Exec::RetType Exec_Precision::Execute(CpptrajState& State, ArgList& argIn) {
// Next string is DataSet(s)/DataFile that command pertains to.
std::string name1 = argIn.GetStringNext();
if (name1.empty()) {
mprinterr("Error: No filename/setname given.\n");
return CpptrajState::ERR;
}
// This will break if dataset name starts with a digit...
int width = argIn.getNextInteger(12);
if (width < 1) {
mprintf("Error: Cannot set width < 1 (%i).\n", width);
return CpptrajState::ERR;
}
int precision = argIn.getNextInteger(4);
if (precision < 0) precision = 0;
DataFile* df = State.DFL().GetDataFile(name1);
if (df != 0) {
mprintf("\tSetting precision for all sets in %s to %i.%i\n", df->DataFilename().base(),
width, precision);
df->SetDataFilePrecision(width, precision);
} else {
State.DSL().SetPrecisionOfDataSets( name1, width, precision );
}
return CpptrajState::OK;
}
// Exec_DataSetCmd::Make2D()
Exec::RetType Exec_DataSetCmd::Make2D(CpptrajState& State, ArgList& argIn) {
std::string name = argIn.GetStringKey("name");
int ncols = argIn.getKeyInt("ncols", 0);
int nrows = argIn.getKeyInt("nrows", 0);
if (ncols <= 0 || nrows <= 0) {
mprinterr("Error: Must specify both ncols and nrows\n");
return CpptrajState::ERR;
}
DataSet* ds1 = State.DSL().GetDataSet( argIn.GetStringNext() );
if (ds1 == 0) return CpptrajState::ERR;
if (ds1->Ndim() != 1) {
mprinterr("Error: make2d only works for 1D data sets.\n");
return CpptrajState::ERR;
}
if (nrows * ncols != (int)ds1->Size()) {
mprinterr("Error: Size of '%s' (%zu) != nrows X ncols.\n", ds1->legend(), ds1->Size());
return CpptrajState::ERR;
}
if (name.empty())
name = State.DSL().GenerateDefaultName("make2d");
MetaData md(name, MetaData::M_MATRIX);
DataSet* ds3 = State.DSL().AddSet( DataSet::MATRIX_DBL, md );
if (ds3 == 0) return CpptrajState::ERR;
mprintf("\tConverting values from 1D set '%s' to 2D matrix '%s' with %i cols, %i rows.\n",
ds1->legend(), ds3->legend(), ncols, nrows);
DataSet_1D const& data = static_cast<DataSet_1D const&>( *ds1 );
DataSet_MatrixDbl& matrix = static_cast<DataSet_MatrixDbl&>( *ds3 );
if (matrix.Allocate2D( ncols, nrows )) return CpptrajState::ERR;
for (unsigned int idx = 0; idx != data.Size(); idx++)
matrix.AddElement( data.Dval(idx) );
return CpptrajState::OK;
}
// Exec_DataSetCmd::MakeXY()
Exec::RetType Exec_DataSetCmd::MakeXY(CpptrajState& State, ArgList& argIn) {
std::string name = argIn.GetStringKey("name");
DataSet* ds1 = State.DSL().GetDataSet( argIn.GetStringNext() );
DataSet* ds2 = State.DSL().GetDataSet( argIn.GetStringNext() );
if (ds1 == 0 || ds2 == 0) return CpptrajState::ERR;
if (ds1->Ndim() != 1 || ds2->Ndim() != 1) {
mprinterr("Error: makexy only works for 1D data sets.\n");
return CpptrajState::ERR;
}
DataSet* ds3 = State.DSL().AddSet( DataSet::XYMESH, name, "XY" );
if (ds3 == 0) return CpptrajState::ERR;
mprintf("\tUsing values from '%s' as X, values from '%s' as Y, output set '%s'\n",
ds1->legend(), ds2->legend(), ds3->legend());
DataSet_1D const& ds_x = static_cast<DataSet_1D const&>( *ds1 );
DataSet_1D const& ds_y = static_cast<DataSet_1D const&>( *ds2 );
DataSet_1D& out = static_cast<DataSet_1D&>( *ds3 );
size_t nframes = std::min( ds_x.Size(), ds_y.Size() );
if (ds_x.Size() != ds_y.Size())
mprintf("Warning: Data sets do not have equal sizes, only using %zu frames.\n", nframes);
double XY[2];
for (size_t i = 0; i != nframes; i++) {
XY[0] = ds_x.Dval(i);
XY[1] = ds_y.Dval(i);
out.Add( i, XY );
}
return CpptrajState::OK;
}
// Exec_CrdAction::ProcessArgs()
Exec::RetType Exec_CrdAction::ProcessArgs(CpptrajState& State, ArgList& argIn) {
std::string setname = argIn.GetStringNext();
if (setname.empty()) {
mprinterr("Error: %s: Specify COORDS dataset name.\n", argIn.Command());
return CpptrajState::ERR;
}
DataSet_Coords* CRD = (DataSet_Coords*)State.DSL().FindCoordsSet( setname );
if (CRD == 0) {
mprinterr("Error: %s: No COORDS set with name %s found.\n", argIn.Command(), setname.c_str());
return CpptrajState::ERR;
}
mprintf("\tUsing set '%s'\n", CRD->legend());
// Start, stop, offset
TrajFrameCounter frameCount;
ArgList crdarg( argIn.GetStringKey("crdframes"), "," );
if (frameCount.CheckFrameArgs( CRD->Size(), crdarg )) return CpptrajState::ERR;
frameCount.PrintInfoLine(CRD->legend());
ArgList actionargs = argIn.RemainingArgs();
actionargs.MarkArg(0);
Cmd const& cmd = Command::SearchTokenType( DispatchObject::ACTION, actionargs.Command() );
if ( cmd.Empty() ) return CpptrajState::ERR;
Action* act = (Action*)cmd.Alloc();
if (act == 0) return CpptrajState::ERR;
CpptrajState::RetType err = DoCrdAction(State, actionargs, CRD, act, frameCount);
delete act;
return err;
}
// Exec_DataSetCmd::ChangeOutputFormat()
Exec::RetType Exec_DataSetCmd::ChangeOutputFormat(CpptrajState const& State, ArgList& argIn)
{
TextFormat::FmtType fmt;
if (argIn.hasKey("double"))
fmt = TextFormat::DOUBLE;
else if (argIn.hasKey("scientific"))
fmt = TextFormat::SCIENTIFIC;
else if (argIn.hasKey("general"))
fmt = TextFormat::GDOUBLE;
else {
mprinterr("Error: Expected either 'double', 'scientific', or 'general'\n");
return CpptrajState::ERR;
}
// Loop over all DataSet arguments
std::string ds_arg = argIn.GetStringNext();
while (!ds_arg.empty()) {
DataSetList dsl = State.DSL().GetMultipleSets( ds_arg );
for (DataSetList::const_iterator ds = dsl.begin(); ds != dsl.end(); ++ds)
if ((*ds)->SetupFormat().SetFormatType(fmt))
mprintf("\tSet '%s' output format changed to '%s'\n",
(*ds)->legend(), TextFormat::typeDescription(fmt));
ds_arg = argIn.GetStringNext();
}
return CpptrajState::OK;
}
Exec::RetType Exec_ParmBox::Execute(CpptrajState& State, ArgList& argIn) {
Box pbox;
bool nobox = false;
if ( argIn.hasKey("nobox") )
nobox = true;
else {
pbox.SetX( argIn.getKeyDouble("x",0) );
pbox.SetY( argIn.getKeyDouble("y",0) );
pbox.SetZ( argIn.getKeyDouble("z",0) );
pbox.SetAlpha( argIn.getKeyDouble("alpha",0) );
pbox.SetBeta( argIn.getKeyDouble("beta",0) );
pbox.SetGamma( argIn.getKeyDouble("gamma",0) );
}
Topology* parm = State.DSL().GetTopByIndex( argIn );
if (parm == 0) return CpptrajState::ERR;
if (nobox)
mprintf("\tRemoving box information from parm %i:%s\n", parm->Pindex(), parm->c_str());
else
// Fill in missing parm box information from specified parm
pbox.SetMissingInfo( parm->ParmBox() );
if (argIn.hasKey("truncoct")) pbox.SetTruncOct();
parm->SetParmBox( pbox );
parm->ParmBox().PrintInfo();
return CpptrajState::OK;
}
Exec::RetType Exec_ParmStrip::Execute(CpptrajState& State, ArgList& argIn) {
Topology* parm = State.DSL().GetTopByIndex( argIn );
if (parm == 0) return CpptrajState::ERR;
// Check if this topology has already been used to set up an input
// trajectory, as this will break the traj read.
bool topology_in_use = false;
const char* fname = 0;
for (TrajinList::trajin_it tIn = State.InputTrajList().trajin_begin();
tIn != State.InputTrajList().trajin_end(); ++tIn)
if ( (*tIn)->Traj().Parm() == parm ) {
topology_in_use = true;
fname = (*tIn)->Traj().Filename().full();
break;
}
if (!topology_in_use) {
for (TrajinList::ensemble_it eIn = State.InputTrajList().ensemble_begin();
eIn != State.InputTrajList().ensemble_end(); ++eIn)
if ( (*eIn)->Traj().Parm() == parm ) {
topology_in_use = true;
fname = (*eIn)->Traj().Filename().full();
break;
}
}
if (topology_in_use) {
mprinterr("Error: Topology '%s' has already been used to set up trajectory '%s'.\n"
"Error: To strip this topology use the 'strip' action.\n",
parm->c_str(), fname);
return CpptrajState::ERR;
}
AtomMask tempMask( argIn.GetMaskNext() );
// Since want to keep atoms outside mask, invert selection
tempMask.InvertMaskExpression();
if (parm->SetupIntegerMask( tempMask )) return CpptrajState::ERR;
mprintf("\tStripping atoms in mask [%s] (%i) from %s\n",tempMask.MaskString(),
parm->Natom() - tempMask.Nselected(), parm->c_str());
Topology* tempParm = parm->modifyStateByMask(tempMask);
if (tempParm==0) {
mprinterr("Error: %s: Could not strip parm.\n", argIn.Command());
return CpptrajState::ERR;
} else {
// Replace parm with stripped version
*parm = *tempParm;
parm->Brief("Stripped parm:");
delete tempParm;
}
return CpptrajState::OK;
}
// Exec_SortEnsembleData::Execute()
Exec::RetType Exec_SortEnsembleData::Execute(CpptrajState& State, ArgList& argIn)
{
debug_ = State.Debug();
DataSetList setsToSort;
std::string dsarg = argIn.GetStringNext();
while (!dsarg.empty()) {
setsToSort += State.DSL().GetMultipleSets( dsarg );
dsarg = argIn.GetStringNext();
}
int err = 0;
# ifdef MPI
// For now, require ensemble mode in parallel.
if (!Parallel::EnsembleIsSetup()) {
rprinterr("Error: Data set ensemble sort requires ensemble mode in parallel.\n");
return CpptrajState::ERR;
}
// Only TrajComm masters have complete data.
if (Parallel::TrajComm().Master()) {
comm_ = Parallel::MasterComm();
# endif
DataSetList OutputSets;
err = SortData( setsToSort, OutputSets );
if (err == 0) {
// Remove unsorted sets.
for (DataSetList::const_iterator ds = setsToSort.begin(); ds != setsToSort.end(); ++ds)
State.DSL().RemoveSet( *ds );
// Add sorted sets.
for (DataSetList::const_iterator ds = OutputSets.begin(); ds != OutputSets.end(); ++ds)
State.DSL().AddSet( *ds );
// Since sorted sets have been transferred to master DSL, OutputSets now
// just has copies.
