// Action_Esander::Init()
Action::RetType Action_Esander::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
# ifdef MPI
trajComm_ = init.TrajComm();
# endif
SANDER_.SetDebug( debugIn );
Init_ = init;
// Get keywords
outfile_ = init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
save_forces_ = actionArgs.hasKey("saveforces");
ReferenceFrame REF = init.DSL().GetReferenceFrame( actionArgs );
if (REF.error()) return Action::ERR;
if (!REF.empty()) {
refFrame_ = REF.Coord();
currentParm_ = REF.ParmPtr();
}
if (SANDER_.SetInput( actionArgs )) return Action::ERR;
// DataSet name and array
setname_ = actionArgs.GetStringNext();
if (setname_.empty())
setname_ = init.DSL().GenerateDefaultName("ENE");
Esets_.clear();
Esets_.resize( (int)Energy_Sander::N_ENERGYTYPES, 0 );
mprintf(" ESANDER: Calculating energy using Sander.\n");
mprintf("\tTemporary topology file name is '%s'\n", SANDER_.TopFilename().full());
if (save_forces_) mprintf("\tSaving force information to frame.\n");
mprintf("\tReference for initialization");
if (!REF.empty())
mprintf(" is '%s'\n", REF.refName());
else
mprintf(" will be first frame.\n");
return Action::OK;
}
// Action_Center::Init()
Action::RetType Action_Center::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
// Get keywords
useMass_ = actionArgs.hasKey("mass");
ReferenceFrame refFrm = init.DSL().GetReferenceFrame( actionArgs );
if (refFrm.error()) return Action::ERR;
// Determine center mode.
if (!refFrm.empty())
centerMode_ = REF;
else if (actionArgs.hasKey("origin"))
centerMode_ = ORIGIN;
else if (actionArgs.hasKey("point")) {
centerMode_ = POINT;
refCenter_[0] = actionArgs.getNextDouble(0.0);
refCenter_[1] = actionArgs.getNextDouble(0.0);
refCenter_[2] = actionArgs.getNextDouble(0.0);
} else
centerMode_ = BOXCTR;
// Get Masks
Mask_.SetMaskString( actionArgs.GetMaskNext() );
// Get reference mask if reference specified.
AtomMask refMask;
if (centerMode_ == REF) {
std::string rMaskExpr = actionArgs.GetMaskNext();
if (rMaskExpr.empty())
rMaskExpr = Mask_.MaskExpression();
refMask.SetMaskString( rMaskExpr );
if (refFrm.Parm().SetupIntegerMask( refMask, refFrm.Coord() ))
return Action::ERR;
// Get center of mask in reference
if (useMass_)
refCenter_ = refFrm.Coord().VCenterOfMass( refMask );
else
refCenter_ = refFrm.Coord().VGeometricCenter( refMask );
}
mprintf(" CENTER: Centering coordinates using");
if (useMass_)
mprintf(" center of mass");
else
mprintf(" geometric center");
mprintf(" of atoms in mask (%s) to\n", Mask_.MaskString());
switch (centerMode_) {
case ORIGIN: mprintf("\tcoordinate origin.\n"); break;
case BOXCTR: mprintf("\tbox center.\n"); break;
case REF:
mprintf("\tcenter of mask (%s) in reference '%s'.\n", refMask.MaskString(),
refFrm.refName());
break;
case POINT: mprintf("\tpoint (%g, %g, %g).\n",
refCenter_[0], refCenter_[1], refCenter_[2]);
break;
}
return Action::OK;
}
// Action_Unwrap::Init()
Action::RetType Action_Unwrap::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
// Get Keywords
center_ = actionArgs.hasKey("center");
if (actionArgs.hasKey("bymol"))
imageMode_ = Image::BYMOL;
else if (actionArgs.hasKey("byres"))
imageMode_ = Image::BYRES;
else if (actionArgs.hasKey("byatom")) {
imageMode_ = Image::BYATOM;
// Unwrapping to center by atom makes no sense
if (center_) center_ = false;
} else
imageMode_ = Image::BYATOM;
// Get reference
ReferenceFrame REF = init.DSL().GetReferenceFrame( actionArgs );
if (REF.error()) return Action::ERR;
if (!REF.empty()) {
RefFrame_ = REF.Coord();
// Get reference parm for frame
RefParm_ = REF.ParmPtr();
}
// Get mask string
maskExpression_ = actionArgs.GetMaskNext();
mprintf(" UNWRAP: By %s", Image::ModeString(imageMode_));
if (!maskExpression_.empty())
mprintf(" using mask '%s'", maskExpression_.c_str());
else
mprintf(" using all atoms");
if (imageMode_ != Image::BYATOM) {
if (center_)
mprintf(" based on center of mass.");
else
mprintf(" based on first atom position.");
}
mprintf("\n");
if ( !REF.empty())
mprintf("\tReference is %s", REF.refName());
else
mprintf("\tReference is first frame.");
mprintf("\n");
return Action::OK;
}
// Action_Center::Init()
Action::RetType Action_Center::Init(ArgList& actionArgs, TopologyList* PFL, DataSetList* DSL, DataFileList* DFL, int debugIn)
{
// Get keywords
if (actionArgs.hasKey("origin"))
centerMode_ = ORIGIN;
else
centerMode_ = BOXCTR;
useMass_ = actionArgs.hasKey("mass");
ReferenceFrame refFrm = DSL->GetReferenceFrame( actionArgs );
if (refFrm.error()) return Action::ERR;
// Get Masks
Mask_.SetMaskString( actionArgs.GetMaskNext() );
// Get reference mask if reference specified.
