// 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_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, 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::RetType Action_Unwrap::Init(ArgList& actionArgs, TopologyList* PFL, FrameList* FL,
DataSetList* DSL, DataFileList* DFL, int debugIn)
{
// Get reference
ReferenceFrame REF = FL->GetFrameFromArgs( actionArgs );
if (REF.error()) return Action::ERR;
if (!REF.empty()) {
RefFrame_ = *(REF.Coord());
// Get reference parm for frame
RefParm_ = REF.Parm();
}
// Get mask string
mask_.SetMaskString( actionArgs.GetMaskNext() );
mprintf(" UNWRAP: (%s), reference is ", mask_.MaskString());
if ( !REF.empty())
mprintf("%s", REF.FrameName().c_str());
else
mprintf("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_Contacts::Init()
Action::RetType Action_Contacts::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
byResidue_ = actionArgs.hasKey("byresidue");
double dist = actionArgs.getKeyDouble("distance", 7.0);
dt_ = actionArgs.getKeyDouble("time", 1.0);
// Square the cutoff
distance_ = dist * dist;
first_ = actionArgs.hasKey("first");
// Get reference
ReferenceFrame REF = init.DSL().GetReferenceFrame( actionArgs );
if (REF.error()) return Action::ERR;
std::string outfilename = actionArgs.GetStringKey("out");
outfile_ = init.DFL().AddCpptrajFile(outfilename, "Contacts", DataFileList::TEXT, true);
if (outfile_ == 0) return Action::ERR;
if (byResidue_) {
if (outfilename.empty()) {
mprinterr("Error: Contacts 'byresidue' requires output filename.\n");
return Action::ERR;
}
outfile2_ = init.DFL().AddCpptrajFile(outfilename + ".native", "Contacts by residue");
if (outfile2_ == 0) return Action::ERR;
}
// Get Mask
std::string mask0 = actionArgs.GetMaskNext();
if (mask0.empty() && byResidue_)
Mask_.SetMaskString("@CA");
else
Mask_.SetMaskString( mask0 );
// Initialize reference. If no reference mask is given mask0 will be used.
// First arg 'nofit' set to true, no fitting with contacts. Allows last arg
// 'RefTrans' to be null.
//if (RefInit(true, false, Mask_.MaskString(), actionArgs, FL, PFL, 0)!=0)
// return 1;
if (!first_ && REF.empty()) {
mprintf("\tNo reference structure specified. Defaulting to first.\n");
first_ = true;
}
if (!first_) {
// TODO: Convert FrameList to return frame reference?
// Set up atom mask for reference frame
if (REF.Parm().SetupIntegerMask(Mask_, REF.Coord())) return Action::ERR;
// Set up reference contacts
SetupContacts(REF.Coord(), REF.Parm());
}
// Output file header - only if not byresidue
if (!byResidue_) {
outfile_->Printf("#time\tContacts\tnative Contacts ");
if (!first_)
outfile_->Printf("(number of natives: %zu)", nativecontacts_.size());
outfile_->Printf("\n");
}
mprintf(" CONTACTS: [%s] Calculating current contacts and comparing results to",
Mask_.MaskString());
if (first_)
mprintf(" first frame.\n");
else
mprintf(" reference structure.\n");
mprintf("\tDistance cutoff is %g angstroms.\n", dist);
mprintf("\tWriting results to %s\n", outfile_->Filename().full());
if (byResidue_)
mprintf("\tResults are output on a per-residue basis to %s.\n", outfile2_->Filename().full());
return Action::OK;
}
/** Called once before traj processing. Set up reference info. */
Action::RetType Action_Rmsd::Init(ArgList& actionArgs, TopologyList* PFL, FrameList* FL,
DataSetList* DSL, DataFileList* DFL, int debugIn)
{
// Check for keywords
GetRmsKeywords( actionArgs );
DataFile* outfile = DFL->AddDataFile(actionArgs.GetStringKey("out"), actionArgs);
// Reference keywords
bool previous = actionArgs.hasKey("previous");
bool first = actionArgs.hasKey("first");
ReferenceFrame REF = FL->GetFrameFromArgs( actionArgs );
std::string reftrajname = actionArgs.GetStringKey("reftraj");
RefParm_ = PFL->GetParm( actionArgs );
// Per-res keywords
perres_ = actionArgs.hasKey("perres");
if (perres_) {
perresout_ = DFL->AddDataFile( actionArgs.GetStringKey("perresout") );
perresinvert_ = actionArgs.hasKey("perresinvert");
ResRange_.SetRange( actionArgs.GetStringKey("range") );
RefRange_.SetRange( actionArgs.GetStringKey("refrange") );
perresmask_ = actionArgs.GetStringKey("perresmask");
if (perresmask_.empty())
perresmask_.assign("");
else {
// If perresmask does not start with ampersand, insert one.
