// DataIO_CCP4::WriteData()
int DataIO_CCP4::WriteData(FileName const& fname, DataSetList const& setList)
{
// Open output file
CpptrajFile outfile;
if (outfile.OpenWrite(fname)) {
mprinterr("Error: Could not open CCP4 output file '%s'.\n", fname.full());
return 1;
}
// Warn about writing multiple sets
if (setList.size() > 1)
mprintf("Warning: %s: Writing multiple 3D sets in CCP4 format not supported.\n"
"Warning: Only writing first set.\n", fname.full());
return WriteSet3D( setList.begin(), outfile );
}
/** Assuming lowest replica filename has been set, search for all other
* replica names assuming a naming scheme of '<PREFIX>.<EXT>[.<CEXT>]',
* where <EXT> is a numerical extension and <CEXT> is an optional
* compression extension.
* \return Found replica filenames, or an empty list on error.
*/
File::NameArray File::SearchForReplicas(FileName const& fname, int debug) {
NameArray replica_filenames;
if (!File::Exists(fname)) {
mprinterr("Error: '%s' does not correspond to a file.\n", fname.full());
return replica_filenames;
}
RepName repName(fname, debug);
if (repName.Error()) return replica_filenames;
// Search for a replica number lower than this. Correct functioning
// of the replica code requires the file specified by trajin be the
// lowest # replica.
if (File::Exists( repName.RepFilename( -1 ) )) {
mprintf("Warning: Replica# found lower than file specified with trajin.\n"
"Warning: Found \"%s\"; 'trajin remdtraj' requires lowest # replica.\n",
repName.RepFilename( -1 ).full());
}
// Add lowest replica filename, search for and add all replicas higher than it.
replica_filenames.push_back( fname );
int rep_offset = 0;
bool search_for_files = true;
FileName trajFilename;
while (search_for_files) {
++rep_offset;
trajFilename = repName.RepFilename( rep_offset );
//mprintf("\t\tChecking for %s\n", trajFilename.full());
if (File::Exists( trajFilename ))
replica_filenames.push_back( trajFilename );
else
search_for_files = false;
}
return replica_filenames;
}
// TODO: Accept const ArgList so arguments are not reset?
CpptrajFile* DataFileList::AddCpptrajFile(FileName const& nameIn,
std::string const& descrip,
CFtype typeIn, bool allowStdout)
{
// If no filename and stdout not allowed, no output desired.
if (nameIn.empty() && !allowStdout) return 0;
FileName name;
CpptrajFile* Current = 0;
int currentIdx = -1;
if (!nameIn.empty()) {
name = nameIn;
// Append ensemble number if set.
if (ensembleNum_ != -1)
name.Append( "." + integerToString(ensembleNum_) );
// Check if filename in use by DataFile.
DataFile* df = GetDataFile(name);
if (df != 0) {
mprinterr("Error: Text output file name '%s' already in use by data file '%s'.\n",
nameIn.full(), df->DataFilename().full());
return 0;
}
// Check if this filename already in use
currentIdx = GetCpptrajFileIdx( name );
if (currentIdx != -1) Current = cfList_[currentIdx];
}
// If no CpptrajFile associated with name, create new CpptrajFile
if (Current==0) {
switch (typeIn) {
case TEXT: Current = new CpptrajFile(); break;
case PDB: Current = (CpptrajFile*)(new PDBfile()); break;
}
Current->SetDebug(debug_);
// Set up file for writing.
//if (Current->SetupWrite( name, debug_ ))
if (Current->OpenWrite( name ))
{
mprinterr("Error: Setting up text output file %s\n", name.full());
delete Current;
return 0;
}
cfList_.push_back( Current );
cfData_.push_back( CFstruct(descrip, typeIn) );
} else {
// If Current type does not match typeIn do not allow.
if (typeIn != cfData_[currentIdx].Type()) {
mprinterr("Error: Cannot change type of text output for '%s'.\n", Current->Filename().full());
return 0;
}
Current->SetDebug(debug_);
// Update description
if (!descrip.empty())
cfData_[currentIdx].UpdateDescrip( descrip );
}
return Current;
}
/** Each rank searches for replica based on lowest replica number. */
int TrajIOarray::SearchForReplicas(FileName const& fname, Parallel::Comm const& ensComm,
Parallel::Comm const& trajComm)
{
RepName repName(fname, debug_);
if (repName.Error()) return 1;
// TODO check for lower replica number?
