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.
//
#ifndef _RD_UFFATOMTYPER_H__
#define _RD_UFFATOMTYPER_H__
#include <vector>
#include <string>
#include <ForceField/UFF/Params.h>
namespace ForceFields {
namespace UFF {
class AtomicParams;
}
}
namespace RDKit {
class ROMol;
class Atom;
namespace UFF {
typedef std::vector<const ForceFields::UFF::AtomicParams *> AtomicParamVect;
std::pair<AtomicParamVect, bool> getAtomTypes(
const ROMol &mol, const std::string &paramData = "");
bool getUFFBondStretchParams(const ROMol &mol, unsigned int idx1,
unsigned int idx2,
ForceFields::UFF::UFFBond &uffBondStretchParams);
bool getUFFAngleBendParams(const ROMol &mol, unsigned int idx1,
unsigned int idx2, unsigned int idx3,
ForceFields::UFF::UFFAngle &uffAngleBendParams);
bool getUFFTorsionParams(const ROMol &mol, unsigned int idx1, unsigned int idx2,
unsigned int idx3, unsigned int idx4,
ForceFields::UFF::UFFTor &uffTorsionParams);
bool getUFFInversionParams(const ROMol &mol, unsigned int idx1,
unsigned int idx2, unsigned int idx3,
unsigned int idx4,
ForceFields::UFF::UFFInv &uffInversionParams);
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.
void addAtomChargeFlags(const Atom *atom, std::string &atomKey,
bool tolerateChargeMismatch = true);
std::string getAtomLabel(const Atom *atom);
}
}
}
#endif
ForceFields::UFF::AtomicParams
class to store atomic parameters for the Universal Force Field
Definition: UFF/Params.h:71
RDKit::UFF::getUFFVdWParams
bool getUFFVdWParams(const ROMol &mol, unsigned int idx1, unsigned int idx2, ForceFields::UFF::UFFVdW &uffVdWParams)
RDKit::UFF::Tools::getAtomLabel
std::string getAtomLabel(const Atom *atom)
RDKit::UFF::getUFFAngleBendParams
bool getUFFAngleBendParams(const ROMol &mol, unsigned int idx1, unsigned int idx2, unsigned int idx3, ForceFields::UFF::UFFAngle &uffAngleBendParams)
RDKit::ROMol
ROMol is a molecule class that is intended to have a fixed topology.
Definition: ROMol.h:102
RDKit::paramData
std::string paramData
ForceFields
Definition: TorsionAngleM6.h:23
RDKit::UFF::getUFFInversionParams
bool getUFFInversionParams(const ROMol &mol, unsigned int idx1, unsigned int idx2, unsigned int idx3, unsigned int idx4, ForceFields::UFF::UFFInv &uffInversionParams)
Params.h
ForceFields::UFF::UFFVdW
class to store UFF parameters for van der Waals interactions
Definition: UFF/Params.h:64
RDKit::UFF::Tools::addAtomChargeFlags
void addAtomChargeFlags(const Atom *atom, std::string &atomKey, bool tolerateChargeMismatch=true)
RDKit
Includes a bunch of functionality for handling Atom and Bond queries.
Definition: Atom.h:28
ForceFields::UFF::UFFBond
class to store UFF parameters for bond stretching
Definition: UFF/Params.h:38
RDKit::UFF::AtomicParamVect
std::vector< const ForceFields::UFF::AtomicParams * > AtomicParamVect
Definition: UFF/AtomTyper.h:27
RDKit::UFF::getUFFBondStretchParams
bool getUFFBondStretchParams(const ROMol &mol, unsigned int idx1, unsigned int idx2, ForceFields::UFF::UFFBond &uffBondStretchParams)
ForceFields::UFF::UFFAngle
class to store UFF parameters for angle bending
Definition: UFF/Params.h:45
RDKit::UFF::getUFFTorsionParams
bool getUFFTorsionParams(const ROMol &mol, unsigned int idx1, unsigned int idx2, unsigned int idx3, unsigned int idx4, ForceFields::UFF::UFFTor &uffTorsionParams)
ForceFields::UFF::UFFInv
class to store UFF parameters for inversions
Definition: UFF/Params.h:58
RDKit::UFF::getAtomTypes
std::pair< AtomicParamVect, bool > getAtomTypes(const ROMol &mol, const std::string &paramData="")
ForceFields::UFF::UFFTor
class to store UFF parameters for torsions
Definition: UFF/Params.h:52
RDKit::Atom
The class for representing atoms.
Definition: Atom.h:67