Changeset 6d0fcaa for molecuilder/src/atom_bondedparticle.cpp

Timestamp:

Feb 2, 2010, 9:43:52 AM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

2bc06b, 31ccb6, 4bb871a

Parents:

49faa8

Message:

Possibility to store all bonds to file added.

So far we only could store the adjacency (i.e. atom along with all bond partners per line) to file.
For plotting molecules with pgfplots (and maybe for other purposes too) we need to have single tupels of two per line.
Hence, the following additions were implemented:

• new functions: BondedParticle::OutputBonds(), molecule::StoreBondsToFile()
• new ParseCommandLineOption: J stores adjacency, j stores bonds.

File:

• molecuilder/src/atom_bondedparticle.cpp (modified) (2 diffs)

molecuilder/src/atom_bondedparticle.cpp

@@ -56 +56 @@
  * \param *AdjacencyFile output stream
  */
-void BondedParticle::OutputAdjacency(ofstream *AdjacencyFile) const
+void BondedParticle::OutputAdjacency(ofstream * const AdjacencyFile) const
 {
   *AdjacencyFile << nr << "\t";
@@ -62 +62 @@
     *AdjacencyFile << (*Runner)->GetOtherAtom(this)->nr << "\t";
   *AdjacencyFile << endl;
+};
+
+/** Output of atom::nr along each bond partner per line.
+ * Only bonds are printed where atom::nr is smaller than the one of the bond partner.
+ * \param *AdjacencyFile output stream
+ */
+void BondedParticle::OutputBonds(ofstream * const BondFile) const
+{
+  for (BondList::const_iterator Runner = ListOfBonds.begin(); Runner != ListOfBonds.end(); (++Runner))
+    if (nr < (*Runner)->GetOtherAtom(this)->nr)
+      *BondFile << nr << "\t" << (*Runner)->GetOtherAtom(this)->nr << "\n";
 };