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//
// Copyright (C) 2022 Sreya Gogineni and other RDKit contributors
//
// @@ 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/BoostStartInclude.h>
#include <boost/lexical_cast.hpp>
#include <RDGeneral/BoostEndInclude.h>
#include "FileParsers.h"
#include "FileParserUtils.h"
#include <RDGeneral/StreamOps.h>
#include <RDGeneral/FileParseException.h>
#include <RDGeneral/BadFileException.h>
#include <exception>
#include <iostream>
#include <fstream>
#include <sstream>
#include <string>
#include <cstdlib>
#include <cstdio>
#include <vector>
namespace RDKit {
void ParseExtraLine(const std::string &extraLine) {
std::string whitespace{" \t"};
if (extraLine.find_first_not_of(whitespace) != std::string::npos) {
std::ostringstream errout;
errout << "More lines than expected" << std::endl;
throw FileParseException(errout.str());
}
}
Atom *ParseXYZFileAtomLine(const std::string &atomLine, RDGeom::Point3D &pos,
unsigned int line) {
std::string whitespace{" \t"};
size_t delims[8];
size_t prev = 0;
for (unsigned int i = 0; i < 7; i++) {
if (i % 2 == 0) {
delims[i] = atomLine.find_first_not_of(whitespace, prev);
} else {
delims[i] = atomLine.find_first_of(whitespace, prev);
}
if (delims[i] == std::string::npos) {
std::ostringstream errout;
errout << "Missing coordinates on line " << line << std::endl;
throw FileParseException(errout.str());
}
prev = delims[i];
}
delims[7] = atomLine.find_last_not_of(whitespace) + 1;
// set conformer
try {
pos.x = FileParserUtils::toDouble(
atomLine.substr(delims[2], delims[3] - delims[2]), false);
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '"
<< atomLine.substr(delims[2], delims[3] - delims[2])
<< "' to double on line " << line << std::endl;
throw FileParseException(errout.str());
}
try {
pos.y = FileParserUtils::toDouble(
atomLine.substr(delims[4], delims[5] - delims[4]), false);
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '"
<< atomLine.substr(delims[4], delims[5] - delims[4])
<< "' to double on line " << line << std::endl;
throw FileParseException(errout.str());
}
try {
pos.z = FileParserUtils::toDouble(
atomLine.substr(delims[6], delims[7] - delims[6]), false);
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Cannot convert '"
<< atomLine.substr(delims[6], delims[7] - delims[6])
<< "' to double on line " << line << std::endl;
throw FileParseException(errout.str());
}
std::string symb{atomLine.substr(delims[0], delims[1] - delims[0])};
if (symb.size() == 2 && symb[1] >= 'A' && symb[1] <= 'Z') {
symb[1] = static_cast<char>(tolower(symb[1]));
}
Atom *atom;
try {
atom = new Atom(PeriodicTable::getTable()->getAtomicNumber(symb));
} catch (const Invar::Invariant &e) {
throw FileParseException(e.what());
}
return atom;
}
namespace v2 {
namespace FileParsers {
std::unique_ptr<RWMol> MolFromXYZDataStream(std::istream &inStream) {
unsigned int numAtoms = 0;
std::string num{getLine(inStream)};
try {
numAtoms = FileParserUtils::toUnsigned(num);
} catch (boost::bad_lexical_cast &) {
std::ostringstream errout;
errout << "Unable to recognize the number of atoms: cannot convert '" << num
<< "' to unsigned int on line 0" << std::endl;
throw FileParseException(errout.str());
}
std::string comment{getLine(inStream)};
auto mol = std::make_unique<RWMol>();
if (numAtoms) {
Conformer *conf = new Conformer(numAtoms);
if (!comment.empty()) {
mol->setProp("_FileComments", comment);
}
for (unsigned int i = 0; i < numAtoms; i++) {
if (inStream.eof()) {
throw FileParseException("EOF hit while reading atoms");
}
RDGeom::Point3D pos;
std::string atomLine{getLine(inStream)};
Atom *atom = ParseXYZFileAtomLine(atomLine, pos, i + 2);
unsigned int idx = mol->addAtom(atom, false, true);
conf->setAtomPos(idx, pos);
}
mol->addConformer(conf);
}
while (!inStream.eof()) {
std::string extraLine{getLine(inStream)};
ParseExtraLine(extraLine);
}
return mol;
}
std::unique_ptr<RWMol> MolFromXYZBlock(const std::string &xyzBlock) {
std::istringstream xyz(xyzBlock);
xyz.peek();
if (!xyz.eof()) {
return MolFromXYZDataStream(xyz);
} else {
return nullptr;
}
}
std::unique_ptr<RWMol> MolFromXYZFile(const std::string &fName) {
std::ifstream xyzFile(fName);
if (!xyzFile || (xyzFile.bad())) {
std::ostringstream errout;
errout << "Bad input file " << fName;
throw BadFileException(errout.str());
}
xyzFile.peek();
if (!xyzFile.eof()) {
return MolFromXYZDataStream(xyzFile);
} else {
return nullptr;
}
}
} // namespace FileParsers
} // namespace v2
} // namespace RDKit
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