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ca41fa5bfd
* Parsing SCSR * add scsrol to mol * removed bad include file * loosen distGeom test slightly * add wrap test for SCSRMol * Add test for scsr in python * tests added for scsr and strict parsing removed * remove extra stuff * More fully specified use of SCSRMol for PR CI build * Added flags for SCSR expansion to not include any leaving groups * Added MolFromScsrParams to Wrap for python * added SCSRMol destructor * Added two tests for RNA macromols, and fixed a bug they revealed * Added new tests abd expected files * changes as per PR review * SCSR Chnages for leaving groups * fixed testScsr.py * hydrogen bond treatment * in SCSR expand, allow Hbond to be autoatically detected * changes as per code review * Adding new test file * chages for SCSR contructors, destructors for CI build * fixed pyton for SCSR hydrogen bond modes, and added tests * Added new test files * fixed edge case for SCSR * fix checksum for inchi * consistent capitalization of SCSR throughout * switch to enum class * make things shorter * simplify * get rid of the ATTCHORD class * New section for SCSR in RDKit_book * addeed section to RDKit_Book * SCSRMol is no longer exposed in Python * fix leak in MolFromSCSRFile() light refactoring * expose MolFromSCSRFile() to python make the MolFromSCSR functions work with default args a bit more testing * removed C++ access to SCSRMol * CXMsiles now ouputs hbonds, fix to template matching, and a few other things * Addl fix for bad aromaticity in Hbond rings * Test files needed * Test files needed * try to fix a CI build errors * CI error fix * Added missing test file * CMake version - for CI build * remove full file compoarison from macromol test file * accidental change to debug restored to release * Code review changes * As per PR review --------- Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
163 lines
7.0 KiB
C++
163 lines
7.0 KiB
C++
//
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// Copyright (C) 2002-2018 Greg Landrum and T5 Informatics GmbH
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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 <RDGeneral/export.h>
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#pragma once
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#include <GraphMol/SubstanceGroup.h>
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#include <RDGeneral/FileParseException.h>
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#include <sstream>
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namespace RDKit {
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namespace SGroupParsing {
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typedef std::map<int, SubstanceGroup> IDX_TO_SGROUP_MAP;
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typedef std::map<int, STR_VECT> IDX_TO_STR_VECT_MAP;
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/* ------------------ V2000 Utils ------------------ */
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unsigned int ParseSGroupIntField(const std::string &text, unsigned int line,
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unsigned int &pos,
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bool isFieldCounter = false);
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unsigned int ParseSGroupIntField(bool &ok, bool strictParsing,
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const std::string &text, unsigned int line,
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unsigned int &pos,
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bool isFieldCounter = false);
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double ParseSGroupDoubleField(const std::string &text, unsigned int line,
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unsigned int &pos);
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double ParseSGroupDoubleField(bool &ok, bool strictParsing,
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const std::string &text, unsigned int line,
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unsigned int &pos);
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SubstanceGroup *FindSgIdx(IDX_TO_SGROUP_MAP &sGroupMap, int sgIdx,
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unsigned int line);
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template <class Exc = FileParseException>
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void SGroupWarnOrThrow(bool strictParsing, const std::string &msg) {
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if (strictParsing) {
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throw Exc(msg);
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} else {
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BOOST_LOG(rdWarningLog) << msg << std::endl;
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}
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}
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void ParseSGroupV2000STYLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol,
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const std::string &text, unsigned int line,
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bool strictParsing = true);
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void ParseSGroupV2000VectorDataLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol,
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const std::string &text, unsigned int line,
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bool strictParsing = true);
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void ParseSGroupV2000SDILine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol,
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const std::string &text, unsigned int line,
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bool strictParsing = true);
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void ParseSGroupV2000SSTLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol,
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const std::string &text, unsigned int &line,
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bool strictParsing = true);
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void ParseSGroupV2000SMTLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol,
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const std::string &text, unsigned int &line,
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bool strictParsing = true);
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void ParseSGroupV2000SLBLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol,
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const std::string &text, unsigned int line,
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bool strictParsing = true);
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void ParseSGroupV2000SCNLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol,
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const std::string &text, unsigned int line,
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bool strictParsing = true);
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void ParseSGroupV2000SDSLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol,
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const std::string &text, unsigned int line,
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bool strictParsing = true);
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void ParseSGroupV2000SBVLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol,
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const std::string &text, unsigned int line,
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bool strictParsing = true);
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void ParseSGroupV2000SDTLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol,
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const std::string &text, unsigned int line,
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bool strictParsing = true);
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void ParseSGroupV2000SDDLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol,
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const std::string &text, unsigned int line,
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bool strictParsing = true);
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void ParseSGroupV2000SCDSEDLine(IDX_TO_SGROUP_MAP &sGroupMap,
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IDX_TO_STR_VECT_MAP &dataFieldsMap, RWMol *mol,
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const std::string &text, unsigned int line,
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bool strictParsing, unsigned int &counter,
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unsigned int &lastDataSGroup,
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std::ostringstream ¤tDataField);
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void ParseSGroupV2000SPLLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol,
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const std::string &text, unsigned int line,
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bool strictParsing = true);
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void ParseSGroupV2000SNCLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol,
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const std::string &text, unsigned int line,
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bool strictParsing = true);
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//! if the SAP line is malformed and has no lvIdx and no id,
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//! lvIdx is set to mol->getNumAtoms() and id is set to " "
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//! the user is responsible for replacing lvIdx with the correct
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//! index: if d_bonds.size() == 1, and one of the bond atom indices
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//! is aIdx, the other can be safely assigned to lvIdx
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void ParseSGroupV2000SAPLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol,
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const std::string &text, unsigned int line,
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bool strictParsing = true);
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void ParseSGroupV2000SCLLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol,
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const std::string &text, unsigned int line,
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bool strictParsing = true);
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void ParseSGroupV2000SBTLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol,
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const std::string &text, unsigned int line,
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bool strictParsing = true);
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/* ------------------ V3000 Utils ------------------ */
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template <class T>
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RDKIT_FILEPARSERS_EXPORT std::vector<T> ParseV3000Array(
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std::stringstream &stream, int maxV = -1, bool strictParsing = false);
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#if defined(_MSC_VER) && defined(RDKIT_DYN_LINK)
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template RDKIT_FILEPARSERS_EXPORT std::vector<int> ParseV3000Array(
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std::stringstream &, int, bool);
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template RDKIT_FILEPARSERS_EXPORT std::vector<unsigned int> ParseV3000Array(
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std::stringstream &, int, bool);
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#endif
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template <class T>
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std::vector<T> ParseV3000Array(const std::string &s, int maxV = -1,
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bool strictParsing = false) {
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std::stringstream stream(s);
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return ParseV3000Array<T>(stream, maxV, strictParsing);
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}
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void ParseV3000CStateLabel(RWMol *mol, SubstanceGroup &sgroup,
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std::stringstream &stream, unsigned int line,
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bool strictParsing = true);
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void ParseV3000SAPLabel(RWMol *mol, SubstanceGroup &sgroup,
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std::stringstream &stream, bool strictParsing = true);
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std::string ParseV3000StringPropLabel(std::stringstream &stream);
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// returns the last line read in the SGroups block
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std::string ParseV3000SGroupsBlock(std::istream *inStream, unsigned int &line,
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unsigned int nSgroups, RWMol *mol,
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bool strictParsing);
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} // namespace SGroupParsing
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} // namespace RDKit
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