FileName replicaFilename = repName.RepFilename( ensComm.Rank() );
// Only traj comm masters actually check for files.
if (trajComm.Master()) {
if (!File::Exists( replicaFilename )) {
File::ErrorMsg( replicaFilename.full() );
rprinterr("Error: File '%s' not accessible.\n", replicaFilename.full());
return 1;
}
}
// At this point each rank has found its replica. Populate filename array.
for (int offset = 0; offset < ensComm.Size(); ++offset)
replica_filenames_.push_back( repName.RepFilename( offset ) );
return 0;
}
bool File::Exists(FileName const& fn) {
if (!fn.empty()) {
FILE* infile = fopen(fn.full(), "rb");
if (infile==0) {
fileErrMsg_.assign( strerror(errno) );
return false;
}
fclose(infile);
return true;
}
return false;
}
/** Each rank searches for replica based on lowest replica number. */
File::NameArray File::SearchForReplicas(FileName const& fname, bool trajCommMaster,
int ensRank, int ensSize, int debug)
{
NameArray replica_filenames;
RepName repName(fname, debug);
if (repName.Error()) return replica_filenames;
// TODO check for lower replica number?
FileName replicaFilename = repName.RepFilename( ensRank );
// Only traj comm masters actually check for files.
if (trajCommMaster) {
if (!File::Exists( replicaFilename )) {
File::ErrorMsg( replicaFilename.full() );
rprinterr("Error: File '%s' not accessible.\n", replicaFilename.full());
return replica_filenames;
}
}
// At this point each rank has found its replica. Populate filename array.
for (int offset = 0; offset < ensSize; ++offset)
replica_filenames.push_back( repName.RepFilename( offset ) );
return replica_filenames;
}
// DataIO_OpenDx::ReadData()
int DataIO_OpenDx::ReadData(FileName const& fname,
DataSetList& datasetlist, std::string const& dsname)
{
// Add grid data set. Default to float for now.
DataSet* ds = datasetlist.AddSet( DataSet::GRID_FLT, dsname, "GRID" );
if (ds==0) return 1;
if (LoadGrid(fname.full(), *ds)) {
// Load failed. Erase grid data set.
datasetlist.RemoveSet( ds );
return 1;
}
return 0;
}
// ParmFile::ReadTopology()
int ParmFile::ReadTopology(Topology& Top, FileName const& fnameIn,
ArgList const& argListIn, int debugIn)
{
if (fnameIn.empty()) {
mprinterr("Error: No input topology name given.\n");
return 1;
}
if (!File::Exists( fnameIn )) {
mprinterr("Error: Topology '%s' does not exist.\n", fnameIn.full());
return 1;
}
parmName_ = fnameIn;
ArgList argIn = argListIn;
ParmFormatType pfType;
ParmIO* parmio = 0;
Top.SetDebug( debugIn );
// Only force bond search when 'bondsearch' is specified.
bool bondsearch = false;
if (argIn.Contains("bondsearch")) {
Top.SetOffset( argIn.getKeyDouble("bondsearch", -1.0) );
bondsearch = true;
}
// 'as' keyword specifies a format
std::string as_arg = argIn.GetStringKey("as");
if (!as_arg.empty()) {
pfType = (ParmFormatType)FileTypes::GetFormatFromString( PF_KeyArray, as_arg, UNKNOWN_PARM );
if (pfType == UNKNOWN_PARM) {
mprinterr("Error: Topology format '%s' not recognized.\n", as_arg.c_str());
return 1;
}
parmio = (ParmIO*)FileTypes::AllocIO( PF_AllocArray, pfType, false );
} else
parmio = DetectFormat( parmName_, pfType );
if (parmio == 0) {
mprinterr("Error: Could not determine format of topology '%s'\n", parmName_.full());
return 1;
}
mprintf("\tReading '%s' as %s\n", parmName_.full(),
FileTypes::FormatDescription(PF_AllocArray, pfType) );
parmio->SetDebug( debugIn );
if (parmio->processReadArgs(argIn)) return 1;
int err = parmio->ReadParm( parmName_.Full(), Top);
// Perform setup common to all parm files.
