Changeset 5f697c for molecuilder/src/builder.cpp

Timestamp:

Oct 30, 2009, 9:05:30 AM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

b84ab4

Parents:

bc8155

git-author:

Frederik Heber <heber@…> (10/30/09 08:30:57)

git-committer:

Frederik Heber <heber@…> (10/30/09 09:05:30)

Message:

New class BondGraph.

• BondGraph parses a file containing bond lengths and basically has a member function which gives lower and upper bounds on when two atoms are bonded and when not.
  • BondGraph::LoadBondLengthTable() - basically uses MatrixContainer::ParseMatrix()
  • BondGraph::ConstructBondGraph() - uses molecule::CreateAdjacency() but with different bounds-function.
  • BondGraph::GetBondLength() - returns entry from parsed bond length matrix
  • BondGraph::CovalentMinMaxDistance() - bounds function using covalent radii of involved elements
  • BondGraph::BondLengthMatrixMinMaxDistance() - bounds function which uses the parsed bond length matrix
• Unit test written for BondGraph.
• molecule::CreateAdjacencyList() - rewritten, takes now a bounds BondGraph member function, if NULL is given, creates its own BondGraph and uses standard covalent bounds function (which does not need any scanning).
• new function BondedParticle::IsBondedTo() which checks whether given BondedPasrticle is contained in ListOfBonds.
• builder.cpp: calls to molecule::CreateAdjacencyList() adapted to new syntax.

File:

• molecuilder/src/builder.cpp (modified) (5 diffs)

molecuilder/src/builder.cpp

@@ -53 +53 @@
 #include "atom.hpp"
 #include "bond.hpp"
+#include "bondgraph.hpp"
 #include "boundary.hpp"
 #include "config.hpp"
@@ -840 +841 @@
           }
           if (mol->first->next != mol->last) // if connect matrix is present already, redo it
-            mol->CreateAdjacencyList((ofstream *)&cout, mol->BondDistance, configuration->GetIsAngstroem());
+            mol->CreateAdjacencyList((ofstream *)&cout, mol->BondDistance, configuration->GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, NULL);
           // free memory
           delete[](Elements);
@@ -896 +897 @@
           cin >> bonddistance;
           start = clock();
-          mol->CreateAdjacencyList((ofstream *)&cout, bonddistance, configuration->GetIsAngstroem());
+          mol->CreateAdjacencyList((ofstream *)&cout, bonddistance, configuration->GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, NULL);
           end = clock();
           cout << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl;
@@ -1555 +1556 @@
                 class StackClass<bond *> *BackEdgeStack = NULL;
                 class StackClass<bond *> *LocalBackEdgeStack = NULL;
-                mol->CreateAdjacencyList((ofstream *)&cout, atof(argv[argptr]), configuration.GetIsAngstroem());
+                mol->CreateAdjacencyList((ofstream *)&cout, atof(argv[argptr]), configuration.GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, NULL);
                 Subgraphs = mol->DepthFirstSearchAnalysis((ofstream *)&cout, BackEdgeStack);
                 if (Subgraphs != NULL) {
@@ -1912 +1913 @@
                 cout << Verbose(0) << "Creating connection matrix..." << endl;
                 start = clock();
-                mol->CreateAdjacencyList((ofstream *)&cout, atof(argv[argptr++]), configuration.GetIsAngstroem());
+                mol->CreateAdjacencyList((ofstream *)&cout, atof(argv[argptr++]), configuration.GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, NULL);
                 cout << Verbose(0) << "Fragmenting molecule with current connection matrix ..." << endl;
                 if (mol->first->next != mol->last) {