if (perresmask_[0] != '&')
perresmask_ = '&' + perresmask_;
}
perrescenter_ = actionArgs.hasKey("perrescenter");
perresavg_ = DFL->AddDataFile( actionArgs.GetStringKey("perresavg") );
}
// Get the RMS mask string for target
std::string mask1 = GetRmsMasks(actionArgs);
// Initialize reference
if (InitRef(previous, first, UseMass(), Fit(), reftrajname, REF, RefParm_, mask1,
actionArgs, "rmsd"))
return Action::ERR;
// Set RefParm for perres if not empty
if (perres_ && RefParm_ == 0 && !REF.empty())
RefParm_ = REF.Parm();
// Set up the RMSD data set.
rmsd_ = DSL->AddSet(DataSet::DOUBLE, actionArgs.GetStringNext(),"RMSD");
if (rmsd_==0) return Action::ERR;
rmsd_->SetScalar( DataSet::M_RMS );
// Add dataset to data file list
if (outfile != 0) outfile->AddSet( rmsd_ );
mprintf(" RMSD: (%s), reference is %s",TgtMask().MaskString(),
RefModeString());
PrintRmsStatus();
// Per-residue RMSD info.
if (perres_) {
mprintf(" No-fit RMSD will also be calculated for ");
if (ResRange_.Empty())
mprintf("each solute residue");
else
mprintf("residues %s",ResRange_.RangeArg());
if (!RefRange_.Empty())
mprintf(" (reference residues %s)",RefRange_.RangeArg());
mprintf(" using mask [:X%s].\n",perresmask_.c_str());
if (perresout_ != 0)
mprintf(" Per-residue output file is %s\n",perresout_->DataFilename().base());
if (perresavg_ != 0)
mprintf(" Avg per-residue output file is %s\n",perresavg_->DataFilename().base());
if (perrescenter_)
mprintf(" perrescenter: Each residue will be centered prior to RMS calc.\n");
if (perresinvert_)
mprintf(" perresinvert: Frames will be written in rows instead of columns.\n");
}
masterDSL_ = DSL;
return Action::OK;
}
int SequenceAlign(CpptrajState& State, ArgList& argIn) {
std::string blastfile = argIn.GetStringKey("blastfile");
if (blastfile.empty()) {
mprinterr("Error: 'blastfile' must be specified.\n");
return 1;
}
ReferenceFrame qref = State.DSL()->GetReferenceFrame(argIn);
if (qref.error() || qref.empty()) {
mprinterr("Error: Must specify reference structure for query.\n");
return 1;
}
std::string outfilename = argIn.GetStringKey("out");
if (outfilename.empty()) {
mprinterr("Error: Must specify output file.\n");
return 1;
}
TrajectoryFile::TrajFormatType fmt = TrajectoryFile::GetFormatFromArg(argIn);
if (fmt != TrajectoryFile::PDBFILE && fmt != TrajectoryFile::MOL2FILE)
fmt = TrajectoryFile::PDBFILE; // Default to PDB
int smaskoffset = argIn.getKeyInt("smaskoffset", 0) + 1;
int qmaskoffset = argIn.getKeyInt("qmaskoffset", 0) + 1;
// Load blast file
mprintf("\tReading BLAST alignment from '%s'\n", blastfile.c_str());
BufferedLine infile;
if (infile.OpenFileRead( blastfile )) return 1;
// Seek down to first Query line.
const char* ptr = infile.Line();
bool atFirstQuery = false;
while (ptr != 0) {
if (*ptr == 'Q') {
if ( strncmp(ptr, "Query", 5) == 0 ) {
atFirstQuery = true;
break;
}
}
ptr = infile.Line();
}
if (!atFirstQuery) {
mprinterr("Error: 'Query' not found.\n");
return 1;
}
// Read alignment. Replacing query with subject.
