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143 lines
3.8 KiB
C++
143 lines
3.8 KiB
C++
// $Id$
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//
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// Copyright (C) 2003-2010 Greg Landrum and Rational Discovery LLC
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <RDGeneral/BadFileException.h>
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#include <RDGeneral/FileParseException.h>
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#include <RDGeneral/RDLog.h>
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#include "MolWriters.h"
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#include "FileParsers.h"
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#include <fstream>
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#include <iostream>
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#include <sstream>
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#include <string>
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#include <boost/any.hpp>
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namespace RDKit {
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SDWriter::SDWriter(std::string fileName) {
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if(fileName!= "-"){
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std::ofstream *tmpStream = new std::ofstream(fileName.c_str());
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df_owner=true;
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if ( !tmpStream || !(*tmpStream) || (tmpStream->bad()) ) {
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std::ostringstream errout;
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errout << "Bad output file " << fileName;
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throw BadFileException(errout.str());
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}
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dp_ostream = static_cast<std::ostream *>(tmpStream);
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} else {
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dp_ostream = static_cast<std::ostream *>(&std::cout);
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df_owner=false;
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}
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d_molid = 0;
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df_kekulize=true;
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df_forceV3000=false;
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}
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SDWriter::SDWriter(std::ostream *outStream,bool takeOwnership) {
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PRECONDITION(outStream,"null stream");
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if (outStream->bad()){
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throw FileParseException("Bad output stream");
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}
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dp_ostream = outStream;
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df_owner = takeOwnership;
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d_molid = 0;
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df_kekulize=true;
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df_forceV3000=false;
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}
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SDWriter::~SDWriter() {
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// close the writer if it's still open:
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if(dp_ostream!=NULL) close();
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}
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void SDWriter::setProps(const STR_VECT &propNames) {
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if (d_molid > 0) {
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BOOST_LOG(rdWarningLog) << "WARNING: Setting property list after a few molecules have been written\n";
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}
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d_props = propNames;
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}
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void SDWriter::write(const ROMol &mol, int confId) {
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PRECONDITION(dp_ostream,"no output stream");
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// write the molecule
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(*dp_ostream) << MolToMolBlock(mol, true, confId, df_kekulize, df_forceV3000);
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// now write the properties
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STR_VECT_CI pi;
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if (d_props.size() > 0) {
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// check if we have any properties the user specified to write out
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// in which loop over them and write them out
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for (pi = d_props.begin(); pi != d_props.end(); pi++) {
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if (mol.hasProp(*pi)) {
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writeProperty(mol, (*pi));
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}
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}
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}
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else {
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// if use did not specify any properties, write all non computed properties
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// out to the file
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STR_VECT properties = mol.getPropList();
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STR_VECT compLst;
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if (mol.hasProp(detail::computedPropName)) {
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mol.getProp(detail::computedPropName, compLst);
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}
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STR_VECT_CI pi;
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for (pi = properties.begin(); pi != properties.end(); pi++) {
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// ignore any of the following properties
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if ( ((*pi) == detail::computedPropName) ||
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((*pi) == "_Name") ||
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((*pi) == "_MolFileInfo") ||
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((*pi) == "_MolFileComments") ||
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((*pi) == "_MolFileChiralFlag")) {
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continue;
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}
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// check if this property is not computed
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if (std::find(compLst.begin(), compLst.end(), (*pi)) == compLst.end()) {
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writeProperty(mol, (*pi));
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}
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}
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}
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// add the $$$$ that marks the end of a molecule
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(*dp_ostream) << "$$$$\n";
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++d_molid;
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}
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void SDWriter::writeProperty(const ROMol &mol, std::string name) {
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PRECONDITION(dp_ostream,"no output stream");
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// write the property value
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// FIX: we will assume for now that the desired property value is
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// catable to a string
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std::string pval;
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try {
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mol.getProp(name, pval);
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} catch (boost::bad_any_cast &){
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return;
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}
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// write the property header line
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(*dp_ostream) << "> <" << name << "> " << "(" << d_molid+1 << ") " << "\n";
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(*dp_ostream) << pval << "\n";
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// empty line after the property
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(*dp_ostream) << "\n";
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}
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}
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