UFF/AtomTyper.h
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//
// Copyright (C) 2004-2006 Rational Discovery LLC
//
// @@ 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 <RDGeneral/export.h>
#ifndef _RD_UFFATOMTYPER_H__
#define _RD_UFFATOMTYPER_H__
#include <vector>
#include <string>
#include <ForceField/UFF/Params.h>
namespace ForceFields {
namespace UFF {
class AtomicParams;
}
} // namespace ForceFields
namespace RDKit {
class ROMol;
class Atom;
namespace UFF {
typedef std::vector<const ForceFields::UFF::AtomicParams *> AtomicParamVect;
RDKIT_FORCEFIELDHELPERS_EXPORT std::pair<AtomicParamVect, bool> getAtomTypes(
const ROMol &mol, const std::string &paramData = "");
RDKIT_FORCEFIELDHELPERS_EXPORT bool getUFFBondStretchParams(
const ROMol &mol, unsigned int idx1, unsigned int idx2,
ForceFields::UFF::UFFBond &uffBondStretchParams);
RDKIT_FORCEFIELDHELPERS_EXPORT bool getUFFAngleBendParams(
const ROMol &mol, unsigned int idx1, unsigned int idx2, unsigned int idx3,
ForceFields::UFF::UFFAngle &uffAngleBendParams);
RDKIT_FORCEFIELDHELPERS_EXPORT bool getUFFTorsionParams(
const ROMol &mol, unsigned int idx1, unsigned int idx2, unsigned int idx3,
unsigned int idx4, ForceFields::UFF::UFFTor &uffTorsionParams);
RDKIT_FORCEFIELDHELPERS_EXPORT bool getUFFInversionParams(
const ROMol &mol, unsigned int idx1, unsigned int idx2, unsigned int idx3,
unsigned int idx4, ForceFields::UFF::UFFInv &uffInversionParams);
RDKIT_FORCEFIELDHELPERS_EXPORT bool getUFFVdWParams(
const ROMol &mol, unsigned int idx1, unsigned int idx2,
ForceFields::UFF::UFFVdW &uffVdWParams);
namespace Tools {
// these functions are primarily exposed so they can be tested.
RDKIT_FORCEFIELDHELPERS_EXPORT void addAtomChargeFlags(
const Atom *atom, std::string &atomKey, bool tolerateChargeMismatch = true);
RDKIT_FORCEFIELDHELPERS_EXPORT std::string getAtomLabel(const Atom *atom);
} // namespace Tools
} // namespace UFF
} // namespace RDKit
#endif
Params.h
ForceFields::UFF::AtomicParams
class to store atomic parameters for the Universal Force Field
Definition: UFF/Params.h:73
ForceFields::UFF::UFFAngle
class to store UFF parameters for angle bending
Definition: UFF/Params.h:47
ForceFields::UFF::UFFBond
class to store UFF parameters for bond stretching
Definition: UFF/Params.h:40
ForceFields::UFF::UFFInv
class to store UFF parameters for inversions
Definition: UFF/Params.h:60
ForceFields::UFF::UFFTor
class to store UFF parameters for torsions
Definition: UFF/Params.h:54
ForceFields::UFF::UFFVdW
class to store UFF parameters for van der Waals interactions
Definition: UFF/Params.h:66
RDKit::Atom
The class for representing atoms.
Definition: Atom.h:68
RDKit::ROMol
Definition: ROMol.h:178
export.h
RDKIT_FORCEFIELDHELPERS_EXPORT
#define RDKIT_FORCEFIELDHELPERS_EXPORT
Definition: export.h:185
ForceFields
Definition: TorsionAngleM6.h:24
RDKit::UFF::Tools::getAtomLabel
RDKIT_FORCEFIELDHELPERS_EXPORT std::string getAtomLabel(const Atom *atom)
RDKit::UFF::Tools::addAtomChargeFlags
RDKIT_FORCEFIELDHELPERS_EXPORT void addAtomChargeFlags(const Atom *atom, std::string &atomKey, bool tolerateChargeMismatch=true)
RDKit::UFF::getUFFVdWParams
RDKIT_FORCEFIELDHELPERS_EXPORT bool getUFFVdWParams(const ROMol &mol, unsigned int idx1, unsigned int idx2, ForceFields::UFF::UFFVdW &uffVdWParams)
RDKit::UFF::getUFFAngleBendParams
RDKIT_FORCEFIELDHELPERS_EXPORT bool getUFFAngleBendParams(const ROMol &mol, unsigned int idx1, unsigned int idx2, unsigned int idx3, ForceFields::UFF::UFFAngle &uffAngleBendParams)
RDKit::UFF::getUFFBondStretchParams
RDKIT_FORCEFIELDHELPERS_EXPORT bool getUFFBondStretchParams(const ROMol &mol, unsigned int idx1, unsigned int idx2, ForceFields::UFF::UFFBond &uffBondStretchParams)
RDKit::UFF::getUFFTorsionParams
RDKIT_FORCEFIELDHELPERS_EXPORT bool getUFFTorsionParams(const ROMol &mol, unsigned int idx1, unsigned int idx2, unsigned int idx3, unsigned int idx4, ForceFields::UFF::UFFTor &uffTorsionParams)
RDKit::UFF::getAtomTypes
RDKIT_FORCEFIELDHELPERS_EXPORT std::pair< AtomicParamVect, bool > getAtomTypes(const ROMol &mol, const std::string &paramData="")
RDKit::UFF::AtomicParamVect
std::vector< const ForceFields::UFF::AtomicParams * > AtomicParamVect
Definition: UFF/AtomTyper.h:28
RDKit::UFF::getUFFInversionParams
RDKIT_FORCEFIELDHELPERS_EXPORT bool getUFFInversionParams(const ROMol &mol, unsigned int idx1, unsigned int idx2, unsigned int idx3, unsigned int idx4, ForceFields::UFF::UFFInv &uffInversionParams)
RDKit
Std stuff.
Definition: Abbreviations.h:18
RDKit::paramData
std::string paramData