if (err == 0)
err = Top.CommonSetup(bondsearch || parmio->NeedsBondSearch());
else
mprinterr("Error reading topology file '%s'\n", parmName_.full());
delete parmio;
if (err > 0) return 1;
return 0;
}
// =============================================================================
// ----- RepName Class ---------------------------------------------------------
// RepName CONSTRUCTOR
File::RepName::RepName(FileName const& fname, int debugIn) :
extChar_('.')
{
if (debugIn > 1)
mprintf("\tREMDTRAJ: FileName=[%s]\n", fname.full());
if ( fname.Ext().empty() ) {
mprinterr("Error: Traj %s has no numerical extension, required for automatic\n"
"Error: detection of replica trajectories. Expected filename format is\n"
"Error: <Prefix>.<#> (with optional compression extension), examples:\n"
"Error: Rep.traj.nc.000, remd.x.01.gz etc.\n", fname.base());
return;
}
// Split off everything before replica extension
size_t found = fname.Full().rfind( fname.Ext() );
Prefix_.assign( fname.Full().substr(0, found) );
ReplicaExt_.assign( fname.Ext() ); // This should be the numeric extension
// Remove leading '.'
if (ReplicaExt_[0] == '.') ReplicaExt_.erase(0,1);
CompressExt_.assign( fname.Compress() );
if (debugIn > 1) {
mprintf("\tREMDTRAJ: Prefix=[%s], #Ext=[%s], CompressExt=[%s]\n",
Prefix_.c_str(), ReplicaExt_.c_str(), CompressExt_.c_str());
}
// CHARMM replica numbers are format <name>_<num>
if ( !validInteger(ReplicaExt_) ) {
size_t uscore = fname.Full().rfind('_');
if (uscore != std::string::npos) {
Prefix_.assign( fname.Full().substr(0, uscore) );
ReplicaExt_.assign( fname.Full().substr(uscore+1) );
extChar_ = '_';
if (debugIn > 0)
mprintf("\tREMDTRAJ: CHARMM style replica names detected, prefix='%s' ext='%s'\n",
Prefix_.c_str(), ReplicaExt_.c_str());
}
}
// Check that the numerical extension is valid.
if ( !validInteger(ReplicaExt_) ) {
mprinterr("Error: Replica extension [%s] is not an integer.\n", ReplicaExt_.c_str());
Prefix_.clear(); // Empty Prefix_ indicates error.
return;
}
ExtWidth_ = (int)ReplicaExt_.size();
if (debugIn > 1)
mprintf("\tREMDTRAJ: Numerical Extension width=%i\n", ExtWidth_);
// Store lowest replica number
lowestRepnum_ = convertToInteger( ReplicaExt_ );
// TODO: Do not allow negative replica numbers?
if (debugIn > 1)
mprintf("\tREMDTRAJ: index of first replica = %i\n", lowestRepnum_);
}
/** Add lowest replica file name and names from comma-separated list. */
int TrajIOarray::AddReplicasFromArgs(FileName const& name0,
std::string const& commaNames)
{
if (name0.empty()) return 1;
if (!File::Exists( name0 )) {
File::ErrorMsg( name0.full() );
return 1;
}
replica_filenames_.push_back( name0 );
ArgList remdtraj_list( commaNames, "," );
for (ArgList::const_iterator fname = remdtraj_list.begin();
fname != remdtraj_list.end(); ++fname)
{
FileName trajFilename( *fname );
if (!File::Exists( trajFilename )) {
File::ErrorMsg( trajFilename.full() );
return 1;
}
replica_filenames_.push_back( trajFilename );
}
return 0;
}
// Parm_CIF::ReadParm()
int Parm_CIF::ReadParm(FileName const& fname, Topology &TopIn) {
CIFfile infile;
CIFfile::DataBlock::data_it line;
if (infile.Read( fname, debug_ )) return 1;
CIFfile::DataBlock const& block = infile.GetDataBlock("_atom_site");
if (block.empty()) {
mprinterr("Error: CIF data block '_atom_site' not found.\n");
return 1;
}
// Does this CIF contain multiple models?
