mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-03 21:44:30 +08:00
ac54eb3209
* reionizer and uncharger and normalizer can now operate in place * add removeUnmatchedAtoms argument to in-place version of runReactant When set to false atoms which are not explicitly removed by the reaction are preserved * Fix a case where transforms were incorrectly updating atomic numbers * add more inplace operations to MolStandardize * support those in the Python layer * support inplace for the rest of the python wrappers * move a few more functions over to the inplace code
97 lines
2.9 KiB
C++
97 lines
2.9 KiB
C++
//
|
|
// 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
|