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270f7b76e5
* add a SmilesParserParams object to prepare for this * add a SmilesParserParams object to prepare for this * add tests for the SmilesParseParmas * support name parsing, should it be the default? * rename CXNSmiles to CXSmiles; add a spirit parser for CXSmiles coordinate that is at least syntax correct * abandon boost::spirit for now; crude atom token parser * support params in smiles parser (not tested, may not build) * can read coords and atom labels along with mol names; crude, but works * read coordinate bonds * remove some compiler warnings with VS2015 * remove a bunch of compiler warnings on windows * remove more warnings on windows * remove more warnings on windows * backup commit: first pass at parsing query features * radical spec parsing * handle attachment points using atom mapping * switch to a named property for atom labels * fix handling of the "A" atom query * add functions to construct A and Q queries (needs more work) * fix a problem created while cleaning up warnings earlier * add some additional convenience functions for making generic atoms. Still need M and to recognize these while writing CXSMILES * add M queries; update some tests * fix a linux compile problem * get the cxsmiles stuff working in python; basic testing * support "M" in CXSMILES
57 lines
1.8 KiB
C++
57 lines
1.8 KiB
C++
//
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// Copyright (C) 2010 Greg Landrum and Rational Discovery LLC
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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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#ifndef _RD_FILEPARSERUTILS_H
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#define _RD_FILEPARSERUTILS_H
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#include <string>
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#include <iostream>
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#include <RDGeneral/BoostStartInclude.h>
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#include <boost/lexical_cast.hpp>
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#include <boost/algorithm/string.hpp>
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#include <RDGeneral/BoostEndInclude.h>
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namespace RDKit {
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class RWMol;
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class Conformer;
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namespace FileParserUtils {
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template <typename T>
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T stripSpacesAndCast(const std::string &input, bool acceptSpaces = false) {
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std::string trimmed = boost::trim_copy(input);
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if (acceptSpaces && trimmed == "") {
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return 0;
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} else {
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return boost::lexical_cast<T>(trimmed);
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}
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}
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int toInt(const std::string &input, bool acceptSpaces = false);
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double toDouble(const std::string &input, bool acceptSpaces = true);
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// reads a line from an MDL v3K CTAB
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std::string getV3000Line(std::istream *inStream, unsigned int &line);
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// nAtoms and nBonds are ignored on input, set on output
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bool ParseV3000CTAB(std::istream *inStream, unsigned int &line, RWMol *mol,
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Conformer *&conf, bool &chiralityPossible,
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unsigned int &nAtoms, unsigned int &nBonds,
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bool strictParsing = true, bool expectMEND = true);
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// nAtoms and nBonds are used
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bool ParseV2000CTAB(std::istream *inStream, unsigned int &line, RWMol *mol,
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Conformer *&conf, bool &chiralityPossible,
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unsigned int &nAtoms, unsigned int &nBonds,
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bool strictParsing = true);
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Atom *replaceAtomWithQueryAtom(RWMol *mol, Atom *atom);
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}
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}
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#endif
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