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// $Id: SDWriter.cpp 1947 2012-01-28 06:04:42Z glandrum $
//
// Copyright (C) 2003-2010 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 "MolWriters.h"
#include "FileParsers.h"
#include <fstream>
#include <iostream>
#include <sstream>
#include <string>
namespace RDKit {
SDWriter::SDWriter(std::string fileName) {
if(fileName!= "-"){
std::ofstream *tmpStream = new std::ofstream(fileName.c_str());
df_owner=true;
if ( !tmpStream || !(*tmpStream) || (tmpStream->bad()) ) {
std::ostringstream errout;
errout << "Bad output file " << fileName;
throw BadFileException(errout.str());
}
dp_ostream = static_cast<std::ostream *>(tmpStream);
} else {
dp_ostream = static_cast<std::ostream *>(&std::cout);
df_owner=false;
}
d_molid = 0;
}
SDWriter::SDWriter(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;
}
SDWriter::~SDWriter() {
// close the writer if it's still open:
if(dp_ostream!=NULL) close();
}
void SDWriter::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 SDWriter::write(ROMol &mol, int confId) {
PRECONDITION(dp_ostream,"no output stream");
// write the molecule
(*dp_ostream) << MolToMolBlock(mol, true, confId);
// 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));
}
}
}
// add the $$$$ that marks the end of a molecule
(*dp_ostream) << "$$$$\n";
++d_molid;
}
void SDWriter::writeProperty(const ROMol &mol, std::string name) {
PRECONDITION(dp_ostream,"no output stream");
// write the property header line
(*dp_ostream) << "> <" << name << "> " << "(" << d_molid+1 << ") " << "\n";
// write the property value
// FIX: we will assume for now that the desired property value is
// catable to a string
std::string pval;
mol.getProp(name, pval);
(*dp_ostream) << pval << "\n";
// empty line after the property
(*dp_ostream) << "\n";
}
}
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