OutputSets.SetHasCopies( true );
mprintf("\tSorted sets:\n");
OutputSets.List();
}
# ifdef MPI
}
if (Parallel::World().CheckError( err ))
# else
if (err != 0)
# endif
return CpptrajState::ERR;
return CpptrajState::OK;
}
Exec::RetType Exec_DataFilter::Execute(CpptrajState& State, ArgList& argIn) {
Action_FilterByData filterAction;
ActionInit state(State.DSL(), State.DFL());
if (filterAction.Init(argIn, state, State.Debug()) != Action::OK)
return CpptrajState::ERR;
size_t nframes = filterAction.DetermineFrames();
if (nframes < 1) {
mprinterr("Error: No data to filter. All sets must contain some data.\n");
return CpptrajState::ERR;
}
ProgressBar progress( nframes );
ActionFrame frm;
for (size_t frame = 0; frame != nframes; frame++) {
progress.Update( frame );
filterAction.DoAction(frame, frm); // Filter does not need frame.
}
// Trigger master datafile write just in case
State.MasterDataFileWrite();
return CpptrajState::OK;
}
// Exec_DataSetCmd::VectorCoord()
Exec::RetType Exec_DataSetCmd::VectorCoord(CpptrajState& State, ArgList& argIn) {
// Keywords
std::string name = argIn.GetStringKey("name");
int idx;
if (argIn.hasKey("X"))
idx = 0;
else if (argIn.hasKey("Y"))
idx = 1;
else if (argIn.hasKey("Z"))
idx = 2;
else {
mprinterr("Error: 'vectorcoord' requires specifying X, Y, or Z.\n");
return CpptrajState::ERR;
}
// Data set
DataSet* ds1 = State.DSL().GetDataSet( argIn.GetStringNext() );
if (ds1 == 0) return CpptrajState::ERR;
if (ds1->Type() != DataSet::VECTOR) {
mprinterr("Error: 'vectorcoord' only works with vector data sets.\n");
return CpptrajState::ERR;
}
if (ds1->Size() < 1) {
mprinterr("Error: '%s' is empty.\n", ds1->legend());
return CpptrajState::ERR;
}
// Create output set.
static const char* XYZ[3] = { "X", "Y", "Z" };
DataSet* out = State.DSL().AddSet( DataSet::DOUBLE, name, "COORD");
if (out == 0) return CpptrajState::ERR;
// Extract data
mprintf("\tExtracting %s coordinate from vector %s to %s\n",
XYZ[idx], ds1->legend(), out->Meta().PrintName().c_str());
DataSet_Vector const& vec = static_cast<DataSet_Vector const&>( *ds1 );
for (unsigned int n = 0; n != vec.Size(); n++) {
double d = vec.VXYZ(n)[idx];
out->Add( n, &d );
}
return CpptrajState::OK;
}
Exec::RetType Exec_ReadData::Execute(CpptrajState& State, ArgList& argIn) {
DataFile dataIn;
dataIn.SetDebug( State.DFL().Debug() );
std::string filenameIn = argIn.GetStringNext();
File::NameArray fnames = File::ExpandToFilenames( filenameIn );
if (fnames.empty()) {
mprinterr("Error: '%s' matches no files.\n", filenameIn.c_str());
return CpptrajState::ERR;
}
int err = 0;
int idx = -1;
bool useIndex = argIn.hasKey("separate");
for (File::NameArray::const_iterator fn = fnames.begin(); fn != fnames.end(); ++fn) {
if (useIndex) idx++;
if (dataIn.ReadDataIn( *fn, argIn, State.DSL(), idx, fnames.size() )!=0) {
mprinterr("Error: Could not read data file '%s'.\n", fn->full());
err++;
}
}
if (err > 0) return CpptrajState::ERR;
return CpptrajState::OK;
}
// Exec_DataSetCmd::Concatenate()
Exec::RetType Exec_DataSetCmd::Concatenate(CpptrajState& State, ArgList& argIn) {
std::string name = argIn.GetStringKey("name");
bool use_offset = !argIn.hasKey("nooffset");
DataSet* ds3 = State.DSL().AddSet( DataSet::XYMESH, name, "CAT" );
if (ds3 == 0) return CpptrajState::ERR;
DataSet_1D& out = static_cast<DataSet_1D&>( *ds3 );
mprintf("\tConcatenating sets into '%s'\n", out.legend());
if (use_offset)
mprintf("\tX values will be offset.\n");
else
mprintf("\tX values will not be offset.\n");
std::string dsarg = argIn.GetStringNext();
double offset = 0.0;
while (!dsarg.empty()) {
DataSetList dsl = State.DSL().GetMultipleSets( dsarg );
double XY[2];
for (DataSetList::const_iterator ds = dsl.begin(); ds != dsl.end(); ++ds)
{
if ( (*ds)->Group() != DataSet::SCALAR_1D )
{
mprintf("Warning: '%s': Concatenation only supported for 1D scalar data sets.\n",
(*ds)->legend());
} else {
DataSet_1D const& set = static_cast<DataSet_1D const&>( *(*ds) );
mprintf("\t\t'%s'\n", set.legend());
for (size_t i = 0; i != set.Size(); i++) {
XY[0] = set.Xcrd( i ) + offset;
XY[1] = set.Dval( i );
out.Add( i, XY ); // NOTE: value of i does not matter for mesh
}
if (use_offset) offset = XY[0];
}
}
dsarg = argIn.GetStringNext();
}
return CpptrajState::OK;
}
Exec::RetType Exec_ParmSolvent::Execute(CpptrajState& State, ArgList& argIn) {
std::string maskexpr;
if (!argIn.hasKey("none")) {
maskexpr = argIn.GetMaskNext();
if ( maskexpr.empty() ) {
mprinterr("Error: solvent: No mask specified.\n");
return CpptrajState::ERR;
}
}
// Get parm index
Topology* parm = State.DSL().GetTopByIndex( argIn );
if (parm == 0) return CpptrajState::ERR;
parm->SetSolvent( maskexpr );
return CpptrajState::OK;
}
Exec::RetType Exec_CrdAction::DoCrdAction(CpptrajState& State, ArgList& actionargs,
DataSet_Coords* CRD, Action* act,
TrajFrameCounter const& frameCount) const
{
Timer total_time;
total_time.Start();
# ifdef MPI
ActionInit state(State.DSL(), State.DFL(), trajComm_);
# else
ActionInit state(State.DSL(), State.DFL());
# endif
if ( act->Init( actionargs, state, State.Debug() ) != Action::OK )
return CpptrajState::ERR;
actionargs.CheckForMoreArgs();
// Set up frame and parm for COORDS.
ActionSetup originalSetup( CRD->TopPtr(), CRD->CoordsInfo(), CRD->Size() );
Frame originalFrame = CRD->AllocateFrame();
ActionFrame frm( &originalFrame, 0 );
// Set up for this topology
Action::RetType setup_ret = act->Setup( originalSetup );
if ( setup_ret == Action::ERR || setup_ret == Action::SKIP )
return CpptrajState::ERR;
// Loop over all frames in COORDS.
ProgressBar progress( frameCount.TotalReadFrames() );
int set = 0;
for (int frame = frameCount.Start(); frame < frameCount.Stop();
frame += frameCount.Offset(), ++set)
{
progress.Update( set );
CRD->GetFrame( frame, originalFrame );
frm.SetTrajoutNum( set );
Action::RetType ret = act->DoAction( set, frm );
if (ret == Action::ERR) {
mprinterr("Error: crdaction: Frame %i, set %i\n", frame + 1, set + 1);
break;
}
// Check if frame was modified. If so, update COORDS.
if ( ret == Action::MODIFY_COORDS )
CRD->SetCRD( frame, frm.Frm() );
}
# ifdef MPI
act->SyncAction();
# endif
// Check if parm was modified. If so, update COORDS.
if ( setup_ret == Action::MODIFY_TOPOLOGY ) {
mprintf("Info: crdaction: Parm for %s was modified by action %s\n",
CRD->legend(), actionargs.Command());
CRD->CoordsSetup( originalSetup.Top(), originalSetup.CoordInfo() );
}
act->Print();
State.MasterDataFileWrite();
total_time.Stop();
mprintf("TIME: Total action execution time: %.4f seconds.\n", total_time.Total());
return CpptrajState::OK;
}
// Exec_DataSetCmd::Execute()
Exec::RetType Exec_DataSetCmd::Execute(CpptrajState& State, ArgList& argIn) {
RetType err = CpptrajState::OK;
if (argIn.Contains("legend")) { // Set legend for one data set
std::string legend = argIn.GetStringKey("legend");
DataSet* ds = State.DSL().GetDataSet( argIn.GetStringNext() );
if (ds == 0) return CpptrajState::ERR;
mprintf("\tChanging legend '%s' to '%s'\n", ds->legend(), legend.c_str());
ds->SetLegend( legend );
// ---------------------------------------------
} else if (argIn.hasKey("outformat")) { // Change double precision set output format
err = ChangeOutputFormat(State, argIn);
// ---------------------------------------------
} else if (argIn.hasKey("remove")) { // Remove data sets by various criteria
err = Remove(State, argIn);
// ---------------------------------------------
} else if (argIn.hasKey("makexy")) { // Combine values from two sets into 1
err = MakeXY(State, argIn);
// ---------------------------------------------
} else if (argIn.hasKey("make2d")) { // Create 2D matrix from 1D set
err = Make2D(State, argIn);
// ---------------------------------------------
} else if (argIn.hasKey("vectorcoord")) { // Extract vector X/Y/Z coord as new set
err = VectorCoord(State, argIn);
// ---------------------------------------------
} else if (argIn.hasKey("filter")) { // Filter points in data set to make new data set
err = Filter(State, argIn);
// ---------------------------------------------
} else if (argIn.hasKey("cat")) { // Concatenate two or more data sets
err = Concatenate(State, argIn);
// ---------------------------------------------
} else if (argIn.hasKey("droppoints")) { // Drop points from set
err = ModifyPoints(State, argIn, true);
// ---------------------------------------------
} else if (argIn.hasKey("keeppoints")) { // Keep points in set
err = ModifyPoints(State, argIn, false);
// ---------------------------------------------
} else if (argIn.hasKey("dim")) { // Modify dimension of set(s)
err = ChangeDim(State, argIn);
// ---------------------------------------------
} else if (argIn.hasKey("invert")) { // Invert set(s) X/Y, create new sets
err = InvertSets(State, argIn);
// ---------------------------------------------
} else { // Default: change mode/type for one or more sets.
