Changeset 388049

Timestamp:

Apr 1, 2010, 1:49:25 PM (15 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

fe238c

Parents:

62c9c0

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@…>

Location:

src

Files:

• analysis_bonds.cpp (modified) (2 diffs)
• analysis_bonds.hpp (modified) (2 diffs)
• bondgraph.cpp (modified) (1 diff)
• bondgraph.hpp (modified) (2 diffs)
• builder.cpp (modified) (1 diff)
• unittests/CountBondsUnitTest.cpp (modified) (1 diff)

src/analysis_bonds.cpp

@@ -9 +9 @@
 #include "atom.hpp"
 #include "bond.hpp"
+#include "element.hpp"
+#include "info.hpp"
 #include "log.hpp"
 #include "molecule.hpp"
@@ -79 +81 @@
   }
 };
+
+
+/** 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 != MolWalker; 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;
+};

src/analysis_bonds.hpp

@@ -18 +18 @@
 #endif
 
+/*********************************************** defines ***********************************/
+
+#define HBRIDGEDISTANCE 3.5   //!< HBridge distance from PCCP Vol 10. 4802-4813
 
 /****************************************** forward declarations *****************************/
 
 class element;
+class MoleculeListClass;
 class molecule;
 
@@ -29 +33 @@
 void MinMeanMaxBondDistanceBetweenElements(const molecule *mol, element *type1, element *type2, double &Min, double &Mean, double &Max);
 
+int CountHydrogenBridgeBonds(MoleculeListClass * const molecules, element * InterfaceElement);
+int CountBondsOfTwo(MoleculeListClass * const molecules, const element * const first, const element * const second);
+int CountBondsOfThree(MoleculeListClass * const molecules, const element * const first, const element * const second, const element * const third);
+
 #endif /* ANALYSIS_BONDS_HPP_ */

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;
-};

src/bondgraph.hpp

@@ -23 +23 @@
 
 #define BONDTHRESHOLD 0.4   //!< CSD threshold in bond check which is the width of the interval whose center is the sum of the covalent radii
-#define HBRIDGEDISTANCE 3.5   //!< HBridge distance from PCCP Vol 10. 4802-4813
 
 /****************************************** forward declarations *****************************/
 
 class molecule;
-class MoleculeListClass;
 class periodentafel;
 class MatrixContainer;
@@ -55 +53 @@
 };
 
-int CountHydrogenBridgeBonds(MoleculeListClass * const molecules, element * InterfaceElement);
-int CountBondsOfTwo(MoleculeListClass * const molecules, const element * const first, const element * const second);
-int CountBondsOfThree(MoleculeListClass * const molecules, const element * const first, const element * const second, const element * const third);
-
 #endif /* BONDGRAPH_HPP_ */

src/builder.cpp

@@ -52 +52 @@
 #include <cstring>
 
+#include "analysis_bonds.hpp"
 #include "analysis_correlation.hpp"
 #include "atom.hpp"

src/unittests/CountBondsUnitTest.cpp

@@ -17 +17 @@
 #include <cstring>
 
+#include "analysis_bonds.hpp"
 #include "atom.hpp"
 #include "bond.hpp"