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// $Id: TDTWriter.cpp 1528 2010-09-26 17:04:37Z glandrum $
//
// Copyright (C) 2005-2010 Greg Landrum and Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <RDGeneral/BadFileException.h>
#include <RDGeneral/FileParseException.h>
#include <RDGeneral/RDLog.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include "MolWriters.h"
#include "FileParsers.h"
#include <fstream>
#include <iostream>
#include <iomanip>
#include <sstream>
#include <string>
#include <boost/algorithm/string.hpp>
namespace RDKit {
TDTWriter::TDTWriter(std::string fileName) {
if(fileName!="-"){
std::ofstream *tmpStream = new std::ofstream(fileName.c_str());
if (!tmpStream || !(*tmpStream) || (tmpStream->bad()) ) {
std::ostringstream errout;
errout << "Bad output file " << fileName;
throw BadFileException(errout.str());
}
dp_ostream = static_cast<std::ostream *>(tmpStream);
df_owner = true;
} else {
dp_ostream = static_cast<std::ostream *>(&std::cout);
df_owner=false;
}
d_molid = 0;
d_numDigits=4;
df_write2D=false;
df_writeNames=true;
}
TDTWriter::TDTWriter(std::ostream *outStream, bool takeOwnership) {
PRECONDITION(outStream,"null stream");
if (outStream->bad()) {
throw FileParseException("Bad output stream");
}
dp_ostream = outStream;
df_owner = takeOwnership;
d_molid = 0;
d_numDigits=4;
df_write2D=false;
df_writeNames=true;
}
TDTWriter::~TDTWriter() {
// if we've written any mols, finish with a "|" line
if (d_molid > 0) {
CHECK_INVARIANT(dp_ostream,"null outstream even though molecules were written");
(*dp_ostream) << "|\n";
}
if (df_owner) {
delete dp_ostream;
}
}
void TDTWriter::setProps(const STR_VECT &propNames) {
if (d_molid > 0) {
BOOST_LOG(rdWarningLog) << "WARNING: Setting property list after a few molecules have been written\n";
}
d_props = propNames;
}
void TDTWriter::write(ROMol &mol, int confId) {
CHECK_INVARIANT(dp_ostream,"no output stream");
//start by writing a "|" line unless this is the first line
if (d_molid > 0) {
(*dp_ostream) << "|\n";
}
// write the molecule
(*dp_ostream) << "$SMI<" << MolToSmiles(mol) << ">\n";
if(df_writeNames && mol.hasProp("_Name")){
std::string name;
mol.getProp("_Name",name);
(*dp_ostream) << "NAME<" << name << ">\n";
}
// do we need to write coordinates?
if(mol.getNumConformers()){
const Conformer &conf = mol.getConformer(confId);
if(df_write2D){
(*dp_ostream) << "2D<";
} else {
(*dp_ostream) << "3D<";
}
const RDGeom::POINT3D_VECT &coords=conf.getPositions();
int nAts=conf.getNumAtoms();
for(int i=0;i<nAts;i++){
(*dp_ostream) << std::setprecision(d_numDigits) << coords[i].x << ",";
(*dp_ostream) << std::setprecision(d_numDigits) << coords[i].y;
if(!df_write2D){
(*dp_ostream) << "," << std::setprecision(d_numDigits) << coords[i].z;
}
if(i!=nAts-1) (*dp_ostream) << ",";
}
(*dp_ostream) << ";>\n";
}
// now write the properties
STR_VECT_CI pi;
if (d_props.size() > 0) {
// check if we have any properties the user specified to write out
// in which loop over them and write them out
for (pi = d_props.begin(); pi != d_props.end(); pi++) {
if (mol.hasProp(*pi)) {
writeProperty(mol, (*pi));
}
}
}
else {
// if use did not specify any properties, write all non computed properties
// out to the file
STR_VECT properties = mol.getPropList();
STR_VECT compLst;
if (mol.hasProp("__computedProps")) {
mol.getProp("__computedProps", compLst);
}
STR_VECT_CI pi;
for (pi = properties.begin(); pi != properties.end(); pi++) {
// ignore any of the following properties
if ( ((*pi) == "__computedProps") ||
((*pi) == "_Name") ||
((*pi) == "_MolFileInfo") ||
((*pi) == "_MolFileComments")) {
continue;
}
// check if this property is not computed
if (std::find(compLst.begin(), compLst.end(), (*pi)) == compLst.end()) {
writeProperty(mol, (*pi));
}
}
}
d_molid++;
}
void TDTWriter::writeProperty(const ROMol &mol, std::string name) {
PRECONDITION(dp_ostream,"no output stream");
(*dp_ostream) << name << "<";
// write the property value
// FIX: we will assume for now that the desired property value is
// catable to a string
std::string pval;
// we need to remove any line breaks in the output, replace them with spaces
mol.getProp(name, pval);
boost::replace_all(pval,"\n"," ");
(*dp_ostream) << pval << ">\n";
}
}
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