typedef std::vector<char> Carray;
typedef std::vector<int> Iarray;
Carray Query; // Query residues
Carray Sbjct; // Sbjct residues
Iarray Smap; // Smap[Sbjct index] = Query index
while (ptr != 0) {
const char* qline = ptr; // query line
const char* aline = infile.Line(); // alignment line
const char* sline = infile.Line(); // subject line
if (aline == 0 || sline == 0) {
mprinterr("Error: Missing alignment line or subject line after Query:\n");
mprinterr("Error: %s", qline);
return 1;
}
for (int idx = 12; qline[idx] != ' '; idx++) {
if (qline[idx] == '-') {
// Sbjct does not have corresponding res in Query
Smap.push_back(-1);
Sbjct.push_back( sline[idx] );
} else if (sline[idx] == '-') {
// Query does not have a corresponding res in Sbjct
Query.push_back( qline[idx] );
} else {
// Direct Query to Sbjct map
Smap.push_back( Query.size() );
Sbjct.push_back( sline[idx] );
Query.push_back( qline[idx] );
}
}
// Scan to next Query
ptr = infile.Line();
while (ptr != 0) {
if (*ptr == 'Q') {
if ( strncmp(ptr, "Query", 5) == 0 ) break;
}
ptr = infile.Line();
}
}
// DEBUG
std::string SmaskExp, QmaskExp;
if (State.Debug() > 0) mprintf(" Map of Sbjct to Query:\n");
for (int sres = 0; sres != (int)Sbjct.size(); sres++) {
if (State.Debug() > 0)
mprintf("%-i %3s %i", sres+smaskoffset, Residue::ConvertResName(Sbjct[sres]),
Smap[sres]+qmaskoffset);
const char* qres = "";
if (Smap[sres] != -1) {
qres = Residue::ConvertResName(Query[Smap[sres]]);
if (SmaskExp.empty())
SmaskExp.assign( integerToString(sres+smaskoffset) );
else
SmaskExp.append( "," + integerToString(sres+smaskoffset) );
if (QmaskExp.empty())
QmaskExp.assign( integerToString(Smap[sres]+qmaskoffset) );
else
QmaskExp.append( "," + integerToString(Smap[sres]+qmaskoffset) );
}
if (State.Debug() > 0) mprintf(" %3s\n", qres);
}
mprintf("Smask: %s\n", SmaskExp.c_str());
mprintf("Qmask: %s\n", QmaskExp.c_str());
// Check that query residues match reference.
for (unsigned int sres = 0; sres != Sbjct.size(); sres++) {
int qres = Smap[sres];
if (qres != -1) {
if (Query[qres] != qref.Parm().Res(qres).SingleCharName()) {
mprintf("Warning: Potential residue mismatch: Query %s reference %s\n",
Residue::ConvertResName(Query[qres]), qref.Parm().Res(qres).c_str());
}
}
}
// Build subject using coordinate from reference.
//AtomMask sMask; // Contain atoms that should be in sTop
Topology sTop;
Frame sFrame;
Iarray placeHolder; // Atom indices of placeholder residues.
for (unsigned int sres = 0; sres != Sbjct.size(); sres++) {
int qres = Smap[sres];
NameType SresName( Residue::ConvertResName(Sbjct[sres]) );
if (qres != -1) {
Residue const& QR = qref.Parm().Res(qres);
Residue SR(SresName, sres+1, ' ', QR.ChainID());
if (Query[qres] == Sbjct[sres]) { // Exact match. All non-H atoms.
for (int qat = QR.FirstAtom(); qat != QR.LastAtom(); qat++)
{
if (qref.Parm()[qat].Element() != Atom::HYDROGEN)
sTop.AddTopAtom( qref.Parm()[qat], SR );
sFrame.AddXYZ( qref.Coord().XYZ(qat) );
//sMask.AddAtom(qat);
}
} else { // Partial match. Copy only backbone and CB.
for (int qat = QR.FirstAtom(); qat != QR.LastAtom(); qat++)
{
if ( qref.Parm()[qat].Name().Match("N" ) ||
qref.Parm()[qat].Name().Match("CA") ||
qref.Parm()[qat].Name().Match("CB") ||
qref.Parm()[qat].Name().Match("C" ) ||
qref.Parm()[qat].Name().Match("O" ) )
{
sTop.AddTopAtom( qref.Parm()[qat], SR );
sFrame.AddXYZ( qref.Coord().XYZ(qat) );
}
}
}
} else {
// Residue in query does not exist for subject. Just put placeholder CA for now.
