int __cdecl _tmain (int argc, TCHAR *argv[])
{
HRESULT result = ProcessArgs(argc, argv);
if (FAILED(result))
return result;
UseImage(QueryContinuously);
return S_OK;
}
void BaseADMImageItem::BaseDraw(IADMDrawer drawer)
{
ASBoolean needNormalDraw = true;
if (UseImage())
{
IADMRect boundsRect;
drawer.GetBoundsRect(boundsRect);
if (fImage && (fImage.GetWidth() != boundsRect.Width() || fImage.GetHeight() != boundsRect.Height()))
{
sADMImage->Destroy(fImage);
fImage = NULL;
}
if (!fImage && boundsRect.Width() != 0 && boundsRect.Height() != 0)
fImage = sADMImage->CreateOffscreen(boundsRect.Width(), boundsRect.Height(), 0);
if (fImage)
{
IADMDrawer imageDrawer = fImage.BeginADMDrawer();
if (imageDrawer)
{
// Make sure we are using the same background color as original drawer
imageDrawer.SetUsePaletteBGColor( drawer.GetUsePaletteBGColor() );
imageDrawer.ClearRect(boundsRect);
Draw(imageDrawer);
fImage.EndADMDrawer();
needNormalDraw = false;
}
IADMPoint point(0, 0);
drawer.DrawADMImage(fImage, point);
}
}
if (needNormalDraw)
Draw(drawer);
}
// Action_Distance::init()
Action::RetType Action_Distance::Init(ArgList& actionArgs, TopologyList* PFL, FrameList* FL,
DataSetList* DSL, DataFileList* DFL, int debugIn)
{
// Get Keywords
InitImaging( !(actionArgs.hasKey("noimage")) );
useMass_ = !(actionArgs.hasKey("geom"));
DataFile* outfile = DFL->AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
DataSet::scalarType stype = DataSet::UNDEFINED;
std::string stypename = actionArgs.GetStringKey("type");
if ( stypename == "hbond" ) stype = DataSet::HBOND;
else if (stypename == "noe" ) stype = DataSet::NOE; // TODO: Grab bound and boundh
// Get Masks
std::string mask1 = actionArgs.GetMaskNext();
std::string mask2 = actionArgs.GetMaskNext();
if (mask1.empty() || mask2.empty()) {
mprinterr("Error: distance: Requires 2 masks\n");
return Action::ERR;
}
Mask1_.SetMaskString(mask1);
Mask2_.SetMaskString(mask2);
// Dataset to store distances
dist_ = DSL->AddSet(DataSet::DOUBLE, actionArgs.GetStringNext(), "Dis");
if (dist_==0) return Action::ERR;
dist_->SetScalar( DataSet::M_DISTANCE, stype );
// Add dataset to data file
if (outfile != 0) outfile->AddSet( dist_ );
mprintf(" DISTANCE: %s to %s",Mask1_.MaskString(), Mask2_.MaskString());
if (!UseImage())
mprintf(", non-imaged");
if (useMass_)
mprintf(", center of mass");
else
mprintf(", geometric center");
mprintf(".\n");
return Action::OK;
}
Action::RetType Action_DNAionTracker::Init(ArgList& actionArgs, TopologyList* PFL, DataSetList* DSL, DataFileList* DFL, int debugIn)
{
// Get keywords
DataFile* outfile = DFL->AddDataFile(actionArgs.GetStringKey("out"), actionArgs);
poffset_ = actionArgs.getKeyDouble("poffset", 5.0);
InitImaging( !actionArgs.hasKey("noimage") );
if (actionArgs.hasKey("shortest"))
bintype_ = SHORTEST;
else if (actionArgs.hasKey("counttopcone"))
bintype_ = TOPCONE;
else if (actionArgs.hasKey("countbottomcone"))
bintype_ = BOTTOMCONE;
else if (actionArgs.hasKey("count"))
bintype_ = COUNT;
// Get masks - 4 must be specified
std::string m1 = actionArgs.GetMaskNext();
std::string m2 = actionArgs.GetMaskNext();
std::string m3 = actionArgs.GetMaskNext();
std::string m4 = actionArgs.GetMaskNext();
if (m1.empty() || m2.empty() || m3.empty() || m4.empty()) {
mprinterr("Error: dnaiontracker requires 4 masks.\n");
return Action::ERR;
}
p1_.SetMaskString(m1);
p2_.SetMaskString(m2);
base_.SetMaskString(m3);
ions_.SetMaskString(m4);
// Add dataset to dataset list (and datafile list if filename specified)
