/** Set up masks and properties for selected atoms. */
Action::RetType Action_Density::HistSetup(ActionSetup& setup) {
properties_.clear();
properties_.reserve( masks_.size() );
for (std::vector<AtomMask>::iterator mask = masks_.begin();
mask != masks_.end();
mask++)
{
if (setup.Top().SetupIntegerMask(*mask) ) return Action::ERR;
std::vector<double> property;
for (AtomMask::const_iterator idx = mask->begin();
idx != mask->end(); idx++)
{
const Atom& atom = setup.Top()[*idx];
switch (property_) {
case NUMBER : property.push_back(1.0); break;
case MASS : property.push_back(atom.Mass() ); break;
case CHARGE : property.push_back(atom.Charge() ); break;
case ELECTRON : property.push_back(atom.AtomicNumber() - atom.Charge() ); break;
}
}
properties_.push_back(property);
mprintf("\t");
mask->BriefMaskInfo();
mprintf("\n");
}
return Action::OK;
}
/** If the current parm does not match the target parm, deactivate. Otherwise
* replace current parm with mapped parm.
*/
Action::RetType Action_AtomMap::Setup(ActionSetup& setup) {
if (maponly_) {
mprintf(" ATOMMAP: maponly was specified, not using atom map during traj read.\n");
return Action::OK;
}
if (setup.Top().Pindex() != TgtFrame_->Top().Pindex() ||
setup.Top().Natom() != TgtFrame_->Top().Natom())
{
mprintf(" ATOMMAP: Map for parm %s -> %s (%i atom).\n",TgtFrame_->Top().c_str(),
RefFrame_->Top().c_str(), TgtFrame_->Top().Natom());
mprintf(" Current parm %s (%i atom).\n",setup.Top().c_str(),
setup.Top().Natom());
mprintf(" Not using map for this parm.\n");
return Action::SKIP;
}
if (rmsfit_) {
mprintf(" ATOMMAP: rmsfit specified, %i atoms.\n",rmsRefFrame_.Natom());
return Action::OK;
}
mprintf(" ATOMMAP: Map for parm %s -> %s (%i atom).\n",TgtFrame_->Top().c_str(),
RefFrame_->Top().c_str(), TgtFrame_->Top().Natom());
setup.SetTopology( newParm_ );
return Action::MODIFY_TOPOLOGY;
}
Action::RetType Action_DNAionTracker::Setup(ActionSetup& setup) {
// Setup masks
if (setup.Top().SetupIntegerMask( p1_ )) return Action::ERR;
if ( p1_.None() ) {
mprinterr("Error: dnaiontracker: No atoms in mask1\n");
return Action::ERR;
}
if (setup.Top().SetupIntegerMask( p2_ )) return Action::ERR;
if ( p2_.None() ) {
mprinterr("Error: dnaiontracker: No atoms in mask2\n");
return Action::ERR;
}
if (setup.Top().SetupIntegerMask( base_ )) return Action::ERR;
if ( base_.None() ) {
mprinterr("Error: dnaiontracker: No atoms in mask3\n");
return Action::ERR;
}
if (setup.Top().SetupIntegerMask( ions_ )) return Action::ERR;
if ( ions_.None() ) {
mprinterr("Error: dnaiontracker: No atoms in mask4\n");
return Action::ERR;
}
SetupImaging( setup.CoordInfo().TrajBox().Type() );
mprintf("\tPhosphate1 Mask [%s] %i atoms.\n", p1_.MaskString(), p1_.Nselected());
mprintf("\tPhosphate2 Mask [%s] %i atoms.\n", p2_.MaskString(), p2_.Nselected());
mprintf("\t Base Mask [%s] %i atoms.\n", base_.MaskString(), base_.Nselected());
mprintf("\t Ions Mask [%s] %i atoms.\n", ions_.MaskString(), ions_.Nselected());
return Action::OK;
}
/** Determine what atoms each mask pertains to for the current parm file.
