/** Given an argument with format, DataSet_Name[,min,max,step,bins], check
* that DataSet_Name exists and is valid. Add the argument to
* dimensionArgs and the corresponding dataset to histdata.
*/
int Analysis_Hist::CheckDimension(std::string const& input, DataSetList& DSLin) {
ArgList arglist;
// Separate input string by ','
arglist.SetList(input, ",");
if (arglist.Nargs()<1) {
mprinterr("Error: No arguments found in histogram argument: %s\n",input.c_str());
return 1;
}
// First argument should specify dataset name
if (debug_>0) mprintf("\tHist: Setting up histogram dimension using dataset %s\n",
arglist.Command());
DataSet* dset = DSLin.GetDataSet( arglist[0] );
if (dset == 0) {
mprinterr("Error: Dataset %s not found.\n",arglist.Command());
return 1;
}
// For now only 1D scalar data sets can be histogrammed
if (dset->Group() != DataSet::SCALAR_1D) {
mprinterr("Error: Cannot histogram data set '%s'\n", dset->legend());
mprinterr("Error: Currently only 1D scalar data sets can be histogrammed.\n");
return 1;
}
// TODO parse remaining args here, create data structure.
dimensionArgs_.push_back( arglist );
histdata_.push_back( (DataSet_1D*)dset );
return 0;
}
/** Read cluster matrix file. Can only get here if file has already been
* determined to be in the proper format, so do no further error checking.
* Expected format:
* <int> <int> <name>
*/
int DataIO_Std::ReadCmatrix(FileName const& fname,
DataSetList& datasetlist, std::string const& dsname)
{
// Allocate output data set
DataSet* ds = datasetlist.AddSet( DataSet::CMATRIX, dsname );
if (ds == 0) return 1;
DataSet_Cmatrix_MEM& Mat = static_cast<DataSet_Cmatrix_MEM&>( *ds );
// Buffer file
BufferedLine buffer;
if (buffer.OpenFileRead( fname )) return 1;
// Read past title. See if optional 'nframes' key is there.
const char* ptr = buffer.Line();
ArgList header;
header.SetList(ptr+1, SEPARATORS );
int nframes = header.getKeyInt("nframes", -1);
// Need to keep track of frame indices so we can check for sieving.
std::vector<char> sieveStatus;
if (nframes > 0)
sieveStatus.assign(nframes, 'T');
// Keep track of matrix values.
std::vector<float> Vals;
// Read file
bool checkSieve = true;
int f1 = -1, f2 = -1, firstf1 = -1;
float val = 0;
while ( (ptr = buffer.Line()) != 0 )
{
if (checkSieve) {
sscanf(ptr, "%i %i %f", &f1, &f2, &val);
if (f2 > (int)sieveStatus.size())
sieveStatus.resize(f2, 'T');
if (firstf1 == -1) {
// First values.
sieveStatus[f1-1] = 'F';
sieveStatus[f2-1] = 'F';
firstf1 = f1;
} else if (f1 > firstf1) {
checkSieve = false;
} else {
sieveStatus[f2-1] = 'F';
}
} else {
sscanf(ptr, "%*i %*i %f", &val);
}
Vals.push_back( val );
}
// DEBUG
//mprintf("Sieved array:\n");
//for (unsigned int i = 0; i < sieveStatus.size(); i++)
// mprintf("\t%6u %c\n", i+1, sieveStatus[i]);
// Try to determine if sieve is random or not.
int sieveDelta = 1;
f1 = -1;
f2 = -1;
int actual_nrows = 0;
for (int i = 0; i < (int)sieveStatus.size(); i++) {
if (sieveStatus[i] == 'F') {
actual_nrows++;
if (sieveDelta != -2) {
if (f1 == -1) {
f1 = i;
} else if (f2 == -1) {
sieveDelta = i - f1;
f1 = i;
f2 = i;
} else {
int newDelta = i - f1;
if (newDelta != sieveDelta) {
// Random. No need to calculate sieveDelta anymore.
sieveDelta = -2;
}
f1 = i;
}
}
}
}
if (sieveDelta == -2) {
// Random sieve. Try to figure out original sieve value.