AtomMask refMask;
if (!refFrm.empty()) {
std::string rMaskExpr = actionArgs.GetMaskNext();
if (rMaskExpr.empty())
rMaskExpr = Mask_.MaskExpression();
refMask.SetMaskString( rMaskExpr );
if (refFrm.Parm().SetupIntegerMask( refMask, refFrm.Coord() ))
return Action::ERR;
// Get center of mask in reference
if (useMass_)
refCenter_ = refFrm.Coord().VCenterOfMass( refMask );
else
refCenter_ = refFrm.Coord().VGeometricCenter( refMask );
centerMode_ = POINT;
}
mprintf(" CENTER: Centering coordinates using");
if (useMass_)
mprintf(" center of mass");
else
mprintf(" geometric center");
mprintf(" of atoms in mask (%s) to\n", Mask_.MaskString());
if (centerMode_ == POINT)
mprintf("\tcenter of mask (%s) in reference '%s'.\n", refMask.MaskString(),
refFrm.refName());
else if (centerMode_ == ORIGIN)
mprintf("\tcoordinate origin.\n");
else
mprintf("\tbox center.\n");
return Action::OK;
}
// Action_NativeContacts::Init()
Action::RetType Action_NativeContacts::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
# ifdef MPI
trajComm_ = init.TrajComm();
# endif
masterDSL_ = init.DslPtr();
debug_ = debugIn;
// Get Keywords
image_.InitImaging( !(actionArgs.hasKey("noimage")) );
double dist = actionArgs.getKeyDouble("distance", 7.0);
byResidue_ = actionArgs.hasKey("byresidue");
resoffset_ = actionArgs.getKeyInt("resoffset", 0) + 1;
if (resoffset_ < 1) {
mprinterr("Error: Residue offset must be >= 0\n");
return Action::ERR;
}
includeSolvent_ = actionArgs.hasKey("includesolvent");
series_ = actionArgs.hasKey("series");
saveNonNative_ = actionArgs.hasKey("savenonnative");
if (actionArgs.hasKey("skipnative"))
determineNativeContacts_ = false;
if (!determineNativeContacts_ && !saveNonNative_) {
mprintf("Warning: 'skipnative' specified; implies 'savenonnative'.\n");
saveNonNative_ = true;
}
# ifdef MPI
if (saveNonNative_) {
mprinterr("Error: Saving non-native contact data not yet supported for MPI\n");
return Action::ERR;
}
# endif
distance_ = dist * dist; // Square the cutoff
first_ = actionArgs.hasKey("first");
DataFile* outfile = init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
Rseries_ = NO_RESSERIES;
if (series_) {
seriesout_ = init.DFL().AddDataFile(actionArgs.GetStringKey("seriesout"), actionArgs);
init.DSL().SetDataSetsPending( true );
if (saveNonNative_)
seriesNNout_ = init.DFL().AddDataFile(actionArgs.GetStringKey("seriesnnout"), actionArgs);
std::string rs_arg = actionArgs.GetStringKey("resseries");
if (!rs_arg.empty()) {
if (rs_arg == "present")
Rseries_ = RES_PRESENT;
else if (rs_arg == "sum")
Rseries_ = RES_SUM;
else {
mprinterr("Error: '%s' is not a valid 'resseries' keyword.\n", rs_arg.c_str());
return Action::ERR;
}
seriesRout_ = init.DFL().AddDataFile(actionArgs.GetStringKey("resseriesout"), actionArgs);
}
} else {
if (KeywordError(actionArgs,"seriesout")) return Action::ERR;
if (KeywordError(actionArgs,"seriesnnout")) return Action::ERR;
if (KeywordError(actionArgs,"resseries")) return Action::ERR;
if (KeywordError(actionArgs,"resseriesout")) return Action::ERR;