*/
Action::RetType Action_LIE::Setup(ActionSetup& setup) {
if (setup.Top().SetupIntegerMask( Mask1_ )) return Action::ERR;
if (setup.Top().SetupIntegerMask( Mask2_ )) return Action::ERR;
mprintf("\tLIE: %i Ligand Atoms, %i Surrounding Atoms\n",
Mask1_.Nselected(), Mask2_.Nselected());
if (setup.CoordInfo().TrajBox().Type() == Box::NOBOX) {
mprinterr("Error: LIE: Must have explicit solvent system with box info\n");
return Action::ERR;
}
if (Mask1_.None() || Mask2_.None()) {
mprintf("Warning: LIE: One or both masks have no atoms.\n");
return Action::SKIP;
}
if (SetupParms(setup.Top()))
return Action::ERR;
// Back up the parm
CurrentParm_ = setup.TopAddress();
return Action::OK;
}
/** For this to be valid the same # of atoms should be selected each time. */
Action::RetType Action_VelocityAutoCorr::Setup(ActionSetup& setup) {
if (setup.Top().SetupIntegerMask( mask_ )) return Action::ERR;
mask_.MaskInfo();
if (mask_.None()) {
mprintf("Warning: No atoms selected by mask.\n");
return Action::SKIP;
}
// If using velocity info, check that it is present.
if (useVelInfo_ && !setup.CoordInfo().HasVel()) {
mprinterr("Error: 'usevelocity' specified but no velocity info assocated with %s\n",
setup.Top().c_str());
return Action::ERR;
}
// If we have already started recording velocities, check that the current
// number of selected atoms has remained the same.
if (!Vel_.empty()) {
if ((int)Vel_.size() != mask_.Nselected()) {
mprinterr("Error: # of selected atoms %i has changed (previously %zu)\n",
mask_.Nselected(), Vel_.size());
return Action::ERR;
}
} else
Vel_.resize( mask_.Nselected() );
return Action::OK;
}
// Action_MultiVector::Setup();
Action::RetType Action_MultiVector::Setup(ActionSetup& setup) {
Range actualRange;
// If range is empty (i.e. no resrange arg given) look through all
// solute residues.
if (resRange_.Empty())
actualRange = setup.Top().SoluteResidues();
else {
// If user range specified, create new range shifted by -1 since internal
// resnums start from 0.
actualRange = resRange_;
actualRange.ShiftBy(-1);
}
// Exit if no residues specified
if (actualRange.Empty()) {
mprintf("Warning: No residues specified for %s\n",setup.Top().c_str());
return Action::SKIP;
}
// Set default DataSet name if not specified.
if (dsetname_.empty())
dsetname_ = masterDSL_->GenerateDefaultName( "MVEC" );
// Search for specified atom names in each residue in the range
CrdIdx1_.clear();
CrdIdx2_.clear();
for (Range::const_iterator res = actualRange.begin(); res != actualRange.end(); ++res)
{
int atom1 = setup.Top().FindAtomInResidue( *res, name1_ );
int atom2 = setup.Top().FindAtomInResidue( *res, name2_ );
if (atom1 != -1 && atom2 != -1) {
MetaData md(dsetname_, atom1+1);
md.SetScalarMode( MetaData::M_VECTOR );
if (ired_) md.SetScalarType( MetaData::IREDVEC );
DataSet_Vector* ds = (DataSet_Vector*)masterDSL_->CheckForSet( md );
if (ds == 0) {
// Create DataSet
ds = (DataSet_Vector*)masterDSL_->AddSet( DataSet::VECTOR, md );
if (ds == 0) return Action::ERR;
ds->SetLegend( "v" + setup.Top().AtomMaskName(atom1) + "->" +
setup.Top().AtomMaskName(atom2) );
if (outfile_ != 0) outfile_->AddDataSet( ds );
}
data_.push_back( ds );
CrdIdx1_.push_back( atom1 * 3 ); // Pre calc coordinate index
CrdIdx2_.push_back( atom2 * 3 );
} else if ((atom1==-1) != (atom2==-1)) {
if (atom1==-1)
mprintf("Warning: '%s' not found but '%s' found for residue %i.\n",
*name1_, *name2_, *res + 1);
else // atom2==-1
mprintf("Warning: '%s' not found but '%s' found for residue %i.\n",
*name2_, *name1_, *res + 1);
}
}
mprintf("\tSelected %zu vectors.\n", CrdIdx1_.size());
for (std::vector<DataSet_Vector*>::const_iterator it = data_.begin();
it != data_.end(); ++it)
mprintf("\t %s\n", (*it)->legend());
return Action::OK;
}
// Action_Principal::Setup()
Action::RetType Action_Principal::Setup(ActionSetup& setup) {
if (setup.Top().SetupIntegerMask(mask_)) return Action::ERR;
mask_.MaskInfo();
if (mask_.None()) {
mprintf("Warning: No atoms selected for %s [%s].\n",setup.Top().c_str(), mask_.MaskString());
return Action::SKIP;
}
return Action::OK;
}
/** Set angle up for this parmtop. Get masks etc.