int o_frames = (int)sieveStatus.size();
int o_sieve_value = o_frames / actual_nrows;
if ( (o_frames % actual_nrows) != 0 )
o_sieve_value++;
sieveDelta = -o_sieve_value;
}
if (debug_ > 0)
mprintf("DEBUG: sieve %i, actual_nrows= %i\n", sieveDelta, actual_nrows);
if (sieveDelta != 1 && nframes == -1)
mprintf("Warning: Pairwise distance matrix file contains sieved frames but\n"
"Warning: number of original frames is not present in file - this\n"
"Warning: may lead to ignored frames in cluster output. Please add\n"
"Warning: 'nframes <# original frames>' to the pairwise distance\n"
"Warning: matrix file header, e.g. '#F1 F2 pw.dat nframes 1000'.\n");
// Save cluster matrix
if (Mat.Allocate( DataSet::SizeArray(1, actual_nrows) )) return 1;
std::copy( Vals.begin(), Vals.end(), Mat.Ptr() );
Mat.SetSieveFromArray(sieveStatus, sieveDelta);
return 0;
}
// ----- M A I N ---------------------------------------------------------------
int main(int argc, char** argv) {
SetWorldSilent(true); // No STDOUT output from cpptraj routines.
std::string topname, crdname, title, bres, pqr, sybyltype, writeconect;
std::string aatm(" pdbatom"), ter_opt(" terbyres"), box(" sg \"P 1\"");
TrajectoryFile::TrajFormatType fmt = TrajectoryFile::PDBFILE;
bool ctr_origin = false;
bool useExtendedInfo = false;
int res_offset = 0;
int debug = 0;
int numSoloArgs = 0;
for (int i = 1; i < argc; ++i) {
std::string arg( argv[i] );
if (arg == "-p" && i+1 != argc && topname.empty()) // Topology
topname = std::string( argv[++i] );
else if (arg == "-c" && i+1 != argc && crdname.empty()) // Coords
crdname = std::string( argv[++i] );
else if (arg == "-tit" && i+1 != argc && title.empty()) // Title
title = " title " + std::string( argv[++i] );
else if (arg == "-offset" && i+1 != argc) // Residue # offset
res_offset = convertToInteger( argv[++i] );
else if ((arg == "-d" || arg == "--debug") && i+1 != argc) // Debug level
debug = convertToInteger( argv[++i] );
else if (arg == "-h" || arg == "--help") { // Help
Help(argv[0], true);
return 0;
} else if (arg == "-v" || arg == "--version") { // Version info
WriteVersion();
return 0;
} else if (arg == "-aatm") // Amber atom names, include extra pts
aatm.assign(" include_ep");
else if (arg == "-sybyl") // Amber atom types to SYBYL
sybyltype.assign(" sybyltype");
else if (arg == "-conect") // Write CONECT records from bond info
writeconect.assign(" conect");
else if (arg == "-ep") // PDB atom names, include extra pts
aatm.append(" include_ep");
else if (arg == "-bres") // PDB residue names
bres.assign(" pdbres");
else if (arg == "-ext") // Use extended PDB info from Topology
useExtendedInfo = true;
else if (arg == "-ctr") // Center on origin
ctr_origin = true;
else if (arg == "-noter") // No TER cards
ter_opt.assign(" noter");
else if (arg == "-nobox") // No CRYST1 record
box.assign(" nobox");
else if (arg == "-pqr") { // Charge/Radii in occ/bfactor cols
pqr.assign(" dumpq");
++numSoloArgs;
} else if (arg == "-mol2") { // output as mol2
fmt = TrajectoryFile::MOL2FILE;
++numSoloArgs;
} else if (Unsupported(arg)) {
mprinterr("Error: Option '%s' is not yet supported.\n\n", arg.c_str());
return 1;
} else {
mprinterr("Error: Unrecognized option '%s'\n", arg.c_str());
Help(argv[0], false);
return 1;
}
}
if (debug > 0) WriteVersion();
// Check command line for errors.