}
cfile_ = init.DFL().AddCpptrajFile(actionArgs.GetStringKey("writecontacts"), "Native Contacts",
DataFileList::TEXT, true);
pfile_ = init.DFL().AddCpptrajFile(actionArgs.GetStringKey("contactpdb"), "Contact PDB",
DataFileList::PDB);
if (saveNonNative_)
nfile_ = init.DFL().AddCpptrajFile(actionArgs.GetStringKey("nncontactpdb"),
"Non-native Contact PDB", DataFileList::PDB);
rfile_ = init.DFL().AddCpptrajFile(actionArgs.GetStringKey("resout"), "Contact Res Pairs",
DataFileList::TEXT, true);
if (cfile_ == 0 || rfile_ == 0) return Action::ERR;
pdbcut_ = (float)actionArgs.getKeyDouble("pdbcut", -1.0);
usepdbcut_ = (pdbcut_ > -1.0);
// Get reference for native contacts. Do this even if we wont be
// determining native contacts in order to set up contact lists.
ReferenceFrame REF = init.DSL().GetReferenceFrame( actionArgs );
if (!first_) {
if (REF.error()) return Action::ERR;
if (REF.empty()) {
mprintf("Warning: No reference structure specified. Defaulting to first.\n");
first_ = true;
}
} else {
if (!REF.empty()) {
mprinterr("Error: Must only specify 'first' or a reference structure, not both.\n");
return Action::ERR;
}
}
// Create data sets
std::string name = actionArgs.GetStringKey("name");
if (name.empty())
name = init.DSL().GenerateDefaultName("Contacts");
numnative_ = init.DSL().AddSet(DataSet::INTEGER, MetaData(name, "native"));
nonnative_ = init.DSL().AddSet(DataSet::INTEGER, MetaData(name, "nonnative"));
if (outfile != 0) {
outfile->AddDataSet(numnative_);
outfile->AddDataSet(nonnative_);
}
if (numnative_ == 0 || nonnative_ == 0) return Action::ERR;
if (actionArgs.hasKey("mindist")) {
mindist_ = init.DSL().AddSet(DataSet::DOUBLE, MetaData(name, "mindist"));
if (mindist_ == 0) return Action::ERR;
if (outfile != 0) outfile->AddDataSet(mindist_);
}
if (actionArgs.hasKey("maxdist")) {
maxdist_ = init.DSL().AddSet(DataSet::DOUBLE, MetaData(name, "maxdist"));
if (maxdist_ == 0) return Action::ERR;
if (outfile != 0) outfile->AddDataSet(maxdist_);
}
DataFile *natmapfile = 0, *nonmapfile = 0;
if (actionArgs.hasKey("map")) {
nativeMap_ = (DataSet_MatrixDbl*)init.DSL().AddSet(DataSet::MATRIX_DBL, MetaData(name, "nativemap"));
if (nativeMap_ == 0) return Action::ERR;
nonnatMap_ = (DataSet_MatrixDbl*)init.DSL().AddSet(DataSet::MATRIX_DBL, MetaData(name, "nonnatmap"));
if (nonnatMap_ == 0) return Action::ERR;
FileName mapFilename;
mapFilename.SetFileName( actionArgs.GetStringKey("mapout") );
if (!mapFilename.empty()) {
natmapfile = init.DFL().AddDataFile(mapFilename.PrependFileName("native."));
if (natmapfile != 0) natmapfile->AddDataSet(nativeMap_);
nonmapfile = init.DFL().AddDataFile(mapFilename.PrependFileName("nonnative."));
if (nonmapfile != 0) nonmapfile->AddDataSet(nonnatMap_);
}
}
// Get Masks
if (Mask1_.SetMaskString( actionArgs.GetMaskNext() )) return Action::ERR;
std::string mask2 = actionArgs.GetMaskNext();
if (!mask2.empty()) {
if (Mask2_.SetMaskString( mask2 )) return Action::ERR;
}
mprintf(" NATIVECONTACTS: Mask1='%s'", Mask1_.MaskString());
