// Find forcefield by name
Forcefield* Aten::findForcefield(QString name) const
{
Messenger::enter("Aten::findForcefield");
Forcefield* ff;
for (ff = forcefields_.first(); ff != NULL; ff = ff->next) if (name == ff->name()) break;
if (ff == NULL) Messenger::print("Forcefield '%s' is not loaded.", qPrintable(name));
Messenger::exit("Aten::findForcefield");
return ff;
}
// Return first forcefield atom type matching supplied name
ForcefieldAtom* ElementMap::forcefieldAtom(QString name)
{
ForcefieldAtom* ffa;
for (Forcefield* ff = aten_->forcefields(); ff != NULL; ff = ff->next)
{
ffa = ff->findType(name);
if (ffa != NULL) return ffa;
}
return NULL;
}
// Convert string from fftype to element number
int ElementMap::ffToZ(const char* s) const
{
ForcefieldAtom* ffa;
int result = -1;
for (Forcefield* ff = duq.forcefields(); ff != NULL; ff = ff->next)
{
ffa = ff->findType(s);
// Found a match, so find out what element it is...
if (ffa != NULL) result = ffa->neta()->characterElement();
if (result != -1) break;
}
return result;
}
ATEN_USING_NAMESPACE
// Add Forcefield
Forcefield* Aten::addForcefield(QString name)
{
Forcefield* newFF = forcefields_.add();
if (name != NULL) newFF->setName(name);
// Set this new forcefield to be the current one
setCurrentForcefield(newFF);
return current_.ff;
}
// Convert string from fftype to element number
int ElementMap::ffToZ(QString s)
{
if (!aten_) return -1;
ForcefieldAtom* ffa;
int result = -1;
for (Forcefield* ff = aten_->forcefields(); ff != NULL; ff = ff->next)
{
ffa = ff->findType(s);
// Found a match, so find out what element it is...
if (ffa != NULL) result = ffa->neta()->characterElement();
if (result != -1) break;
}
return result;
}
// Load forcefield
Forcefield* Aten::loadForcefield(QString ffFile)
{
Messenger::enter("Aten::loadForcefield");
// Try some different locations to find the supplied forcefield.
QString filename;
QFileInfo fileInfo;
bool result;
Forcefield* newff = forcefields_.add();
// First try - actual / absolute path
fileInfo.setFile(ffFile);
Messenger::print(Messenger::Verbose, "Looking for forcefield in absolute path (%s)...", qPrintable(ffFile));
if (fileInfo.exists()) result = newff->load(ffFile);
else
{
// Second try - aten.dataDir/ff
filename = dataDirectoryFile("ff/"+ffFile);
fileInfo.setFile(filename);
Messenger::print(Messenger::Verbose, "Looking for forcefield in installed location (%s)...", qPrintable(filename));
if (fileInfo.exists()) result = newff->load(filename);
else
{
// Last try - user home datadir/ff
filename = atenDirectoryFile("ff/"+ffFile);
fileInfo.setFile(filename);
Messenger::print(Messenger::Verbose, "Looking for forcefield in user's data directory (%s)...", qPrintable(filename));
if (fileInfo.exists()) result = newff->load(filename);
else
{
Messenger::print("Can't find forcefield file '%s' in any location.", qPrintable(ffFile));
result = false;
}
}
}
if (result) setCurrentForcefield(newff);
else
{
Messenger::print("Couldn't load forcefield file '%s'.", qPrintable(ffFile));
forcefields_.remove(newff);
newff = NULL;
}
Messenger::exit("Aten::loadForcefield");
return newff;
}
// Close window (accepted)
void AtenPrefs::on_PrefsOkButton_clicked(bool checked)
{
// Recalculate forcefield energy terms if the glboal energy unit was changed
if (prefsBackup_.energyUnit() != prefs.energyUnit()) for (Forcefield* ff = parent_.aten().forcefields(); ff != NULL; ff = ff->next) ff->convertParameters();
updateAfterViewPrefs();
accept();
}
void TestRefiner_FromStage2( int argc, char** argv)
{
ASSERT( argc == 6, ArgumentException, "Give me traname, startres, length, branchCount\n" );
std::string traFile( argv[1] );
int startRes = atoi( argv[2] );
int nRes = atoi( argv[3] );
double dielec = atof( argv[4] );
int execID = atoi( argv[5] );
int endRes = startRes + nRes - 1;
std::string stem = traPathToStem( traFile, dielec ) + "_out";
// set a standard random number seed for this test.
