Changeset 5f697c for molecuilder/src/molecule.hpp

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/molecule.hpp (modified) (2 diffs)

molecuilder/src/molecule.hpp

@@ -35 +35 @@
 class atom;
 class bond;
+class BondedParticle;
+class BondGraph;
 class element;
 class ForceMatrix;
@@ -238 +240 @@
   /// Initialising routines in fragmentation
   void CreateAdjacencyListFromDbondFile(ofstream *out, ifstream *output);
-  void CreateAdjacencyList(ofstream *out, double bonddistance, bool IsAngstroem);
+  void CreateAdjacencyList(ofstream *out, double bonddistance, bool IsAngstroem, void (BondGraph::*f)(BondedParticle * const , BondedParticle * const , double &, double &, bool), BondGraph *BG = NULL);
   int CorrectBondDegree(ofstream *out);
   void OutputBondsList(ofstream *out);