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89 lines
3.0 KiB
C++
89 lines
3.0 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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#include <RDGeneral/export.h>
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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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RDKIT_STRUCTCHECKER_EXPORT 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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RDKIT_STRUCTCHECKER_EXPORT int FixDubious3DMolecule(RWMol &mol);
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// Removes ill-defined stereodescriptors.
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RDKIT_STRUCTCHECKER_EXPORT 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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RDKIT_STRUCTCHECKER_EXPORT 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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RDKIT_STRUCTCHECKER_EXPORT 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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RDKIT_STRUCTCHECKER_EXPORT int AtomParity(const ROMol &mol, unsigned iatom,
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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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RDKIT_STRUCTCHECKER_EXPORT int CisTransPerception(
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const ROMol &mol, const std::vector<RDGeom::Point3D> &points,
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const std::vector<unsigned> &numbering, std::vector<unsigned> &bondColor);
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} // namespace StructureCheck
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} // namespace RDKit
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