Changeset b84ab4 for molecuilder/src/builder.cpp

Timestamp:

Oct 30, 2009, 3:49:38 PM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

245826

Parents:

5f697c

git-author:

Frederik Heber <heber@…> (10/30/09 15:33:51)

git-committer:

Frederik Heber <heber@…> (10/30/09 15:49:38)

Message:

BondGraph is parsed if command line switch '-g' is given.

• builder.cpp: case 'g' which gives a bond length table file which is parsed after the configuration and before other command line options.
• BondGraph::BondLengthMatrixMinMaxDistance() falls back to CovalentMinMaxDistance() if no table parsed.
• Bond Length Table was changed to have first row _and_ column each enlist all the elements and does not have a "#" in front anymore.
• The unit test has been changed accordingly.

Signed-off-by: Frederik Heber <heber@…>

File:

• molecuilder/src/builder.cpp (modified) (6 diffs)

molecuilder/src/builder.cpp

@@ -1357 +1357 @@
   int argptr;
   molecule *mol = NULL;
+  string BondGraphFileName("");
   strncpy(configuration.databasepath, LocalPath, MAXSTRINGSIZE-1);
 
@@ -1384 +1385 @@
             cout << "\t-E <id> <Z>\tChange atom <id>'s element to <Z>, <id> begins at 0." << endl;
             cout << "\t-f/F <dist> <order>\tFragments the molecule in BOSSANOVA manner (with/out rings compressed) and stores config files in same dir as config (return code 0 - fragmented, 2 - no fragmentation necessary)." << endl;
+            cout << "\t-g <file>\tParses a bond length table from the given file." << endl;
             cout << "\t-h/-H/-?\tGive this help screen." << endl;
             cout << "\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;
@@ -1420 +1422 @@
             }
             break;
+          case 'g':
+            if ((argptr >= argc) || (argv[argptr][0] == '-')) {
+              cerr << "Not enough or invalid arguments for specifying bond length table: -g <table file>" << endl;
+            } else {
+              BondGraphFileName = argv[argptr];
+              cout << "Using " << BondGraphFileName << " as bond length table." << endl;
+              argptr+=1;
+            }
+            break;
           case 'n':
             cout << "I won't parse trajectories." << endl;
@@ -1432 +1443 @@
     } while (argptr < argc);
 
-    // 2. Parse the element database
+    // 3a. Parse the element database
     if (periode->LoadPeriodentafel(configuration.databasepath)) {
       cout << Verbose(0) << "Element list loaded successfully." << endl;
@@ -1440 +1451 @@
       return 1;
     }
-    // 3. Find config file name and parse if possible
+    // 3b. Find config file name and parse if possible
     if (argv[1][0] != '-') {
       // simply create a new molecule, wherein the config file is loaded and the manipulation takes place
@@ -1483 +1494 @@
     } else
       configPresent = absent;
+    // 3c. parse the bond graph file if given
+    configuration.BG = new BondGraph(configuration.GetIsAngstroem());
+    if (configuration.BG->LoadBondLengthTable((ofstream *)&cout, BondGraphFileName)) {
+      cout << Verbose(0) << "Bond length table loaded successfully." << endl;
+    } else {
+      cout << Verbose(0) << "Bond length table loading failed." << endl;
+      return 1;
+    }
     // 4. parse again through options, now for those depending on elements db and config presence
     argptr = 1;