Changeset 1cbf47 for src

Timestamp:

Mar 18, 2010, 3:38:56 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:

f18185

Parents:

c7b1e7

git-author:

Frederik Heber <heber@…> (03/18/10 15:29:54)

git-committer:

Frederik Heber <heber@…> (03/18/10 15:38:56)

Message:

Introduced CountHydrogenBridgeBonds() function.

• CountHydrogenBridgeBonds() in bondgraph.cpp counts hydrogen bridges in a system.
• MergeMolecules has a new case 'h'. The placement is this menu is however nonsense and should be corrected, when MeasureAtoms has a MoleculeListClass as parameter instead of a single molecule.

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

Location:

src

Files:

• bondgraph.cpp (modified) (4 diffs)
• bondgraph.hpp (modified) (2 diffs)
• builder.cpp (modified) (2 diffs)

src/bondgraph.cpp

@@ -9 +9 @@
 
 #include "atom.hpp"
+#include "bond.hpp"
 #include "bondgraph.hpp"
 #include "element.hpp"
@@ -86 +87 @@
 bool BondGraph::ConstructBondGraph(molecule * const mol)
 {
-  bool status = true;
+  Info FunctionInfo(__func__);
+bool status = true;
 
   if (mol->start->next == mol->end) // only construct if molecule is not empty
@@ -119 +121 @@
 double BondGraph::SetMaxDistanceToMaxOfCovalentRadii(const molecule * const mol)
 {
+  Info FunctionInfo(__func__);
   max_distance = 0.;
 
@@ -169 +172 @@
 };
 
+/** 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;
+  atom *Hydrogen = NULL;
+  atom *OtherHydrogen = NULL;
+  Vector OHBond;
+  Vector OOBond;
+  int count = 0;
+  bool HydrogenFlag = false;
+  bool OtherHydrogenFlag = false;
+  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 < HBRIDGEDISTANCE*HBRIDGEDISTANCE) {
+              // get hydrogen, check for InterfaceElement
+              HydrogenFlag = false;
+              OtherHydrogenFlag = false;
+              InterfaceFlag = (InterfaceElement == NULL);
+              // on other atom(Runner) we check for bond to interface element
+              for (BondList::const_iterator BondRunner = Runner->ListOfBonds.begin(); BondRunner != Runner->ListOfBonds.end(); BondRunner++) {
+                atom * const OtherAtom = (*BondRunner)->GetOtherAtom(Walker);
+                if (!OtherHydrogenFlag && (OtherAtom->type->Z == 1)) {
+                  OtherHydrogen = OtherAtom;
+                  OtherHydrogen = true;
+                }
+                InterfaceFlag = InterfaceFlag || (OtherAtom->type == InterfaceElement);
+              }
+              // 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 (!HydrogenFlag && (OtherAtom->type->Z == 1)) {
+                  Hydrogen = OtherAtom;
+                  HydrogenFlag = true;
+                }
+              }
+              if (InterfaceFlag && HydrogenFlag) {
+                if ((Walker->nr < Runner->nr) || (!OtherHydrogenFlag)) {
+                  // check angle
+                  OHBond.CopyVector(&Walker->x);
+                  OHBond.SubtractVector(&Hydrogen->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 << ", " << Hydrogen->Name << " and " << Runner->Name << " have a hydrogen bridge bond with " << sqrt(distance) << " and at angle " << (180./M_PI)*angle << " degrees." << endl);
+                    count++;
+                  }
+                }
+              }
+            }
+          }
+        }
+      }
+    }
+  }
+  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;
@@ -53 +55 @@
 };
 
+int CountHydrogenBridgeBonds(MoleculeListClass * const molecules, element * InterfaceElement);
+
 #endif /* BONDGRAPH_HPP_ */

src/builder.cpp

@@ -1090 +1090 @@
   Log() << Verbose(0) << "a - simple add of one molecule to another" << endl;
   Log() << Verbose(0) << "e - embedding merge of two molecules" << endl;
+  Log() << Verbose(0) << "h - count the number of hydrogen bonds" << endl;
   Log() << Verbose(0) << "m - multi-merge of all molecules" << endl;
   Log() << Verbose(0) << "s - scatter merge of two molecules" << endl;
@@ -1140 +1141 @@
         if ((src != -1) && (dest != -1))
           molecules->EmbedMerge(destmol, srcmol);
+      }
+      break;
+
+    case 'h':
+      {
+        int Z;
+        cout << "Please enter interface element: ";
+        cin >> Z;
+        element * const InterfaceElement = periode->FindElement(Z);
+        cout << endl << "There are " << CountHydrogenBridgeBonds(molecules, InterfaceElement) << " hydrogen bridges with connections to " << (InterfaceElement != 0 ? InterfaceElement->name : "None") << "." << endl;
       }
       break;