Changeset 08b88b for molecuilder/src/bondgraph.cpp

Timestamp:

Nov 3, 2009, 2:34:02 PM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

c1b4a4

Parents:

5f9f8b

git-author:

Frederik Heber <heber@…> (11/03/09 14:27:15)

git-committer:

Frederik Heber <heber@…> (11/03/09 14:34:02)

Message:

Fixing not created adjacency list, partially fixing subgraph dissection in config::Load()

• CreateAdjacencyList() was called with zero bonddistance.
• this was due to max_distance not being initialised in the constructor to 0 and subsequently not set if Bond Length Table was not found.
• new function SetMaxDistanceToMaxOfCovalentRadii() which sets the max_distance to twice the max of covalent radii of all elements.
• config::Load() - atoms in copied molecule (by DepthFirstSearchAnalysis()) are made their own father (and originals are removed).

File:

• molecuilder/src/bondgraph.cpp (modified) (3 diffs)

molecuilder/src/bondgraph.cpp

@@ -13 +13 @@
 #include "molecule.hpp"
 #include "parser.hpp"
+#include "periodentafel.hpp"
 #include "vector.hpp"
 
@@ -18 +19 @@
  * This classes contains typical bond lengths and thus may be used to construct a bond graph for a given molecule.
  */
-BondGraph::BondGraph(bool IsA) : BondLengthMatrix(NULL), IsAngstroem(IsA)
+BondGraph::BondGraph(bool IsA) : BondLengthMatrix(NULL), max_distance(0), IsAngstroem(IsA)
 {
 };
@@ -104 +105 @@
 };
 
+/** Determines the maximum of all element::CovalentRadius.
+ * \param *out output stream for debugging
+ * \param *periode periodentafel with all elements.
+ */
+double BondGraph::SetMaxDistanceToMaxOfCovalentRadii(ofstream * const out, const periodentafel * const periode)
+{
+  max_distance = 0.;
+
+  element * Runner = periode->start;
+  while (Runner->next != periode->end) {
+    Runner = Runner->next;
+    if (Runner->CovalentRadius > max_distance)
+      max_distance = Runner->CovalentRadius;
+  }
+  max_distance *= 2.;
+
+  return max_distance;
+};
+
 /** Returns bond criterion for given pair based on covalent radius.
  * \param *Walker first BondedParticle