// 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::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;
}
// 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;
}
/** Determine what atoms each mask pertains to for the current parm file.
*/
Action::RetType Action_NMRrst::Setup(ActionSetup& setup) {
if (!viewrst_.empty() && rsttop_ == 0) rsttop_ = setup.TopAddress();
// ---------------------------------------------
// Set up NOEs from file.
for (noeDataArray::iterator noe = NOEs_.begin(); noe != NOEs_.end(); ++noe) {
if (setup.Top().SetupIntegerMask( noe->dMask1_ )) return Action::ERR;
if (setup.Top().SetupIntegerMask( noe->dMask2_ )) return Action::ERR;
if (noe->dMask1_.None() || noe->dMask2_.None()) {
mprintf("Warning: One or both masks for NOE '%s' have no atoms (%i and %i).\n",
noe->dist_->legend(), noe->dMask1_.Nselected(),
noe->dMask2_.Nselected());
noe->active_ = false;
} else
noe->active_ = true;
}
// ---------------------------------------------
// Set up potential NOE sites.
if (findNOEs_) {
if (setup.Top().SetupCharMask( Mask_ )) return Action::ERR;
Mask_.MaskInfo();
if (Mask_.None()) return Action::SKIP;
SiteArray potentialSites; // .clear();
AtomMap resMap;
resMap.SetDebug( debug_ );
std::vector<bool> selected;
Range soluteRes = setup.Top().SoluteResidues();
for (Range::const_iterator res = soluteRes.begin(); res != soluteRes.end(); ++res)
{
int res_first_atom = setup.Top().Res(*res).FirstAtom();
selected.assign( setup.Top().Res(*res).NumAtoms(), false );
// Find symmetric atom groups.
AtomMap::AtomIndexArray symmGroups;
if (resMap.SymmetricAtoms(setup.Top(), symmGroups, *res)) return Action::ERR;
// DEBUG
if (debug_ > 0) {
mprintf("DEBUG: Residue %i: symmetric atom groups:\n", *res + 1);
for (AtomMap::AtomIndexArray::const_iterator grp = symmGroups.begin();
grp != symmGroups.end(); ++grp)
{
mprintf("\t\t");
for (AtomMap::Iarray::const_iterator at = grp->begin();
at != grp->end(); ++at)
mprintf(" %s", setup.Top().TruncAtomNameNum( *at ).c_str());
mprintf("\n");
}
}
// Each symmetric hydrogen atom group is a site.
for (AtomMap::AtomIndexArray::const_iterator grp = symmGroups.begin();
grp != symmGroups.end(); ++grp)
{ // NOTE: If first atom is H all should be H.
if ( setup.Top()[ grp->front() ].Element() == Atom::HYDROGEN )
{
Iarray symmAtomGroup;
for (Iarray::const_iterator at = grp->begin();
at != grp->end(); ++at)
if (Mask_.AtomInCharMask( *at ))
symmAtomGroup.push_back( *at );
if (!symmAtomGroup.empty()) {
potentialSites.push_back( Site(*res, symmAtomGroup) );
// Mark symmetric atoms as selected.
for (AtomMap::Iarray::const_iterator at = grp->begin();
at != grp->end(); ++at)
selected[ *at - res_first_atom ] = true;
}
}
}
// All other non-selected hydrogens bonded to same heavy atom are sites.
