RDKit: ReCharge.h Source File

| RDKit Open-source cheminformatics and machine learning.

- Main Page
- Namespaces
- Classes
- Files

- File List
- File Members

ReCharge.h
Go to the documentation of this file.
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 #pragma once
11 #include "StructChecker.h"
12 #include "Pattern.h"
13 #include "Utilites.h"
14
15 namespace RDKit {
16 namespace StructureCheck {
17 /*
18 * Returns the total charge of all atoms in molecule.
19 */
20 int TotalCharge(const ROMol &mol);
21
22 class ChargeFix {
23 const StructCheckerOptions &Options;
24 RWMol &Mol;
25 std::vector<unsigned> BondColor;
26 std::vector<unsigned> AtomColor;
27 std::vector<double> AtompKaValue;
28 std::vector<double> AtomOldpKaValue;
29
30 public:
31 ChargeFix(const StructCheckerOptions &op, RWMol &mol)
32 : Options(op), Mol(mol) {
33 resetColors();
34 resetValues();
35 }
36 /*
37 * Removes hydrogens from *mp until desired_charge is reached. The
38 * positions for hydrogen removal are selected by "acidity" combined
39 * with a refinement algorithm. It returns TRUE if molecule could be
40 * neutralized and FALSE if any problem were encountered.
41 * *ndeprot and *nrefine are set to the number of deprotonations
42 * and refinement cycles performed.
43 */
44 bool rechargeMolecule(unsigned &ndeprot, unsigned &nrefine);
45
46 private: // internal helpers:
47 bool setpKaValues();
48 void decrementMarkedCharges();
49 int markMostAcidicAtoms(double &pKa_value, double &gap);
50 int refineAcidicAtoms(std::vector<unsigned> &numbering);
51 void resetColors();
52 void resetValues();
53 };
54 }
55 }
RDKit::StructureCheck::ChargeFix::rechargeMolecule
bool rechargeMolecule(unsigned &ndeprot, unsigned &nrefine)
Utilites.h
RDKit::RWMol
RWMol is a molecule class that is intended to be edited.
Definition: RWMol.h:30
StructChecker.h
Contains the public API of the StructChecker.
RDKit::StructureCheck::TotalCharge
int TotalCharge(const ROMol &mol)
RDKit::StructureCheck::ChargeFix
Definition: ReCharge.h:22
RDKit::StructureCheck::StructCheckerOptions
Structure Check Options.
Definition: StructChecker.h:120
RDKit
Std stuff.
Definition: Atom.h:29
Pattern.h
RDKit::StructureCheck::ChargeFix::ChargeFix
ChargeFix(const StructCheckerOptions &op, RWMol &mol)
Definition: ReCharge.h:31