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* collection of doxygen fixes * more files with fixed doxygen comments * more doxygen fixes * more doxygen fixes * last set of doxygen comment fixes Co-authored-by: Jason Biggs <jasonb@wolfram.com>
212 lines
8.3 KiB
C++
212 lines
8.3 KiB
C++
//
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// Copyright (C) 2012-2021 Greg Landrum
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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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/*! \file ConnectivityDescriptors.h
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\brief Use MolDescriptors.h in client code.
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*/
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#include <RDGeneral/export.h>
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#ifndef __RD_CONNECTIVITYDESCRIPTORS_H__
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#define __RD_CONNECTIVITYDESCRIPTORS_H__
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#include <string>
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#include <vector>
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#include <boost/smart_ptr.hpp>
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namespace RDKit {
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class ROMol;
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namespace Descriptors {
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//! From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
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/*!
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\param mol the molecule of interest
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\param force forces the value to be recalculated instead
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of pulled from the cache
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*/
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RDKIT_DESCRIPTORS_EXPORT double calcChi0v(const ROMol &mol, bool force = false);
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const std::string chi0vVersion = "1.2.0";
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//! From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
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/*!
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\param mol the molecule of interest
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\param force forces the value to be recalculated instead
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of pulled from the cache
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*/
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RDKIT_DESCRIPTORS_EXPORT double calcChi1v(const ROMol &mol, bool force = false);
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const std::string chi1vVersion = "1.2.0";
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//! From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
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/*!
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\param mol the molecule of interest
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\param force forces the value to be recalculated instead
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of pulled from the cache
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*/
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RDKIT_DESCRIPTORS_EXPORT double calcChi2v(const ROMol &mol, bool force = false);
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const std::string chi2vVersion = "1.2.0";
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//! From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
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/*!
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\param mol the molecule of interest
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\param force forces the value to be recalculated instead
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of pulled from the cache
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*/
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RDKIT_DESCRIPTORS_EXPORT double calcChi3v(const ROMol &mol, bool force = false);
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const std::string chi3vVersion = "1.2.0";
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//! From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
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/*!
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\param mol the molecule of interest
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\param force forces the value to be recalculated instead
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of pulled from the cache
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*/
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RDKIT_DESCRIPTORS_EXPORT double calcChi4v(const ROMol &mol, bool force = false);
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const std::string chi4vVersion = "1.2.0";
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//! From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
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/*!
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\param mol the molecule of interest
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\param n the order of the connectivity index
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\param force forces the value to be recalculated instead
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of pulled from the cache
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*/
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RDKIT_DESCRIPTORS_EXPORT double calcChiNv(const ROMol &mol, unsigned int n,
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bool force = false);
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const std::string chiNvVersion = "1.2.0";
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//! Similar to Hall Kier ChiXv, but uses nVal instead of valence
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//! This makes a big difference after we get out of the first row.
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/*!
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\param mol the molecule of interest
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\param force forces the value to be recalculated instead
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of pulled from the cache
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*/
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RDKIT_DESCRIPTORS_EXPORT double calcChi0n(const ROMol &mol, bool force = false);
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const std::string chi0nVersion = "1.2.0";
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//! Similar to Hall Kier ChiXv, but uses nVal instead of valence
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//! This makes a big difference after we get out of the first row.
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/*!
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\param mol the molecule of interest
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\param force forces the value to be recalculated instead
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of pulled from the cache
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*/
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RDKIT_DESCRIPTORS_EXPORT double calcChi1n(const ROMol &mol, bool force = false);
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const std::string chi1nVersion = "1.2.0";
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//! Similar to Hall Kier ChiXv, but uses nVal instead of valence
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//! This makes a big difference after we get out of the first row.
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/*!
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\param mol the molecule of interest
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\param force forces the value to be recalculated instead
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of pulled from the cache
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*/
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RDKIT_DESCRIPTORS_EXPORT double calcChi2n(const ROMol &mol, bool force = false);
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const std::string chi2nVersion = "1.2.0";
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//! Similar to Hall Kier ChiXv, but uses nVal instead of valence
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//! This makes a big difference after we get out of the first row.
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/*!
