1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175
|
// $Id$
//
// 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(const std::string &fileName) {
if (fileName != "-") {
auto *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() throw() {
// 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(const 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";
std::string name;
if (df_writeNames && mol.getPropIfPresent(common_properties::_Name, name)) {
(*dp_ostream) << "NAME<" << name << ">\n";
}
// do we need to write coordinates?
if (mol.getNumConformers()) {
// get the ordering of the atoms in the output SMILES:
std::vector<unsigned int> atomOrdering;
mol.getProp(common_properties::_smilesAtomOutputOrder, atomOrdering);
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 = atomOrdering.size();
for (int i = 0; i < nAts; i++) {
(*dp_ostream) << std::setprecision(d_numDigits)
<< coords[atomOrdering[i]].x << ",";
(*dp_ostream) << std::setprecision(d_numDigits)
<< coords[atomOrdering[i]].y;
if (!df_write2D) {
(*dp_ostream) << "," << std::setprecision(d_numDigits)
<< coords[atomOrdering[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;
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()) {
writeProperty(mol, (*pi));
}
}
}
d_molid++;
}
void TDTWriter::writeProperty(const ROMol &mol, const 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";
}
} // namespace RDKit
|