*/
Action::RetType Action_Esander::Setup(ActionSetup& setup) {
if (currentParm_ != 0 && currentParm_->Pindex() != setup.Top().Pindex())
{
mprintf("Warning: Current topology is %i:%s but reference is %i:%s. Skipping.\n",
setup.Top().Pindex(), setup.Top().c_str(),
currentParm_->Pindex(), currentParm_->c_str());
return Action::SKIP;
}
// Check for LJ terms
if (!setup.Top().Nonbond().HasNonbond())
{
mprinterr("Error: Topology '%s' does not have non-bonded parameters.\n", setup.Top().c_str());
return Action::ERR;
}
// If reference specified, init now. Otherwise using first frame.
if (currentParm_ != 0 ) {
if ( InitForRef() ) return Action::ERR;
} else
currentParm_ = setup.TopAddress();
// If saving of forces is requested, make sure CoordinateInfo has force.
if (save_forces_) {
cInfo_ = setup.CoordInfo();
cInfo_.SetForce( true );
newFrame_.SetupFrameV( setup.Top().Atoms(), cInfo_ );
setup.SetCoordInfo( &cInfo_ );
ret_ = Action::MODIFY_COORDS;
return Action::MODIFY_TOPOLOGY;
}
ret_ = Action::OK;
return Action::OK;
}
// Action_Outtraj::Setup()
Action::RetType Action_Outtraj::Setup(ActionSetup& setup) {
if (associatedParm_->Pindex() != setup.Top().Pindex())
return Action::SKIP;
if (!isSetup_) { // TODO: Trajout IsOpen?
if (outtraj_.SetupTrajWrite(setup.TopAddress(), setup.CoordInfo(), setup.Nframes()))
return Action::ERR;
outtraj_.PrintInfo(0);
isSetup_ = true;
}
return Action::OK;
}
/** Determine what atoms each mask pertains to for the current parm file.
*/
Action::RetType Action_ReplicateCell::Setup(ActionSetup& setup) {
if (setup.Top().SetupIntegerMask( Mask1_ )) return Action::ERR;
mprintf("\t%s (%i atoms)\n",Mask1_.MaskString(), Mask1_.Nselected());
if (Mask1_.None()) {
mprintf("Warning: One or both masks have no atoms.\n");
return Action::SKIP;
}
// Set up imaging info for this parm
image_.SetupImaging( setup.CoordInfo().TrajBox().Type() );
if (!image_.ImagingEnabled()) {
mprintf("Warning: Imaging cannot be performed for topology %s\n", setup.Top().c_str());
return Action::SKIP;
}
// Create combined topology.
if (combinedTop_.Natom() > 0) {
// Topology already set up. Check that # atoms matches.
if (Mask1_.Nselected() * ncopies_ != combinedTop_.Natom()) {
mprintf("Warning: Unit cell can currently only be replicated for"
" topologies with same # atoms.\n");
return Action::SKIP;
}
// Otherwise assume top does not change.
} else {
// Set up topology and frame.
Topology* stripParm = setup.Top().modifyStateByMask( Mask1_ );
if (stripParm == 0) return Action::ERR;
for (int cell = 0; cell != ncopies_; cell++)
combinedTop_.AppendTop( *stripParm );
combinedTop_.Brief("Combined parm:");
delete stripParm;
if (!parmfilename_.empty()) {
ParmFile pfile;
if (pfile.WriteTopology(combinedTop_, parmfilename_, ParmFile::UNKNOWN_PARM, 0)) {
mprinterr("Error: Topology file %s not written.\n", parmfilename_.c_str());
return Action::ERR;
}
}
// Only coordinates for now. FIXME
combinedFrame_.SetupFrameM(combinedTop_.Atoms());
// Set up COORDS / output traj if necessary.