if (topname.empty()) topname.assign("prmtop");
if (debug > 0 && crdname.empty())
mprinterr("| Reading Amber restart from STDIN\n");
if (numSoloArgs > 1) {
mprinterr("Error: Only one alternate output format option may be specified (found %i)\n",
numSoloArgs);
Help(argv[0], true);
return 1;
}
if (!sybyltype.empty() && fmt != TrajectoryFile::MOL2FILE) {
mprinterr("Warning: -sybyl is only valid for MOL2 file output.\n");
sybyltype.clear();
}
if (debug > 0) {
mprinterr("Warning: debug is %i; debug info will be written to STDOUT.\n", debug);
SetWorldSilent(false);
}
// Topology
ParmFile pfile;
Topology parm;
if (pfile.ReadTopology(parm, topname, debug)) {
if (topname == "prmtop") Help(argv[0], false);
return 1;
}
if (!useExtendedInfo)
parm.ResetPDBinfo();
if (res_offset != 0)
for (int r = 0; r < parm.Nres(); r++)
parm.SetRes(r).SetOriginalNum( parm.Res(r).OriginalResNum() + res_offset );
ArgList trajArgs;
// Input coords
Frame TrajFrame;
CoordinateInfo cInfo;
if (!crdname.empty()) {
Trajin_Single trajin;
if (trajin.SetupTrajRead(crdname, trajArgs, &parm)) return 1;
cInfo = trajin.TrajCoordInfo();
TrajFrame.SetupFrameV(parm.Atoms(), cInfo);
trajin.BeginTraj();
if (trajin.ReadTrajFrame(0, TrajFrame)) return 1;
trajin.EndTraj();
} else {
// Assume Amber restart from STDIN
// Check that input is from a redirect.
if ( isatty(fileno(stdin)) ) {
mprinterr("Error: No coordinates specified with '-c' and no STDIN '<'.\n");
return 1;
}
Traj_AmberRestart restartIn;
restartIn.SetDebug( debug );
//restartIn.processReadArgs( trajArgs );
int total_frames = restartIn.setupTrajin("", &parm);
if (total_frames < 1) return 1;
cInfo = restartIn.CoordInfo();
TrajFrame.SetupFrameV(parm.Atoms(), cInfo);
if (restartIn.openTrajin()) return 1;
if (restartIn.readFrame(0, TrajFrame)) return 1;
restartIn.closeTraj();
}
if (ctr_origin)
TrajFrame.CenterOnOrigin(false);
// Output coords
Trajout_Single trajout;
trajArgs.SetList( aatm + bres + pqr + title + ter_opt + box + sybyltype + writeconect, " " );
if ( trajout.PrepareStdoutTrajWrite(trajArgs, &parm, cInfo, 1, fmt) ) return 1;
trajout.WriteSingle(0, TrajFrame);
trajout.EndTraj();
return 0;
}
// DataIO_Std::Read_1D()
int DataIO_Std::Read_1D(std::string const& fname,
DataSetList& datasetlist, std::string const& dsname)
{
ArgList labels;
bool hasLabels = false;
// Buffer file
BufferedLine buffer;
if (buffer.OpenFileRead( fname )) return 1;
// Read the first line. Attempt to determine the number of columns
const char* linebuffer = buffer.Line();
if (linebuffer == 0) return 1;
int ntoken = buffer.TokenizeLine( SEPARATORS );
if ( ntoken == 0 ) {
mprinterr("Error: No columns detected in %s\n", buffer.Filename().full());
return 1;
}
// Try to skip past any comments. If line begins with a '#', assume it
// contains labels.
bool isCommentLine = true;
const char* ptr = linebuffer;
while (isCommentLine) {
// Skip past any whitespace
while ( *ptr != '\0' && isspace(*ptr) ) ++ptr;
// Assume these are column labels until proven otherwise.
if (*ptr == '#') {
labels.SetList(ptr+1, SEPARATORS );
if (!labels.empty()) {
hasLabels = true;
// If first label is Frame assume it is the index column
if (labels[0] == "Frame" && indexcol_ == -1)
indexcol_ = 0;
}
linebuffer = buffer.Line();
ptr = linebuffer;
if (ptr == 0) {
mprinterr("Error: No data found in file.\n");
return 1;
}
} else
// Not a recognized comment character, assume data.
isCommentLine = false;
}
// Special case: check if labels are '#F1 F2 <name> [nframes <#>]'. If so, assume
// this is a cluster matrix file.