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\param mol the molecule of interest
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\param force forces the value to be recalculated instead
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of pulled from the cache
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*/
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RDKIT_DESCRIPTORS_EXPORT double calcChi3n(const ROMol &mol, bool force = false);
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const std::string chi3nVersion = "1.2.0";
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//! Similar to Hall Kier ChiXv, but uses nVal instead of valence
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//! This makes a big difference after we get out of the first row.
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/*!
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\param mol the molecule of interest
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\param force forces the value to be recalculated instead
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of pulled from the cache
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*/
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RDKIT_DESCRIPTORS_EXPORT double calcChi4n(const ROMol &mol, bool force = false);
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const std::string chi4nVersion = "1.2.0";
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//! Similar to Hall Kier ChiXv, but uses nVal instead of valence
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//! This makes a big difference after we get out of the first row.
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/*!
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\param mol the molecule of interest
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\param n the order of the connectivity index
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\param force forces the value to be recalculated instead
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of pulled from the cache
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*/
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RDKIT_DESCRIPTORS_EXPORT double calcChiNn(const ROMol &mol, unsigned int n,
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bool force = false);
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const std::string chiNnVersion = "1.2.0";
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//! calculate the Hall-Kier alpha value for a molecule
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//! From equation (58) of Rev. Comp. Chem. vol 2, 367-422, (1991)
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//!
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//! \note Because hybridization is used to calculate this, results may differ
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//! from other implementations which have different conventions for assigning
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//! hybridization
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/*!
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\param mol the molecule of interest
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\param atomContribs if provided, this will be used to return the
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contributions
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of the individual atoms to the value. These do not
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necessarily sum to the full value.
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Note: this can be a time-consuming calculation.
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*/
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RDKIT_DESCRIPTORS_EXPORT double calcHallKierAlpha(
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const ROMol &mol, std::vector<double> *atomContribs = nullptr);
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const std::string hallKierAlphaVersion = "1.2.0";
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//! calculate the Hall-Kier kappa1 value for a molecule
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//! From equations (58) and (59) of Rev. Comp. Chem. vol 2, 367-422, (1991)
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//!
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//! \note Because hybridization is used to calculate this, results may differ
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//! from other implementations which have different conventions for assigning
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//! hybridization
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/*!
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\param mol the molecule of interest
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*/
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RDKIT_DESCRIPTORS_EXPORT double calcKappa1(const ROMol &mol);
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const std::string kappa1Version = "1.1.0";
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//! calculate the Hall-Kier kappa2 value for a molecule
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//! From equations (58) and (60) of Rev. Comp. Chem. vol 2, 367-422, (1991)
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//!
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//! \note Because hybridization is used to calculate this results may differ
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//! from other implementations which have different conventions for assigning
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//! hybridization
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/*!
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\param mol the molecule of interest
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*/
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RDKIT_DESCRIPTORS_EXPORT double calcKappa2(const ROMol &mol);
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const std::string kappa2Version = "1.1.0";
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//! calculate the Hall-Kier kappa3 value for a molecule
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//! From equations (58), (61) and (62) of Rev. Comp. Chem. vol 2, 367-422,
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/// 1991)
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//!
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//! \note Because hybridization is used to calculate this results may differ
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//! from other implementations which have different conventions for assigning
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//! hybridization
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/*!
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\param mol the molecule of interest
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*/
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RDKIT_DESCRIPTORS_EXPORT double calcKappa3(const ROMol &mol);
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const std::string kappa3Version = "1.1.0";
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//! calculate the Kier Phi value for a molecule
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//! From Quantitative Structure-Activity Relationships 8, 221–224 (1989).
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//!
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//! \note Because hybridization is used to calculate this results may differ
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//! from other implementations which have different conventions for assigning
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//! hybridization
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/*!
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\param mol the molecule of interest
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*/
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RDKIT_DESCRIPTORS_EXPORT double calcPhi(const ROMol &mol);
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const std::string PhiVersion = "1.0.0";
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namespace detail {
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RDKIT_DESCRIPTORS_EXPORT void hkDeltas(const ROMol &mol,
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std::vector<double> &deltas, bool force);
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}
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} // end of namespace Descriptors
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} // namespace RDKit
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#endif
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