if (coords_ != 0)
coords_->CoordsSetup( combinedTop_, CoordinateInfo() );
if (!trajfilename_.empty()) {
if ( outtraj_.PrepareEnsembleTrajWrite(trajfilename_, trajArgs_,
&combinedTop_, CoordinateInfo(),
setup.Nframes(), TrajectoryFile::UNKNOWN_TRAJ,
ensembleNum_) )
return Action::ERR;
}
}
return Action::OK;
}
// Action_CheckStructure::Setup()
Action::RetType Action_CheckStructure::Setup(ActionSetup& setup) {
CurrentParm_ = setup.TopAddress();
if (SeparateSetup( setup.Top(), setup.CoordInfo().TrajBox().Type(),bondcheck_ ))
return Action::ERR;
// Print imaging info for this parm
if (bondcheck_)
mprintf("\tChecking %u bonds.\n", bondList_.size());
if (image_.ImagingEnabled())
mprintf("\tImaging on.\n");
else
mprintf("\timaging off.\n");
return Action::OK;
}
// Action_Unwrap::Setup()
Action::RetType Action_Unwrap::Setup(ActionSetup& setup) {
// Ensure same number of atoms in current parm and ref parm
if ( RefParm_!=0 ) {
if ( setup.Top().Natom() != RefParm_->Natom() ) {
mprinterr("Error: unwrap: # atoms in reference parm %s is not\n", RefParm_->c_str());
mprinterr("Error: equal to # atoms in parm %s\n", setup.Top().c_str());
return Action::ERR;
}
}
// Check box type
if (setup.CoordInfo().TrajBox().Type()==Box::NOBOX) {
mprintf("Error: unwrap: Parm %s does not contain box information.\n",
setup.Top().c_str());
return Action::ERR;
}
orthogonal_ = false;
if (setup.CoordInfo().TrajBox().Type()==Box::ORTHO)
orthogonal_ = true;
// Setup atom pairs to be unwrapped.
imageList_ = Image::CreatePairList(setup.Top(), imageMode_, maskExpression_);
if (imageList_.empty()) {
mprintf("Warning: Mask selects no atoms for topology '%s'.\n", setup.Top().c_str());
return Action::SKIP;
}
mprintf("\tNumber of %ss to be unwrapped is %zu\n",
Image::ModeString(imageMode_), imageList_.size()/2);
// Use current parm as reference if not already set
if (RefParm_ == 0)
RefParm_ = setup.TopAddress();
return Action::OK;
}
/** Set angle up for this parmtop. Get masks etc.
*/
Action::RetType Action_Angle::Setup(ActionSetup& setup) {
if (setup.Top().SetupIntegerMask(Mask1_)) return Action::ERR;
if (setup.Top().SetupIntegerMask(Mask2_)) return Action::ERR;
if (setup.Top().SetupIntegerMask(Mask3_)) return Action::ERR;
mprintf("\t");
Mask1_.BriefMaskInfo();
Mask2_.BriefMaskInfo();
Mask3_.BriefMaskInfo();
mprintf("\n");
if (Mask1_.None() || Mask2_.None() || Mask3_.None()) {
mprintf("Warning: angle: One or more masks contain 0 atoms.\n");
return Action::SKIP;
}
return Action::OK;
}
// Action_GridFreeEnergy::setup()
Action::RetType Action_GridFreeEnergy::Setup(ActionSetup& setup) {
// Setup grid, checks box info.
if (GridSetup( setup.Top(), setup.CoordInfo() )) return Action::ERR;
// Setup mask
if (setup.Top().SetupIntegerMask( mask_ ))
return Action::ERR;
mask_.MaskInfo();
if (mask_.None()) {
mprinterr("Warning: No atoms selected for parm %s\n", setup.Top().c_str());
return Action::SKIP;
}
return Action::OK;
}
// Action_Outtraj::Setup()
Action::RetType Action_Outtraj::Setup(ActionSetup& setup) {
if (!isActive_ || associatedParm_->Pindex() != setup.Top().Pindex()) {
mprintf("\tOutput trajectory not active for topology '%s'\n", setup.Top().c_str());
return Action::SKIP;
}
if (!isSetup_) { // TODO: Trajout IsOpen?
if (outtraj_.SetupTrajWrite(setup.TopAddress(), setup.CoordInfo(), setup.Nframes()))
return Action::ERR;
mprintf(" "); //TODO this is a kludge; PrintInfo should be a string.
outtraj_.PrintInfo(0);
mprintf("\tHas %s\n", outtraj_.Traj().CoordInfo().InfoString().c_str());
isSetup_ = true;
}
return Action::OK;
}
// Action_Center::Setup()
Action::RetType Action_Center::Setup(ActionSetup& setup) {
if ( setup.Top().SetupIntegerMask(Mask_) ) return Action::ERR;
Mask_.MaskInfo();
if (Mask_.None()) {
mprintf("Warning: Mask contains 0 atoms.\n");
return Action::SKIP;
}
if (centerMode_ == BOXCTR && setup.CoordInfo().TrajBox().Type()==Box::NOBOX) {
mprintf("Warning: Box center specified but no box information.\n");
return Action::SKIP;
}
return Action::OK;
}
/** Called every time the trajectory changes. Set up TgtMask for the new
* parmtop and allocate space for selected atoms from the Frame.