for (int ratom = res_first_atom; ratom != setup.Top().Res(*res).LastAtom(); ++ratom)
{
if ( setup.Top()[ratom].Element() != Atom::HYDROGEN ) {
Iarray heavyAtomGroup;
for (Atom::bond_iterator ba = setup.Top()[ratom].bondbegin();
ba != setup.Top()[ratom].bondend(); ++ba)
if ( Mask_.AtomInCharMask(*ba) &&
*ba >= res_first_atom &&
*ba < setup.Top().Res(*res).LastAtom() )
{
if ( !selected[ *ba - res_first_atom ] &&
setup.Top()[ *ba ].Element() == Atom::HYDROGEN )
heavyAtomGroup.push_back( *ba );
}
if (!heavyAtomGroup.empty())
potentialSites.push_back( Site(*res, heavyAtomGroup) );
}
}
}
mprintf("\t%zu potential NOE sites:\n", potentialSites.size());
for (SiteArray::const_iterator site = potentialSites.begin();
site != potentialSites.end(); ++site)
{
mprintf(" %u\tRes %i:", site - potentialSites.begin(), site->ResNum()+1);
for (unsigned int idx = 0; idx != site->Nindices(); ++idx)
mprintf(" %s", setup.Top().TruncAtomNameNum( site->Idx(idx) ).c_str());
mprintf("\n");
}
if (noeArray_.empty()) {
size_t siteArraySize = 0;
// Set up all potential NOE pairs. Keep track of size.
for (SiteArray::const_iterator site1 = potentialSites.begin();
site1 != potentialSites.end(); ++site1)
{
for (SiteArray::const_iterator site2 = site1 + 1;
site2 != potentialSites.end(); ++site2)
{
if (site1->ResNum() != site2->ResNum()) {
std::string legend = site1->SiteLegend(setup.Top()) + "--" +
site2->SiteLegend(setup.Top());
DataSet* ds = 0;
if (series_) {
ds = masterDSL_->AddSet(DataSet::FLOAT,
MetaData(setname_, "foundNOE", noeArray_.size()));
if (ds == 0) return Action::ERR;
// Construct a data set name.
ds->SetLegend(legend);
}
noeArray_.push_back( NOEtype(*site1, *site2, ds, legend) );
siteArraySize += (2 * sizeof(int) * site1->Nindices()) +
(2 * sizeof(int) * site2->Nindices());
}
}
}
numNoePairs_ = noeArray_.size();
size_t siteSize = sizeof(int) + (2 * sizeof(Iarray)) + sizeof(Site);
size_t noeSize = (2 * siteSize) + sizeof(DataSet*) + sizeof(double)
+ sizeof(NOEtype);
if (series_) noeSize += sizeof(std::vector<float>);
size_t noeArraySize = (noeSize * numNoePairs_) + siteArraySize;
if (series_)
noeArraySize += (setup.Nframes() * numNoePairs_ * sizeof(float));
mprintf("\t%zu potential NOE pairs. Estimated memory usage is %s\n",
numNoePairs_, ByteString(noeArraySize, BYTE_DECIMAL).c_str());
} else if (numNoePairs_ != potentialSites.size()) {
mprinterr("Warning: Found NOE matrix has already been set up for %zu potential\n"
"Warning: NOEs, but %zu NOEs currently found.\n", numNoePairs_,
potentialSites.size());
return Action::SKIP;
}
}
// ---------------------------------------------
// Set up NOEs specified on the command line
if (!Pairs_.empty()) {
if (!specifiedNOEs_.empty()) {
mprintf("Warning: Specifying NOEs currently only works with first topology used.\n");
return Action::SKIP;
}
for (MaskPairArray::iterator mp = Pairs_.begin(); mp != Pairs_.end(); mp++) {
if (setup.Top().SetupIntegerMask( mp->first )) return Action::ERR;
int res1 = CheckSameResidue(setup.Top(), mp->first);
if (res1 < 0) continue;
if (setup.Top().SetupIntegerMask( mp->second )) return Action::ERR;
int res2 = CheckSameResidue(setup.Top(), mp->second);
