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//
// 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 <fstream>
#include <iostream>
#include <sstream>
#include <string>
#include <RDGeneral/BoostStartInclude.h>
#include <boost/any.hpp>
#include <RDGeneral/BoostEndInclude.h>
#include <RDGeneral/BadFileException.h>
#include <RDGeneral/FileParseException.h>
#include <RDGeneral/RDLog.h>
#ifdef RDK_BUILD_MAEPARSER_SUPPORT
#undef RDK_BUILD_MAEPARSER_SUPPORT
#endif
#include "MolWriters.h"
#include "FileParsers.h"
namespace RDKit {
SDWriter::SDWriter(const std::string &fileName) {
if (fileName != "-") {
auto *tmpStream = new std::ofstream(fileName.c_str());
df_owner = true;
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);
} else {
dp_ostream = static_cast<std::ostream *>(&std::cout);
df_owner = false;
}
d_molid = 0;
df_kekulize = true;
df_forceV3000 = false;
}
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;
df_kekulize = true;
df_forceV3000 = false;
}
SDWriter::~SDWriter() {
// close the writer if it's still open:
if (dp_ostream != nullptr) {
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;
}
namespace {
void _writePropToStream(std::ostream *dp_ostream, const ROMol &mol,
const std::string &name, int d_molid) {
PRECONDITION(dp_ostream, "no output stream");
// write the property value
// FIX: we will assume for now that the desired property value is
// catable to a string
std::string pval;
try {
mol.getProp(name, pval);
} catch (std::bad_any_cast &) {
return;
}
// warn and skip if we include a new line
if (name.find("\n") != std::string::npos) {
BOOST_LOG(rdWarningLog)
<< "WARNING: Skipping property " << name
<< " because the name includes a newline" << std::endl;
return;
}
if (pval.find("\r\n\r\n") != std::string::npos ||
pval.find("\n\n") != std::string::npos) {
BOOST_LOG(rdWarningLog)
<< "WARNING: Skipping property " << name
<< " because the value includes an illegal blank line" << std::endl;
return;
}
// write the property header line
(*dp_ostream) << "> <" << name << "> ";
if (d_molid >= 0) {
(*dp_ostream) << "(" << d_molid + 1 << ") ";
}
(*dp_ostream) << "\n";
(*dp_ostream) << pval << "\n";
// empty line after the property
(*dp_ostream) << "\n";
}
void _MolToSDStream(std::ostream *dp_ostream, const ROMol &mol, int confId,
bool df_kekulize, bool df_forceV3000, int d_molid,
STR_VECT *props) {
PRECONDITION(dp_ostream, "no output stream");
// write the molecule
(*dp_ostream) << MolToMolBlock(mol, true, confId, df_kekulize, df_forceV3000);
// now write the properties
STR_VECT_CI pi;
if (props && 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 = props->begin(); pi != props->end(); pi++) {
if (mol.hasProp(*pi)) {
_writePropToStream(dp_ostream, mol, (*pi), d_molid);
}
}
} 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;
mol.getPropIfPresent(RDKit::detail::computedPropName, compLst);
STR_VECT_CI pi;
for (pi = properties.begin(); pi != properties.end(); pi++) {
// ignore any of the following properties
if (((*pi) == RDKit::detail::computedPropName) ||
((*pi) == common_properties::_Name) || ((*pi) == "_MolFileInfo") ||
((*pi) == "_MolFileComments") ||
((*pi) == common_properties::_MolFileChiralFlag)) {
continue;
}
// check if this property is not computed
if (std::find(compLst.begin(), compLst.end(), (*pi)) == compLst.end()) {
_writePropToStream(dp_ostream, mol, (*pi), d_molid);
}
}
}
// add the $$$$ that marks the end of a molecule
(*dp_ostream) << "$$$$\n";
}
} // namespace
std::string SDWriter::getText(const ROMol &mol, int confId, bool kekulize,
bool forceV3000, int molid, STR_VECT *propNames) {
std::stringstream sstr;
_MolToSDStream(&sstr, mol, confId, kekulize, forceV3000, molid, propNames);
return sstr.str();
};
void SDWriter::write(const ROMol &mol, int confId) {
PRECONDITION(dp_ostream, "no output stream");
_MolToSDStream(dp_ostream, mol, confId, df_kekulize, df_forceV3000, d_molid,
&d_props);
++d_molid;
}
void SDWriter::writeProperty(const ROMol &mol, const std::string &name) {
PRECONDITION(dp_ostream, "no output stream");
_writePropToStream(dp_ostream, mol, name, d_molid);
}
} // namespace RDKit
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