*/
Action::RetType Action_DistRmsd::Setup(ActionSetup& setup) {
if ( setup.Top().SetupIntegerMask(TgtMask_) ) return Action::ERR;
if ( TgtMask_.None() ) {
mprintf("Warning: No atoms in mask.\n");
return Action::SKIP;
}
// Allocate space for selected atoms in the frame. This will also put the
// correct masses in based on the mask.
SelectedTgt_.SetupFrameFromMask(TgtMask_, setup.Top().Atoms());
if (refHolder_.SetupRef(setup.Top(), TgtMask_.Nselected(), "distrmsd"))
return Action::ERR;
return Action::OK;
}
// Action_NativeContacts::Setup()
Action::RetType Action_NativeContacts::Setup(ActionSetup& setup) {
// Setup potential contact lists for this topology
if (SetupContactLists( setup.Top(), Frame()))
return Action::SKIP;
mprintf("\t%zu potential contact sites for '%s'\n", Mask1_.Nselected(), Mask1_.MaskString());
if (Mask2_.MaskStringSet())
mprintf("\t%zu potential contact sites for '%s'\n", Mask2_.Nselected(), Mask2_.MaskString());
// Set up imaging info for this parm
image_.SetupImaging( setup.CoordInfo().TrajBox().Type() );
if (image_.ImagingEnabled())
mprintf("\tImaging enabled.\n");
else
mprintf("\tImaging disabled.\n");
CurrentParm_ = setup.TopAddress();
return Action::OK;
}
// Action_Density::DensitySetup()
Action::RetType Action_Density::DensitySetup(ActionSetup& setup) {
// Total system density setup
image_.SetupImaging( setup.CoordInfo().TrajBox().Type() );
if (!image_.ImagingEnabled()) {
mprintf("Warning: No unit cell information, total density cannot be calculated for '%s'\n",
setup.Top().c_str());
return Action::SKIP;
}
// delta_ will hold sum of masses
delta_ = 0.0;
for (int idx = 0; idx != setup.Top().Natom(); idx++)
delta_ += setup.Top()[idx].Mass();
mprintf("\tSum of masses is %g amu\n", delta_);
return Action::OK;
}
/** Set angle up for this parmtop. Get masks etc.
*/
Action::RetType Action_Energy::Setup(ActionSetup& setup) {
if (setup.Top().SetupCharMask(Mask1_)) return Action::ERR;
if (Mask1_.None()) {
mprintf("Warning: Mask '%s' selects no atoms.\n", Mask1_.MaskString());
return Action::SKIP;
}
Mask1_.MaskInfo();
Imask_ = AtomMask(Mask1_.ConvertToIntMask(), Mask1_.Natom());
// Check for LJ terms
for (calc_it calc = Ecalcs_.begin(); calc != Ecalcs_.end(); ++calc)
if ((*calc == N14 || *calc == NBD) && !setup.Top().Nonbond().HasNonbond())
{
mprinterr("Error: Nonbonded energy calc requested but topology '%s'\n"
"Error: does not have non-bonded parameters.\n", setup.Top().c_str());
return Action::ERR;
}
currentParm_ = setup.TopAddress();
return Action::OK;
}
/** Determine what atoms each mask pertains to for the current parm file.
* Imaging is checked for in Action::Setup.
