Changeset 6d0fcaa for molecuilder/src/molecule_graph.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/molecule_graph.cpp (modified) (1 diff)

molecuilder/src/molecule_graph.cpp

@@ -992 +992 @@
   Log() << Verbose(1) << "Saving adjacency list ... ";
   if (AdjacencyFile != NULL) {
+    AdjacencyFile << "m\tn" << endl;
     ActOnAllAtoms(&atom::OutputAdjacency, &AdjacencyFile);
     AdjacencyFile.close();
+    Log() << Verbose(1) << "done." << endl;
+  } else {
+    Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl;
+    status = false;
+  }
+
+  return status;
+}
+;
+
+/** Storing the bond structure of a molecule to file.
+ * Simply stores Atom::nr and then the Atom::nr of all bond partners, one per line.
+ * \param *out output stream for debugging
+ * \param *path path to file
+ * \return true - file written successfully, false - writing failed
+ */
+bool molecule::StoreBondsToFile(char *path)
+{
+  ofstream BondFile;
+  stringstream line;
+  bool status = true;
+
+  line << path << "/" << FRAGMENTPREFIX << ADJACENCYFILE;
+  BondFile.open(line.str().c_str(), ios::out);
+  Log() << Verbose(1) << "Saving adjacency list ... ";
+  if (BondFile != NULL) {
+    BondFile << "m\tn" << endl;
+    ActOnAllAtoms(&atom::OutputBonds, &BondFile);
+    BondFile.close();
     Log() << Verbose(1) << "done." << endl;
   } else {