err = ChangeModeType(State, argIn);
}
return err;
}
// Exec_Analyze::Execute()
Exec::RetType Exec_Analyze::Execute(CpptrajState& State, ArgList& argIn) {
// Remove 'analyze'
ArgList arg = argIn;
arg.RemoveFirstArg();
if (arg.empty()) {
mprinterr("Error: No analysis command specified.\n");
return CpptrajState::ERR;
}
mprintf("Warning: The 'analyze' prefix is no longer necessary and may be soon deprecated.\n");
if (arg.CommandIs("matrix"))
mprintf("Warning: NOTE: 'analyze matrix' is now 'diagmatrix'.\n");
else
mprintf("Warning: To add an analysis command the the queue, only the command name needs\n"
"Warning: to be specified, e.g. '%s <args>'.\n", arg.Command());
Cmd const& cmd = Command::SearchTokenType(DispatchObject::ANALYSIS, arg.Command());
if (cmd.Empty()) {
mprinterr("Error: Analysis command '%s' not found.\n", arg.Command());
return CpptrajState::ERR;
}
return State.AddToAnalysisQueue( (Analysis*)cmd.Alloc(), arg );
}
Exec::RetType Exec_LoadTraj::Execute(CpptrajState& State, ArgList& argIn) {
// Get Keywords
std::string setname = argIn.GetStringKey("name");
if (setname.empty()) {
mprinterr("Error: Must provide data set name ('name <setname>')\n");
return CpptrajState::ERR;
}
DataSet_Coords_TRJ* trj = (DataSet_Coords_TRJ*)
State.DSL().FindSetOfType(setname, DataSet::TRAJ);
if (trj == 0)
trj = (DataSet_Coords_TRJ*)
State.DSL().AddSet(DataSet::TRAJ, setname, "__DTRJ__");
if (trj == 0) {
mprinterr("Error: Could not set up TRAJ data set.\n");
return CpptrajState::ERR;
}
std::string trajname = argIn.GetStringNext();
if (trajname.empty()) {
// Add all existing input trajectories
if (State.InputTrajList().empty()) {
mprinterr("Error: No input trajectories loaded.\n");
return CpptrajState::ERR;
}
if (State.InputTrajList().Mode() != TrajinList::NORMAL) {
mprinterr("Error: Cannot convert ensemble input trajectories to data.\n");
return CpptrajState::ERR;
}
mprintf("\tSaving currently loaded input trajectories as data set with name '%s'\n",
setname.c_str());
for (TrajinList::trajin_it Trajin = State.InputTrajList().trajin_begin();
Trajin != State.InputTrajList().trajin_end(); ++Trajin)
if (trj->AddInputTraj( *Trajin )) return CpptrajState::ERR;
// TODO: Clear input trajectories from trajinList?
} else {
// Add the named trajectory
if (trj->AddSingleTrajin( trajname, argIn, State.DSL().GetTopology(argIn) ))
return CpptrajState::ERR;
}
return CpptrajState::OK;
}
/** Set up variable with value. In this case allow any amount of whitespace,
* so re-tokenize the original argument line (minus the command).
*/
CpptrajState::RetType
Control_Set::SetupControl(CpptrajState& State, ArgList& argIn, Varray& CurrentVars)
{
ArgList remaining = argIn.RemainingArgs();
size_t pos0 = remaining.ArgLineStr().find_first_of("=");
if (pos0 == std::string::npos) {
mprinterr("Error: Expected <var>=<value>\n");
return CpptrajState::ERR;
}
size_t pos1 = pos0;
bool append = false;
if (pos0 > 0 && remaining.ArgLineStr()[pos0-1] == '+') {
pos0--;
append = true;
}
std::string variable = NoWhitespace( remaining.ArgLineStr().substr(0, pos0) );
if (variable.empty()) {
mprinterr("Error: No variable name.\n");
return CpptrajState::ERR;
}
ArgList equals( NoLeadingWhitespace(remaining.ArgLineStr().substr(pos1+1)) );
std::string value;
if (equals.Contains("inmask")) {
AtomMask mask( equals.GetStringKey("inmask") );
Topology* top = State.DSL().GetTopByIndex( equals );
if (top == 0) return CpptrajState::ERR;
if (top->SetupIntegerMask( mask )) return CpptrajState::ERR;
if (equals.hasKey("atoms"))
value = integerToString( mask.Nselected() );
else if (equals.hasKey("residues")) {
int curRes = -1;
int nres = 0;
for (AtomMask::const_iterator at = mask.begin(); at != mask.end(); ++at) {
int res = (*top)[*at].ResNum();
if (res != curRes) {
nres++;
curRes = res;
}
}
value = integerToString( nres );
} else if (equals.hasKey("molecules")) {
int curMol = -1;
int nmol = 0;
for (AtomMask::const_iterator at = mask.begin(); at != mask.end(); ++at) {
int mol = (*top)[*at].MolNum();
if (mol != curMol) {
nmol++;
curMol = mol;
}
}
value = integerToString( nmol );
} else {
mprinterr("Error: Expected 'atoms', 'residues', or 'molecules'.\n");
return CpptrajState::ERR;
}
} else if (equals.hasKey("trajinframes")) {
value = integerToString(State.InputTrajList().MaxFrames());
} else
value = equals.ArgLineStr();
if (append)
CurrentVars.AppendVariable( "$" + variable, value );
else
CurrentVars.UpdateVariable( "$" + variable, value );
mprintf("\tVariable '%s' set to '%s'\n", variable.c_str(), value.c_str());
for (int iarg = 0; iarg < argIn.Nargs(); iarg++)
argIn.MarkArg( iarg );
return CpptrajState::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;
}
// Exec_DataSetCmd::Remove()
Exec::RetType Exec_DataSetCmd::Remove(CpptrajState& State, ArgList& argIn) {
std::string status;
// Get criterion type
CriterionType criterion = UNKNOWN_C;
for (int i = 1; i < (int)N_C; i++)
if (argIn.hasKey( CriterionKeys[i] )) {
criterion = (CriterionType)i;
status.assign( CriterionKeys[i] );
break;
}
if (criterion == UNKNOWN_C) {
mprinterr("Error: No criterion specified for 'remove'.\n");
return CpptrajState::ERR;
}
// Get select type
SelectType select = UNKNOWN_S;
std::string val1, val2;
for (const SelectPairType* ptr = SelectKeys; ptr->key_ != 0; ptr++)
if (argIn.Contains( ptr->key_ )) {
select = ptr->type_;
val1 = argIn.GetStringKey( ptr->key_ );
status.append( " " + std::string(ptr->key_) + " " + val1 );
// Get 'and' value for between/outside. TODO put nargs in SelectPairType?
if (select == BETWEEN || select == OUTSIDE) {
val2 = argIn.GetStringKey("and");
if (val2.empty()) {
mprinterr("Error: Missing 'and' value for selection '%s'\n", ptr->key_);
return CpptrajState::ERR;
}
status.append(" and " + val2);
}
break;
}
if (select == UNKNOWN_S || val1.empty()) {
mprinterr("Error: No selection specified for 'remove'.\n");
return CpptrajState::ERR;
}
if ( (criterion == SMODE || criterion == STYPE) &&
(select != EQUAL && select != NOT_EQUAL) )
{
mprinterr("Error: Specified select not valid for criterion '%s'\n", CriterionKeys[criterion]);
return CpptrajState::ERR;
}
mprintf("\tRemoving data sets");
std::string setSelectArg = argIn.GetStringNext();
if (setSelectArg.empty())
setSelectArg.assign("*");
else
mprintf(" within selection '%s'", setSelectArg.c_str());
mprintf(" %s\n", status.c_str());
DataSetList tempDSL = State.DSL().GetMultipleSets( setSelectArg );
if (tempDSL.empty()) {
mprinterr("Error: No data sets selected.\n");
return CpptrajState::ERR;
}
// Remove sets
unsigned int Nremoved = 0;
if ( criterion == AVERAGE ) {
if (!validDouble( val1 )) {
mprinterr("Error: '%s' is not a valid number\n", val1.c_str());
return CpptrajState::ERR;
}
double d_val1 = convertToDouble( val1 );
double d_val2 = d_val1;
if (!val2.empty()) {
if (!validDouble( val2 )) {
mprinterr("Error: '%s' is not a valid number\n", val2.c_str());
return CpptrajState::ERR;
}
d_val2 = convertToDouble( val2 );
}
for (DataSetList::const_iterator ds = tempDSL.begin(); ds != tempDSL.end(); ++ds)
{
if ( (*ds)->Group() != DataSet::SCALAR_1D )
mprintf("Warning: '%s' is not a valid data set for 'average' criterion.\n", (*ds)->legend());
else {
DataSet_1D const& ds1 = static_cast<DataSet_1D const&>( *(*ds) );
double avg = ds1.Avg();
bool remove = false;
switch (select) {
case EQUAL : remove = (avg == d_val1); break;
case NOT_EQUAL : remove = (avg != d_val1); break;
case LESS_THAN : remove = (avg < d_val1); break;
case GREATER_THAN : remove = (avg > d_val1); break;
case BETWEEN : remove = (avg > d_val1 && avg < d_val2); break;
case OUTSIDE : remove = (avg < d_val1 || avg > d_val2); break;
case UNKNOWN_S:
case N_S : return CpptrajState::ERR; // Sanity check
}
if (remove) {
mprintf("\t Removing set '%s' (avg is %g)\n", (*ds)->legend(), avg);
State.RemoveDataSet( *ds );
++Nremoved;
}
}
}
} else if ( criterion == SIZE ) {
if (!validInteger( val1 )) {
mprinterr("Error: '%s' is not a valid number\n", val1.c_str());
return CpptrajState::ERR;
}
unsigned int i_val1 = (unsigned int)convertToInteger( val1 );
unsigned int i_val2 = i_val1;
if (!val2.empty()) {
if (!validInteger( val2 )) {
mprinterr("Error: '%s' is not a valid number\n", val2.c_str());
return CpptrajState::ERR;
}
i_val2 = convertToInteger( val2 );
}
for (DataSetList::const_iterator ds = tempDSL.begin(); ds != tempDSL.end(); ++ds)
{
unsigned int size = (*ds)->Size();
bool remove = false;
switch ( select ) {
case EQUAL : remove = (size == i_val1); break;
case NOT_EQUAL : remove = (size != i_val1); break;
case LESS_THAN : remove = (size < i_val1); break;
case GREATER_THAN : remove = (size > i_val1); break;
case BETWEEN : remove = (size > i_val1 && size < i_val2); break;
case OUTSIDE : remove = (size < i_val1 || size > i_val2); break;
case UNKNOWN_S:
case N_S : return CpptrajState::ERR; // Sanity check
}
if (remove) {
mprintf("\t Removing set '%s' (size is %u)\n", (*ds)->legend(), size);
State.RemoveDataSet( *ds );
++Nremoved;
}
}
} else if ( criterion == SMODE ) {
MetaData::scalarMode mode_val = MetaData::ModeFromKeyword( val1 );
if (mode_val == MetaData::UNKNOWN_MODE) {
mprinterr("Error: '%s' is not a valid mode.\n", val1.c_str());
return CpptrajState::ERR;
}
for (DataSetList::const_iterator ds = tempDSL.begin(); ds != tempDSL.end(); ++ds)
{
bool remove = false;
MetaData::scalarMode mode = (*ds)->Meta().ScalarMode();
if (select == EQUAL ) remove = ( mode == mode_val );
else if (select == NOT_EQUAL) remove = ( mode != mode_val );
else return CpptrajState::ERR; // Sanity check
if (remove) {
mprintf("\t Removing set '%s' (mode is '%s')\n", (*ds)->legend(), MetaData::ModeString(mode));
State.RemoveDataSet( *ds );
++Nremoved;
}
}
} else if ( criterion == STYPE ) {
MetaData::scalarType type_val = MetaData::TypeFromKeyword( val1, MetaData::UNKNOWN_MODE );
if (type_val == MetaData::UNDEFINED) {
mprinterr("Error: '%s' is not a valid type.\n", val1.c_str());
return CpptrajState::ERR;
}
for (DataSetList::const_iterator ds = tempDSL.begin(); ds != tempDSL.end(); ++ds)
{
bool remove = false;
MetaData::scalarType type = (*ds)->Meta().ScalarType();
if (select == EQUAL ) remove = ( type == type_val );
else if (select == NOT_EQUAL) remove = ( type != type_val );
else return CpptrajState::ERR; // Sanity check
if (remove) {
mprintf("\t Removing set '%s' (typeis '%s')\n", (*ds)->legend(), MetaData::TypeString(type));
State.RemoveDataSet( *ds );
++Nremoved;
}
}
} else {
mprinterr("Internal Error: Criterion not yet implemented.\n");
return CpptrajState::ERR;
}
mprintf("\tRemoved %u of %zu sets.\n", Nremoved, tempDSL.size());
return CpptrajState::OK;
}
Exec::RetType Exec_CrdAction::DoCrdAction(CpptrajState& State, ArgList& actionargs,
DataSet_Coords* CRD, Action* act,
TrajFrameCounter const& frameCount) const
{
Timer total_time;
total_time.Start();
# ifdef MPI
ActionInit state(State.DSL(), State.DFL(), trajComm_);
# else
ActionInit state(State.DSL(), State.DFL());
# endif
if ( act->Init( actionargs, state, State.Debug() ) != Action::OK )
return CpptrajState::ERR;
actionargs.CheckForMoreArgs();
// Set up frame and parm for COORDS.
