// 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_LIE::init()
Action::RetType Action_LIE::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
// Always use imaged distances
InitImaging(true);
double cut;
// Get Keywords
doelec_ = !(actionArgs.hasKey("noelec"));
dovdw_ = !(actionArgs.hasKey("novdw"));
DataFile* datafile = init.DFL().AddDataFile(actionArgs.GetStringKey("out"), actionArgs);
dielc_ = actionArgs.getKeyDouble("diel", 1.0);
cut = actionArgs.getKeyDouble("cutvdw", 12.0);
cut2vdw_ = cut * cut; // store square of cut for computational efficiency
cut = actionArgs.getKeyDouble("cutelec", 12.0);
cut2elec_ = cut * cut; // store square of cut for computational efficiency
onecut2_ = 1 / cut2elec_;
bool has_mask2 = false;
if (!doelec_ && !dovdw_) {
mprinterr("Error: LIE: Cannot skip both ELEC and VDW calcs\n");
return Action::ERR;
}
// Get Masks
Mask1_.SetMaskString( actionArgs.GetMaskNext() );
std::string refmask = actionArgs.GetMaskNext();
if (!refmask.empty()) {
Mask2_.SetMaskString(refmask);
has_mask2 = true;
}
else {
Mask2_ = Mask1_;
Mask2_.InvertMaskExpression();
}
// Get data set name
std::string ds_name = actionArgs.GetStringNext();
if (ds_name.empty())
ds_name = init.DSL().GenerateDefaultName("LIE");
// Datasets
if (doelec_) {
elec_ = init.DSL().AddSet(DataSet::DOUBLE, MetaData(ds_name, "EELEC"));
if (elec_ == 0) return Action::ERR;
if (datafile != 0) datafile->AddDataSet(elec_);
}
if (dovdw_) {
vdw_ = init.DSL().AddSet(DataSet::DOUBLE, MetaData(ds_name, "EVDW"));
if (vdw_ == 0) return Action::ERR;
if (datafile != 0) datafile->AddDataSet(vdw_);
}
mprintf(" LIE: Ligand mask is %s. Surroundings are ", Mask1_.MaskString());
if (!has_mask2)
mprintf("everything else. ");
else
mprintf("atoms in mask %s. ", Mask2_.MaskString());
mprintf("Cutoff is %.3lf Ang. ", cut);
if (!doelec_)
mprintf("Skipping Electrostatic Calc. ");
if (!dovdw_)
mprintf("Skipping VDW Calc. ");
mprintf("\n");
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;
}
// Action_Spam::init()
Action::RetType Action_Spam::Init(ArgList& actionArgs, TopologyList* PFL, DataSetList* DSL, DataFileList* DFL, int debugIn)
{
// Always use imaged distances
InitImaging(true);
// This is needed everywhere in this function scope
FileName filename;
// See if we're doing pure water. If so, we don't need a peak file
purewater_ = actionArgs.hasKey("purewater");
if (purewater_) {
// We still need the cutoff
double cut = actionArgs.getKeyDouble("cut", 12.0);
cut2_ = cut * cut;
doublecut_ = 2 * cut;
onecut2_ = 1 / cut2_;
// See if we write to a data file
datafile_ = actionArgs.GetStringKey("out");
// Generate the data set name, and hold onto the master data set list
std::string ds_name = actionArgs.GetStringKey("name");
if (ds_name.empty())
ds_name = myDSL_.GenerateDefaultName("SPAM");
// We only have one data set averaging over every water. Add it here
myDSL_.AddSet(DataSet::DOUBLE, ds_name, NULL);
solvname_ = actionArgs.GetStringKey("solv");
if (solvname_.empty())
solvname_ = std::string("WAT");
}else {
// Get the file name with the peaks defined in it
filename.SetFileName( actionArgs.GetStringNext() );
if (filename.empty() || !File::Exists(filename)) {
mprinterr("Spam: Error: Peak file [%s] does not exist!\n", filename.full());
return Action::ERR;
}
// Get the remaining optional arguments
solvname_ = actionArgs.GetStringKey("solv");
if (solvname_.empty())
solvname_ = std::string("WAT");
reorder_ = actionArgs.hasKey("reorder");
bulk_ = actionArgs.getKeyDouble("bulk", 0.0);
double cut = actionArgs.getKeyDouble("cut", 12.0);
cut2_ = cut * cut;
doublecut_ = 2 * cut;
onecut2_ = 1 / cut2_;
std::string infoname = actionArgs.GetStringKey("info");