*/
Action::RetType Action_Distance::Setup(ActionSetup& setup) {
if (setup.Top().SetupIntegerMask( Mask1_ )) return Action::ERR;
if (setup.Top().SetupIntegerMask( Mask2_ )) return Action::ERR;
mprintf("\t%s (%i atoms) to %s (%i atoms)",Mask1_.MaskString(), Mask1_.Nselected(),
Mask2_.MaskString(),Mask2_.Nselected());
if (Mask1_.None() || Mask2_.None()) {
mprintf("\nWarning: One or both masks have no atoms.\n");
return Action::SKIP;
}
// Set up imaging info for this parm
image_.SetupImaging( setup.CoordInfo().TrajBox().Type() );
if (image_.ImagingEnabled())
mprintf(", imaged");
else
mprintf(", imaging off");
mprintf(".\n");
return Action::OK;
}
Action::RetType Action_AtomicCorr::Setup(ActionSetup& setup) {
if (setup.Top().SetupIntegerMask( mask_ )) return Action::ERR;
mask_.MaskInfo();
if (mask_.None()) return Action::SKIP;
if (acorr_mode_ == ATOM) {
// Setup output array; labels and index
atom_vectors_.clear();
for (AtomMask::const_iterator atom = mask_.begin(); atom != mask_.end(); ++atom)
atom_vectors_.push_back( AtomVector(integerToString( *atom + 1 ), *atom) );
} else {
std::map<int,AtomMask> rmaskmap;
// Find which residues selected atoms belong to.
for (AtomMask::const_iterator atom = mask_.begin(); atom != mask_.end(); ++atom)
{
int current_res = setup.Top()[*atom].ResNum();
std::map<int,AtomMask>::iterator rmask = rmaskmap.find( current_res );
if ( rmask == rmaskmap.end() ) {
// Residue not yet in map.
AtomMask newmask;
newmask.AddAtom( *atom );
rmaskmap.insert( std::pair<int,AtomMask>( current_res, newmask ) );
} else {
// Residue is already in map. Add this atom.
rmask->second.AddAtom( *atom );
}
}
// Place selected residues in mask vector and setup output array; labels and index.
resmasks_.clear();
atom_vectors_.clear();
for (std::map<int,AtomMask>::const_iterator rmask = rmaskmap.begin();
rmask != rmaskmap.end(); ++rmask)
{
if (debug_ > 0)
mprintf("DBG:\tRes mask for %i has %i atoms\n", rmask->first, rmask->second.Nselected());
resmasks_.push_back( rmask->second );
atom_vectors_.push_back( AtomVector( setup.Top().TruncResNameNum( rmask->first ),
rmask->first ) );
}
mprintf("\tSelected %zu residues.\n", resmasks_.size());
}
return Action::OK;
}
Action::RetType Action_Channel::Setup(ActionSetup& setup) {
// Initial grid setup
if (grid_->Size() == 0) {
DataSet_3D& GRID = static_cast<DataSet_3D&>( *grid_ );
Box const& box = setup.Top().ParmBox();
if (box.Type() == Box::NOBOX) {
mprinterr("Error: No box information to set up grid.\n");
return Action::ERR;
} else if (box.Type() == Box::ORTHO) {
// FIXME: May need to update parm box info or set up on first frame.
if (GRID.Allocate_X_C_D(box.Lengths(), box.Center(), dxyz_)) return Action::ERR;
} else {
Vec3 nxyz = box.Lengths() / dxyz_;
if (GRID.Allocate_N_O_Box((size_t)nxyz[0], (size_t)nxyz[1], (size_t)nxyz[2],
Vec3(0.0), box)) return Action::ERR;
}
GRID.GridInfo();
}
// Set up masks
if (setup.Top().SetupIntegerMask( soluteMask_ ) ||
setup.Top().SetupIntegerMask( solventMask_) )
return Action::ERR;
soluteMask_.MaskInfo();
if (soluteMask_.None()) {
mprintf("Warning: No solute atoms selected.\n");
return Action::SKIP;
}
solventMask_.MaskInfo();
if (solventMask_.None()) {
mprintf("Warning: No solvent atoms selected.\n");
return Action::SKIP;
}
// Set up solute van der Waals. FIXME: Handle case where no LJ params
radii_.clear();
for (AtomMask::const_iterator uAtom = soluteMask_.begin();
uAtom != soluteMask_.end(); ++uAtom)
radii_.push_back( setup.Top().GetVDWradius( *uAtom ) );
return Action::OK;
}
// Action_CreateReservoir::Setup()
Action::RetType Action_CreateReservoir::Setup(ActionSetup& setup) {
// Check that input parm matches current parm
if (original_trajparm_->Pindex() != setup.Top().Pindex()) {
mprintf("Info: createreservoir was set up for topology %s\n", original_trajparm_->c_str());
mprintf("Info: skipping topology %s\n", setup.Top().c_str());
return Action::SKIP;
}
if (!trajIsOpen_) {
mprintf("\tCreating reservoir file %s\n", filename_.full());
CoordinateInfo cinfo = setup.CoordInfo();
if (!useVelocity_) cinfo.SetVelocity(false);
if (!useForce_) cinfo.SetForce(false);
if (reservoir_.InitReservoir(filename_, title_, cinfo, setup.Top().Natom(),
(bin_ != 0), reservoirT_, iseed_))
{
mprinterr("Error: Could not set up NetCDF reservoir.\n");
return Action::ERR;
}
trajIsOpen_ = true;
nframes_ = 0;
}
return Action::OK;
}
// Action_Vector::Setup()
Action::RetType Action_Vector::Setup(ActionSetup& setup) {
if (needBoxInfo_) {
// Check for box info
if (setup.CoordInfo().TrajBox().Type() == Box::NOBOX) {
mprinterr("Error: vector box: No box information.\n",
setup.Top().c_str());
return Action::ERR;
}
}
if (mask_.MaskStringSet()) {
// Setup mask 1
if (setup.Top().SetupIntegerMask(mask_)) return Action::ERR;
mask_.MaskInfo();
if (mask_.None()) {
mprinterr("Error: First vector mask is empty.\n");
return Action::ERR;
}
}
// Allocate space for CORRPLANE.