ActionSetup originalSetup( CRD->TopPtr(), CRD->CoordsInfo(), CRD->Size() );
Frame originalFrame = CRD->AllocateFrame();
// Set up for this topology
Action::RetType setup_ret = act->Setup( originalSetup );
if ( setup_ret == Action::ERR || setup_ret == Action::SKIP )
return CpptrajState::ERR;
// If the topology was modified, we will need a new COORDS set.
DataSet_Coords* crdOut = 0;
if ( setup_ret == Action::MODIFY_TOPOLOGY ) {
// This will not work for a TRJ set.
switch ( CRD->Type() ) {
case DataSet::TRAJ : mprinterr("Error: Cannot modify TRAJ data sets.\n"); break;
case DataSet::COORDS : crdOut = (DataSet_Coords*)new DataSet_Coords_CRD(); break;
case DataSet::REF_FRAME : crdOut = (DataSet_Coords*)new DataSet_Coords_REF(); break;
default: crdOut = 0; // SANITY
}
if (crdOut == 0) return CpptrajState::ERR;
mprintf("Info: crdaction: COORDS set '%s' will be modified by action '%s'\n",
CRD->legend(), actionargs.Command());
if (frameCount.TotalReadFrames() != (int)CRD->Size())
mprintf("Info: crdaction: Previous size= %zu, new size is %i\n",
CRD->Size(), frameCount.TotalReadFrames());
// Set up set, copy original metadata
crdOut->SetMeta( CRD->Meta() );
if (crdOut->CoordsSetup( originalSetup.Top(), originalSetup.CoordInfo() ))
return CpptrajState::ERR;
DataSet::SizeArray mfArray(1, frameCount.TotalReadFrames());
if (crdOut->Allocate( mfArray )) return CpptrajState::ERR;
}
// Loop over all frames in COORDS.
ProgressBar* progress = 0;
if (State.ShowProgress())
progress = new ProgressBar( frameCount.TotalReadFrames() );
int set = 0;
for (int frame = frameCount.Start(); frame < frameCount.Stop();
frame += frameCount.Offset(), ++set)
{
// Since Frame can be modified by actions, save original and use currentFrame
ActionFrame frm( &originalFrame, set );
if (progress != 0) progress->Update( set );
CRD->GetFrame( frame, originalFrame );
Action::RetType ret = act->DoAction( set, frm );
if (ret == Action::ERR) {
mprinterr("Error: crdaction: Frame %i, set %i\n", frame + 1, set + 1);
break;
}
// Check if frame was modified. If so, update COORDS.
if ( ret == Action::MODIFY_COORDS ) {
if (crdOut != 0)
crdOut->AddFrame( frm.Frm() );
else
CRD->SetCRD( frame, frm.Frm() );
}
}
if (progress != 0) delete progress;
# ifdef MPI
act->SyncAction();
# endif
// If topology was modified, replace old set with new.
if ( setup_ret == Action::MODIFY_TOPOLOGY ) {
mprintf("Info: crdaction: Topology for '%s' was modified by action '%s'\n",
CRD->legend(), actionargs.Command());
State.DSL().RemoveSet( CRD );
State.DSL().AddSet( crdOut );
}
act->Print();
State.MasterDataFileWrite();
total_time.Stop();
mprintf("TIME: Total action execution time: %.4f seconds.\n", total_time.Total());
return CpptrajState::OK;
}
// Exec_PermuteDihedrals::Execute()
Exec::RetType Exec_PermuteDihedrals::Execute(CpptrajState& State, ArgList& argIn) {
debug_ = State.Debug();
mode_ = INTERVAL;
// Get Keywords - first determine mode
if (argIn.hasKey("random"))
mode_ = RANDOM;
else if (argIn.hasKey("interval"))
mode_ = INTERVAL;
// Get input COORDS set
std::string setname = argIn.GetStringKey("crdset");
if (setname.empty()) {
mprinterr("Error: Specify COORDS dataset name with 'crdset'.\n");
return CpptrajState::ERR;
}
DataSet_Coords* CRD = (DataSet_Coords*)State.DSL().FindCoordsSet( setname );
if (CRD == 0) {
mprinterr("Error: Could not find COORDS set '%s'\n", setname.c_str());
return CpptrajState::ERR;
}
mprintf(" PERMUTEDIHEDRALS: Using COORDS '%s'\n", CRD->legend());
// Get residue range
Range resRange;
resRange.SetRange(argIn.GetStringKey("resrange"));
if (!resRange.Empty())
resRange.ShiftBy(-1); // User res args start from 1
mprintf("\tPermutating dihedrals in");
if (resRange.Empty())
mprintf(" all solute residues.\n");
else
mprintf(" residue range [%s]\n", resRange.RangeArg());
// Determine which angles to search for
DihedralSearch dihSearch;
dihSearch.SearchForArgs(argIn);
// If nothing is enabled, enable all
dihSearch.SearchForAll();
mprintf("\tSearching for types:");
dihSearch.PrintTypes();
mprintf("\n");
// Setup output trajectory
outframe_ = 0;
std::string outfilename = argIn.GetStringKey("outtraj");
if (!outfilename.empty()) {
mprintf("\tCoordinates output to '%s'\n", outfilename.c_str());
Topology* outtop = State.DSL().GetTopology( argIn );
if (outtop == 0) {
mprinterr("Error: No topology for output traj.\n");
return CpptrajState::ERR;
}
// Setup output trajectory FIXME: Correct frames for # of rotations
if (outtraj_.PrepareTrajWrite(outfilename, argIn, CRD->TopPtr(), CRD->CoordsInfo(),
CRD->Size(), TrajectoryFile::UNKNOWN_TRAJ))
return CpptrajState::ERR;
}
// Setup output coords
outfilename = argIn.GetStringKey("crdout");
if (!outfilename.empty()) {
mprintf("\tCoordinates saved to set '%s'\n", outfilename.c_str());
crdout_ = (DataSet_Coords_CRD*)State.DSL().AddSet(DataSet::COORDS, outfilename);
if (crdout_ == 0) return CpptrajState::ERR;
crdout_->CoordsSetup( CRD->Top(), CRD->CoordsInfo() );
}
// Get specific mode options.
double interval_in_deg = 60.0;
if ( mode_ == INTERVAL ) {
interval_in_deg = argIn.getNextDouble(60.0);
mprintf("\tDihedrals will be rotated at intervals of %.2f degrees.\n", interval_in_deg);
} else if (mode_ == RANDOM) {
check_for_clashes_ = argIn.hasKey("check");
checkAllResidues_ = argIn.hasKey("checkallresidues");
cutoff_ = argIn.getKeyDouble("cutoff",0.8);
rescutoff_ = argIn.getKeyDouble("rescutoff",10.0);
backtrack_ = argIn.getKeyInt("backtrack",4);
increment_ = argIn.getKeyInt("increment",1);
max_factor_ = argIn.getKeyInt("maxfactor",2);
int iseed = argIn.getKeyInt("rseed",-1);
// Output file for # of problems
DataFile* problemFile = State.DFL().AddDataFile(argIn.GetStringKey("out"), argIn);
// Dataset to store number of problems
number_of_problems_ = State.DSL().AddSet(DataSet::INTEGER, argIn.GetStringNext(),"Nprob");
if (number_of_problems_==0) return CpptrajState::ERR;
// Add dataset to data file list
if (problemFile != 0) problemFile->AddDataSet(number_of_problems_);
// Check validity of args
if (cutoff_ < Constants::SMALL) {
mprinterr("Error: cutoff too small.\n");
return CpptrajState::ERR;
}
if (rescutoff_ < Constants::SMALL) {
mprinterr("Error: rescutoff too small.\n");
return CpptrajState::ERR;
}
if (backtrack_ < 0) {
mprinterr("Error: backtrack value must be >= 0\n");
return CpptrajState::ERR;
}
if ( increment_<1 || (360 % increment_)!=0 ) {
mprinterr("Error: increment must be a factor of 360.\n");
return CpptrajState::ERR;
}
// Calculate max increment
max_increment_ = 360 / increment_;
// Seed random number gen
RN_.rn_set( iseed );
// Print info
mprintf("\tDihedrals will be rotated to random values.\n");
if (iseed==-1)
mprintf("\tRandom number generator will be seeded using time.\n");
else
mprintf("\tRandom number generator will be seeded using %i\n",iseed);
if (check_for_clashes_) {
mprintf("\tWill attempt to recover from bad steric clashes.\n");
if (checkAllResidues_)
mprintf("\tAll residues will be checked.\n");
else
mprintf("\tResidues up to the currenly rotating dihedral will be checked.\n");
mprintf("\tAtom cutoff %.2f, residue cutoff %.2f, backtrack = %i\n",
cutoff_, rescutoff_, backtrack_);
mprintf("\tWhen clashes occur dihedral will be incremented by %i\n",increment_);
mprintf("\tMax # attempted rotations = %i times number dihedrals.\n",
max_factor_);
}
// Square cutoffs to compare to dist^2 instead of dist
cutoff_ *= cutoff_;
rescutoff_ *= rescutoff_;
// Increment backtrack by 1 since we need to skip over current res
++backtrack_;
// Initialize CheckStructure
if (checkStructure_.SetOptions( false, false, false, State.Debug(), "*", "", 0.8, 1.15, 4.0 )) {
mprinterr("Error: Could not set up structure check.\n");
return CpptrajState::ERR;
}
// Set up CheckStructure for this parm (false = nobondcheck)
if (checkStructure_.Setup(CRD->Top(), CRD->CoordsInfo().TrajBox()))
return CpptrajState::ERR;
}
// Determine from selected mask atoms which dihedrals will be rotated.