int Nmodels = 0;
int model_col = block.ColumnIndex("pdbx_PDB_model_num");
if (model_col != -1) {
line = block.end();
--line;
Nmodels = convertToInteger( (*line)[model_col] );
if (Nmodels > 1)
mprintf("Warning: CIF '%s' contains %i models. Using first model for topology.\n",
fname.full(), Nmodels);
}
// Get essential columns
int COL[NENTRY];
for (int i = 0; i < (int)NENTRY; i++) {
COL[i] = block.ColumnIndex(Entries[i]);
if (COL[i] == -1) {
mprinterr("Error: In CIF file '%s' could not find entry '%s' in block '%s'\n",
fname.full(), Entries[i], block.Header().c_str());
return 1;
}
if (debug_>0) mprintf("DEBUG: '%s' column = %i\n", Entries[i], COL[i]);
}
// Get optional columns
int occ_col = block.ColumnIndex("occupancy");
int bfac_col = block.ColumnIndex("B_iso_or_equiv");
int icode_col = block.ColumnIndex("pdbx_PDB_ins_code");
int altloc_col = block.ColumnIndex("label_alt_id");
std::vector<AtomExtra> extra;
// Loop over all atom sites
int current_res = 0;
double XYZ[3];
double occupancy = 1.0;
double bfactor = 0.0;
char altloc = ' ';
char icode;
icode = ' ';
Frame Coords;
for (line = block.begin(); line != block.end(); ++line) {
// If more than 1 model check if we are done.
if (Nmodels > 1) {
if ( convertToInteger( (*line)[model_col] ) > 1 )
break;
}
if (occ_col != -1) occupancy = convertToDouble( (*line)[ occ_col ] );
if (bfac_col != -1) bfactor = convertToDouble( (*line)[ bfac_col ] );
if (altloc_col != -1) altloc = (*line)[ altloc_col ][0];
// '.' altloc means blank?
if (altloc == '.') altloc = ' ';
extra.push_back( AtomExtra(occupancy, bfactor, altloc) );
if (icode_col != -1) {
icode = (*line)[ icode_col ][0];
// '?' icode means blank
if (icode == '?') icode = ' ';
}
XYZ[0] = convertToDouble( (*line)[ COL[X] ] );
XYZ[1] = convertToDouble( (*line)[ COL[Y] ] );
XYZ[2] = convertToDouble( (*line)[ COL[Z] ] );
NameType currentResName( (*line)[ COL[RNAME] ] );
// It seems that in some CIF files, there doesnt have to be a residue
// number. Check if residue name has changed.
if ( (*line)[ COL[RNUM] ][0] == '.' ) {
Topology::res_iterator lastResidue = TopIn.ResEnd();
--lastResidue;
if ( currentResName != (*lastResidue).Name() )
current_res = TopIn.Nres() + 1;
} else
current_res = convertToInteger( (*line)[ COL[RNUM] ] );
TopIn.AddTopAtom( Atom((*line)[ COL[ANAME] ], " "),
Residue(currentResName, current_res, icode,
(*line)[ COL[CHAINID] ][0]) );
Coords.AddXYZ( XYZ );
}
if (TopIn.SetExtraAtomInfo( 0, extra )) return 1;
// Search for bonds // FIXME nobondsearch?
BondSearch( TopIn, Coords, Offset_, debug_ );
// Get title.
CIFfile::DataBlock const& entryblock = infile.GetDataBlock("_entry");
std::string ciftitle;
if (!entryblock.empty())
ciftitle = entryblock.Data("id");
TopIn.SetParmName( ciftitle, infile.CIFname() );
// Get unit cell parameters if present.
