Changeset 32b6dc for molecuilder/src/builder.cpp

Timestamp:

Jun 7, 2008, 1:21:53 PM (17 years ago)

Author:

Frederik Heber <heber@…>

Children:

d11f22

Parents:

a89a22

Message:

Working version of PAS transformation (tested on C-S-H cluster) and code scaffold of VolumeOfConvexEnvelope that's untested so far

PAS simply calculates inertia tensor, diagonalizes it via GSL and transforms molecule into eigenvector system such that z axis is eigenvector of biggest eigenvalue.

File:

• molecuilder/src/builder.cpp (modified) (7 diffs)

molecuilder/src/builder.cpp

@@ -484 +484 @@
  * \param *mol the molecule with all the atoms
  */
-static void MeasureAtoms(periodentafel *periode, molecule *mol)
+static void MeasureAtoms(periodentafel *periode, molecule *mol, config *configuration)
 {
   atom *first, *second, *third;
@@ -496 +496 @@
   cout << Verbose(0) << " b - calculate bond length between two atoms" << endl;
   cout << Verbose(0) << " c - calculate bond angle" << endl;
+  cout << Verbose(0) << " d - calculate principal axis of the system" << endl;
+  cout << Verbose(0) << " e - calculate volume of the convex envelope" << endl;
   cout << Verbose(0) << "all else - go back" << endl;
   cout << Verbose(0) << "===============================================" << endl;
@@ -553 +555 @@
       cout << Verbose(0) << (acos(x.ScalarProduct((const vector *)&y)/(y.Norm()*x.Norm()))/M_PI*180.) << " degrees" << endl;         
       break;
+    case 'd':
+        cout << Verbose(0) << "Evaluating prinicipal axis." << endl;
+        cout << Verbose(0) << "Shall we rotate? [0/1]: ";
+        cin >> Z;
+        if ((Z >=0) && (Z <=1))
+          mol->PrincipalAxisSystem((ofstream *)&cout, (bool)Z);
+        else
+          mol->PrincipalAxisSystem((ofstream *)&cout, false);
+        break;
+    case 'e':
+        cout << Verbose(0) << "Evaluating volume of the convex envelope.";
+        mol->VolumeOfConvexEnvelope((ofstream *)&cout, configuration->GetIsAngstroem());
+        break;
   }
 };
@@ -745 +760 @@
             cout << "\t-f <dist> <order>\tFragments the molecule in BOSSANOVA manner and stores config files in same dir as config." << endl;
             cout << "\t-h/-H/-?\tGive this help screen." << endl;
+            cout << "\t-m\tAlign in PAS with greatest EV along z axis." << endl;
             cout << "\t-p <file>\tParse given xyz file and create raw config file from it." << endl;
             cout << "\t-r\t\tConvert file from an old pcp syntax." << endl;
@@ -945 +961 @@
               }
               break;
+            case 'm':
+              ExitFlag = 1;
+              cout << Verbose(0) << "Evaluating prinicipal axis." << endl;
+              mol->PrincipalAxisSystem((ofstream *)&cout, true);
+              break;
             default:   // no match? Step on
               argptr++;
@@ -1151 +1172 @@
 
       case 'l': // measure distances or angles
-        MeasureAtoms(periode, mol);
+        MeasureAtoms(periode, mol, &configuration);
         break;
 
@@ -1164 +1185 @@
         mol->CreateAdjacencyList((ofstream *)&cout, tmp1, configuration.GetIsAngstroem());
         //mol->CreateListOfBondsPerAtom((ofstream *)&cout);
-        Subgraphs = mol->DepthFirstSearchAnalysis((ofstream *)&cout, false, MinimumRingSize);
+        Subgraphs = mol->DepthFirstSearchAnalysis((ofstream *)&cout, MinimumRingSize);
         while (Subgraphs->next != NULL) {
           Subgraphs = Subgraphs->next;