RDKit
Open-source cheminformatics and machine learning.
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 
18 namespace ForceFields {
19 namespace UFF {
20 class AtomicParams;
21 }
22 } // namespace ForceFields
23 namespace RDKit {
24 class ROMol;
25 class 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 = "");
33  const ROMol &mol, unsigned int idx1, unsigned int idx2,
34  ForceFields::UFF::UFFBond &uffBondStretchParams);
36  const ROMol &mol, unsigned int idx1, unsigned int idx2, unsigned int idx3,
37  ForceFields::UFF::UFFAngle &uffAngleBendParams);
39  const ROMol &mol, unsigned int idx1, unsigned int idx2, unsigned int idx3,
40  unsigned int idx4, ForceFields::UFF::UFFTor &uffTorsionParams);
42  const ROMol &mol, unsigned int idx1, unsigned int idx2, unsigned int idx3,
43  unsigned int idx4, ForceFields::UFF::UFFInv &uffInversionParams);
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.
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
RDKit::UFF::Tools::addAtomChargeFlags
RDKIT_FORCEFIELDHELPERS_EXPORT void addAtomChargeFlags(const Atom *atom, std::string &atomKey, bool tolerateChargeMismatch=true)
RDKit::UFF::AtomicParamVect
std::vector< const ForceFields::UFF::AtomicParams * > AtomicParamVect
Definition: UFF/AtomTyper.h:28
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)
ForceFields::UFF::UFFVdW
class to store UFF parameters for van der Waals interactions
Definition: UFF/Params.h:66
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
RDKit::Atom
The class for representing atoms.
Definition: Atom.h:69
RDKit::ROMol
Definition: ROMol.h:171
ForceFields::UFF::UFFTor
class to store UFF parameters for torsions
Definition: UFF/Params.h:54
RDKit::paramData
std::string paramData
RDKit::UFF::getUFFVdWParams
RDKIT_FORCEFIELDHELPERS_EXPORT bool getUFFVdWParams(const ROMol &mol, unsigned int idx1, unsigned int idx2, ForceFields::UFF::UFFVdW &uffVdWParams)
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)
ForceFields::UFF::UFFAngle
class to store UFF parameters for angle bending
Definition: UFF/Params.h:47
ForceFields
Definition: TorsionAngleM6.h:24
RDKit::UFF::getUFFAngleBendParams
RDKIT_FORCEFIELDHELPERS_EXPORT bool getUFFAngleBendParams(const ROMol &mol, unsigned int idx1, unsigned int idx2, unsigned int idx3, ForceFields::UFF::UFFAngle &uffAngleBendParams)
Params.h
RDKit
Std stuff.
Definition: Atom.h:30
RDKit::UFF::Tools::getAtomLabel
RDKIT_FORCEFIELDHELPERS_EXPORT std::string getAtomLabel(const Atom *atom)
ForceFields::UFF::AtomicParams
class to store atomic parameters for the Universal Force Field
Definition: UFF/Params.h:73
RDKIT_FORCEFIELDHELPERS_EXPORT
#define RDKIT_FORCEFIELDHELPERS_EXPORT
Definition: export.h:268
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)
export.h