distance_ = DSL->AddSet(DataSet::DOUBLE, MetaData(actionArgs.GetStringNext(),
MetaData::M_DISTANCE), "DNAion");
if (distance_==0) return Action::ERR;
if (outfile != 0)
outfile->AddDataSet( distance_ );
// INFO
mprintf(" DNAIONTRACKER: Data representing the ");
switch (bintype_) {
case COUNT :
mprintf("count within the cone will be\n"); break;
case SHORTEST:
mprintf("shortest distance to a phosphate or base centroid will be\n"); break;
case TOPCONE:
mprintf("count in the top half of the cone (and sort-of bound) will be\n"); break;
case BOTTOMCONE:
mprintf("count in the bottom half of the cone will be\n"); break;
}
mprintf(" saved to array named %s\n", distance_->legend());
mprintf(" Perpendicular offset for cone is %5.2f angstroms\n", poffset_);
if (!UseImage())
mprintf(" Imaging has been disabled\n");
mprintf("\tPhosphate1 Mask [%s]\n", p1_.MaskString());
mprintf("\tPhosphate2 Mask [%s]\n", p2_.MaskString());
mprintf("\tBase Mask [%s]\n", base_.MaskString());
mprintf("\tIons Mask [%s]\n", ions_.MaskString());
if (outfile != 0)
mprintf("\tData will be printed to a file named %s\n", outfile->DataFilename().full());
return Action::OK;
}
// Action_Watershell::init()
Action::RetType Action_Watershell::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
InitImaging( !actionArgs.hasKey("noimage") );
// Get keywords
std::string filename = actionArgs.GetStringKey("out");
lowerCutoff_ = actionArgs.getKeyDouble("lower", 3.4);
upperCutoff_ = actionArgs.getKeyDouble("upper", 5.0);
// Get solute mask
std::string maskexpr = actionArgs.GetMaskNext();
if (maskexpr.empty()) {
mprinterr("Error: Solute mask must be specified.\n");
return Action::ERR;
}
soluteMask_.SetMaskString( maskexpr );
// Check for solvent mask
solventmaskexpr_ = actionArgs.GetMaskNext();
// For backwards compat., if no 'out' assume next string is
if (filename.empty() && actionArgs.Nargs() > 2 && !actionArgs.Marked(2))
filename = actionArgs.GetStringNext();
DataFile* outfile = init.DFL().AddDataFile( filename, actionArgs );
// Set up datasets
std::string dsname = actionArgs.GetStringNext();
if (dsname.empty())
dsname = init.DSL().GenerateDefaultName("WS");
lower_ = init.DSL().AddSet(DataSet::INTEGER, MetaData(dsname, "lower"));
upper_ = init.DSL().AddSet(DataSet::INTEGER, MetaData(dsname, "upper"));
if (lower_ == 0 || upper_ == 0) return Action::ERR;
if (outfile != 0) {
outfile->AddDataSet(lower_);
outfile->AddDataSet(upper_);
}
# ifdef _OPENMP
// Determine number of parallel threads
#pragma omp parallel
{
if (omp_get_thread_num()==0)
numthreads_ = omp_get_num_threads();
}
# endif
mprintf(" WATERSHELL:");
if (outfile != 0) mprintf(" Output to %s", outfile->DataFilename().full());
mprintf("\n");
if (!UseImage())
mprintf("\tImaging is disabled.\n");
mprintf("\tThe first shell will contain water < %.3f angstroms from\n",
lowerCutoff_);
mprintf("\t the solute; the second shell < %.3f angstroms...\n",
upperCutoff_);
mprintf("\tSolute atoms will be specified by [%s]\n",soluteMask_.MaskString());
if (!solventmaskexpr_.empty()) {
mprintf("\tSolvent atoms will be specified by [%s]\n",
solventmaskexpr_.c_str());
solventMask_.SetMaskString( solventmaskexpr_ );
}
if (numthreads_ > 1)
mprintf("\tParallelizing calculation with %i threads.\n", numthreads_);
mprintf("\t# waters in 'lower' shell stored in set '%s'\n", lower_->legend());
mprintf("\t# waters in 'upper' shell stored in set '%s'\n", upper_->legend());
// Pre-square upper and lower cutoffs
lowerCutoff_ *= lowerCutoff_;
upperCutoff_ *= upperCutoff_;
return Action::OK;
}
