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Metal.h
Go to the documentation of this file.
//
// Copyright (C) 2018-2021 Susan H. Leung and other RDKit contributors
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
/*! \file Metal.h
\brief Defines the MetalDisconnector class.
*/
#include <RDGeneral/export.h>
#ifndef RD_METAL_H
#define RD_METAL_H
#include <GraphMol/ROMol.h>
namespace RDKit {
class RWMol;
class ROMol;
namespace MolStandardize {
//! The MetalDisconnector class contains tools for disconnecting metal atoms
//! that are defined as covalently bonded to non-metals.
/*!
<b>Notes:</b>
-
*/
struct RDKIT_MOLSTANDARDIZE_EXPORT MetalDisconnectorOptions {
bool splitGrignards = false; // Whether to split Grignard-type complexes.
bool splitAromaticC = false; // Whether to split metal-aromatic C bonds.
bool adjustCharges = true; // Whether to adjust charges on ligand atoms.
bool removeHapticDummies =
false; // Whether to remove the dummy atoms representing haptic bonds.
// Such dummies are bonded to the metal with a bond
// that has the _MolFileBondEndPts prop set.
};
class RDKIT_MOLSTANDARDIZE_EXPORT MetalDisconnector {
public:
MetalDisconnector(
const MetalDisconnectorOptions &options = MetalDisconnectorOptions());
MetalDisconnector(const MetalDisconnector &other);
~MetalDisconnector();
ROMol *getMetalNof(); // {return dp_metal_nof;}
ROMol *getMetalNon(); // {return dp_metal_non;}
void setMetalNof(const ROMol &mol);
void setMetalNon(const ROMol &mol);
//! Break covalent bonds between metals and organic atoms under certain
//! conditions.
/*!
<b>Notes:</b>
The algorithm works as follows:
- Disconnect N, O, F from any metal.
- Disconnect other non-metals from transition metals + Al (but not Hg, Ga, Ge,
In, Sn, As, Tl, Pb, Bi, Po).
- For every bond broken, adjust the charges of the begin and end atoms
accordingly.
*/
ROMol *disconnect(const ROMol &mol);
//! overload
/// modifies the molecule in place
void disconnect(RWMol &mol);
void disconnectInPlace(RWMol &mol) { disconnect(mol); };
private:
struct NonMetal {
int cutBonds{0};
std::vector<int> boundMetalIndices;
};
int chargeAdjustment(const Atom *a, int order);
ROMOL_SPTR dp_metal_nof;
ROMOL_SPTR dp_metal_non;
ROMOL_SPTR dp_metalDummy;
const MetalDisconnectorOptions d_options;
void adjust_charges(RDKit::RWMol &mol, std::map<int, NonMetal> &nonMetals,
std::map<int, int> &metalChargeExcess);
// Remove any dummy atoms that are bonded to a metal and have the ENDPTS
// prop. These are assumed to marking a haptic bond from the aotms in
// ENDPTS to the metal, e.g. in ferrocene.
void remove_haptic_dummies(RDKit::RWMol &mol);
}; // class Metal
} // namespace MolStandardize
} // namespace RDKit
#endif
ROMol.h
Defines the primary molecule class ROMol as well as associated typedefs.
RDKit::MolStandardize::MetalDisconnector
Definition Metal.h:44
RDKit::MolStandardize::MetalDisconnector::MetalDisconnector
MetalDisconnector(const MetalDisconnectorOptions &options=MetalDisconnectorOptions())
RDKit::MolStandardize::MetalDisconnector::getMetalNof
ROMol * getMetalNof()
RDKit::MolStandardize::MetalDisconnector::disconnect
void disconnect(RWMol &mol)
RDKit::MolStandardize::MetalDisconnector::getMetalNon
ROMol * getMetalNon()
RDKit::MolStandardize::MetalDisconnector::setMetalNon
void setMetalNon(const ROMol &mol)
RDKit::MolStandardize::MetalDisconnector::MetalDisconnector
MetalDisconnector(const MetalDisconnector &other)
RDKit::MolStandardize::MetalDisconnector::disconnectInPlace
void disconnectInPlace(RWMol &mol)
Definition Metal.h:71
RDKit::MolStandardize::MetalDisconnector::~MetalDisconnector
~MetalDisconnector()
RDKit::MolStandardize::MetalDisconnector::setMetalNof
void setMetalNof(const ROMol &mol)
RDKit::MolStandardize::MetalDisconnector::disconnect
ROMol * disconnect(const ROMol &mol)
RDKit::ROMol
Definition ROMol.h:199
RDKit::RWMol
RWMol is a molecule class that is intended to be edited.
Definition RWMol.h:32
export.h
RDKIT_MOLSTANDARDIZE_EXPORT
#define RDKIT_MOLSTANDARDIZE_EXPORT
Definition export.h:353
RDKit
Std stuff.
Definition Abbreviations.h:19
RDKit::MolStandardize::MetalDisconnectorOptions
Definition Metal.h:34