if (Mask2_.MaskStringSet())
mprintf(" Mask2='%s'", Mask2_.MaskString());
if (determineNativeContacts_) {
mprintf(", native contacts set up based on");
if (first_)
mprintf(" first frame.\n");
else
mprintf("'%s'.\n", REF.refName());
} else {
mprintf(", skipping native contacts set up.\n");
}
if (byResidue_) {
mprintf("\tContacts will be ignored for residues spaced < %i apart.\n", resoffset_);
if (nativeMap_ != 0)
mprintf("\tMap will be printed by residue.\n");
}
if (saveNonNative_)
mprintf("\tSaving non-native contacts as well (may use a lot of memory).\n");
mprintf("\tDistance cutoff is %g Angstroms,", sqrt(distance_));
if (!image_.UseImage())
mprintf(" imaging is off.\n");
else
mprintf(" imaging is on.\n");
if (includeSolvent_)
mprintf("\tMask selection will including solvent.\n");
else
mprintf("\tMask selection will not include solvent.\n");
mprintf("\tData set name: %s\n", name.c_str());
if (maxdist_ != 0)
mprintf("\tSaving maximum observed distances in set '%s'\n", maxdist_->legend());
if (mindist_ != 0)
mprintf("\tSaving minimum observed distances in set '%s'\n", mindist_->legend());
if (outfile != 0)
mprintf("\tOutput to '%s'\n", outfile->DataFilename().full());
mprintf("\tContact stats will be written to '%s'\n", cfile_->Filename().full());
mprintf("\tContact res pairs will be written to '%s'\n", rfile_->Filename().full());
if (pfile_ != 0) {
mprintf("\tContact PDB will be written to '%s'\n", pfile_->Filename().full());
if (usepdbcut_) mprintf("\tOnly atoms with values > %g will be written to PDB.\n", pdbcut_);
}
if (nfile_ != 0) {
mprintf("\tNon-native contact PDB will be written to '%s'\n", nfile_->Filename().full());
if (usepdbcut_) mprintf("\tOnly atoms with values > %g will be written to PDB.\n", pdbcut_);
}
if (nativeMap_ != 0) {
mprintf("\tNative contacts map will be saved as set '%s'\n"
"\tNon-native contacts map will be saved as set '%s'\n",
nativeMap_->legend(), nonnatMap_->legend());
if (natmapfile!=0) mprintf("\tNative map output to '%s'\n",natmapfile->DataFilename().full());
if (nonmapfile!=0) mprintf("\tNative map output to '%s'\n",nonmapfile->DataFilename().full());
}
if (series_) {
mprintf("\tSaving native contact time series %s[NC].\n", name.c_str());
if (seriesout_ != 0) mprintf("\tWriting native contact time series to %s\n",
seriesout_->DataFilename().full());
if (saveNonNative_) {
mprintf("\tSaving non-native contact time series %s[NN]\n", name.c_str());
if (seriesNNout_ != 0) mprintf("\tWriting non-native contact time series to %s\n",
seriesNNout_->DataFilename().full());
}
if (Rseries_ != NO_RESSERIES) {
if (Rseries_ == RES_PRESENT)
mprintf("\tResidue contact time series will reflect presence of individual contacts.\n");
else if (Rseries_ == RES_SUM)
mprintf("\tResidue contact time series will reflect sum of individual contacts.\n");
if (seriesRout_ != 0) mprintf("\tWriting residue contact time series to %s\n",
seriesRout_->DataFilename().full());
}
}
// Set up reference if necessary.