CIFfile::DataBlock const& cellblock = infile.GetDataBlock("_cell");
if (!cellblock.empty()) {
double cif_box[6];
cif_box[0] = convertToDouble( cellblock.Data("length_a") );
cif_box[1] = convertToDouble( cellblock.Data("length_b") );
cif_box[2] = convertToDouble( cellblock.Data("length_c") );
cif_box[3] = convertToDouble( cellblock.Data("angle_alpha") );
cif_box[4] = convertToDouble( cellblock.Data("angle_beta" ) );
cif_box[5] = convertToDouble( cellblock.Data("angle_gamma") );
mprintf("\tRead cell info from CIF: a=%g b=%g c=%g alpha=%g beta=%g gamma=%g\n",
cif_box[0], cif_box[1], cif_box[2], cif_box[3], cif_box[4], cif_box[5]);
TopIn.SetParmBox( Box(cif_box) );
}
return 0;
}
// DataIO_Mdout::ReadData()
int DataIO_Mdout::ReadData(FileName const& fname,
DataSetList& datasetlist, std::string const& dsname)
{
mprintf("\tReading from mdout file: %s\n", fname.full());
BufferedLine buffer;
if (buffer.OpenFileRead( fname )) return 1;
const char* ptr = buffer.Line();
if (ptr == 0) {
mprinterr("Error: Nothing in MDOUT file: %s\n", fname.full());
return 1;
}
// ----- PARSE THE INPUT SECTION -----
int imin = -1; // imin for this file
const char* Trigger = 0; // Trigger for storing energies, must be 8 chars long.
int frame = 0; // Frame counter for this file
double dt = 1.0; // Timestep for this file (MD)
double t0 = 0.0; // Initial time for this file (MD)
int ntpr = 1; // Value of ntpr
int irest = 0; // Value of irest
while ( ptr != 0 && strncmp(ptr, " 2. CONTROL DATA", 20) != 0 )
ptr = buffer.Line();
if (ptr == 0) return EOF_ERROR();
// Determine whether this is dynamics or minimization, get dt
ptr = buffer.Line(); // Dashes
ptr = buffer.Line(); // Blank
ptr = buffer.Line(); // title line
while ( strncmp(ptr, " 3. ATOMIC", 13) != 0 )
{
ArgList mdin_args( ptr, " ,=" ); // Remove commas, equal signs
// Scan for stuff we want
//mprintf("DEBUG:\tInput[%i] %s", mdin_args.Nargs(), mdin_args.ArgLine());
for (int col=0; col < mdin_args.Nargs(); col += 2) {
int col1 = col + 1;
if (mdin_args[col] == "imin") {
imin = convertToInteger( mdin_args[ col1 ] );
if (debug_ > 0) mprintf("\t\tMDIN: imin is %i\n", imin);
// Set a trigger for printing. For imin5 this is the word minimization.
// For imin0 or imin1 this is NSTEP.
if (imin==0) Trigger = " NSTEP =";
else if (imin==1) Trigger = " NSTEP";
else if (imin==5) Trigger = "minimiza";
// Since imin0 and imin1 first trigger has no data, set frame 1 lower.
if (imin==1 || imin==0) frame = -1;
} else if (mdin_args[col] == "dt") {
dt = convertToDouble( mdin_args[ col1 ] );
if (debug_ > 0) mprintf("\t\tMDIN: dt is %f\n", dt);
} else if (mdin_args[col] == "t") {
t0 = convertToDouble( mdin_args[ col1 ] );
if (debug_ > 0) mprintf("\t\tMDIN: t is %f\n", t0);
} else if (mdin_args[col] == "ntpr") {
ntpr = convertToInteger( mdin_args[ col1 ] );
if (debug_ > 0) mprintf("\t\tMDIN: ntpr is %i\n", ntpr);
} else if (mdin_args[col] == "irest") {
irest = convertToInteger( mdin_args[ col1 ] );
if (debug_ > 0) mprintf("\t\tMDIN: irest is %i\n", irest);
}
}
ptr = buffer.Line();
if (ptr == 0) return EOF_ERROR();
}
if (Trigger == 0) {
mprinterr("Error: Could not determine whether MDOUT is md, min, or post-process.\n");
return 1;
}
// ----- PARSE THE ATOMIC ... SECTION -----
while ( ptr != 0 && strncmp(ptr, " 4. RESULTS", 14) != 0 )
{
ptr = buffer.Line();
// If run is a restart, set the initial time value.
