RDKit
Open-source cheminformatics and machine learning.
OopBend.h
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//
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// Copyright (C) 2013 Paolo Tosco
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//
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// Copyright (C) 2004-2006 Rational Discovery LLC
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <
RDGeneral/export.h
>
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#ifndef __RD_MMFFOopBend_H__
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#define __RD_MMFFOopBend_H__
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#include <
ForceField/Contrib.h
>
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#include <
Geometry/point.h
>
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namespace
ForceFields
{
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namespace
MMFF {
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class
MMFFOop;
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//! the out-of-plane term for MMFF
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class
RDKIT_FORCEFIELD_EXPORT
OopBendContrib
:
public
ForceFieldContrib
{
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public
:
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OopBendContrib
() : d_at1Idx(-1), d_at2Idx(-1), d_at3Idx(-1), d_at4Idx(-1){};
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//! Constructor
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/*!
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The Wilson angle is between the vector formed by atom2-atom4
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and the angle formed by atom1-atom2-atom3
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\param owner pointer to the owning ForceField
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\param idx1 index of atom1 in the ForceField's positions
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\param idx2 index of atom2 in the ForceField's positions
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\param idx3 index of atom3 in the ForceField's positions
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\param idx4 index of atom4 in the ForceField's positions
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*/
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OopBendContrib
(
ForceField
*owner,
unsigned
int
idx1,
unsigned
int
idx2,
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unsigned
int
idx3,
unsigned
int
idx4,
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const
MMFFOop
*mmffOopParams);
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double
getEnergy(
double
*pos)
const
;
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void
getGrad(
double
*pos,
double
*grad)
const
;
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virtual
OopBendContrib
*
copy
()
const
{
return
new
OopBendContrib
(*
this
); };
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private
:
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int
d_at1Idx, d_at2Idx, d_at3Idx, d_at4Idx;
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double
d_koop;
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};
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namespace
Utils {
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//! calculates and returns the Wilson angle (in degrees)
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RDKIT_FORCEFIELD_EXPORT
double
calcOopChi
(
const
RDGeom::Point3D
&iPoint,
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const
RDGeom::Point3D
&jPoint,
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const
RDGeom::Point3D
&kPoint,
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const
RDGeom::Point3D
&lPoint);
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//! returns the out-of-plane force constant koop
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RDKIT_FORCEFIELD_EXPORT
double
calcOopBendForceConstant
(
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const
MMFFOop *mmffOopParams);
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//! calculates and returns the out-of-plane MMFF energy
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RDKIT_FORCEFIELD_EXPORT
double
calcOopBendEnergy
(
const
double
chi,
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const
double
koop);
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}
// namespace Utils
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}
// namespace MMFF
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}
// namespace ForceFields
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#endif
ForceFields::MMFF::Utils::calcOopChi
RDKIT_FORCEFIELD_EXPORT double calcOopChi(const RDGeom::Point3D &iPoint, const RDGeom::Point3D &jPoint, const RDGeom::Point3D &kPoint, const RDGeom::Point3D &lPoint)
calculates and returns the Wilson angle (in degrees)
point.h
RDGeom::Point3D
Definition:
point.h:46
ForceFields::MMFF::MMFFOop
class to store MMFF parameters for out-of-plane bending
Definition:
MMFF/Params.h:126
ForceFields::ForceField
A class to store forcefields and handle minimization.
Definition:
ForceField.h:79
ForceFields::MMFF::OopBendContrib::OopBendContrib
OopBendContrib()
Definition:
OopBend.h:26
ForceFields::MMFF::Utils::calcOopBendEnergy
RDKIT_FORCEFIELD_EXPORT double calcOopBendEnergy(const double chi, const double koop)
calculates and returns the out-of-plane MMFF energy
ForceFields::MMFF::Utils::calcOopBendForceConstant
RDKIT_FORCEFIELD_EXPORT double calcOopBendForceConstant(const MMFFOop *mmffOopParams)
returns the out-of-plane force constant koop
ForceFields::ForceFieldContrib
abstract base class for contributions to ForceFields
Definition:
Contrib.h:18
RDKIT_FORCEFIELD_EXPORT
#define RDKIT_FORCEFIELD_EXPORT
Definition:
export.h:255
ForceFields::MMFF::OopBendContrib::copy
virtual OopBendContrib * copy() const
return a copy
Definition:
OopBend.h:43
ForceFields
Definition:
TorsionAngleM6.h:24
Contrib.h
ForceFields::MMFF::OopBendContrib
the out-of-plane term for MMFF
Definition:
OopBend.h:24
export.h
ForceField
MMFF
OopBend.h
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