RDKit: ReCharge.h Source File

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ReCharge.h
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1//
2// Copyright (C) 2016 Novartis Institutes for BioMedical Research
3//
4// @@ All Rights Reserved @@
5// This file is part of the RDKit.
6// The contents are covered by the terms of the BSD license
7// which is included in the file license.txt, found at the root
8// of the RDKit source tree.
9//
10#include <RDGeneral/export.h>
11#pragma once
12#include "StructChecker.h"
13#include "Pattern.h"
14#include "Utilites.h"
15
16namespace RDKit {
17namespace StructureCheck {
18/*
19 * Returns the total charge of all atoms in molecule.
20 */
21 int TotalCharge(const ROMol &mol);
22
23 class RDKIT_STRUCTCHECKER_EXPORT ChargeFix {
24 const StructCheckerOptions &Options;
25 RWMol &Mol;
26 std::vector<unsigned> BondColor;
27 std::vector<unsigned> AtomColor;
28 std::vector<double> AtompKaValue;
29 std::vector<double> AtomOldpKaValue;
30
31 public:
32 ChargeFix(const StructCheckerOptions &op, RWMol &mol)
33 : Options(op), Mol(mol) {
34 resetColors();
35 resetValues();
36 }
37 /*
38 * Removes hydrogens from *mp until desired_charge is reached. The
39 * positions for hydrogen removal are selected by "acidity" combined
40 * with a refinement algorithm. It returns TRUE if molecule could be
41 * neutralized and FALSE if any problem were encountered.
42 * *ndeprot and *nrefine are set to the number of deprotonations
43 * and refinement cycles performed.
44 */
45 bool rechargeMolecule(unsigned &ndeprot, unsigned &nrefine);
46
47 private: // internal helpers:
48 bool setpKaValues();
49 void decrementMarkedCharges();
50 int markMostAcidicAtoms(double &pKa_value, double &gap);
51 int refineAcidicAtoms(std::vector<unsigned> &numbering);
52 void resetColors();
53 void resetValues();
54};
55} // namespace StructureCheck
56} // namespace RDKit
Pattern.h
StructChecker.h
Contains the public API of the StructChecker.
Utilites.h
RDKit::ROMol
Definition ROMol.h:199
RDKit::RWMol
RWMol is a molecule class that is intended to be edited.
Definition RWMol.h:32
RDKit::StructureCheck::ChargeFix::rechargeMolecule
bool rechargeMolecule(unsigned &ndeprot, unsigned &nrefine)
RDKit::StructureCheck::ChargeFix::ChargeFix
ChargeFix(const StructCheckerOptions &op, RWMol &mol)
Definition ReCharge.h:32
export.h
RDKIT_STRUCTCHECKER_EXPORT
#define RDKIT_STRUCTCHECKER_EXPORT
Definition export.h:545
RDKit::StructureCheck
Definition Pattern.h:16
RDKit::StructureCheck::TotalCharge
int TotalCharge(const ROMol &mol)
RDKit
Std stuff.
Definition Abbreviations.h:19
RDKit::StructureCheck::StructCheckerOptions
Definition StructChecker.h:121