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// $Id$
//
// Copyright (C) 2007-2008 Greg Landrum
//
// @@ 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 "FileParsers.h"
#include <RDGeneral/RDLog.h>
#include <sstream>
#include <fstream>
#include <RDGeneral/FileParseException.h>
#include <RDGeneral/BadFileException.h>
namespace RDKit {
namespace TPLWriter {
void writeAtom(const ROMol &mol, unsigned int atomId,
ROMol::ConstConformerIterator confIt, std::ostringstream &dest,
std::string partialChargeProp) {
const Atom *atom = mol.getAtomWithIdx(atomId);
dest << atomId + 1;
dest << " " << atom->getSymbol();
dest << " " << atom->getFormalCharge();
std::string propVal;
if (atom->hasProp(partialChargeProp)) {
atom->getProp(partialChargeProp, propVal);
} else {
propVal = "0.0";
}
dest << " " << propVal;
const RDGeom::Point3D &pos = (*confIt)->getAtomPos(atomId);
dest << " " << 100. * pos.x << " " << 100. * pos.y << " " << 100. * pos.z;
ROMol::ADJ_ITER nbrIdx, endNbrs;
boost::tie(nbrIdx, endNbrs) = mol.getAtomNeighbors(atom);
dest << " " << (endNbrs - nbrIdx);
while (nbrIdx != endNbrs) {
dest << " " << (*nbrIdx + 1);
++nbrIdx;
}
// FIX: get this right:
dest << " "
<< "U";
dest << std::endl;
}
void writeBond(const ROMol &mol, unsigned int bondId,
ROMol::ConstConformerIterator confIt, std::ostringstream &dest) {
RDUNUSED_PARAM(confIt);
const Bond *bond = mol.getBondWithIdx(bondId);
dest << bondId + 1;
std::string bondLabel;
switch (bond->getBondType()) {
case Bond::SINGLE:
if (bond->getIsAromatic()) {
bondLabel = "1.5";
} else {
bondLabel = "1.0";
}
break;
case Bond::DOUBLE:
if (bond->getIsAromatic()) {
bondLabel = "1.5";
} else {
bondLabel = "2.0";
}
break;
case Bond::AROMATIC:
bondLabel = "1.5";
break;
case Bond::TRIPLE:
bondLabel = "3.0";
break;
default:
BOOST_LOG(rdWarningLog) << "TPL files only support single, double, "
"aromatic, and triple bonds." << std::endl;
BOOST_LOG(rdWarningLog) << "Bond of with type " << bond->getBondType()
<< " written as single in output." << std::endl;
bondLabel = "1.0";
}
dest << " " << bondLabel;
dest << " " << bond->getBeginAtomIdx() + 1 << " "
<< bond->getEndAtomIdx() + 1;
// FIX: add these
dest << " "
<< "0"
<< " "
<< "0";
dest << std::endl;
}
}
std::string MolToTPLText(const ROMol &mol, const std::string &partialChargeProp,
bool writeFirstConfTwice) {
if (!mol.getNumConformers()) {
BOOST_LOG(rdErrorLog)
<< "Cannot write molecules with no conformers to TPL files\n";
return "";
}
std::ostringstream res;
std::string tempStr;
res << "BioCAD format, all rights reserved" << std::endl;
res << "Output from RDKit" << std::endl;
if (!mol.hasProp(common_properties::_Name)) {
BOOST_LOG(rdWarningLog)
<< "Molecule has no name; arbitrary name assigned.\n";
tempStr = "Unnamed molecule";
} else {
mol.getProp(common_properties::_Name, tempStr);
}
res << "NAME " << tempStr << std::endl;
res << "PROP 7 1" << std::endl;
res << mol.getNumAtoms() << " " << mol.getNumBonds() << std::endl;
auto confIt = mol.beginConformers();
// write the atoms:
for (unsigned int i = 0; i < mol.getNumAtoms(); ++i) {
TPLWriter::writeAtom(mol, i, confIt, res, partialChargeProp);
}
// write the bonds:
for (unsigned int i = 0; i < mol.getNumBonds(); ++i) {
TPLWriter::writeBond(mol, i, confIt, res);
}
// write the additional conformations:
res << "CONFS " << mol.getNumConformers() - 1 << std::endl;
if (!writeFirstConfTwice) ++confIt;
while (confIt != mol.endConformers()) {
std::stringstream tmpStrm;
std::string confName;
tmpStrm << "conformer_" << (*confIt)->getId();
confName = tmpStrm.str();
res << "NAME " << confName << std::endl;
for (unsigned int i = 0; i < mol.getNumAtoms(); ++i) {
const RDGeom::Point3D &pos = (*confIt)->getAtomPos(i);
res << " " << 100. * pos.x << " " << 100. * pos.y << " " << 100. * pos.z
<< std::endl;
}
++confIt;
if (confIt != mol.endConformers()) {
res << std::endl;
}
}
return res.str();
}
void MolToTPLFile(const ROMol &mol, const std::string &fName,
const std::string &partialChargeProp,
bool writeFirstConfTwice) {
auto *outStream = new std::ofstream(fName.c_str());
if (!outStream || !(*outStream) || outStream->bad()) {
std::ostringstream errout;
errout << "Bad output file " << fName;
throw BadFileException(errout.str());
}
std::string outString =
MolToTPLText(mol, partialChargeProp, writeFirstConfTwice);
*outStream << outString;
delete outStream;
}
}
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