void MoleculeURLListProperty::loadMolecules(bool selectedOnly /*= false*/, bool removeOnFailure /*= false*/) {
std::vector<std::string> failedURLs;
for (size_t i=0; i<value_.size(); i++) {
std::string url = value_[i];
if (selectedOnly && !isSelected(url))
continue;
if (getMolecule(url))
continue;
try {
loadMolecule(url);
}
catch (tgt::FileException& e) {
LERROR(e.what());
failedURLs.push_back(url);
}
catch (std::bad_alloc&) {
LERROR("bad allocation while loading molecule: " << url);
failedURLs.push_back(url);
}
catch (tgt::Exception& e) {
LERROR("unknown exception while loading molecule '" << url << "':" << e.what());
failedURLs.push_back(url);
}
}
if (removeOnFailure) {
for (size_t i=0; i<failedURLs.size(); i++)
removeURL(failedURLs.at(i));
}
}
int main(int argc, char** argv)
{
float s;
clock_t t;
char inner = 0;
float k = 0;
if (argc!=5)
{
printf("Usage: levelSet <pdb File> <gridSize> <probeSize> <inner caves(1) or outer surface(0)\n");
return 1;
}
t = clock();
mol = loadMolecule(argv[1]);
catrace = loadCATrace(argv[1]);
printf("Number of CA atoms = %d\n",catrace->npoints);
printf("Molecule loading time %f seconds\n",(clock()-t)/(float)CLOCKS_PER_SEC);
N = (short)atoi(argv[2]);
PR = (float)atof(argv[3]);
inner = argv[4][0]-'0';
printf("Number of atoms: %d\n",mol->npoints);
t = clock();
ttime = clock();
s = centerMolecule(mol, catrace);
printf("Molecule centering time %f seconds\n",(clock()-t)/(float)CLOCKS_PER_SEC);
PR = PR*s;
t = clock();
grid = createGrid(N);
printf("Grid creation time %f seconds\n",(clock()-t)/(float)CLOCKS_PER_SEC);
t = clock();
signDistanceGridMol(grid,mol,PR);
printf("Grid initialization time %f seconds\n",(clock()-t)/(float)CLOCKS_PER_SEC);
t = clock();
shrink(grid,PR);
/* c = findProbesMol(grid,PR);
printf("There are %d probes.\n",c);
printf("ProbesMol time %f seconds.\n",(clock()-t)/(float)CLOCKS_PER_SEC);
*/
printf("Shrinking time %f seconds.\n",(clock()-t)/(float)CLOCKS_PER_SEC);
t = clock();
k = s/(512/N);
k = k * k * k;
printf("Total cavity/molecule volume = %f\n",fastMarching(grid,inner)/k);
printf("Fast marching time %f seconds\n",(clock()-t)/(float)CLOCKS_PER_SEC);
init();
return 0;
}
/* initialization */
void initEvent()
{
vl::Log::notify(appletInfo());
/* initialize the text actor */
mText->setText("Drop a MOL2 file inside the window.");
mText->setFont( vl::defFontManager()->acquireFont("/font/bitstream-vera/VeraMono.ttf", 10) );
mText->setAlignment( vl::AlignHCenter | vl::AlignTop );
mText->setViewportAlignment( vl::AlignHCenter | vl::AlignTop );
mText->setTextAlignment(vl::TextAlignCenter);
mText->translate(0,-5,0);
mText->setColor(vl::white);
vl::ref<vl::Effect> effect = new vl::Effect;
effect->shader()->enable(vl::EN_BLEND);
sceneManager()->tree()->addActor(mText.get(), effect.get());
loadMolecule("/mol/molecule.mol2");
}
/* loads a MOL2 file when it is dropped in the window */
void fileDroppedEvent(const std::vector<vl::String>& files)
{
/*loads only the first .mol2 file if more are dropped*/
loadMolecule( files[0] );
}