if ((labels.Nargs() == 3 || labels.Nargs() == 5) && labels[0] == "F1" && labels[1] == "F2")
{
mprintf("Warning: Header format '#F1 F2 <name>' detected, assuming cluster pairwise matrix.\n");
return IS_ASCII_CMATRIX;
}
// Column user args start from 1
if (indexcol_ > -1)
mprintf("\tUsing column %i as index column.\n", indexcol_ + 1);
// Should be at first data line. Tokenize the line.
ntoken = buffer.TokenizeLine( SEPARATORS );
// If # of data columns does not match # labels, clear labels.
if ( !labels.empty() && ntoken != labels.Nargs() ) {
labels.ClearList();
hasLabels = false;
}
// Index column checks
if (indexcol_ != -1 ) {
if (indexcol_ >= ntoken) {
mprinterr("Error: Specified index column %i is out of range (%i columns).\n",
indexcol_+1, ntoken);
return 1;
}
if (!onlycols_.Empty() && !onlycols_.InRange(indexcol_)) {
mprinterr("Error: Index column %i specified, but not in given column range '%s'\n",
indexcol_+1, onlycols_.RangeArg());
return 1;
}
}
// Determine the type of data stored in each column. Assume numbers should
// be read with double precision.
MetaData md( dsname );
DataSetList::DataListType inputSets;
unsigned int nsets = 0;
for (int col = 0; col != ntoken; ++col) {
std::string token( buffer.NextToken() );
if (!onlycols_.Empty() && !onlycols_.InRange( col )) {
mprintf("\tSkipping column %i\n", col+1);
inputSets.push_back( 0 );
} else {
md.SetIdx( col+1 );
if (hasLabels) md.SetLegend( labels[col] );
if ( col == indexcol_ ) {
// Always save the index column as floating point
inputSets.push_back( new DataSet_double() );
} else if (validInteger(token)) {
// Integer number
inputSets.push_back( datasetlist.Allocate(DataSet::INTEGER) );
} else if (validDouble(token)) {
// Floating point number
inputSets.push_back( new DataSet_double() );
} else {
// Assume string. Not allowed for index column.
if (col == indexcol_) {
mprintf("Warning: '%s' index column %i has string values. No indices will be read.\n",
buffer.Filename().full(), indexcol_+1);
indexcol_ = -1;
}
inputSets.push_back( new DataSet_string() );
}
inputSets.back()->SetMeta( md );
nsets++;
}
}
if (inputSets.empty() || nsets == 0) {
mprinterr("Error: No data detected.\n");
return 1;
}
// Read in data
while (linebuffer != 0) {
if ( buffer.TokenizeLine( SEPARATORS ) != ntoken ) {
PrintColumnError(buffer.LineNumber());
break;
}
// Convert data in columns
for (int i = 0; i < ntoken; ++i) {
const char* token = buffer.NextToken();
if (inputSets[i] != 0) {
if (inputSets[i]->Type() == DataSet::DOUBLE)
((DataSet_double*)inputSets[i])->AddElement( atof(token) );
else if (inputSets[i]->Type() == DataSet::INTEGER)
((DataSet_integer*)inputSets[i])->AddElement( atoi(token) );
else
((DataSet_string*)inputSets[i])->AddElement( std::string(token) );
}
}
//Ndata++;
linebuffer = buffer.Line();
}
buffer.CloseFile();
mprintf("\tDataFile %s has %i columns, %i lines.\n", buffer.Filename().full(),
ntoken, buffer.LineNumber());
// Create list containing only data sets.
DataSetList::DataListType mySets;
DataSet_double* Xptr = 0;
for (int idx = 0; idx != (int)inputSets.size(); idx++) {
if (inputSets[idx] != 0) {
if ( idx != indexcol_ )
mySets.push_back( inputSets[idx] );
else
Xptr = (DataSet_double*)inputSets[idx];
}
}
mprintf("\tRead %zu data sets.\n", mySets.size());
std::string Xlabel;
if (indexcol_ != -1 && indexcol_ < labels.Nargs())
Xlabel = labels[indexcol_];
if (Xptr == 0)
datasetlist.AddOrAppendSets(Xlabel, DataSetList::Darray(), mySets);
else {
datasetlist.AddOrAppendSets(Xlabel, Xptr->Data(), mySets);
delete Xptr;
}
return 0;
}