if (res2 < 0) continue;
Site site1( res1, mp->first.Selected() );
Site site2( res2, mp->second.Selected() );
std::string legend = site1.SiteLegend(setup.Top()) + "--" +
site2.SiteLegend(setup.Top());
DataSet* ds = 0;
if (series_) {
ds = masterDSL_->AddSet(DataSet::FLOAT,
MetaData(setname_, "specNOE", specifiedNOEs_.size()));
if (ds == 0) return Action::ERR;
ds->SetLegend(legend);
}
specifiedNOEs_.push_back( NOEtype(site1, site2, ds, legend) );
}
}
// Set up imaging info for this parm
Image_.SetupImaging( setup.CoordInfo().TrajBox().Type() );
if (Image_.ImagingEnabled())
mprintf("\tImaged.\n");
else
mprintf("\tImaging off.\n");
return Action::OK;
}
// Action_LESsplit::Setup()
Action::RetType Action_LESsplit::Setup(ActionSetup& setup) {
if ( !setup.Top().LES().HasLES() ) {
mprintf("Warning: No LES parameters in '%s', skipping.\n", setup.Top().c_str());
return Action::SKIP;
}
if (lesParm_ == 0) { // First time setup
// Set up masks for all copies
lesMasks_.clear();
lesMasks_.resize( setup.Top().LES().Ncopies() );
unsigned int atom = 0;
for (LES_Array::const_iterator les = setup.Top().LES().Array().begin();
les != setup.Top().LES().Array().end(); ++les, ++atom)
{
// Copy 0 is in all copies
if ( les->Copy() == 0 ) {
for (MaskArray::iterator mask = lesMasks_.begin(); mask != lesMasks_.end(); ++mask)
mask->AddAtom( atom );
} else
lesMasks_[ les->Copy() - 1 ].AddAtom( atom );
}
for (unsigned int i = 0; i < lesMasks_.size(); i++) {
mprintf("\t%i atoms in LES copy %u\n", lesMasks_[i].Nselected(), i+1);
if ( lesMasks_[i].Nselected() != lesMasks_[0].Nselected() ) {
mprinterr("Error: Currently all LES copies MUST have same # atoms.\n");
return Action::ERR;
}
}
// Create topology for first copy
lesParm_ = setup.Top().modifyStateByMask( lesMasks_[0] );
if (lesParm_ == 0) return Action::ERR;
// Set up frames to hold individual copies
lesFrames_.resize( lesMasks_.size() );
lesFrames_.SetupFrames(lesParm_->Atoms(), setup.CoordInfo());
lesPtrs_.resize( lesMasks_.size() );
for (unsigned int i = 0; i != lesMasks_.size(); i++)
lesPtrs_[i] = &lesFrames_[i];
if (lesSplit_) {
// Set up output ensemble FIXME check overwrites TODO combine init/setup?
if (lesTraj_.InitEnsembleWrite(trajfilename_, trajArgs_, lesMasks_.size(),
TrajectoryFile::UNKNOWN_TRAJ))
return Action::ERR;
if (lesTraj_.SetupEnsembleWrite(lesParm_, setup.CoordInfo(), setup.Nframes()))
return Action::ERR;
lesTraj_.PrintInfo(0);
}
if (lesAverage_) {
// For average only care about coords.
avgFrame_.SetupFrame( lesParm_->Natom() );
if (avgTraj_.PrepareTrajWrite( avgfilename_, trajArgs_, lesParm_,
CoordinateInfo(), setup.Nframes(),
TrajectoryFile::UNKNOWN_TRAJ ))
return Action::ERR;
avgTraj_.PrintInfo(0);
}
} else {
if (lesParm_->Pindex() != setup.Top().Pindex()) {
mprintf("Warning: Already set up for LES parm '%s'. Skipping '%s'\n",
lesParm_->c_str(), setup.Top().c_str());
return Action::SKIP;
}
}
return Action::OK;
}
/** Determine from selected mask atoms which dihedrals will be rotated. */
Action::RetType Action_DihedralScan::Setup(ActionSetup& setup) {
DihedralScanType dst;
// If range is empty (i.e. no resrange arg given) look through all
// solute residues.
