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da6cd73168
* run clang-format-18 across Code/*.cpp and Code/*.h * run clang-format-18 across External
64 lines
1.8 KiB
C++
64 lines
1.8 KiB
C++
// Copyright (C) 2019 Eisuke Kawashima
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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 "FileParsers.h"
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#include <fstream>
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#include <sstream>
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#include <boost/format.hpp>
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#include <RDGeneral/BadFileException.h>
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namespace RDKit {
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std::string MolToXYZBlock(const ROMol &mol, int confId,
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unsigned int precision) {
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if (!mol.getNumConformers()) {
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BOOST_LOG(rdErrorLog)
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<< "Cannot write molecules with no conformers to XYZ block\n";
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return "";
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}
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const auto &conf = mol.getConformer(confId);
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const unsigned int nAtoms = mol.getNumAtoms();
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std::stringstream ss;
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ss << nAtoms << '\n';
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unsigned fieldWidth = 5 + precision;
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std::stringstream formatString;
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formatString << "%-3s %" << fieldWidth << "." << precision << "f %"
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<< fieldWidth << "." << precision << "f %" << fieldWidth << "."
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<< precision << "f\n";
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std::string name;
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if (mol.getPropIfPresent(common_properties::_Name, name)) {
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ss << name.substr(0, name.find_first_of('\n'));
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}
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ss << '\n';
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for (unsigned int i = 0; i < nAtoms; i++) {
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const auto &symbol = mol.getAtomWithIdx(i)->getSymbol();
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const auto &pos = conf.getAtomPos(i);
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ss << boost::format{formatString.str()} % symbol % pos.x % pos.y % pos.z;
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}
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return ss.str();
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}
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void MolToXYZFile(const ROMol &mol, const std::string &fName, int confId,
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unsigned int precision) {
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std::ofstream outStream(fName);
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if (!outStream) {
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std::ostringstream errout;
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errout << "Bad output file " << fName;
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throw BadFileException(errout.str());
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}
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outStream << MolToXYZBlock(mol, confId, precision);
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}
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} // namespace RDKit
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