PermuteDihedralsType dst;
// If range is empty (i.e. no resrange arg given) look through all
// solute residues.
Range actualRange;
if (resRange.Empty())
actualRange = CRD->Top().SoluteResidues();
else
actualRange = resRange;
// Search for dihedrals
if (dihSearch.FindDihedrals(CRD->Top(), actualRange))
return CpptrajState::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(CRD->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 = CRD->Top()[dih->A1()].ResNum();
for (int maskatom = CRD->Top().Res(a1res).FirstAtom();
maskatom < CRD->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",
CRD->Top().TruncResAtomName(dih->A0()).c_str(),
CRD->Top().TruncResAtomName(dih->A1()).c_str(),
CRD->Top().TruncResAtomName(dih->A2()).c_str(),
CRD->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 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 = CRD->Top().ResStart();
residue != CRD->Top().ResEnd(); ++residue)
{
rct.resnum = res++;
rct.start = residue->FirstAtom();
rct.stop = residue->LastAtom();
rct.checkatom = rct.start;
ResCheck_.push_back(rct);
}
}
// Perform dihedral permute
Frame currentFrame = CRD->AllocateFrame();
for (unsigned int set = 0; set != CRD->Size(); set++)
{
CRD->GetFrame(set, currentFrame);
int n_problems = 0;
switch (mode_) {
case RANDOM:
RandomizeAngles(currentFrame, CRD->Top());
// Check the resulting structure
n_problems = checkStructure_.CheckOverlaps( currentFrame );
//mprintf("%i\tResulting structure has %i problems.\n",frameNum,n_problems);
number_of_problems_->Add(set, &n_problems);
if (outtraj_.IsInitialized()) outtraj_.WriteSingle(outframe_++, currentFrame);
if (crdout_ != 0) crdout_->AddFrame( currentFrame );
break;
case INTERVAL: IntervalAngles(currentFrame, CRD->Top(), interval_in_deg); break;
}
}
if (outtraj_.IsInitialized()) outtraj_.EndTraj();
return CpptrajState::OK;
}
// Exec_RotateDihedral::Execute()
Exec::RetType Exec_RotateDihedral::Execute(CpptrajState& State, ArgList& argIn) {
// Get input COORDS set
std::string setname = argIn.GetStringKey("crdset");
if (setname.empty()) {
mprinterr("Error: Specify COORDS dataset name with 'crdset'.\n");
return CpptrajState::ERR;
}
DataSet_Coords* CRD = (DataSet_Coords*)State.DSL().FindCoordsSet( setname );
if (CRD == 0) {
mprinterr("Error: Could not find COORDS set '%s'\n", setname.c_str());
return CpptrajState::ERR;
}
if (CRD->Size() < 1) {
mprinterr("Error: COORDS set is empty.\n");
return CpptrajState::ERR;
}
int frame = argIn.getKeyInt("frame", 0);
if (frame < 0 || frame >= (int)CRD->Size()) {
mprinterr("Error: Specified frame %i is out of range.\n", frame+1);
return CpptrajState::ERR;
}
mprintf(" ROTATEDIHEDRAL: Using COORDS '%s', frame %i\n", CRD->legend(), frame+1);
// Get target frame
Frame FRM = CRD->AllocateFrame();
CRD->GetFrame(frame, FRM);
// Save as reference
Frame refFrame = FRM;
// Create output COORDS set if necessary
DataSet_Coords* OUT = 0;
int outframe = 0;
std::string outname = argIn.GetStringKey("name");
if (outname.empty()) {
// This will not work for TRAJ data sets
if (CRD->Type() == DataSet::TRAJ) {
mprinterr("Error: Using TRAJ as input set requires use of 'name' keyword for output.\n");
return CpptrajState::ERR;
}
OUT = CRD;
outframe = frame;
} else {
// Create new output set with 1 empty frame.
OUT = (DataSet_Coords*)State.DSL().AddSet( DataSet::COORDS, outname );
if (OUT == 0) return CpptrajState::ERR;
OUT->Allocate( DataSet::SizeArray(1, 1) );
OUT->CoordsSetup( CRD->Top(), CRD->CoordsInfo() );
OUT->AddFrame( CRD->AllocateFrame() );
mprintf("\tOutput to set '%s'\n", OUT->legend());
}
// Determine whether we are setting or incrementing.
enum ModeType { SET = 0, INCREMENT };
ModeType mode = SET;
if (argIn.Contains("value"))
mode = SET;
else if (argIn.Contains("increment"))
mode = INCREMENT;
else {
mprinterr("Error: Specify 'value <value>' or 'increment <increment>'\n");
return CpptrajState::ERR;
}
double value = argIn.getKeyDouble(ModeStr[mode], 0.0);
switch (mode) {
case SET: mprintf("\tDihedral will be set to %g degrees.\n", value); break;
case INCREMENT: mprintf("\tDihedral will be incremented by %g degrees.\n", value); break;
}
// Convert to radians
value *= Constants::DEGRAD;
// Select dihedral atoms
int A1, A2, A3, A4;
if (argIn.Contains("type")) {
// By type
ArgList typeArg = argIn.GetStringKey("type");
if (typeArg.empty()) {
mprinterr("Error: No dihedral type specified after 'type'\n");
return CpptrajState::ERR;
}
DihedralSearch dihSearch;
dihSearch.SearchForArgs( typeArg );
if (dihSearch.NoDihedralTokens()) {
mprinterr("Error: Specified dihedral type not recognized.\n");
return CpptrajState::ERR;
}
// Get residue
int res = argIn.getKeyInt("res", -1);
if (res <= 0) {
mprinterr("Error: If 'type' specified 'res' must be specified and > 0.\n");
return CpptrajState::ERR;
}
// Search for dihedrals. User residue #s start from 1.
if (dihSearch.FindDihedrals(CRD->Top(), Range(res-1)))
return CpptrajState::ERR;
DihedralSearch::mask_it dih = dihSearch.begin();
A1 = dih->A0();
A2 = dih->A1();
A3 = dih->A2();
A4 = dih->A3();
} else {
// By masks
AtomMask m1( argIn.GetMaskNext() );
AtomMask m2( argIn.GetMaskNext() );
AtomMask m3( argIn.GetMaskNext() );
AtomMask m4( argIn.GetMaskNext() );
if (CRD->Top().SetupIntegerMask( m1 )) return CpptrajState::ERR;
if (CRD->Top().SetupIntegerMask( m2 )) return CpptrajState::ERR;
if (CRD->Top().SetupIntegerMask( m3 )) return CpptrajState::ERR;
if (CRD->Top().SetupIntegerMask( m4 )) return CpptrajState::ERR;
if (m1.Nselected() != 1) return MaskError( m1 );
if (m2.Nselected() != 1) return MaskError( m2 );
if (m3.Nselected() != 1) return MaskError( m3 );
if (m4.Nselected() != 1) return MaskError( m4 );
A1 = m1[0];
A2 = m2[0];
A3 = m3[0];
A4 = m4[0];
}
mprintf("\tRotating dihedral defined by atoms '%s'-'%s'-'%s'-'%s'\n",
CRD->Top().AtomMaskName(A1).c_str(),
CRD->Top().AtomMaskName(A2).c_str(),
CRD->Top().AtomMaskName(A3).c_str(),
CRD->Top().AtomMaskName(A4).c_str());
// Set mask of atoms that will move during dihedral rotation
AtomMask Rmask = DihedralSearch::MovingAtoms(CRD->Top(), A2, A3);
// Calculate current value of dihedral
double torsion = Torsion( FRM.XYZ(A1), FRM.XYZ(A2), FRM.XYZ(A3), FRM.XYZ(A4) );
// Calculate delta needed to get to target value.
double delta;
switch (mode) {
case SET: delta = value - torsion; break;
case INCREMENT: delta = value; break;
}
mprintf("\tOriginal torsion is %g, rotating by %g degrees.\n",
torsion*Constants::RADDEG, delta*Constants::RADDEG);
// Set axis of rotation
Vec3 axisOfRotation = FRM.SetAxisOfRotation( A2, A3 );
// Calculate rotation matrix for delta.
Matrix_3x3 rotationMatrix;
rotationMatrix.CalcRotationMatrix(axisOfRotation, delta);
// Rotate around axis
FRM.Rotate(rotationMatrix, Rmask);
// RMS-fit the non-moving part of the coords back on original
AtomMask refMask = Rmask;
refMask.InvertMask();
FRM.Align( refFrame, refMask );
// Update coords
OUT->SetCRD( outframe, FRM );
return CpptrajState::OK;
}
// Exec_UpdateParameters::Execute()
Exec::RetType Exec_UpdateParameters::Execute(CpptrajState& State, ArgList& argIn)
{
std::string dsname = argIn.GetStringKey("setname");
if (dsname.empty()) {
mprinterr("Error: Specify parameter set.\n");
return CpptrajState::ERR;
}
DataSet* ds = State.DSL().GetDataSet( dsname );
if (ds == 0) {
mprinterr("Error: Parameter data set '%s' not found.\n", dsname.c_str());
return CpptrajState::ERR;
}
if (ds->Type() != DataSet::PARAMETERS) {
mprinterr("Error: Set '%s' is not a parameter data set.\n", ds->legend());
return CpptrajState::ERR;
}
DataSet_Parameters const& prm = static_cast<DataSet_Parameters const&>( *ds );
Topology* dstop = State.DSL().GetTopology( argIn );
if (dstop == 0) {
mprinterr("Error: No topology specified.\n");
return CpptrajState::ERR;
}
Topology& top = static_cast<Topology&>( *dstop );
mprintf("\tUpdating parameters in topology '%s' using those in set '%s'\n",
top.c_str(), prm.legend());
// Get list of existing parameters.
// We assume a parameter in topology is never repeated, so as soon
// as it is found we can move to the next one.
