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// $Id$
//
// Copyright (C) 2003-2008 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 <sstream>
#include <string>
namespace RDKit {
SmilesWriter::SmilesWriter(const std::string &fileName,
const std::string &delimiter,
const std::string &nameHeader, bool includeHeader,
bool isomericSmiles, bool kekuleSmiles) {
if (fileName != "-") {
auto *tmpStream = new std::ofstream(fileName.c_str());
if (!(*tmpStream) || (tmpStream->bad())) {
delete tmpStream;
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;
}
this->init(delimiter, nameHeader, includeHeader, isomericSmiles,
kekuleSmiles);
}
SmilesWriter::SmilesWriter(std::ostream *outStream, std::string delimiter,
std::string nameHeader, bool includeHeader,
bool takeOwnership, bool isomericSmiles,
bool kekuleSmiles) {
PRECONDITION(outStream, "null stream");
if (outStream->bad()) {
throw FileParseException("Bad output stream.");
}
dp_ostream = outStream;
df_owner = takeOwnership;
this->init(delimiter, nameHeader, includeHeader, isomericSmiles,
kekuleSmiles);
}
void SmilesWriter::init(const std::string &delimiter,
const std::string &nameHeader, bool includeHeader,
bool isomericSmiles, bool kekuleSmiles) {
d_molid = 0;
d_delim = delimiter;
d_nameHeader = nameHeader;
df_includeHeader = includeHeader;
df_isomericSmiles = isomericSmiles;
df_kekuleSmiles = kekuleSmiles;
// these are set by the setProps function as required
d_props.clear();
}
void SmilesWriter::setProps(const STR_VECT &propNames) {
if (d_molid > 0) {
BOOST_LOG(rdErrorLog)
<< "ERROR: Atleast one molecule has already been written\n";
BOOST_LOG(rdErrorLog)
<< "ERROR: Cannot set properties now - ignoring setProps\n";
return;
}
d_props = propNames;
}
void SmilesWriter::dumpHeader() const {
CHECK_INVARIANT(dp_ostream, "no output stream");
if (df_includeHeader) {
(*dp_ostream) << "SMILES" << d_delim;
if (d_nameHeader != "") {
(*dp_ostream) << d_nameHeader << d_delim;
}
if (d_props.size() > 0) {
auto pi = d_props.begin();
(*dp_ostream) << (*pi);
pi++;
while (pi != d_props.end()) {
(*dp_ostream) << d_delim << (*pi);
pi++;
}
}
(*dp_ostream) << "\n";
}
}
SmilesWriter::~SmilesWriter() {
// close the writer if it's still open:
if (dp_ostream != nullptr) {
close();
}
}
void SmilesWriter::write(const ROMol &mol, int) {
CHECK_INVARIANT(dp_ostream, "no output stream");
if (d_molid <= 0 && df_includeHeader) {
dumpHeader();
}
std::string name = "";
std::string smi = MolToSmiles(mol, df_isomericSmiles, df_kekuleSmiles);
(*dp_ostream) << smi;
if (d_nameHeader != "") {
if (!mol.getPropIfPresent(common_properties::_Name, name) ||
name.size() == 0) {
std::stringstream tstream;
tstream << d_molid;
name = tstream.str();
}
(*dp_ostream) << d_delim << name;
}
STR_VECT_CI pi;
for (pi = d_props.begin(); pi != d_props.end(); pi++) {
std::string pval;
// FIX: we will assume that any property that the user requests is castable
// to
// a std::string
if (mol.getPropIfPresent(*pi, pval)) {
(*dp_ostream) << d_delim << pval;
} else {
(*dp_ostream) << d_delim << "";
}
}
(*dp_ostream) << "\n";
d_molid++;
}
} // namespace RDKit
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