Maths::FastRandom::getInstance()->reinitialise(100);
std::string libPath = "./";
// Load the replay InTra
if( !IO::fileExists( traFile ) )
{
throw IOException("Cant find tra!");
}
// Load our anglsest
Library::AngleSet as;
as.loadFromFile(libPath + "big.loop.angleset");
as.info();
// Load our forcefield parameters
FFParamSet ffps;
ffps.readLib(libPath + "amber03aa.ff");
Library::RotamerLibrary rotLib( ffps );
//rotLib.readLib( libPath + "lib/rotlib/shetty.rotamer" );
// Use the HIGH resolution lib for refinement
rotLib.convertLib(libPath + "scl-B30-occ1.0-rmsd0.5-prop20.0", Library::RotLibConvert_Shetty() );
//rotLib.convertLib(libPath + "scl-B30-occ1.0-rmsd0.2-prop20.0", Library::RotLibConvert_Shetty() );
//rotLib.convertLib(libPath + "scl-B30-occ1.0-rmsd1.0-prop20.0", Library::RotLibConvert_Shetty() );
//rotLib.writeLib( libPath + "shetty.rotamer" );
// Load our tra
System sys(ffps);
IO::InTra_BTF traInput( traFile );
traInput.loadIntoSystem( sys, -1 );
// Make a full workspace from the imported system
WorkSpace wspace( sys );
wspace.info();
RotBond replacement; // Must stay in scope for the lifetime of this wspace...
wspace.setRotatableBondList( &replacement ); // Override the internal dummy rotbond array
IO::OutTra_BTF& tra = wspace.addStdTra(stem); // tra
IO::BTF_Block_Comment* cmnt = new IO::BTF_Block_Comment();
tra.addOwnedBlock(cmnt);
// Write what we have interpreted from the import file
PDB_Writer(stem + ".imported.pdb").write(wspace); // pdb
// Forcefield config
bool useBrokenBonded = true; // Flag the use of the bonded forcefield that allows bond breaks.
Forcefield ffs = createffts(wspace,useBrokenBonded,false);
Forcefield ff = createff(wspace,useBrokenBonded,dielec,false);
SegmentDef def(wspace,startRes,endRes,SegBreakCentre);
def.info();
// Loop stitcher
Protocol::ArcusReplay loopBuild(ffs,ff,as,rotLib,traInput);
loopBuild.UpdateNList = 5;
loopBuild.OutputLevel = Verbosity::Eleven; // I love that flag :-D
loopBuild.enableComments( cmnt );
loopBuild.buildAddExplicit( def ); // turn off auto-detection of what to build and explicitly define it
// Override to split protocol ...
ArcusRefine_CGMin minimisingRefiner;
minimisingRefiner.OutputLevel = Verbosity::Normal;
minimisingRefiner.enableRotamerPack( rotLib );
minimisingRefiner.UpdateNList = 10;
loopBuild.setRefiner( minimisingRefiner );
Printf("All setup complete... Rolling the primary loop. Hold onto your hat!\n");
int result = loopBuild.run();
ff.calcEnergies();
cmnt->setFormat("**Final Best** Structure According to FF! Ene: %8.3f, BB-cRMS: %8.3f, Heavy-cRMS: %8.3f\n")
(wspace.ene.epot / (Physics::PhysicsConst::kcal2J / Physics::PhysicsConst::Na))
(def.cCRMS_BB())
(def.cCRMS_Heavy());
cmnt->toScreen();
wspace.outtra.append();
Printf("Complete! :-D\n");
return;
}