ParmHolder<int> ParmIndices;
// Bond parameters
BondTypes(ParmIndices, top, top.Bonds());
BondTypes(ParmIndices, top, top.BondsH());
for (ParmHolder<BondParmType>::const_iterator it1 = prm.BP().begin();
it1 != prm.BP().end(); ++it1)
{
for (ParmHolder<int>::const_iterator it0 = ParmIndices.begin();
it0 != ParmIndices.end(); ++it0)
{
if (it1->first == it0->first)
{
BondParmType& bp = top.SetBondParm(it0->second);
mprintf("\tUpdating bond parameter %s - %s from %f %f to %f %f\n",
*(it0->first[0]), *(it0->first[1]), bp.Rk(), bp.Req(),
it1->second.Rk(), it1->second.Req());
bp = it1->second;
break;
}
}
}
ParmIndices.clear();
// Angle parameters
AngleTypes(ParmIndices, top, top.Angles());
AngleTypes(ParmIndices, top, top.AnglesH());
for (ParmHolder<AngleParmType>::const_iterator it1 = prm.AP().begin();
it1 != prm.AP().end(); ++it1)
{
for (ParmHolder<int>::const_iterator it0 = ParmIndices.begin();
it0 != ParmIndices.end(); ++it0)
{
if (it1->first == it0->first)
{
AngleParmType& bp = top.SetAngleParm(it0->second);
mprintf("\tUpdating angle parameter %s - %s - %s from %f %f to %f %f\n",
*(it0->first[0]), *(it0->first[1]), *(it0->first[2]), bp.Tk(), bp.Teq(),
it1->second.Tk(), it1->second.Teq());
bp = it1->second;
break;
}
}
}
ParmIndices.clear();
// Dihedral parameters
DihedralTypes(ParmIndices, top, top.Dihedrals());
DihedralTypes(ParmIndices, top, top.DihedralsH());
for (ParmHolder<DihedralParmType>::const_iterator it1 = prm.DP().begin();
it1 != prm.DP().end(); ++it1)
{
for (ParmHolder<int>::const_iterator it0 = ParmIndices.begin();
it0 != ParmIndices.end(); ++it0)
{
if (it1->first == it0->first)
{
DihedralParmType& bp = top.SetDihedralParm(it0->second);
mprintf("\tUpdating dihedral parameter %s - %s - %s %s from %f %f %f to %f %f %f\n",
*(it0->first[0]), *(it0->first[1]), *(it0->first[2]), *(it0->first[3]),
bp.Pk(), bp.Pn(), bp.Phase(),
it1->second.Pk(), it1->second.Pn(), it1->second.Phase());
bp = it1->second;
break;
}
}
}
ParmIndices.clear();
if (top.Chamber().HasChamber()) {
ChamberParmType& chm = top.SetChamber();
// UB parameters
BondTypes(ParmIndices, top, chm.UB());
for (ParmHolder<BondParmType>::const_iterator it1 = prm.UB().begin();
it1 != prm.UB().end(); ++it1)
{
for (ParmHolder<int>::const_iterator it0 = ParmIndices.begin();
it0 != ParmIndices.end(); ++it0)
{
if (it1->first == it0->first)
{
BondParmType& bp = chm.SetUBparm(it0->second);
mprintf("\tUpdating UB parameter %s - %s from %f %f to %f %f\n",
*(it0->first[0]), *(it0->first[1]), bp.Rk(), bp.Req(),
it1->second.Rk(), it1->second.Req());
bp = it1->second;
break;
}
}
}
ParmIndices.clear();
// Improper parameters
DihedralTypes(ParmIndices, top, chm.Impropers());
for (ParmHolder<DihedralParmType>::const_iterator it1 = prm.IP().begin();
it1 != prm.IP().end(); ++it1)
{
for (ParmHolder<int>::const_iterator it0 = ParmIndices.begin();
it0 != ParmIndices.end(); ++it0)
{
if (it1->first == it0->first)
{
DihedralParmType& bp = chm.SetImproperParm(it0->second);
mprintf("\tUpdating improper parameter %s - %s - %s %s from %f %f %f to %f %f %f\n",
*(it0->first[0]), *(it0->first[1]), *(it0->first[2]), *(it0->first[3]),
bp.Pk(), bp.Pn(), bp.Phase(),
it1->second.Pk(), it1->second.Pn(), it1->second.Phase());
bp = it1->second;
break;
}
}
}
ParmIndices.clear();
}
//for (ParmHolder<int>::const_iterator it = ParmIndices.begin(); it != ParmIndices.end(); ++it)
// mprintf("\t%s %s %i\n", *(it->first[0]), *(it->first[1]), it->second);
return CpptrajState::OK;
}
// Exec_ParallelAnalysis::Execute()
Exec::RetType Exec_ParallelAnalysis::Execute(CpptrajState& State, ArgList& argIn)
{
Timer t_total;
t_total.Start();
Timer t_sync;
bool syncToMaster = argIn.hasKey("sync");
std::vector<unsigned int> setSizesBefore;
if (syncToMaster) {
t_sync.Start();
setSizesBefore.reserve( State.DSL().size() );
for (DataSetList::const_iterator it = State.DSL().begin(); it != State.DSL().end(); ++it)
setSizesBefore.push_back( (*it)->Size() );
t_sync.Stop();
}
// DEBUG - Have each thread report what analyses it knows about and what
// data sets it has.
/*
for (int rank = 0; rank < Parallel::World().Size(); rank++) {
if (rank == Parallel::World().Rank()) {
printf("Rank %i, %u analyses, %zu data sets:\n", rank, State.Analyses().size(),
State.DSL().size());
for (DataSetList::const_iterator it = State.DSL().begin(); it != State.DSL().end(); ++it)
printf("\t'%s' (%zu)\n", (*it)->Meta().PrintName().c_str(), (*it)->Size());
}
Parallel::World().Barrier();
}
Parallel::World().Barrier();
*/
mprintf(" PARALLELANALYSIS: Will attempt to run current Analyses in parallel.\n\n"
"*** THIS COMMAND IS STILL EXPERIMENTAL! ***\n\n");
if (syncToMaster)
mprintf("\tResulting data sets will be synced back to master.\n");
// Naively divide up all analyses among threads.
int my_start, my_stop;
int nelts = Parallel::World().DivideAmongProcesses( my_start, my_stop, State.Analyses().size() );
rprintf("Dividing %zu analyses among %i threads: %i to %i (%i)\n",
State.Analyses().size(), Parallel::World().Size(), my_start, my_stop, nelts);
// Each thread runs the analyses they are responsible for.
int nerr = 0;
for (int na = my_start; na != my_stop; na++) {
// TODO check setup status
if (State.Analyses().Ana(na).Analyze() != Analysis::OK) {
rprinterr("Error: Analysis failed: '%s'\n", State.Analyses().Args(na).ArgLine());
nerr++;
}
}
// This error check serves as a barrier
if (Parallel::World().CheckError( nerr )) return CpptrajState::ERR;
State.DFL().AllThreads_WriteAllDF();
State.Analyses().Clear();
if (syncToMaster) {
t_sync.Start();
// Check which sizes have changed.
if (setSizesBefore.size() != State.DSL().size()) {
mprintf("Warning: Number of sets have changed. Not attempting to sync sets to master.\n");
} else {
for (unsigned int idx = 0; idx != State.DSL().size(); idx++) {
int setHasChanged = 0;
if (!Parallel::World().Master()) {
if (setSizesBefore[idx] != State.DSL()[idx]->Size()) {
if (State.Debug() > 0)
rprintf("Set '%s' size has changed from %u to %zu\n",
State.DSL()[idx]->legend(), setSizesBefore[idx], State.DSL()[idx]->Size());
setHasChanged = 1;
}
}
int totalChanged;
Parallel::World().AllReduce(&totalChanged, &setHasChanged, 1, MPI_INT, MPI_SUM);
if (totalChanged > 0) {
if (totalChanged == 1) {
int sourceRank = 0;
if (setHasChanged == 1)
setHasChanged = Parallel::World().Rank();
Parallel::World().ReduceMaster(&sourceRank, &setHasChanged, 1, MPI_INT, MPI_SUM);
if (State.Debug() > 0)
mprintf("DEBUG: Need to sync '%s' from %i\n", State.DSL()[idx]->legend(), sourceRank);
if (Parallel::World().Master())
State.DSL()[idx]->RecvSet( sourceRank, Parallel::World() );
else if (setHasChanged == Parallel::World().Rank())
State.DSL()[idx]->SendSet( 0, Parallel::World() );
} else
mprintf("Warning: '%s' exists on multiple threads. Not syncing.\n",
State.DSL()[idx]->legend());
}
}
}
t_sync.Stop();
}
t_total.Stop();
if (syncToMaster)
t_sync.WriteTiming(2, "Sync:", t_total.Total());
t_total.WriteTiming(1, "Total:");
return CpptrajState::OK;
}
// Exec_DataSetCmd::Filter()
Exec::RetType Exec_DataSetCmd::Filter(CpptrajState& State, ArgList& argIn) {
std::string name = argIn.GetStringKey("name");
int rowmin = argIn.getKeyInt("rowmin", -1);
int rowmax = argIn.getKeyInt("rowmax", -1);
int colmin = argIn.getKeyInt("colmin", -1);
int colmax = argIn.getKeyInt("colmax", -1);
DataSet* ds1 = State.DSL().GetDataSet( argIn.GetStringNext() );
if (ds1 == 0) return CpptrajState::ERR;
if ( ds1->Group() == DataSet::SCALAR_1D ) {
mprinterr("Error: Not yet set up for 1D sets.\n");
return CpptrajState::ERR;
} else if (ds1->Group() == DataSet::MATRIX_2D) {
DataSet_2D const& matrixIn = static_cast<DataSet_2D const&>( *ds1 );
if (rowmin < 0) rowmin = 0;
if (rowmax < 0) rowmax = matrixIn.Nrows();
int nrows = rowmax - rowmin;
if (nrows < 1) {
mprinterr("Error: Keeping less than 1 row.\n");
return CpptrajState::ERR;
} else if (nrows > (int)matrixIn.Nrows())
nrows = matrixIn.Nrows();
if (colmin < 0) colmin = 0;
if (colmax < 0) colmax = matrixIn.Ncols();
int ncols = colmax - colmin;
if (ncols < 1) {
mprinterr("Error: Keeping less than 1 column.\n");
return CpptrajState::ERR;
} else if (ncols > (int)matrixIn.Ncols())
ncols = matrixIn.Ncols();
mprintf("\tMatrix to filter: %s\n", ds1->legend());
mprintf("\tKeeping rows >= %i and < %i\n", rowmin, rowmax);
mprintf("\tKeeping cols >= %i and < %i\n", colmin, colmax);
mprintf("\tCreating new matrix with %i rows and %i columns.\n", nrows, ncols);
DataSet* ds3 = State.DSL().AddSet( DataSet::MATRIX_DBL, name, "make2d" );
if (ds3 == 0) return CpptrajState::ERR;
DataSet_MatrixDbl& matrixOut = static_cast<DataSet_MatrixDbl&>( *ds3 );
matrixOut.Allocate2D(ncols, nrows);
matrixOut.SetDim( Dimension::X, Dimension(matrixIn.Dim(0).Coord(colmin),
matrixIn.Dim(0).Step(),
matrixIn.Dim(0).Label()) );
matrixOut.SetDim( Dimension::Y, Dimension(matrixIn.Dim(1).Coord(rowmin),