if (irest == 1) {
if (strncmp(ptr, " begin time", 11) == 0) {
sscanf(ptr, " begin time read from input coords = %lf", &t0);
if (debug_ > 0) mprintf("\t\tMD restart initial time= %f\n", t0);
}
}
}
if (ptr == 0) return EOF_ERROR();
// ----- PARSE THE RESULTS SECTION -----
bool finalE = false;
int nstep;
int minStep = 0; // For imin=1 only
if (irest == 0)
nstep = 0;
else
nstep = ntpr;
double Energy[N_FIELDTYPES];
std::fill( Energy, Energy+N_FIELDTYPES, 0.0 );
std::vector<bool> EnergyExists(N_FIELDTYPES, false);
DataSetList::Darray TimeVals;
DataSetList::DataListType inputSets(N_FIELDTYPES, 0);
Sarray Name(2);
double time = 0.0;
while (ptr != 0) {
// Check for end of imin 0 or 1 run; do not record Average and Stdevs
if ( (imin == 1 && (strncmp(ptr, " FINAL", 25) == 0 ||
strncmp(ptr, " 5. TIMINGS", 14) == 0 )) ||
(imin == 0 && strncmp(ptr, " A V", 9) == 0))
finalE = true;
// Check for '| TI region 2' to prevent reading duplicate energies
if ( strncmp(ptr, "| TI region 2", 14) == 0 ) {
while (ptr != 0 && !(ptr[0] == ' ' && ptr[1] == '-'))
ptr = buffer.Line();
if (ptr == 0) return EOF_ERROR();
}
// Record set for energy post-processing
if (imin == 5 && strncmp(ptr, "minimizing", 10) == 0)
nstep = atoi( ptr + 22 );
// MAIN OUTPUT ROUTINE
// If the trigger has been reached print output.
// For imin0 and imin1 the first trigger will have no data.
// If the end of the file has been reached print then exit.
if ( strncmp(ptr, Trigger, 8) == 0 || finalE ) {
if (frame > -1) {
// Store all energies present.
for (int i = 0; i < (int)N_FIELDTYPES; i++) {
if (EnergyExists[i]) {
if (inputSets[i] == 0) {
MetaData md( dsname, Enames[i] );
md.SetLegend( dsname + "_" + Enames[i] );
inputSets[i] = new DataSet_double();
inputSets[i]->SetMeta( md );
}
// Since energy terms can appear and vanish over the course of the
// mdout file, resize if necessary.
if (frame > (int)inputSets[i]->Size())
((DataSet_double*)inputSets[i])->Resize( frame );
((DataSet_double*)inputSets[i])->AddElement( Energy[i] );
}
}
TimeVals.push_back( time );
nstep += ntpr;
}
frame++;
if (finalE) break;
}
// Check for NSTEP in minimization or post-processing. Values will be
// on the next line. NOTE: NSTEP means something different for imin=5.
if ((imin == 1 || imin == 5) && strncmp(ptr, " NSTEP", 8) == 0) {
ptr = buffer.Line(); // Get next line
//sscanf(ptr, " %6lf %13lE %13lE %13lE", Energy+NSTEP, Energy+EPtot, Energy+RMS, Energy+GMAX);
sscanf(ptr, " %i %lE %lE %lE", &minStep, Energy+EPtot, Energy+RMS, Energy+GMAX);
EnergyExists[EPtot] = true;
EnergyExists[RMS] = true;
EnergyExists[GMAX] = true;
ptr = buffer.Line();
}
// Tokenize line, scan through until '=' is reached; value after is target.
int ntokens = buffer.TokenizeLine(" ");
if (ntokens > 0) {
int nidx = 0;
Name[0].clear();
Name[1].clear();
for (int tidx = 0; tidx < ntokens; tidx++) {
const char* tkn = buffer.NextToken();
if (tkn[0] == '=') {
FieldType Eindex = getEindex(Name);
tkn = buffer.NextToken();
++tidx;
if (tkn == 0)
mprintf("Warning: No numerical value, line %i column %i. Skipping.\n",
buffer.LineNumber(), tidx+1);
else if (tkn[0] == '*' || tkn[0] == 'N') // Assume if number begins with N it is NaN
mprintf("Warning: Numerical overflow detected, line %i column %i. Skipping.\n",
buffer.LineNumber(), tidx+1);
else {
if (Eindex != N_FIELDTYPES) {
Energy[Eindex] = atof( tkn );
EnergyExists[Eindex] = true;
}
}
nidx = 0;
Name[0].clear();
Name[1].clear();
} else {
if (nidx > 1) break; // Two tokens, no '=' found. Not an E line.
