Changeset 5f697c for molecuilder/src/Makefile.am

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/Makefile.am (modified) (1 diff)

molecuilder/src/Makefile.am

@@ -2 +2 @@
 ATOMHEADER = atom.hpp atom_atominfo.hpp atom_bondedparticle.hpp atom_bondedparticleinfo.hpp atom_graphnode.hpp atom_graphnodeinfo.hpp atom_particleinfo.hpp atom_trajectoryparticle.hpp atom_trajectoryparticleinfo.hpp
 
-SOURCE = analysis_correlation.cpp ${ATOMSOURCE} bond.cpp boundary.cpp config.cpp element.cpp ellipsoid.cpp graph.cpp helpers.cpp leastsquaremin.cpp linkedcell.cpp memoryusageobserver.cpp moleculelist.cpp molecule.cpp molecule_dynamics.cpp molecule_fragmentation.cpp molecule_geometry.cpp molecule_graph.cpp molecule_pointcloud.cpp parser.cpp periodentafel.cpp tesselation.cpp tesselationhelpers.cpp vector.cpp verbose.cpp
-HEADER = analysis_correlation.hpp ${ATOMHEADER} bond.hpp boundary.hpp config.hpp defs.hpp element.hpp ellipsoid.hpp graph.hpp helpers.hpp leastsquaremin.hpp linkedcell.hpp lists.hpp memoryallocator.hpp memoryusageobserver.hpp molecule.hpp molecule_template.hpp parser.hpp periodentafel.hpp stackclass.hpp tesselation.hpp tesselationhelpers.hpp vector.hpp verbose.hpp
+SOURCE = analysis_correlation.cpp ${ATOMSOURCE} bond.cpp bondgraph.cpp boundary.cpp config.cpp element.cpp ellipsoid.cpp graph.cpp helpers.cpp leastsquaremin.cpp linkedcell.cpp memoryusageobserver.cpp moleculelist.cpp molecule.cpp molecule_dynamics.cpp molecule_fragmentation.cpp molecule_geometry.cpp molecule_graph.cpp molecule_pointcloud.cpp parser.cpp periodentafel.cpp tesselation.cpp tesselationhelpers.cpp vector.cpp verbose.cpp
+HEADER = analysis_correlation.hpp ${ATOMHEADER} bond.hpp bondgraph.hpp boundary.hpp config.hpp defs.hpp element.hpp ellipsoid.hpp graph.hpp helpers.hpp leastsquaremin.hpp linkedcell.hpp lists.hpp memoryallocator.hpp memoryusageobserver.hpp molecule.hpp molecule_template.hpp parser.hpp periodentafel.hpp stackclass.hpp tesselation.hpp tesselationhelpers.hpp vector.hpp verbose.hpp
 
 BOOST_LIB = $(BOOST_LDFLAGS) $(BOOST_MPL_LIB)