mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-05 22:04:27 +08:00
c08ea49bda
* - enable building DLLs on Windows * - export.h and test.h are now auto-generated by CMake
57 lines
1.6 KiB
C++
57 lines
1.6 KiB
C++
//
|
|
// Copyright (C) 2016 Novartis Institutes for BioMedical Research
|
|
//
|
|
// @@ 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.
|
|
//
|
|
#include <RDBoost/export.h>
|
|
#pragma once
|
|
#include "StructChecker.h"
|
|
#include "Pattern.h"
|
|
#include "Utilites.h"
|
|
|
|
namespace RDKit {
|
|
namespace StructureCheck {
|
|
/*
|
|
* Returns the total charge of all atoms in molecule.
|
|
*/
|
|
int TotalCharge(const ROMol &mol);
|
|
|
|
class RDKIT_STRUCTCHECKER_EXPORT ChargeFix {
|
|
const StructCheckerOptions &Options;
|
|
RWMol &Mol;
|
|
std::vector<unsigned> BondColor;
|
|
std::vector<unsigned> AtomColor;
|
|
std::vector<double> AtompKaValue;
|
|
std::vector<double> AtomOldpKaValue;
|
|
|
|
public:
|
|
ChargeFix(const StructCheckerOptions &op, RWMol &mol)
|
|
: Options(op), Mol(mol) {
|
|
resetColors();
|
|
resetValues();
|
|
}
|
|
/*
|
|
* Removes hydrogens from *mp until desired_charge is reached. The
|
|
* positions for hydrogen removal are selected by "acidity" combined
|
|
* with a refinement algorithm. It returns TRUE if molecule could be
|
|
* neutralized and FALSE if any problem were encountered.
|
|
* *ndeprot and *nrefine are set to the number of deprotonations
|
|
* and refinement cycles performed.
|
|
*/
|
|
bool rechargeMolecule(unsigned &ndeprot, unsigned &nrefine);
|
|
|
|
private: // internal helpers:
|
|
bool setpKaValues();
|
|
void decrementMarkedCharges();
|
|
int markMostAcidicAtoms(double &pKa_value, double &gap);
|
|
int refineAcidicAtoms(std::vector<unsigned> &numbering);
|
|
void resetColors();
|
|
void resetValues();
|
|
};
|
|
}
|
|
}
|