Name[nidx++].assign( tkn );
}
}
}
// Set time
switch (imin) {
case 5: time = (double)nstep + t0; break;
case 1: time = (double)minStep + t0; break;
case 0: time = ((double)nstep * dt) + t0; break;
}
// Read in next line
ptr = buffer.Line();
}
mprintf("\t%i frames\n", frame);
buffer.CloseFile();
std::string Xlabel;
if (imin == 5) Xlabel.assign("Set");
else if (imin == 1) Xlabel.assign("Nstep");
else Xlabel.assign("Time"); // imin == 0
if (datasetlist.AddOrAppendSets( Xlabel, TimeVals, inputSets )) return 1;
return 0;
}
/** Free the given temporary file name. */
void FreeTempName(FileName const& temp) {
TempFileNames_.remove( temp );
if (Exists(temp)) remove(temp.full());
}
// DataIO_OpenDx::WriteData()
int DataIO_OpenDx::WriteData(FileName const& fname, DataSetList const& setList)
{
// Open output file
CpptrajFile outfile;
if (outfile.OpenWrite(fname)) {
mprinterr("Error: Could not open OpenDX output file.\n");
return 1;
}
// Warn about writing multiple sets
if (setList.size() > 1)
mprintf("Warning: %s: Writing multiple 3D sets in OpenDX format may result in unexpected behavior\n", fname.full());
int err = 0;
for (DataSetList::const_iterator set = setList.begin(); set != setList.end(); ++set)
err += WriteSet3D( *(*set), outfile );
return err;
}
// Action_Spam::init()
Action::RetType Action_Spam::Init(ArgList& actionArgs, TopologyList* PFL, DataSetList* DSL, DataFileList* DFL, int debugIn)
{
// Always use imaged distances
InitImaging(true);
// This is needed everywhere in this function scope
FileName filename;
// See if we're doing pure water. If so, we don't need a peak file
purewater_ = actionArgs.hasKey("purewater");
if (purewater_) {
// We still need the cutoff
double cut = actionArgs.getKeyDouble("cut", 12.0);
cut2_ = cut * cut;
doublecut_ = 2 * cut;
onecut2_ = 1 / cut2_;
// See if we write to a data file
datafile_ = actionArgs.GetStringKey("out");
// Generate the data set name, and hold onto the master data set list
std::string ds_name = actionArgs.GetStringKey("name");
if (ds_name.empty())
ds_name = myDSL_.GenerateDefaultName("SPAM");
// We only have one data set averaging over every water. Add it here
myDSL_.AddSet(DataSet::DOUBLE, ds_name, NULL);
solvname_ = actionArgs.GetStringKey("solv");
if (solvname_.empty())
solvname_ = std::string("WAT");
}else {
// Get the file name with the peaks defined in it
filename.SetFileName( actionArgs.GetStringNext() );
if (filename.empty() || !File::Exists(filename)) {
mprinterr("Spam: Error: Peak file [%s] does not exist!\n", filename.full());
return Action::ERR;
}
// Get the remaining optional arguments
solvname_ = actionArgs.GetStringKey("solv");
if (solvname_.empty())
solvname_ = std::string("WAT");
reorder_ = actionArgs.hasKey("reorder");
bulk_ = actionArgs.getKeyDouble("bulk", 0.0);
double cut = actionArgs.getKeyDouble("cut", 12.0);
cut2_ = cut * cut;
doublecut_ = 2 * cut;
onecut2_ = 1 / cut2_;
std::string infoname = actionArgs.GetStringKey("info");
if (infoname.empty())
infoname = std::string("spam.info");
infofile_ = DFL->AddCpptrajFile(infoname, "SPAM info");
if (infofile_ == 0) return Action::ERR;
// The default maskstr is the Oxygen atom of the solvent
summaryfile_ = actionArgs.GetStringKey("summary");
// Divide site size by 2 to make it half the edge length (or radius)
