Changes in src/builder.cpp [68f03d:b32dbb]

File:

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

src/builder.cpp ¶

@@ -70 +70 @@
 #include "molecule.hpp"
 #include "periodentafel.hpp"
+#include "tesselationhelpers.hpp"
 #include "UIElements/UIFactory.hpp"
 #include "UIElements/MainWindow.hpp"
@@ -1519 +1520 @@
         switch(argv[argptr-1][1]) {
           case 'h':
-          case 'H':
           case '?':
             DoLog(0) && (Log() << Verbose(0) << "MoleCuilder suite" << endl << "==================" << endl << endl);
@@ -1538 +1538 @@
             DoLog(0) && (Log() << Verbose(0) << "\t-FF <MaxDistance> <xyz of filler> <dist_x> <dist_y> <dist_z> <epsilon> <randatom> <randmol> <DoRotate>\tFilling Box with water molecules." << endl);
             DoLog(0) && (Log() << Verbose(0) << "\t-g <file>\tParses a bond length table from the given file." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-h/-H/-?\tGive this help screen." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-h/-?\tGive this help screen." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-H\tCount Hydrogen bridge bonds." << endl);
             DoLog(0) && (Log() << Verbose(0) << "\t-I\t Dissect current system of molecules into a set of disconnected (subgraphs of) molecules." << endl);
             DoLog(0) && (Log() << Verbose(0) << "\t-j\t<path> Store all bonds to file." << endl);
@@ -1819 +1820 @@
               }
               break;
+            case 'H':
+              if ((argptr+1 >= argc) || (argv[argptr][0] == '-') || (argv[argptr+1][0] == '-')) {
+                ExitFlag = 255;
+                DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for calculating hydrogen bridge bonds: -H <Z1> <Z2>" << endl);
+                performCriticalExit();
+              } else {
+                if (ExitFlag == 0) ExitFlag = 1;
+                const element *elemental = periode->FindElement((const int) atoi(argv[argptr]));
+                const element *elemental2 = periode->FindElement((const int) atoi(argv[argptr+1]));
+                cout << endl << "There are " << CountHydrogenBridgeBonds(molecules, elemental, elemental2) << " hydrogen bridges with connections to " << (elemental != 0 ? elemental->name : "None") << " and " << (elemental2 != 0 ? elemental2->name : "None") << "." << endl;
+                argptr+=1;
+              }
+              break;
             case 'C':
               {
@@ -2089 +2103 @@
               } else {
                 class Tesselation *T = NULL;
+                class Tesselation *Convex = NULL;
                 const LinkedCell *LCList = NULL;
+                const LinkedCell *LCListConvex = NULL;
                 molecule * Boundary = NULL;
                 //string filename(argv[argptr+1]);
@@ -2109 +2125 @@
                 if (!FindNonConvexBorder(Boundary, T, LCList, atof(argv[argptr]), argv[argptr+1]))
                   ExitFlag = 255;
+                const double ConvexRadius = 20.;
+                LCListConvex = new LinkedCell(Boundary, 2.*ConvexRadius);
+//                setVerbosity(3);
+                if (!FindNonConvexBorder(Boundary, Convex, LCListConvex, ConvexRadius, "ConvexEnvelope"))
+                  ExitFlag = 255;
+                CalculateConstrictionPerBoundaryPoint(T, Convex);
+                StoreTrianglesinFile(mol, (const Tesselation *&)T, argv[argptr+1], "");
                 //FindDistributionOfEllipsoids(T, &LCList, N, number, filename.c_str());
                 end = clock();