if (mode_ == CORRPLANE) {
if (vcorr_!=0) delete[] vcorr_;
vcorr_ = new double[ 3 * mask_.Nselected() ];
}
// Setup mask 2
if (mask2_.MaskStringSet()) {
if (setup.Top().SetupIntegerMask(mask2_)) return Action::ERR;
mask2_.MaskInfo();
if (mask2_.None()) {
mprinterr("Error: Second vector mask is empty.\n");
return Action::ERR;
}
}
CurrentParm_ = setup.TopAddress();
return Action::OK;
}
Action::RetType Action_Contacts::Setup(ActionSetup& setup) {
//if (first_)
// RefParm_ = currentParm;
// Set up atom mask
if (setup.Top().SetupIntegerMask(Mask_)) return Action::ERR;
// Determine which residues are active based on the mask
activeResidues_.clear();
for (AtomMask::const_iterator atom = Mask_.begin();
atom != Mask_.end(); ++atom)
{
int resnum = setup.Top()[*atom].ResNum();
activeResidues_.insert( resnum );
}
// byresidue header - only on first time through
if (residueContacts_.empty() && byResidue_) {
outfile_->Printf("#time");
outfile2_->Printf("#time");
for (std::set<int>::iterator res = activeResidues_.begin();
res != activeResidues_.end(); ++res)
{
outfile_->Printf("\tresidue %i", *res);
outfile2_->Printf("\tresidue %i", *res);
}
outfile_->Printf("\tTotal\n");
outfile2_->Printf("\tTotal\n");
}
// Reserve space for residue contact counts
residueContacts_.reserve( setup.Top().Nres() );
residueNative_.reserve( setup.Top().Nres() );
CurrentParm_ = setup.TopAddress();
return Action::OK;
}
Action::RetType Action_CreateCrd::Setup(ActionSetup& setup) {
// Set COORDS topology now if not already set.
if (setup.Top().Pindex() == pindex_ && coords_->Top().Natom() == 0) {
coords_->CoordsSetup( setup.Top(), setup.CoordInfo() );
// Estimate memory usage
mprintf("\tEstimated memory usage (%i frames): %s\n",
setup.Nframes(),
ByteString(coords_->SizeInBytes(setup.Nframes()), BYTE_DECIMAL).c_str());
}
// If # atoms in currentParm does not match coords, warn user.
if (setup.Top().Natom() != coords_->Top().Natom()) {
if (check_) {
mprinterr("Error: # atoms in current topology (%i) != # atoms in coords set \"%s\" (%i)\n",
setup.Top().Natom(), coords_->legend(), coords_->Top().Natom());
return Action::ERR;
} else {
mprintf("Warning: # atoms in current topology (%i) != # atoms in coords set \"%s\" (%i)\n"
"Warning: The resulting COORDS data set may have problems.\n",
setup.Top().Natom(), coords_->legend(), coords_->Top().Natom());
}
}
return Action::OK;
}
/** Set up mask, allocate memory for exclusion list.
