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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
88 lines
2.7 KiB
C++
88 lines
2.7 KiB
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 "StructChecker.h"
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#include "Utilites.h"
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namespace RDKit {
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namespace StructureCheck {
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// ??? stereo parity
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static const int ODD = 1;
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static const int EVEN = 2;
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static const int UNMARKED = 3;
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static const int ALLENE_PARITY = -2;
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static const int ILLEGAL_REPRESENTATION = -1;
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static const int UNDEFINED_PARITY = 0;
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static const int ODD_PARITY = 1;
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static const int EVEN_PARITY = 2;
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static inline int INVERT_PARITY(int p) { return ((p) == 0 ? (0) : (3 - (p))); }
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// bond color:
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static const int CIS = 1;
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static const int TRANS = 2;
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// return codes for DubiousStereochemistry()
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static const int EITHER_BOND_FOUND = 1;
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static const int STEREO_BOND_AT_NON_STEREO_ATOM = 2;
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static const int ZEROED_Z_COORDINATES = 4;
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static const int CONVERTED_TO_2D = 8;
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/* DubiousStereochemistry:
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* Checks if there is some ill-defined stereochemistry in the
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* molecule *mp. The function returns a bit set integer which defines
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* the problems encountered.
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*/
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int DubiousStereochemistry(RWMol &mol);
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/* FixDubious3DMolecule:
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* Checks if the structure has 3D coordinates and/or flat sp3-carbons with
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* stereo-bonds and
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* converts the designation to 2D, clearing away any Z-component of the
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* coordinates.
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* Real 3D structures without stereo designations go through untouched.
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*/
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int FixDubious3DMolecule(RWMol &mol);
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// Removes ill-defined stereodescriptors.
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void RemoveDubiousStereochemistry(RWMol &mol);
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/*
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* Checks if all potential stereocenters are either completely undefined
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* or attributed with hashes and wedges according to MDL rules.
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*/
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bool CheckStereo(const ROMol &mol);
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/*
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* Checks if any two atoms in *mp come closer than 10% of the
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* average bond length or if an atom is too close the line
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* between two bonded atoms.
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*/
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bool AtomClash(RWMol &mol, double clash_limit);
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/*
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* Computes the stereo parity of atom number iatom in *mp relative
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* to its numbering. The immediate neighbours are defined by *nbp
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* to speed up processing.
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*/
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int AtomParity(const ROMol &mol, unsigned iatom, const Neighbourhood &nbp);
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/*
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* Sets the color field of the defined double bonds in *mp to CIS,
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* TRANS, or NONE depending on the ligands with the lowest numbering[].
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* It returns the number of defined double bonds found.
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*/
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int CisTransPerception(const ROMol &mol,
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const std::vector<RDGeom::Point3D> &points,
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const std::vector<unsigned> &numbering,
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std::vector<unsigned> &bondColor);
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}
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}
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