Vec3 Zero(0.0);
placeHolder.push_back( sTop.Natom() );
sTop.AddTopAtom( Atom("CA", "C "), Residue(SresName, sres+1, ' ', ' ') );
sFrame.AddXYZ( Zero.Dptr() );
}
}
//sTop.PrintAtomInfo("*");
mprintf("\tPlaceholder residue indices:");
for (Iarray::const_iterator p = placeHolder.begin(); p != placeHolder.end(); ++p)
mprintf(" %i", *p + 1);
mprintf("\n");
// Try to give placeholders more reasonable coordinates.
if (!placeHolder.empty()) {
Iarray current_indices;
unsigned int pidx = 0;
while (pidx < placeHolder.size()) {
if (current_indices.empty()) {
current_indices.push_back( placeHolder[pidx++] );
// Search for the end of this segment
for (; pidx != placeHolder.size(); pidx++) {
if (placeHolder[pidx] - current_indices.back() > 1) break;
current_indices.push_back( placeHolder[pidx] );
}
// DEBUG
mprintf("\tSegment:");
for (Iarray::const_iterator it = current_indices.begin();
it != current_indices.end(); ++it)
mprintf(" %i", *it + 1);
// Get coordinates of residues bordering segment.
int prev_res = sTop[current_indices.front()].ResNum() - 1;
int next_res = sTop[current_indices.back() ].ResNum() + 1;
mprintf(" (prev_res=%i, next_res=%i)\n", prev_res+1, next_res+1);
Vec3 prev_crd(sFrame.XYZ(current_indices.front() - 1));
Vec3 next_crd(sFrame.XYZ(current_indices.back() + 1));
prev_crd.Print("prev_crd");
next_crd.Print("next_crd");
Vec3 crd_step = (next_crd - prev_crd) / (double)(current_indices.size()+1);
crd_step.Print("crd_step");
double* xyz = sFrame.xAddress() + (current_indices.front() * 3);
for (unsigned int i = 0; i != current_indices.size(); i++, xyz += 3) {
prev_crd += crd_step;
xyz[0] = prev_crd[0];
xyz[1] = prev_crd[1];
xyz[2] = prev_crd[2];
}
current_indices.clear();
}
}
}
//Topology* sTop = qref.Parm().partialModifyStateByMask( sMask );
//if (sTop == 0) return 1;
//Frame sFrame(qref.Coord(), sMask);
// Write output traj
Trajout_Single trajout;
if (trajout.PrepareTrajWrite(outfilename, argIn, &sTop, CoordinateInfo(), 1, fmt)) return 1;
if (trajout.WriteSingle(0, sFrame)) return 1;
trajout.EndTraj();
return 0;
}
// ReferenceAction::InitRef()
int ReferenceAction::InitRef(bool previousIn, bool firstIn, bool massIn, bool fitIn,
std::string const& reftrajname, ReferenceFrame const& REF,
Topology* RefParm, std::string const& refmaskIn,
ArgList& actionArgs, const char* call)
{
refmode_ = UNKNOWN_REF;
previous_ = previousIn;
if (firstIn || previous_)
refmode_ = FIRST;
else {
if (REF.error()) return 1;
if (REF.empty()) {
if (!reftrajname.empty()) {
if (RefParm == 0) {
mprinterr("Error: %s: No parm found for reftraj %s. Make sure parm has been loaded.\n",
call, reftrajname.c_str());
return 1;
}
refmode_ = REFTRAJ;
} else {
// No reference keywords specified. Default to first.
mprintf("Warning: %s: No reference structure given. Defaulting to first.\n",call);
refmode_ = FIRST;
}
} else
refmode_ = REFFRAME;
}
// Set the reference mask expression
refMask_.SetMaskString(refmaskIn);
// Initialize reference if not 'first'
if (refmode_ != FIRST) {
if ( !reftrajname.empty() ) {
// Reference trajectory
if (SetRefMask( *RefParm, call )!=0) return 1;
// Attempt to open reference traj.
