OOBond.SubtractVector(central);
-  const double angle = OHBond.Angle(&OOBond);
-  return angle;
-};
-
-/** Checks whether the angle between \a *Oxygen and \a *Hydrogen and \a *Oxygen and \a *OtherOxygen is less than 30 degrees.
- * Note that distance criterion is not checked.
- * \param *Oxygen first oxygen atom, bonded to \a *Hydrogen
- * \param *Hydrogen hydrogen bonded to \a *Oxygen
- * \param *OtherOxygen other oxygen atom
- * \return true - angle criteria fulfilled, false - criteria not fulfilled, angle greater than 30 degrees.
- */
-bool CheckHydrogenBridgeBondAngle(atom *Oxygen, atom *Hydrogen, atom *OtherOxygen)
-{
-  Info FunctionInfo(__func__);
-
-  // check angle
-  if (CalculateAngle(&Hydrogen->x, &Oxygen->x, &OtherOxygen->x) < M_PI*(30./180.)) {
-    return true;
-  } else {
-    return false;
-  }
-};
-
-/** 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)
-{
-  atom *Walker = NULL;
-  atom *Runner = NULL;
-  int count = 0;
-  int OtherHydrogens = 0;
-  double Otherangle = 0.;
-  bool InterfaceFlag = false;
-  bool OtherHydrogenFlag = true;
-  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 ((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
-              // on other atom(Runner) we check for bond to interface element and
-              // check that O-O line is not in between the shanks of the two connected hydrogens (Otherangle > 104.5)
-              OtherHydrogenFlag = true;
-              Otherangle = 0.;
-              OtherHydrogens = 0;
-              InterfaceFlag = (InterfaceElement == NULL);
-              for (BondList::const_iterator BondRunner = Runner->ListOfBonds.begin(); BondRunner != Runner->ListOfBonds.end(); BondRunner++) {
-                atom * const OtherAtom = (*BondRunner)->GetOtherAtom(Runner);
-                // if hydrogen, check angle to be greater(!) than 30 degrees
-                if (OtherAtom->type->Z == 1) {
-                  const double angle = CalculateAngle(&OtherAtom->x, &Runner->x, &Walker->x);
-                  OtherHydrogenFlag = OtherHydrogenFlag && (angle > M_PI*(30./180.) + MYEPSILON);
-                  Otherangle += angle;
-                  OtherHydrogens++;
-                }
-                InterfaceFlag = InterfaceFlag || (OtherAtom->type == InterfaceElement);
-              }
-              DoLog(1) && (Log() << Verbose(1) << "Otherangle is " << Otherangle << " for " << OtherHydrogens << " hydrogens." << endl);
-              switch (OtherHydrogens) {
-                case 0:
-                case 1:
-                  break;
-                case 2:
-                  OtherHydrogenFlag = OtherHydrogenFlag && (Otherangle > M_PI*(104.5/180.) + MYEPSILON);
-                  break;
-                default: // 3 or more hydrogens ...
-                  OtherHydrogenFlag = false;
-                  break;
-              }
-              if (InterfaceFlag && 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++) {
-                  atom * const OtherAtom = (*BondRunner)->GetOtherAtom(Walker);
-                  if (OtherAtom->type->Z == 1) {
-                    // check angle
-                    if (CheckHydrogenBridgeBondAngle(Walker, OtherAtom, Runner)) {
-                      DoLog(1) && (Log() << Verbose(1) << Walker->Name << ", " << OtherAtom->Name << " and " << Runner->Name << " has a hydrogen bridge bond with distance " << sqrt(distance) << " and angle " << CalculateAngle(&OtherAtom->x, &Walker->x, &Runner->x)*(180./M_PI) << "." << 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;
-};