matrixIn.Dim(1).Step(),
matrixIn.Dim(1).Label()) );
for (int row = 0; row < (int)matrixIn.Nrows(); row++)
{
if (row >= rowmin && row < rowmax)
{
for (int col = 0; col < (int)matrixIn.Ncols(); col++)
{
if (col >= colmin && col < colmax)
{
double val = matrixIn.GetElement(col, row);
matrixOut.SetElement( col-colmin, row-rowmin, val );
//mprintf("DEBUG:\tmatrixIn(%i, %i) = %f to matrixOut(%i, %i)\n",
// col, row, val, col-colmin, row-rowmin);
}
}
}
}
}
return CpptrajState::OK;
}
// Exec_DataSetCmd::ChangeDim()
Exec::RetType Exec_DataSetCmd::ChangeDim(CpptrajState const& State, ArgList& argIn) {
int ndim = -1;
if (argIn.hasKey("xdim"))
ndim = 0;
else if (argIn.hasKey("ydim"))
ndim = 1;
else if (argIn.hasKey("zdim"))
ndim = 2;
else
ndim = argIn.getKeyInt("ndim", -1);
if (ndim < 0) {
mprinterr("Error: Specify xdim/ydim/zdim or dimension number with ndim.\n");
return CpptrajState::ERR;
}
if (ndim < 3) {
static const char DIMSTR[3] = { 'X', 'Y', 'Z' };
mprintf("\tChanging the following in the %c dimension:\n", DIMSTR[ndim]);
} else
mprintf("\tChanging the following in dimension %i\n", ndim);
bool changeLabel, changeMin, changeStep;
std::string label;
double min = 0.0;
double step = 0.0;
if (argIn.Contains("label")) {
label = argIn.GetStringKey("label");
changeLabel = true;
mprintf("\tNew Label: %s\n", label.c_str());
} else
changeLabel = false;
if (argIn.Contains("step")) {
step = argIn.getKeyDouble("step", 0.0);
changeStep = true;
mprintf("\tNew step: %g\n", step);
} else
changeStep = false;
if (argIn.Contains("min")) {
min = argIn.getKeyDouble("min", 0.0);
changeMin = true;
mprintf("\tNew min: %g\n", min);
} else
changeMin = false;
// Loop over all DataSet arguments
std::string ds_arg = argIn.GetStringNext();
while (!ds_arg.empty()) {
DataSetList dsl = State.DSL().GetMultipleSets( ds_arg );
for (DataSetList::const_iterator ds = dsl.begin(); ds != dsl.end(); ++ds)
{
if (ndim < (int)(*ds)->Ndim()) {
mprintf("\t%s\n", (*ds)->legend());
Dimension dim = (*ds)->Dim(ndim);
if (changeLabel) dim.SetLabel( label );
if (changeMin) dim.ChangeMin( min );
if (changeStep) dim.ChangeStep( step );
(*ds)->SetDim(ndim, dim);
} else
mprintf("Warning: Set '%s' has fewer then %i dimensions - skipping.\n",
(*ds)->legend(), ndim);
}
ds_arg = argIn.GetStringNext();
}
return CpptrajState::OK;
}
// Exec_DataSetCmd::ChangeModeType()
Exec::RetType Exec_DataSetCmd::ChangeModeType(CpptrajState const& State, ArgList& argIn) {
std::string modeKey = argIn.GetStringKey("mode");
std::string typeKey = argIn.GetStringKey("type");
if (modeKey.empty() && typeKey.empty()) {
mprinterr("Error: No valid keywords specified.\n");
return CpptrajState::ERR;
}
// First determine mode if specified.
MetaData::scalarMode dmode = MetaData::UNKNOWN_MODE;
if (!modeKey.empty()) {
dmode = MetaData::ModeFromKeyword( modeKey );
if (dmode == MetaData::UNKNOWN_MODE) {
mprinterr("Error: Invalid mode keyword '%s'\n", modeKey.c_str());
return CpptrajState::ERR;
}
}
// Next determine type if specified.
MetaData::scalarType dtype = MetaData::UNDEFINED;
if (!typeKey.empty()) {
dtype = MetaData::TypeFromKeyword( typeKey, dmode );
if (dtype == MetaData::UNDEFINED) {
mprinterr("Error: Invalid type keyword '%s'\n", typeKey.c_str());
return CpptrajState::ERR;
}
}
// Additional options for type 'noe'
AssociatedData_NOE noeData;
if (dtype == MetaData::NOE) {
if (noeData.NOE_Args(argIn))
return CpptrajState::ERR;
}
if (dmode != MetaData::UNKNOWN_MODE)
mprintf("\tDataSet mode = %s\n", MetaData::ModeString(dmode));
if (dtype != MetaData::UNDEFINED)
mprintf("\tDataSet type = %s\n", MetaData::TypeString(dtype));
// Loop over all DataSet arguments
std::string ds_arg = argIn.GetStringNext();
while (!ds_arg.empty()) {
DataSetList dsl = State.DSL().GetMultipleSets( ds_arg );
for (DataSetList::const_iterator ds = dsl.begin(); ds != dsl.end(); ++ds)
{
if (dmode != MetaData::UNKNOWN_MODE) {
// Warn if mode does not seem appropriate for the data set type.
if ( dmode >= MetaData::M_DISTANCE &&
dmode <= MetaData::M_RMS &&
(*ds)->Group() != DataSet::SCALAR_1D )
mprintf("Warning: '%s': Expected scalar 1D data set type for mode '%s'\n",
(*ds)->legend(), MetaData::ModeString(dmode));
else if ( dmode == MetaData::M_VECTOR &&
(*ds)->Type() != DataSet::VECTOR )
mprintf("Warning: '%s': Expected vector data set type for mode '%s'\n",
(*ds)->legend(), MetaData::ModeString(dmode));
else if ( dmode == MetaData::M_MATRIX &&
(*ds)->Group() != DataSet::MATRIX_2D )
mprintf("Warning: '%s': Expected 2D matrix data set type for mode '%s'\n",
(*ds)->legend(), MetaData::ModeString(dmode));
}
if ( dtype == MetaData::NOE ) (*ds)->AssociateData( &noeData );
mprintf("\t\t'%s'\n", (*ds)->legend());
MetaData md = (*ds)->Meta();
md.SetScalarMode( dmode );
md.SetScalarType( dtype );
(*ds)->SetMeta( md );
}
ds_arg = argIn.GetStringNext();
}
return CpptrajState::OK;
}
/** Syntax: dataset invert <set arg0> ... name <new name> */
Exec::RetType Exec_DataSetCmd::InvertSets(CpptrajState& State, ArgList& argIn) {
DataSetList& DSL = State.DSL();
// Get keywords
DataSet* inputNames = 0;
std::string dsname = argIn.GetStringKey("legendset");
if (!dsname.empty()) {
inputNames = DSL.GetDataSet( dsname );
if (inputNames == 0) {
mprinterr("Error: Name set '%s' not found.\n", dsname.c_str());
return CpptrajState::ERR;
}
if (inputNames->Type() != DataSet::STRING) {
mprinterr("Error: Set '%s' does not contain strings.\n", inputNames->legend());
return CpptrajState::ERR;
}
mprintf("\tUsing names from set '%s' as legends for inverted sets.\n", inputNames->legend());
}
dsname = argIn.GetStringKey("name");
if (dsname.empty()) {
mprinterr("Error: 'invert' requires that 'name <new set name>' be specified.\n");
return CpptrajState::ERR;
}
mprintf("\tNew sets will be named '%s'\n", dsname.c_str());
DataFile* outfile = State.DFL().AddDataFile( argIn.GetStringKey("out"), argIn );
if (outfile != 0)
mprintf("\tNew sets will be output to '%s'\n", outfile->DataFilename().full());
// TODO determine type some other way
DataSet::DataType outtype = DataSet::DOUBLE;
// Get input DataSets
std::vector<DataSet_1D*> input_sets;
std::string dsarg = argIn.GetStringNext();
while (!dsarg.empty()) {
DataSetList sets = DSL.GetMultipleSets( dsarg );
for (DataSetList::const_iterator ds = sets.begin(); ds != sets.end(); ++ds)
{
if ( (*ds)->Group() != DataSet::SCALAR_1D ) {
mprintf("Warning: '%s': Inversion only supported for 1D scalar data sets.\n",
(*ds)->legend());
} else {
if (!input_sets.empty()) {
if ( (*ds)->Size() != input_sets.back()->Size() ) {
mprinterr("Error: Set '%s' has different size (%zu) than previous set (%zu)\n",
(*ds)->legend(), (*ds)->Size(), input_sets.back()->Size());
return CpptrajState::ERR;
}
}
input_sets.push_back( (DataSet_1D*)*ds );
}
}
dsarg = argIn.GetStringNext();
}
if (input_sets.empty()) {
mprinterr("Error: No sets selected.\n");
return CpptrajState::ERR;
}
if (inputNames != 0 && inputNames->Size() != input_sets.front()->Size()) {
mprinterr("Error: Name set '%s' size (%zu) differs from # data points (%zu).\n",
inputNames->legend(), inputNames->Size(), input_sets.front()->Size());
return CpptrajState::ERR;
}
mprintf("\t%zu input sets; creating %zu output sets.\n",
input_sets.size(), input_sets.front()->Size());
// Need an output data set for each point in input sets
std::vector<DataSet*> output_sets;
int column = 1;
for (int idx = 0; idx != (int)input_sets[0]->Size(); idx++, column++) {
DataSet* ds = 0;
ds = DSL.AddSet(outtype, MetaData(dsname, column));
if (ds == 0) return CpptrajState::ERR;
if (inputNames != 0)
ds->SetLegend( (*((DataSet_string*)inputNames))[idx] );
output_sets.push_back( ds );
if (outfile != 0) outfile->AddDataSet( ds );
}
// Create a data set containing names of each input data set
DataSet* nameset = DSL.AddSet(DataSet::STRING, MetaData(dsname, column));
if (nameset == 0) return CpptrajState::ERR;
if (inputNames != 0)
nameset->SetLegend("Names");
if (outfile != 0) outfile->AddDataSet( nameset );
// Populate output data sets
for (int jdx = 0; jdx != (int)input_sets.size(); jdx++)
{
DataSet_1D const& INP = static_cast<DataSet_1D const&>( *(input_sets[jdx]) );
nameset->Add( jdx, INP.legend() );
for (unsigned int idx = 0; idx != INP.Size(); idx++)
{
double dval = INP.Dval( idx );
output_sets[idx]->Add( jdx, &dval );
}
}
return CpptrajState::OK;
}
/** Set up each mask/integer loop. */
int ControlBlock_For::SetupBlock(CpptrajState& State, ArgList& argIn) {
mprintf(" Setting up 'for' loop.\n");
Vars_.clear();
Topology* currentTop = 0;
static const char* TypeStr[] = { "ATOMS ", "RESIDUES ", "MOLECULES ",
"MOL_FIRST_RES ", "MOL_LAST_RES " };
static const char* OpStr[] = {"+=", "-=", "<", ">"};
description_.assign("for (");
int MaxIterations = -1;
int iarg = 0;
while (iarg < argIn.Nargs())
{
// Advance to next unmarked argument.