if (refTraj_.SetupTrajRead( reftrajname, actionArgs, RefParm)) {
mprinterr("Error: %s: Could not set up reftraj %s\n", call, reftrajname.c_str());
return 1;
}
refFrame_.SetupFrameV(RefParm->Atoms(), refTraj_.TrajCoordInfo());
if (refTraj_.BeginTraj()) {
mprinterr("Error: %s: Could not open reftraj %s\n", call, reftrajname.c_str());
return 1;
}
} else {
// Reference Frame
if (SetRefMask( REF.Parm(), call ) != 0) return 1;
SetRefStructure( REF.Coord(), fitIn, massIn );
}
}
// Set reference mode string
if (previous_)
modeString_ = "previous frame";
else if (refmode_ == FIRST)
modeString_ = "first frame";
else if (refmode_==REFTRAJ)
modeString_ = "trajectory " + refTraj_.Traj().Filename().Full();
else // REFFRAME
modeString_ = "\"" + REF.RefName() + "\"";
modeString_ += " (" + refMask_.MaskExpression() + ")";
return 0;
}
// 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;
}
/** Called once before traj processing. Set up reference info. */
Action::RetType Action_Rmsd::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
debug_ = debugIn;
// Check for keywords
fit_ = !actionArgs.hasKey("nofit");
if (fit_)
rotate_ = !actionArgs.hasKey("norotate");
useMass_ = actionArgs.hasKey("mass");
DataFile* outfile = init.DFL().AddDataFile(actionArgs.GetStringKey("out"), actionArgs);
bool saveMatrices = actionArgs.hasKey("savematrices");
// Reference keywords
bool previous = actionArgs.hasKey("previous");
bool first = actionArgs.hasKey("first");
ReferenceFrame refFrm = init.DSL().GetReferenceFrame( actionArgs );
std::string reftrajname = actionArgs.GetStringKey("reftraj");
if (!reftrajname.empty())
RefParm_ = init.DSL().GetTopology( actionArgs );
// Per-res keywords
perres_ = actionArgs.hasKey("perres");
if (perres_) {
perresout_ = init.DFL().AddDataFile( actionArgs.GetStringKey("perresout") );
perresinvert_ = actionArgs.hasKey("perresinvert");
TgtRange_.SetRange( actionArgs.GetStringKey("range") );
RefRange_.SetRange( actionArgs.GetStringKey("refrange") );
perresmask_ = actionArgs.GetStringKey("perresmask");
if (perresmask_.empty())
perresmask_.assign("");
else {
// If perresmask does not start with ampersand, insert one.
if (perresmask_[0] != '&')
perresmask_ = '&' + perresmask_;
}
perrescenter_ = actionArgs.hasKey("perrescenter");
perresavg_ = init.DFL().AddDataFile( actionArgs.GetStringKey("perresavg") );
}
// Get the RMS mask string for target
std::string tMaskExpr = actionArgs.GetMaskNext();
tgtMask_.SetMaskString(tMaskExpr);
// Get the RMS mask string for reference
std::string rMaskExpr = actionArgs.GetMaskNext();
if (rMaskExpr.empty())
rMaskExpr = tMaskExpr;
// Initialize reference
if (REF_.InitRef(previous, first, useMass_, fit_, reftrajname, refFrm,
RefParm_, rMaskExpr, actionArgs, "rmsd"))
return Action::ERR;
// Set RefParm for perres if not empty
if (perres_ && RefParm_ == 0 && !refFrm.empty())
RefParm_ = refFrm.ParmPtr();
// Set up the RMSD data set.
MetaData md( actionArgs.GetStringNext(), MetaData::M_RMS );
rmsd_ = init.DSL().AddSet(DataSet::DOUBLE, md, "RMSD");
if (rmsd_==0) return Action::ERR;
// Add dataset to data file list
if (outfile != 0) outfile->AddDataSet( rmsd_ );
// Set up rotation matrix data set if specified
if (saveMatrices) {
md.SetAspect("RM");
if (!fit_) {
mprinterr("Error: Must be fitting in order to save rotation matrices.\n");
return Action::ERR;
}
rmatrices_ = init.DSL().AddSet(DataSet::MAT3X3, md);
if (rmatrices_ == 0) return Action::ERR;
}
mprintf(" RMSD: (%s), reference is %s", tgtMask_.MaskString(),
REF_.RefModeString());
if (!fit_)
mprintf(", no fitting");
else {
mprintf(", with fitting");
if (!rotate_)
mprintf(" (no rotation)");
}
if (useMass_)
mprintf(", mass-weighted");
mprintf(".\n");
if (rmatrices_ != 0)
mprintf("\tRotation matrices will be saved to set '%s'\n", rmatrices_->legend());
// Per-residue RMSD info.
if (perres_) {
mprintf(" No-fit RMSD will also be calculated for ");
if (TgtRange_.Empty())
mprintf("each solute residue");
else
mprintf("residues %s",TgtRange_.RangeArg());
if (!RefRange_.Empty())
mprintf(" (reference residues %s)",RefRange_.RangeArg());
mprintf(" using mask [:X%s].\n",perresmask_.c_str());
if (perresout_ != 0)
mprintf(" Per-residue output file is %s\n",perresout_->DataFilename().base());
if (perresavg_ != 0)
mprintf(" Avg per-residue output file is %s\n",perresavg_->DataFilename().base());
if (perrescenter_)
mprintf(" perrescenter: Each residue will be centered prior to RMS calc.\n");
if (perresinvert_)
mprintf(" perresinvert: Frames will be written in rows instead of columns.\n");
}
if (perres_)
init.DSL().SetDataSetsPending(true);
masterDSL_ = init.DslPtr();
return Action::OK;
}