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* StructChecker changes. Initial commit. First implementation. Added some tests. * StructChecker: add GoodAtoms and AcidicAtoms. new updates * StructChecker: add new tests * StructChecker: added TransformAugmentedAtoms() * StructCheck: add structCheck to GraphMol. Fix compilation errors. * StructChecker: add stereo verification and some utilities. * StructChecker: function FixDubious3DMolecule was added * StructChecker: checkStereo added. done with stereo. * StructChecker: add StripSmallFragments() * StructChecker: add AtomClash() function. Some cosmetic + tests * StructChecker: checkAtoms() was started * StructChecker: checkAtoms is ready * StructChecker: user RingInfo from RDkit. Start regarge * StructChecker: ReCharge molecule method prototype * StructChecker: updates for ReCharge. Almost finished * StructChecker: all ReCharge is done except external data tables loading * StructChecker: add path tables into API. ReCharge completed * Adds augmented atom data Signed-off-by: Brian Kelley <brian.kelley@novartis.com> * Removes extra files Signed-off-by: Brian Kelley <brian.kelley@novartis.com> * Adds path to test data via RDBASE environment Signed-off-by: Brian Kelley <brian.kelley@novartis.com> * Revert "Struct checker apr15" * StructChecker: add missing tautomer tests * Updates test to use RDBASE * Adds initialization of data from data section * Adds Python API and tests * Fixes namespace for enum * StructChecker: update/imporve strip small fragments * StructChecker: fix acidic atoms (but logic does not work) * StructChecker: fix match issue for CheckAtoms * Adds macro guards * Adds loading API and proper constructor * Fixes tests, adds stereo test * Fixes crash bug, matches[0] was being accessed from an empty match vector * Reverts crash fix - conflicts with previous * Adds the rest of the structure checker options * StructChecker: fix atom matching for aromatic rings * StructChecker: add tautomers checks. Update some tests * StructChecker: stereo fixes. Add some tests * StructChecker: fix check atoms. Start ligand symbol list * StructChecker: fix some check atoms validation. Add Tranform to query lists. Start correct loading augmented atoms * update * another set of fixes * StructChecker: fix loadDefaultAugmentedAtoms. Some changes in CheckAtom + tests + debug conditional breakpoints (TEMP operators) * StructChecker: rewrited RecMatch() to sequential. Changed bond matching algorithm. small bug fixes * Adds better logging of mismatched atoms * Removes duplicated negative charge * Fixes charges * Adds nitro group test * StructChecker: add better logging * remove double logging * Reformats code using RDKit's clang-format style * StructChecker: Fix charge reformat using RDKit format. * StructChecker: compilation restore after merge * restore bond matching * Removes the same fragments that strucheck does in case of ties * Don't resanitize - this adds aromaticity which mucks things up * Adds empty molecule checks * Fixes atom clashes. * Removes debug printing * Removes debug logging info * First pass at stereo fixes * Fixes off by one error for dubious stereo fix * Fixes more off by one errors * Fixes more off by one errors * More off by one fixes. * Another off by one * Fixes chiral flag set in molfile check * Copies chiral flag over to largest fragment if necessary * Poor man’s parity check. * Find unspecified chiral centers ala Avalon. * StructChecker: fix recursive match. Fix transformations * StructChecker: fix transformation for atom list (using query atoms) * Fixes checks && to & * StructChecker: fix carboxylic acids tranform issue. Atom list is changed only if different * StructChecker: documentation was updated * Fixes snprintf and silences some warnings * Adds Get/Set StructCheckerOptions * Adds default AugmentedAtomTransforms
32 lines
948 B
C++
32 lines
948 B
C++
//
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// Copyright (C) 2016 Novartis Institutes for BioMedical Research
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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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#pragma once
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#include "../RDKitBase.h"
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#include "StructChecker.h"
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namespace RDKit {
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namespace StructureCheck {
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struct Neighbourhood { // a set of an atom neighbours
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std::vector<unsigned> Atoms; // indices of atoms
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std::vector<unsigned> Bonds; // indices of bonds
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};
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void SetupNeighbourhood(const ROMol &mol,
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std::vector<Neighbourhood> &neighbour_array);
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bool getMolAtomPoints(const ROMol &mol,
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std::vector<RDGeom::Point3D> &atomPoint, bool twod=false);
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std::string LogNeighbourhood(
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const ROMol &mol, unsigned int idx,
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const std::vector<Neighbourhood> &bneighbour_array);
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}
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}
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