RDKit: StretchBend.h Source File

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StretchBend.h
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1 //
2 // Copyright (C) 2013 Paolo Tosco
3 //
4 // Copyright (C) 2004-2006 Rational Discovery LLC
5 //
6 // @@ All Rights Reserved @@
7 // This file is part of the RDKit.
8 // The contents are covered by the terms of the BSD license
9 // which is included in the file license.txt, found at the root
10 // of the RDKit source tree.
11 //
12 #ifndef __RD_MMFFSTRETCHBEND_H__
13 #define __RD_MMFFSTRETCHBEND_H__
14
15 #include <utility>
16 #include <ForceField/Contrib.h>
17
18 namespace ForceFields {
19 namespace MMFF {
20 class MMFFBond;
21 class MMFFAngle;
22 class MMFFStbn;
23 class MMFFProp;
24
25 //! The angle-bend term for MMFF
26 class StretchBendContrib : public ForceFieldContrib {
27 public:
28 StretchBendContrib() : d_at1Idx(-1), d_at2Idx(-1), d_at3Idx(-1){};
29 //! Constructor
30 /*!
31 The angle is between atom1 - atom2 - atom3
32
33 \param owner pointer to the owning ForceField
34 \param idx1 index of atom1 in the ForceField's positions
35 \param idx2 index of atom2 in the ForceField's positions
36 \param idx3 index of atom3 in the ForceField's positions
37 \param angleType MMFF type of the angle (as an unsigned int)
38
39 */
40 StretchBendContrib(ForceField *owner, const unsigned int idx1,
41 const unsigned int idx2, const unsigned int idx3,
42 const MMFFStbn *mmffStbnParams,
43 const MMFFAngle *mmffAngleParams,
44 const MMFFBond *mmffBondParams1,
45 const MMFFBond *mmffBondParams2);
46
47 double getEnergy(double *pos) const;
48 void getGrad(double *pos, double *grad) const;
49 virtual StretchBendContrib *copy() const {
50 return new StretchBendContrib(*this);
51 };
52
53 private:
54 int d_at1Idx, d_at2Idx, d_at3Idx;
55 double d_restLen1, d_restLen2, d_theta0;
56 std::pair<double, double> d_forceConstants;
57 };
58 namespace Utils {
59 //! returns the std::pair of stretch-bend force constants for an angle
60 std::pair<double, double> calcStbnForceConstants(
61 const MMFFStbn *mmffStbnParams);
62 //! calculates and returns the stretch-bending MMFF energy
63 std::pair<double, double> calcStretchBendEnergy(
64 const double deltaDist1, const double deltaDist2, const double deltaTheta,
65 const std::pair<double, double> forceConstants);
66 }
67 }
68 }
69 #endif
ForceFields::MMFF::StretchBendContrib::getEnergy
double getEnergy(double *pos) const
returns our contribution to the energy of a position
ForceFields::MMFF::MMFFAngle
class to store MMFF parameters for angle bending
Definition: MMFF/Params.h:110
ForceFields::ForceFieldContrib
abstract base class for contributions to ForceFields
Definition: Contrib.h:17
Contrib.h
ForceFields
Definition: TorsionAngleM6.h:23
ForceFields::MMFF::Utils::calcStbnForceConstants
std::pair< double, double > calcStbnForceConstants(const MMFFStbn *mmffStbnParams)
returns the std::pair of stretch-bend force constants for an angle
ForceFields::MMFF::MMFFStbn
class to store MMFF parameters for stretch-bending
Definition: MMFF/Params.h:117
ForceFields::MMFF::MMFFBond
class to store MMFF parameters for bond stretching
Definition: MMFF/Params.h:86
ForceFields::MMFF::StretchBendContrib::StretchBendContrib
StretchBendContrib()
Definition: StretchBend.h:28
ForceFields::MMFF::StretchBendContrib::getGrad
void getGrad(double *pos, double *grad) const
calculates our contribution to the gradients of a position
ForceFields::MMFF::StretchBendContrib
The angle-bend term for MMFF.
Definition: StretchBend.h:26
ForceFields::MMFF::StretchBendContrib::copy
virtual StretchBendContrib * copy() const
return a copy
Definition: StretchBend.h:49
ForceFields::ForceField
A class to store forcefields and handle minimization.
Definition: ForceField.h:56
ForceFields::MMFF::Utils::calcStretchBendEnergy
std::pair< double, double > calcStretchBendEnergy(const double deltaDist1, const double deltaDist2, const double deltaTheta, const std::pair< double, double > forceConstants)
calculates and returns the stretch-bending MMFF energy