int main(int argc, const char **argv) {
seed();
physics::settings_type physics_settings;
scene::settings_type scene_settings;
Helix::settings_type helix_settings;
std::string input_file, output_file;
parse_settings::parse(argc, argv, physics_settings, scene_settings, helix_settings, input_file, output_file);
if (input_file.empty() || output_file.empty() || argc < 3) {
std::cerr << parse_settings::usage(argv[0]) << std::endl;
return 0;
}
scene mesh(scene_settings, helix_settings);
physics phys(physics_settings);
try {
if (!mesh.read(phys, input_file)) {
std::cerr << "Failed to read scene \"" << input_file << "\"" << std::endl;
return 1;
}
}
catch (const std::runtime_error & e) {
std::cerr << "Failed to read scene \"" << input_file << "\": " << e.what() << std::endl;
return 1;
}
physics::real_type initialmin, initialmax, initialaverage, initialtotal, min, max, average, total;
mesh.getTotalSeparationMinMaxAverage(initialmin, initialmax, initialaverage, initialtotal);
std::cerr << "Running simulation for scene loaded from \"" << input_file << " outputting to " << output_file << "\"." << std::endl
<< "Initial: min: " << initialmin << ", max: " << initialmax << ", average: " << initialaverage << ", total: " << initialtotal << " nm" << std::endl
<< "Connect with NVIDIA PhysX Visual Debugger to " << PVD_HOST << ':' << PVD_PORT << " to visualize the progress. " << std::endl
<< "Press ^C to stop the relaxation...." << std::endl;
setinterrupthandler<handle_exit>();
SceneDescription best_scene;
Helix helix1 = Helix(helix_settings, phys, 20, physics::transform_type(physics::vec3_type(1,20,1)));
Helix helix2 = Helix(helix_settings, phys, 20, physics::transform_type(physics::vec3_type(1, 20, 8)));
helix1.attach(phys, helix2, Helix::AttachmentPoint::kBackwardFivePrime, Helix::AttachmentPoint::kBackwardThreePrime);
#if 0
best_scene = simulated_rectification(mesh, phys, []() { return running; });
#else
#if 0
simulated_annealing(mesh, phys, 100, 0, 7, 1,
[&best_scene](scene & mesh, float e) { std::cerr << "Store best energy: " << e << std::endl; best_scene = SceneDescription(mesh); },
[]() { return running; });
#else
gradient_descent(mesh, phys, 7,
[&best_scene, &min, &max, &average, &total](scene & mesh, physics::real_type min_, physics::real_type max_, physics::real_type average_, physics::real_type total_) { min = min_; max = max_; average = average_; total = total_; std::cerr << "State: min: " << min << ", max: " << max << ", average: " << average << " total: " << total << " nm" << std::endl; best_scene = SceneDescription(mesh); },
[]() { return running; });
#endif
#endif
std::cerr << "Result: min: " << min << ", max: " << max << ", average: " << average << ", total: " << total << " nm" << std::endl;
{
std::ofstream outfile(output_file);
outfile << "# Relaxation of original " << input_file << " file. " << mesh.getHelixCount() << " helices." << std::endl
<< "# Total separation: Initial: min: " << initialmin << ", max: " << initialmax << ", average: " << initialaverage << ", total: " << initialtotal << " nm" << ", final: min: " << min << ", max: " << max << ", average: " << average << ", total: " << total << " nm" << std::endl;
if (!best_scene.write(outfile))
std::cerr << "Failed to write resulting mesh to \"" << output_file << "\"" << std::endl;
outfile.close();
}
sleepms(2000);
return 0;
}
int main(int argc, char **argv)
{
CHAIN **Chain;
HBOND **HBond;
COMMAND *Cmd;
int Cn, NChain=0, NHBond=0, ValidChain=0;
float **PhiPsiMapHelix, **PhiPsiMapSheet;
register int i;
/* argc = ccommand(&argv); */ /* For Macintosh only, see readme.mac */
Chain = (CHAIN **)ckalloc(MAX_CHAIN*sizeof(CHAIN *));
HBond = (HBOND **)ckalloc(MAXHYDRBOND*sizeof(HBOND *));
Cmd = (COMMAND *)ckalloc(sizeof(COMMAND));
ProcessStrideOptions(argv,argc,Cmd);
if( !ReadPDBFile(Chain,&NChain,Cmd) || !NChain )
die("Error reading PDB file %s\n",Cmd->InputFile);
for( Cn=0; Cn<NChain; Cn++ )
ValidChain += CheckChain(Chain[Cn],Cmd);
/* if( Cmd->Stringent )
* exit(0);
*/
if( !ValidChain )
die("No valid chain in %s\n",Chain[0]->File);
if( Cmd->BrookhavenAsn )
GetPdbAsn(Chain,NChain);
if( Cmd->DsspAsn )
GetDsspAsn(Chain,NChain,Cmd);
BackboneAngles(Chain,NChain);
if( Cmd->OutSeq )
OutSeq(Chain,NChain,Cmd);
if( Cmd->ContactOrder )
ContactOrder(Chain,NChain,Cmd);
if( Cmd->ContactMap )
ContactMap(Chain,NChain,Cmd);
if( !strlen(Cmd->MapFileHelix) )
PhiPsiMapHelix = DefaultHelixMap(Cmd);
else
ReadPhiPsiMap(Cmd->MapFileHelix,&PhiPsiMapHelix,Cmd);
if( !strlen(Cmd->MapFileSheet) )
PhiPsiMapSheet = DefaultSheetMap(Cmd);
else
ReadPhiPsiMap(Cmd->MapFileSheet,&PhiPsiMapSheet,Cmd);
for( Cn=0; Cn<NChain; Cn++ )
PlaceHydrogens(Chain[Cn]);
if( (NHBond = FindHydrogenBonds(Chain,Cn,HBond,Cmd)) == 0 )
die("No hydrogen bonds found in %s\n",Cmd->InputFile);
NoDoubleHBond(HBond,NHBond);
DiscrPhiPsi(Chain,NChain,Cmd);
if(Cmd->ExposedArea)
Area(Chain,NChain,Cmd);
for( Cn=0; Cn<NChain; Cn++ ) {
if( Chain[Cn]->Valid ) {
Helix(Chain,Cn,HBond,Cmd,PhiPsiMapHelix);
for( i=0; i<NChain; i++ )
if( Chain[i]->Valid )
Sheet(Chain,Cn,i,HBond,Cmd,PhiPsiMapSheet);
BetaTurn(Chain,Cn);
GammaTurn(Chain,Cn,HBond);
}
}
Report(Chain,NChain,HBond,Cmd);
if( Cmd->MolScript )
MolScript(Chain,NChain,Cmd);
for( i=0; i<Cn; i++ ) free(Chain[i]);
for( i=0; i<NHBond; i++ ) free(HBond[i]);
free(Cmd);
return(0);
}