site_size_ = actionArgs.getKeyDouble("site_size", 2.5) / 2.0;
sphere_ = actionArgs.hasKey("sphere");
// If it's a sphere, square the radius to compare with
if (sphere_)
site_size_ *= site_size_;
datafile_ = actionArgs.GetStringKey("out");
std::string ds_name = actionArgs.GetStringKey("name");
if (ds_name.empty())
ds_name = myDSL_.GenerateDefaultName("SPAM");
// Parse through the peaks file and extract the peaks
CpptrajFile peakfile;
if (peakfile.OpenRead(filename)) {
mprinterr("SPAM: Error: Could not open %s for reading!\n", filename.full());
return Action::ERR;
}
std::string line = peakfile.GetLine();
int npeaks = 0;
while (!line.empty()) {
if (sscanf(line.c_str(), "%d", &npeaks) != 1) {
line = peakfile.GetLine();
continue;
}
line = peakfile.GetLine();
break;
}
while (!line.empty()) {
double x, y, z, dens;
if (sscanf(line.c_str(), "C %lg %lg %lg %lg", &x, &y, &z, &dens) != 4) {
line = peakfile.GetLine();
continue;
}
line = peakfile.GetLine();
peaks_.push_back(Vec3(x, y, z));
}
peakfile.CloseFile();
// Check that our initial number of peaks matches our parsed peaks. Warn
// otherwise
if (npeaks != (int)peaks_.size())
mprinterr("SPAM: Warning: %s claims to have %d peaks, but really has %d!\n",
filename.full(), npeaks, peaks_.size());
// Now add all of the data sets
MetaData md(ds_name);
for (int i = 0; i < (int)peaks_.size(); i++) {
md.SetAspect( integerToString(i+1) ); // TODO: Should this be Idx?
if (myDSL_.AddSet(DataSet::DOUBLE, md) == 0) return Action::ERR;
// Add a new list of integers to keep track of omitted frames
std::vector<int> vec;
peakFrameData_.push_back(vec);
}
}
// Print info now
if (purewater_) {
mprintf("SPAM: Calculating bulk value for pure solvent\n");
if (!datafile_.empty())
mprintf("SPAM: Printing solvent energies to %s\n", datafile_.c_str());
mprintf("SPAM: Using a %.2f Angstrom non-bonded cutoff with shifted EEL.\n",
sqrt(cut2_));
if (reorder_)
mprintf("SPAM: Warning: Re-ordering makes no sense for pure solvent.\n");
if (!summaryfile_.empty())
mprintf("SPAM: Printing solvent SPAM summary to %s\n", summaryfile_.c_str());
}else {
mprintf("SPAM: Solvent [%s] density peaks taken from %s.\n",
solvname_.c_str(), filename.base());
mprintf("SPAM: %d density peaks will be analyzed from %s.\n",
peaks_.size(), filename.base());
mprintf("SPAM: Occupation information printed to %s.\n", infofile_->Filename().full());
mprintf("SPAM: Sites are ");
if (sphere_)
mprintf("spheres with diameter %.3lf\n", site_size_);
else
mprintf("boxes with edge length %.3lf\n", site_size_);
if (reorder_) {
mprintf("SPAM: Re-ordering trajectory so each site always has ");
mprintf("the same water molecule.\n");
}
if (summaryfile_.empty() && datafile_.empty()) {
if (!reorder_) {
mprinterr("SPAM: Error: Not re-ordering trajectory or calculating energies. ");
mprinterr("Nothing to do!\n");
return Action::ERR;
}
mprintf("SPAM: Not calculating any SPAM energies\n");
}else {
mprintf("SPAM: Using a non-bonded cutoff of %.2lf Ang. with a EEL shifting function.\n",
sqrt(cut2_));
mprintf("SPAM: Bulk solvent SPAM energy taken as %.3lf kcal/mol\n", bulk_);
}
}
mprintf("#Citation: Cui, G.; Swails, J.M.; Manas, E.S.; \"SPAM: A Simple Approach\n"
"# for Profiling Bound Water Molecules\"\n"
"# J. Chem. Theory Comput., 2013, 9 (12), pp 5539–5549.\n");
return Action::OK;
}
