Changeset 6d0fcaa for molecuilder/src/builder.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/builder.cpp (modified) (3 diffs)

molecuilder/src/builder.cpp

@@ -1422 +1422 @@
             Log() << Verbose(0) << "\t-h/-H/-?\tGive this help screen." << endl;
             Log() << Verbose(0) << "\t-I\t Dissect current system of molecules into a set of disconnected (subgraphs of) molecules." << endl;
+            Log() << Verbose(0) << "\t-j\t<path> Store all bonds to file." << endl;
+            Log() << Verbose(0) << "\t-J\t<path> Store adjacency per atom to file." << endl;
             Log() << Verbose(0) << "\t-L <step0> <step1> <prefix>\tStore a linear interpolation between two configurations <step0> and <step1> into single config files with prefix <prefix> and as Trajectories into the current config file." << endl;
             Log() << Verbose(0) << "\t-m <0/1>\tCalculate (0)/ Align in(1) PAS with greatest EV along z axis." << endl;
@@ -1709 +1711 @@
                 CorrelationToSurfaceMap *surfacemap = PeriodicCorrelationToSurface( molecules, elemental, TesselStruct, LCList, ranges );
                 OutputCorrelationToSurface(&output, surfacemap);
-                BinPairMap *binmap = BinData( surfacemap, 0.5, 0., 0. );
+                BinPairMap *binmap = BinData( surfacemap, 0.5, 0., 20. );
                 OutputCorrelation ( &binoutput, binmap );
                 output.close();
@@ -1793 +1795 @@
               }
               break;
+
+            case 'J':
+              if (ExitFlag == 0) ExitFlag = 1;
+              if ((argptr >= argc) || (argv[argptr][0] == '-')) {
+                ExitFlag =255;
+                eLog() << Verbose(0) << "Missing path of adjacency file: -j <path>" << endl;
+                performCriticalExit();
+              } else {
+                Log() << Verbose(0) << "Storing adjacency to path " << argv[argptr] << "." << endl;
+                configuration.BG->ConstructBondGraph(mol);
+                mol->StoreAdjacencyToFile(argv[argptr]);
+                argptr+=1;
+              }
+              break;
+
+            case 'j':
+              if (ExitFlag == 0) ExitFlag = 1;
+              if ((argptr >= argc) || (argv[argptr][0] == '-')) {
+                ExitFlag =255;
+                eLog() << Verbose(0) << "Missing path of bonds file: -j <path>" << endl;
+                performCriticalExit();
+              } else {
+                Log() << Verbose(0) << "Storing bonds to path " << argv[argptr] << "." << endl;
+                configuration.BG->ConstructBondGraph(mol);
+                mol->StoreBondsToFile(argv[argptr]);
+                argptr+=1;
+              }
+              break;
+
             case 'N':
               if (ExitFlag == 0) ExitFlag = 1;