while (iarg < argIn.Nargs() && argIn.Marked(iarg)) iarg++;
if (iarg == argIn.Nargs()) break;
// Determine 'for' type
ForType ftype = UNKNOWN;
bool isMaskFor = true;
int argToMark = iarg;
if ( argIn[iarg] == "atoms" ) ftype = ATOMS;
else if ( argIn[iarg] == "residues" ) ftype = RESIDUES;
else if ( argIn[iarg] == "molecules" ) ftype = MOLECULES;
else if ( argIn[iarg] == "molfirstres" ) ftype = MOLFIRSTRES;
else if ( argIn[iarg] == "mollastres" ) ftype = MOLLASTRES;
else if ( argIn[iarg].find(";") != std::string::npos ) {
isMaskFor = false;
ftype = INTEGER;
}
// If type is still unknown, check for list.
if (ftype == UNKNOWN) {
if (iarg+1 < argIn.Nargs() && argIn[iarg+1] == "in") {
ftype = LIST;
isMaskFor = false;
argToMark = iarg+1;
}
}
// Exit if type could not be determined.
if (ftype == UNKNOWN) {
mprinterr("Error: for loop type not specfied.\n");
return 1;
}
argIn.MarkArg(argToMark);
Vars_.push_back( LoopVar() );
LoopVar& MH = Vars_.back();
int Niterations = -1;
// Set up for specific type
if (description_ != "for (") description_.append(", ");
// -------------------------------------------
if (isMaskFor)
{
// {atoms|residues|molecules} <var> inmask <mask> [TOP KEYWORDS]
if (argIn[iarg+2] != "inmask") {
mprinterr("Error: Expected 'inmask', got %s\n", argIn[iarg+2].c_str());
return 1;
}
AtomMask currentMask;
if (currentMask.SetMaskString( argIn.GetStringKey("inmask") )) return 1;
MH.varType_ = ftype;
Topology* top = State.DSL().GetTopByIndex( argIn );
if (top != 0) currentTop = top;
if (currentTop == 0) return 1;
MH.varname_ = argIn.GetStringNext();
if (MH.varname_.empty()) {
mprinterr("Error: 'for inmask': missing variable name.\n");
return 1;
}
MH.varname_ = "$" + MH.varname_;
// Set up mask
if (currentTop->SetupIntegerMask( currentMask )) return 1;
currentMask.MaskInfo();
if (currentMask.None()) return 1;
// Set up indices
if (MH.varType_ == ATOMS)
MH.Idxs_ = currentMask.Selected();
else if (MH.varType_ == RESIDUES) {
int curRes = -1;
for (AtomMask::const_iterator at = currentMask.begin(); at != currentMask.end(); ++at) {
int res = (*currentTop)[*at].ResNum();
if (res != curRes) {
MH.Idxs_.push_back( res );
curRes = res;
}
}
} else if (MH.varType_ == MOLECULES ||
MH.varType_ == MOLFIRSTRES ||
MH.varType_ == MOLLASTRES)
{
int curMol = -1;
for (AtomMask::const_iterator at = currentMask.begin(); at != currentMask.end(); ++at) {
int mol = (*currentTop)[*at].MolNum();
if (mol != curMol) {
if (MH.varType_ == MOLECULES)
MH.Idxs_.push_back( mol );
else {
int res;
if (MH.varType_ == MOLFIRSTRES)
res = (*currentTop)[ currentTop->Mol( mol ).BeginAtom() ].ResNum();
else // MOLLASTRES
res = (*currentTop)[ currentTop->Mol( mol ).EndAtom()-1 ].ResNum();
MH.Idxs_.push_back( res );
}
curMol = mol;
}
}
}
Niterations = (int)MH.Idxs_.size();
description_.append(std::string(TypeStr[MH.varType_]) +
MH.varname_ + " inmask " + currentMask.MaskExpression());
// -------------------------------------------
} else if (ftype == INTEGER) {
// [<var>=<start>;[<var><OP><end>;]<var><OP>[<value>]]
MH.varType_ = ftype;
ArgList varArg( argIn[iarg], ";" );
if (varArg.Nargs() < 2 || varArg.Nargs() > 3) {
mprinterr("Error: Malformed 'for' loop variable.\n"
"Error: Expected '[<var>=<start>;[<var><OP><end>;]<var><OP>[<value>]]'\n"
"Error: Got '%s'\n", argIn[iarg].c_str());
return 1;
}
// First argument: <var>=<start>
ArgList startArg( varArg[0], "=" );
if (startArg.Nargs() != 2) {
mprinterr("Error: Malformed 'start' argument.\n"
"Error: Expected <var>=<start>, got '%s'\n", varArg[0].c_str());
return 1;
}
MH.varname_ = startArg[0];
if (!validInteger(startArg[1])) {
// TODO allow variables
mprinterr("Error: Start argument must be an integer.\n");
return 1;
} else
MH.start_ = convertToInteger(startArg[1]);
// Second argument: <var><OP><end>
size_t pos0 = MH.varname_.size();
size_t pos1 = pos0 + 1;
MH.endOp_ = NO_OP;
int iargIdx = 1;
if (varArg.Nargs() == 3) {
iargIdx = 2;
if ( varArg[1][pos0] == '<' )
MH.endOp_ = LESS_THAN;
else if (varArg[1][pos0] == '>')
MH.endOp_ = GREATER_THAN;
if (MH.endOp_ == NO_OP) {
mprinterr("Error: Unrecognized end op: '%s'\n",
varArg[1].substr(pos0, pos1-pos0).c_str());
return 1;
}
std::string endStr = varArg[1].substr(pos1);
if (!validInteger(endStr)) {
// TODO allow variables
mprinterr("Error: End argument must be an integer.\n");
return 1;
} else
MH.end_ = convertToInteger(endStr);
}
// Third argument: <var><OP>[<value>]
pos1 = pos0 + 2;
MH.incOp_ = NO_OP;
bool needValue = false;
if ( varArg[iargIdx][pos0] == '+' ) {
if (varArg[iargIdx][pos0+1] == '+') {
MH.incOp_ = INCREMENT;
MH.inc_ = 1;
} else if (varArg[iargIdx][pos0+1] == '=') {
MH.incOp_ = INCREMENT;
needValue = true;
}
} else if ( varArg[iargIdx][pos0] == '-' ) {
if (varArg[iargIdx][pos0+1] == '-' ) {
MH.incOp_ = DECREMENT;
MH.inc_ = 1;
} else if (varArg[iargIdx][pos0+1] == '=') {
MH.incOp_ = DECREMENT;
needValue = true;
}
}
if (MH.incOp_ == NO_OP) {
mprinterr("Error: Unrecognized increment op: '%s'\n",
varArg[iargIdx].substr(pos0, pos1-pos0).c_str());
return 1;
}
if (needValue) {
std::string incStr = varArg[iargIdx].substr(pos1);
if (!validInteger(incStr)) {
mprinterr("Error: increment value is not a valid integer.\n");
return 1;
}
MH.inc_ = convertToInteger(incStr);
if (MH.inc_ < 1) {
mprinterr("Error: Extra '-' detected in increment.\n");
return 1;
}
}
// Description
MH.varname_ = "$" + MH.varname_;
std::string sval = integerToString(MH.start_);
description_.append("(" + MH.varname_ + "=" + sval + "; ");
std::string eval;
if (iargIdx == 2) {
// End argument present
eval = integerToString(MH.end_);
description_.append(MH.varname_ + std::string(OpStr[MH.endOp_]) + eval + "; ");
// Check end > start for increment, start > end for decrement
int maxval, minval;
if (MH.incOp_ == INCREMENT) {
if (MH.start_ >= MH.end_) {
mprinterr("Error: start must be less than end for increment.\n");
return 1;
}
minval = MH.start_;
maxval = MH.end_;
} else {
if (MH.end_ >= MH.start_) {
mprinterr("Error: end must be less than start for decrement.\n");
return 1;
}
minval = MH.end_;
maxval = MH.start_;
}
// Figure out number of iterations
Niterations = (maxval - minval) / MH.inc_;
if (((maxval-minval) % MH.inc_) > 0) Niterations++;
}
description_.append( MH.varname_ + std::string(OpStr[MH.incOp_]) +
integerToString(MH.inc_) + ")" );
// If decrementing just negate value
if (MH.incOp_ == DECREMENT)
MH.inc_ = -MH.inc_;
// DEBUG
//mprintf("DEBUG: start=%i endOp=%i end=%i incOp=%i val=%i startArg=%s endArg=%s\n",
// MH.start_, (int)MH.endOp_, MH.end_, (int)MH.incOp_, MH.inc_,
// MH.startArg_.c_str(), MH.endArg_.c_str());
// -------------------------------------------
} else if (ftype == LIST) {
// <var> in <string0>[,<string1>...]
MH.varType_ = ftype;
// Variable name
MH.varname_ = argIn.GetStringNext();
if (MH.varname_.empty()) {
mprinterr("Error: 'for in': missing variable name.\n");
return 1;
}
MH.varname_ = "$" + MH.varname_;
// Comma-separated list of strings
std::string listArg = argIn.GetStringNext();
if (listArg.empty()) {
mprinterr("Error: 'for in': missing comma-separated list of strings.\n");
return 1;
}
ArgList list(listArg, ",");
if (list.Nargs() < 1) {
mprinterr("Error: Could not parse '%s' for 'for in'\n", listArg.c_str());
return 1;
}
for (int il = 0; il != list.Nargs(); il++) {
// Check if file name expansion should occur
if (list[il].find_first_of("*?") != std::string::npos) {
File::NameArray files = File::ExpandToFilenames( list[il] );
for (File::NameArray::const_iterator fn = files.begin(); fn != files.end(); ++fn)
MH.List_.push_back( fn->Full() );
} else
MH.List_.push_back( list[il] );
}
Niterations = (int)MH.List_.size();
// Description
description_.append( MH.varname_ + " in " + listArg );
}
// Check number of values
if (MaxIterations == -1)
MaxIterations = Niterations;
else if (Niterations != -1 && Niterations != MaxIterations) {
mprintf("Warning: # iterations %i != previous # iterations %i\n",
Niterations, MaxIterations);
MaxIterations = std::min(Niterations, MaxIterations);
}
}
mprintf("\tLoop will execute for %i iterations.\n", MaxIterations);
if (MaxIterations < 1) {
mprinterr("Error: Loop has less than 1 iteration.\n");
return 1;
}
description_.append(") do");
return 0;
}