if (infoname.empty())
infoname = std::string("spam.info");
infofile_ = DFL->AddCpptrajFile(infoname, "SPAM info");
if (infofile_ == 0) return Action::ERR;
// The default maskstr is the Oxygen atom of the solvent
summaryfile_ = actionArgs.GetStringKey("summary");
// Divide site size by 2 to make it half the edge length (or radius)
site_size_ = actionArgs.getKeyDouble("site_size", 2.5) / 2.0;
sphere_ = actionArgs.hasKey("sphere");
// If it's a sphere, square the radius to compare with
if (sphere_)
site_size_ *= site_size_;
datafile_ = actionArgs.GetStringKey("out");
std::string ds_name = actionArgs.GetStringKey("name");
if (ds_name.empty())
ds_name = myDSL_.GenerateDefaultName("SPAM");
// Parse through the peaks file and extract the peaks
CpptrajFile peakfile;
if (peakfile.OpenRead(filename)) {
mprinterr("SPAM: Error: Could not open %s for reading!\n", filename.full());
return Action::ERR;
}
std::string line = peakfile.GetLine();
int npeaks = 0;
while (!line.empty()) {
if (sscanf(line.c_str(), "%d", &npeaks) != 1) {
line = peakfile.GetLine();
continue;
}
line = peakfile.GetLine();
break;
}
while (!line.empty()) {
double x, y, z, dens;
if (sscanf(line.c_str(), "C %lg %lg %lg %lg", &x, &y, &z, &dens) != 4) {
line = peakfile.GetLine();
continue;
}
line = peakfile.GetLine();
peaks_.push_back(Vec3(x, y, z));
}
peakfile.CloseFile();
// Check that our initial number of peaks matches our parsed peaks. Warn
// otherwise
if (npeaks != (int)peaks_.size())
mprinterr("SPAM: Warning: %s claims to have %d peaks, but really has %d!\n",
filename.full(), npeaks, peaks_.size());
// Now add all of the data sets
MetaData md(ds_name);
for (int i = 0; i < (int)peaks_.size(); i++) {
md.SetAspect( integerToString(i+1) ); // TODO: Should this be Idx?
if (myDSL_.AddSet(DataSet::DOUBLE, md) == 0) return Action::ERR;
// Add a new list of integers to keep track of omitted frames
std::vector<int> vec;
peakFrameData_.push_back(vec);
}
}
// Print info now
if (purewater_) {
mprintf("SPAM: Calculating bulk value for pure solvent\n");
if (!datafile_.empty())
mprintf("SPAM: Printing solvent energies to %s\n", datafile_.c_str());
mprintf("SPAM: Using a %.2f Angstrom non-bonded cutoff with shifted EEL.\n",
sqrt(cut2_));
if (reorder_)
mprintf("SPAM: Warning: Re-ordering makes no sense for pure solvent.\n");
if (!summaryfile_.empty())
mprintf("SPAM: Printing solvent SPAM summary to %s\n", summaryfile_.c_str());
}else {
mprintf("SPAM: Solvent [%s] density peaks taken from %s.\n",
solvname_.c_str(), filename.base());
mprintf("SPAM: %d density peaks will be analyzed from %s.\n",
peaks_.size(), filename.base());
mprintf("SPAM: Occupation information printed to %s.\n", infofile_->Filename().full());
mprintf("SPAM: Sites are ");
if (sphere_)
mprintf("spheres with diameter %.3lf\n", site_size_);
else
mprintf("boxes with edge length %.3lf\n", site_size_);
if (reorder_) {
mprintf("SPAM: Re-ordering trajectory so each site always has ");
mprintf("the same water molecule.\n");
}
if (summaryfile_.empty() && datafile_.empty()) {
if (!reorder_) {
mprinterr("SPAM: Error: Not re-ordering trajectory or calculating energies. ");
mprinterr("Nothing to do!\n");
return Action::ERR;
}
mprintf("SPAM: Not calculating any SPAM energies\n");
}else {
mprintf("SPAM: Using a non-bonded cutoff of %.2lf Ang. with a EEL shifting function.\n",
sqrt(cut2_));
mprintf("SPAM: Bulk solvent SPAM energy taken as %.3lf kcal/mol\n", bulk_);
}
}
mprintf("#Citation: Cui, G.; Swails, J.M.; Manas, E.S.; \"SPAM: A Simple Approach\n"
"# for Profiling Bound Water Molecules\"\n"
"# J. Chem. Theory Comput., 2013, 9 (12), pp 5539–5549.\n");
return Action::OK;
}
