RDKit: AtomTyper.h Source File

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UFF/AtomTyper.h
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1//
2// Copyright (C) 2004-2006 Rational Discovery LLC
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#ifndef _RD_UFFATOMTYPER_H__
12#define _RD_UFFATOMTYPER_H__
13
14#include <vector>
15#include <string>
16#include <ForceField/UFF/Params.h>
17
18namespace ForceFields {
19 namespace UFF {
20class AtomicParams;
21}
22} // namespace ForceFields
23namespace RDKit {
24class ROMol;
25class Atom;
26
27 namespace UFF {
28 typedef std::vector<const ForceFields::UFF::AtomicParams *> AtomicParamVect;
29
30 RDKIT_FORCEFIELDHELPERS_EXPORT std::pair<AtomicParamVect, bool> getAtomTypes(
31 const ROMol &mol, const std::string &paramData = "");
32 RDKIT_FORCEFIELDHELPERS_EXPORT bool getUFFBondStretchParams(
33 const ROMol &mol, unsigned int idx1, unsigned int idx2,
34 ForceFields::UFF::UFFBond &uffBondStretchParams);
35 RDKIT_FORCEFIELDHELPERS_EXPORT bool getUFFAngleBendParams(
36 const ROMol &mol, unsigned int idx1, unsigned int idx2, unsigned int idx3,
37 ForceFields::UFF::UFFAngle &uffAngleBendParams);
38 RDKIT_FORCEFIELDHELPERS_EXPORT bool getUFFTorsionParams(
39 const ROMol &mol, unsigned int idx1, unsigned int idx2, unsigned int idx3,
40 unsigned int idx4, ForceFields::UFF::UFFTor &uffTorsionParams);
41 RDKIT_FORCEFIELDHELPERS_EXPORT bool getUFFInversionParams(
42 const ROMol &mol, unsigned int idx1, unsigned int idx2, unsigned int idx3,
43 unsigned int idx4, ForceFields::UFF::UFFInv &uffInversionParams);
44 RDKIT_FORCEFIELDHELPERS_EXPORT bool getUFFVdWParams(
45 const ROMol &mol, unsigned int idx1, unsigned int idx2,
46 ForceFields::UFF::UFFVdW &uffVdWParams);
47
48 namespace Tools {
49// these functions are primarily exposed so they can be tested.
50 RDKIT_FORCEFIELDHELPERS_EXPORT void addAtomChargeFlags(
51 const Atom *atom, std::string &atomKey, bool tolerateChargeMismatch = true);
52 RDKIT_FORCEFIELDHELPERS_EXPORT std::string getAtomLabel(const Atom *atom);
53} // namespace Tools
54} // namespace UFF
55} // namespace RDKit
56
57#endif
Params.h
ForceFields::UFF::AtomicParams
class to store atomic parameters for the Universal Force Field
Definition UFF/Params.h:68
ForceFields::UFF::UFFAngle
class to store UFF parameters for angle bending
Definition UFF/Params.h:42
ForceFields::UFF::UFFBond
class to store UFF parameters for bond stretching
Definition UFF/Params.h:35
ForceFields::UFF::UFFInv
class to store UFF parameters for inversions
Definition UFF/Params.h:55
ForceFields::UFF::UFFTor
class to store UFF parameters for torsions
Definition UFF/Params.h:49
ForceFields::UFF::UFFVdW
class to store UFF parameters for van der Waals interactions
Definition UFF/Params.h:61
RDKit::Atom
The class for representing atoms.
Definition Atom.h:74
RDKit::ROMol
Definition ROMol.h:199
export.h
RDKIT_FORCEFIELDHELPERS_EXPORT
#define RDKIT_FORCEFIELDHELPERS_EXPORT
Definition export.h:209
ForceFields::UFF
Definition UFF/AtomTyper.h:19
ForceFields
Definition TorsionAngleContribs.h:21
RDKit::UFF::Tools
Definition UFF/AtomTyper.h:48
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
Definition UFF/AtomTyper.h:27
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::getAtomTypes
RDKIT_FORCEFIELDHELPERS_EXPORT std::pair< AtomicParamVect, bool > getAtomTypes(const ROMol &mol, const std::string &paramData="")
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::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:19
RDKit::paramData
std::string paramData