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