*/
Action::RetType Action_Pairwise::Setup(ActionSetup& setup) {
// Set up mask
if ( setup.Top().SetupIntegerMask( Mask0_ ) ) return Action::ERR;
if (Mask0_.None()) {
mprintf("Warning: Mask has no atoms.\n");
return Action::SKIP;
}
// Set up exclusion list and determine total # interactions.
int N_interactions = SetupNonbondParm(Mask0_, setup.Top());
if (N_interactions == -1) return Action::ERR;
// Allocate matrix memory
int previous_size = (int)vdwMat_->Size();
if (previous_size == 0) {
vdwMat_->AllocateTriangle( setup.Top().Natom() );
eleMat_->AllocateTriangle( setup.Top().Natom() );
} else {
if (previous_size != N_interactions) {
mprinterr("Error: Attempting to reallocate matrix with different size.\n"
"Error: Original size= %i, new size= %i\n"
"Error: This can occur when different #s of atoms are selected in\n"
"Error: different topology files.\n", previous_size, N_interactions);
return Action::ERR;
}
}
// If comparing to a reference frame for atom-by-atom comparison make sure
// the number of interactions is the same in reference and parm.
if (nb_calcType_==COMPARE_REF) {
if (N_interactions != N_ref_interactions_) {
mprinterr("Error: # reference interactions (%i) != # interactions for this parm (%i)\n",
N_ref_interactions_, N_interactions);
return Action::ERR;
}
}
// Set up cumulative energy arrays
atom_eelec_.clear();
atom_eelec_.resize(setup.Top().Natom(), 0.0);
atom_evdw_.clear();
atom_evdw_.resize(setup.Top().Natom(), 0.0);
// Print pairwise info for this parm
Mask0_.MaskInfo();
CurrentParm_ = setup.TopAddress();
return Action::OK;
}
// Action_SymmetricRmsd::Setup()
Action::RetType Action_SymmetricRmsd::Setup(ActionSetup& setup) {
// Setup target mask.
if (setup.Top().SetupIntegerMask( tgtMask_ )) return Action::ERR;
tgtMask_.MaskInfo();
if (tgtMask_.None()) {
mprintf("Warning: No atoms selected by mask '%s'\n", tgtMask_.MaskString());
return Action::SKIP;
}
// Allocate space for selected atoms in target frame. This will also
// put the correct masses in based on the mask.
selectedTgt_.SetupFrameFromMask(tgtMask_, setup.Top().Atoms());
// Setup Symmetric RMSD calc (target mask, symmetric atoms etc)
if (SRMSD_.SetupSymmRMSD( setup.Top(), tgtMask_, remap_ )) return Action::ERR;
if (remap_) {
// Allocate space for remapped frame; same # atoms as original frame
remapFrame_.SetupFrameV( setup.Top().Atoms(), setup.CoordInfo() );
targetMap_.resize( setup.Top().Natom() );
}
// Reference frame setup
if (REF_.SetupRef(setup.Top(), tgtMask_.Nselected(), "symmrmsd"))
return Action::ERR;
return Action::OK;
}
/** Called every time the trajectory changes. Set up FrameMask for the new
* parmtop and allocate space for selected atoms from the Frame.
*/
Action::RetType Action_Rmsd::Setup(ActionSetup& setup) {
// Target setup
if ( setup.Top().SetupIntegerMask( tgtMask_ ) ) return Action::ERR;
mprintf("\tTarget mask:");
tgtMask_.BriefMaskInfo();
mprintf("\n");
if ( tgtMask_.None() ) {
mprintf("Warning: No atoms in mask '%s'.\n", tgtMask_.MaskString());
return Action::SKIP;
}
// Allocate space for selected atoms in the frame. This will also put the
// correct masses in based on the mask.
tgtFrame_.SetupFrameFromMask(tgtMask_, setup.Top().Atoms());
// Reference setup
if (REF_.SetupRef(setup.Top(), tgtMask_.Nselected(), "rmsd"))
return Action::SKIP;
// Per residue rmsd setup
if (perres_) {
// If RefParm is still NULL probably 'first', set now.
if (RefParm_ == 0)
RefParm_ = setup.TopAddress();
int err = perResSetup(setup.Top(), *RefParm_);
if (err == 1) return Action::SKIP;
else if (err == 2) return Action::ERR;
}
// Warn if PBC and rotating
if (rotate_ && setup.CoordInfo().TrajBox().Type() != Box::NOBOX) {
mprintf("Warning: Coordinates are being rotated and box coordinates are present.\n"
"Warning: Unit cell vectors are NOT rotated; imaging will not be possible\n"
"Warning: after the RMS-fit is performed.\n");
}
return Action::OK;
}