Range actualRange;
if (resRange_.Empty())
actualRange = setup.Top().SoluteResidues();
else
actualRange = resRange_;
// Search for dihedrals
if (dihSearch_.FindDihedrals(setup.Top(), actualRange))
return Action::ERR;
// For each found dihedral, set up mask of atoms that will move upon
// rotation. Also set up mask of atoms in this residue that will not
// move, including atom2.
if (debug_>0)
mprintf("DEBUG: Dihedrals:\n");
for (DihedralSearch::mask_it dih = dihSearch_.begin();
dih != dihSearch_.end(); ++dih)
{
dst.checkAtoms.clear();
// Set mask of atoms that will move during dihedral rotation.
dst.Rmask = DihedralSearch::MovingAtoms(setup.Top(), dih->A1(), dih->A2());
// If randomly rotating angles, check for atoms that are in the same
// residue as A1 but will not move. They need to be checked for clashes
// since further rotations will not help them.
if (mode_ == RANDOM && check_for_clashes_) {
CharMask cMask( dst.Rmask.ConvertToCharMask(), dst.Rmask.Nselected() );
int a1res = setup.Top()[dih->A1()].ResNum();
for (int maskatom = setup.Top().Res(a1res).FirstAtom();
maskatom < setup.Top().Res(a1res).LastAtom(); ++maskatom)
if (!cMask.AtomInCharMask(maskatom))
dst.checkAtoms.push_back( maskatom );
dst.checkAtoms.push_back(dih->A1()); // TODO: Does this need to be added first?
// Since only the second atom and atoms it is bonded to move during
// rotation, base the check on the residue of the second atom.
dst.resnum = a1res;
}
dst.atom0 = dih->A0(); // FIXME: This duplicates info
dst.atom1 = dih->A1();
dst.atom2 = dih->A2();
dst.atom3 = dih->A3();
BB_dihedrals_.push_back(dst);
// DEBUG: List dihedral info.
if (debug_ > 0) {
mprintf("\t%s-%s-%s-%s\n",
setup.Top().TruncResAtomName(dih->A0()).c_str(),
setup.Top().TruncResAtomName(dih->A1()).c_str(),
setup.Top().TruncResAtomName(dih->A2()).c_str(),
setup.Top().TruncResAtomName(dih->A3()).c_str() );
if (debug_ > 1 && mode_ == RANDOM && check_for_clashes_) {
mprintf("\t\tCheckAtoms=");
for (std::vector<int>::const_iterator ca = dst.checkAtoms.begin();
ca != dst.checkAtoms.end(); ++ca)
mprintf(" %i", *ca + 1);
mprintf("\n");
}
if (debug_ > 2) {
mprintf("\t\t");
dst.Rmask.PrintMaskAtoms("Rmask:");
}
}
}
// Set up CheckStructure for this parm (false = nobondcheck)
if (checkStructure_.SeparateSetup(setup.Top(),
setup.CoordInfo().TrajBox().Type(), false) != Action::OK)
return Action::ERR;
// Set the overall max number of rotations to try
max_rotations_ = (int) BB_dihedrals_.size();
max_rotations_ *= max_factor_;
// Set up simple structure check. First step is coarse; check distances
// between a certain atom in each residue (first, COM, CA, some other atom?)
// to see if residues are in each others neighborhood. Second step is to
// check the atoms in each close residue.
if (check_for_clashes_) {
ResidueCheckType rct;
int res = 0;
for (Topology::res_iterator residue = setup.Top().ResStart();
residue != setup.Top().ResEnd(); ++residue)
{
rct.resnum = res++;
rct.start = residue->FirstAtom();
rct.stop = residue->LastAtom();
rct.checkatom = rct.start;
ResCheck_.push_back(rct);
}
}
if (!outfilename_.empty() && CurrentParm_ == 0) // FIXME: Correct frames for # of rotations
outtraj_.SetupTrajWrite(setup.TopAddress(), setup.CoordInfo(), setup.Nframes());
CurrentParm_ = setup.TopAddress();
return Action::OK;
}
