FileParserUtils.h
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//
// Copyright (C) 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.
//
#ifndef _RD_FILEPARSERUTILS_H
#define _RD_FILEPARSERUTILS_H
#include <string>
#include <iostream>
#include <boost/lexical_cast.hpp>
#include <boost/algorithm/string.hpp>
namespace RDKit {
class RWMol;
class Conformer;
namespace FileParserUtils {
template <typename T>
T stripSpacesAndCast(const std::string &input, bool acceptSpaces = false) {
std::string trimmed = boost::trim_copy(input);
if (acceptSpaces && trimmed == "") {
return 0;
} else {
return boost::lexical_cast<T>(trimmed);
}
}
int toInt(const std::string &input, bool acceptSpaces = false);
double toDouble(const std::string &input, bool acceptSpaces = true);
// reads a line from an MDL v3K CTAB
std::string getV3000Line(std::istream *inStream, unsigned int &line);
// nAtoms and nBonds are ignored on input, set on output
bool ParseV3000CTAB(std::istream *inStream, unsigned int &line, RWMol *mol,
Conformer *&conf, bool &chiralityPossible,
unsigned int &nAtoms, unsigned int &nBonds,
bool strictParsing = true, bool expectMEND = true);
// nAtoms and nBonds are used
bool ParseV2000CTAB(std::istream *inStream, unsigned int &line, RWMol *mol,
Conformer *&conf, bool &chiralityPossible,
unsigned int &nAtoms, unsigned int &nBonds,
bool strictParsing = true);
Atom *replaceAtomWithQueryAtom(RWMol *mol, Atom *atom);
}
}
#endif
RDKit::RWMol
RWMol is a molecule class that is intended to be edited.
Definition: RWMol.h:30
RDKit::FileParserUtils::getV3000Line
std::string getV3000Line(std::istream *inStream, unsigned int &line)
RDKit::FileParserUtils::toDouble
double toDouble(const std::string &input, bool acceptSpaces=true)
RDKit::FileParserUtils::toInt
int toInt(const std::string &input, bool acceptSpaces=false)
RDKit
Includes a bunch of functionality for handling Atom and Bond queries.
Definition: Atom.h:28
RDKit::FileParserUtils::replaceAtomWithQueryAtom
Atom * replaceAtomWithQueryAtom(RWMol *mol, Atom *atom)
RDKit::FileParserUtils::stripSpacesAndCast
T stripSpacesAndCast(const std::string &input, bool acceptSpaces=false)
Definition: FileParserUtils.h:24
RDKit::FileParserUtils::ParseV3000CTAB
bool ParseV3000CTAB(std::istream *inStream, unsigned int &line, RWMol *mol, Conformer *&conf, bool &chiralityPossible, unsigned int &nAtoms, unsigned int &nBonds, bool strictParsing=true, bool expectMEND=true)
RDKit::FileParserUtils::ParseV2000CTAB
bool ParseV2000CTAB(std::istream *inStream, unsigned int &line, RWMol *mol, Conformer *&conf, bool &chiralityPossible, unsigned int &nAtoms, unsigned int &nBonds, bool strictParsing=true)
RDKit::Conformer
The class for representing 2D or 3D conformation of a molecule.
Definition: Conformer.h:41
RDKit::Atom
The class for representing atoms.
Definition: Atom.h:67