if (!first_) {
// Set up imaging info for ref parm
image_.SetupImaging( REF.CoordsInfo().TrajBox().Type() );
if (image_.ImageType() == NONORTHO)
REF.Coord().BoxCrd().ToRecip(ucell_, recip_);
if (DetermineNativeContacts( REF.Parm(), REF.Coord() )) return Action::ERR;
}
return Action::OK;
}
// Action_Pairwise::Init()
Action::RetType Action_Pairwise::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
// Get Keywords
DataFile* dataout = init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
DataFile* vmapout = init.DFL().AddDataFile( actionArgs.GetStringKey("vmapout"), actionArgs );
DataFile* emapout = init.DFL().AddDataFile( actionArgs.GetStringKey("emapout"), actionArgs );
avgout_ = actionArgs.GetStringKey("avgout");
std::string eout = actionArgs.GetStringKey("eout");
cut_eelec_ = fabs(actionArgs.getKeyDouble("cuteelec",1.0));
cut_evdw_ = fabs(actionArgs.getKeyDouble("cutevdw",1.0));
mol2Prefix_ = actionArgs.GetStringKey("cutout");
std::string pdbout = actionArgs.GetStringKey("pdbout");
ReferenceFrame REF = init.DSL().GetReferenceFrame( actionArgs );
// Get Masks
Mask0_.SetMaskString( actionArgs.GetMaskNext() );
std::string refmask = actionArgs.GetMaskNext();
if (!refmask.empty())
RefMask_.SetMaskString(refmask);
else
RefMask_.SetMaskString( Mask0_.MaskString() );
// Datasets
std::string ds_name = actionArgs.GetStringNext();
if (ds_name.empty())
ds_name = init.DSL().GenerateDefaultName("PW");
ds_vdw_ = init.DSL().AddSet(DataSet::DOUBLE, MetaData(ds_name, "EVDW"));
ds_elec_ = init.DSL().AddSet(DataSet::DOUBLE, MetaData(ds_name, "EELEC"));
if (ds_vdw_ == 0 || ds_elec_ == 0) return Action::ERR;
// Add DataSets to data file list
if (dataout != 0) {
dataout->AddDataSet(ds_vdw_);
dataout->AddDataSet(ds_elec_);
}
vdwMat_ = (DataSet_MatrixDbl*)init.DSL().AddSet(DataSet::MATRIX_DBL, MetaData(ds_name, "VMAP"));
eleMat_ = (DataSet_MatrixDbl*)init.DSL().AddSet(DataSet::MATRIX_DBL, MetaData(ds_name, "EMAP"));
if (vdwMat_ == 0 || eleMat_ == 0) return Action::ERR;
if (vmapout != 0) vmapout->AddDataSet(vdwMat_);
if (emapout != 0) emapout->AddDataSet(eleMat_);
// Get reference structure
if (REF.error()) return Action::ERR;
if (!REF.empty()) {
// Set up reference mask
if ( REF.Parm().SetupIntegerMask(RefMask_) ) return Action::ERR;
if (RefMask_.None()) {
mprinterr("Error: No atoms selected in reference mask.\n");
return Action::ERR;
}
// Set up nonbonded params for reference
if ( (N_ref_interactions_=SetupNonbondParm( RefMask_, REF.Parm() )) == -1 )
return Action::ERR;
// Calculate energy for reference
nb_calcType_ = SET_REF;
NonbondEnergy(REF.Coord(), REF.Parm(), RefMask_);
nb_calcType_ = COMPARE_REF;
}
// Output for individual atom energy | dEnergy
if (!eout.empty()) {
Eout_ = init.DFL().AddCpptrajFile(eout, "Atom Energies");
if (Eout_ == 0) {
mprinterr("Error: Could not set up file %s for eout.\n",eout.c_str());
return Action::ERR;
}
}
// Set up output pdb
if (!pdbout.empty()) {
if (PdbOut_.OpenWrite( pdbout )) return Action::ERR;
}
// Action Info
mprintf(" PAIRWISE: Atoms in mask [%s].\n",Mask0_.MaskString());
if (!eout.empty())
mprintf("\tEnergy info for each atom will be written to %s\n",eout.c_str());
if (nb_calcType_ == COMPARE_REF) {
mprintf("\tReference %s, mask [%s]\n", REF.refName(), RefMask_.MaskString());
mprintf("\tReference energy (kcal/mol): EVDW= %12.5e EELEC= %12.5e\n", ELJ_, Eelec_);
mprintf("\tSize of reference energy array is %zu elements (%s)\n",
ref_nonbondEnergy_.size(),
ByteString(ref_nonbondEnergy_.size() * 2 * sizeof(double), BYTE_DECIMAL).c_str());
}
mprintf("\tEelec absolute cutoff (kcal/mol): %.4f\n", cut_eelec_);
mprintf("\tEvdw absolute cutoff (kcal/mol) : %.4f\n", cut_evdw_);
if (!mol2Prefix_.empty())
mprintf("\tAtoms satisfying cutoff will be printed to %s.e<type>.mol2\n",
mol2Prefix_.c_str());
if (PdbOut_.IsOpen())
mprintf("\tPDB with evdw/eelec in occ/b-fac columns will be written to %s\n",
PdbOut_.Filename().full());
return Action::OK;
}