RDKit: Params.h Source File

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UFF/Params.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 #ifndef __RD_UFFPARAMS_H__
11 #define __RD_UFFPARAMS_H__
12
13 #include <string>
14 #include <cmath>
15 #include <map>
16
17 #ifndef M_PI
18 #define M_PI 3.14159265358979323846
19 #endif
20
21 namespace ForceFields {
22 namespace UFF {
23
24 const double DEG2RAD = M_PI / 180.0;
25 const double RAD2DEG = 180.0 / M_PI;
26 inline bool isDoubleZero(const double x) {
27 return ((x < 1.0e-10) && (x > -1.0e-10));
28 }
29 inline void clipToOne(double &x) {
30 if (x > 1.0) {
31 x = 1.0;
32 } else if (x < -1.0) {
33 x = -1.0;
34 }
35 }
36
37 //! class to store UFF parameters for bond stretching
38 class UFFBond {
39 public:
40 double kb;
41 double r0;
42 };
43
44 //! class to store UFF parameters for angle bending
45 class UFFAngle {
46 public:
47 double ka;
48 double theta0;
49 };
50
51 //! class to store UFF parameters for torsions
52 class UFFTor {
53 public:
54 double V;
55 };
56
57 //! class to store UFF parameters for inversions
58 class UFFInv {
59 public:
60 double K;
61 };
62
63 //! class to store UFF parameters for van der Waals interactions
64 class UFFVdW {
65 public:
66 double x_ij;
67 double D_ij;
68 };
69
70 //! class to store atomic parameters for the Universal Force Field
71 class AtomicParams {
72 public:
73 double r1; //!< valence bond radius
74 double theta0; //!< valence angle
75 double x1; //!< vdW characteristic length
76 double D1; //!< vdW atomic energy
77 double zeta; //!< vdW scaling term
78 double Z1; //!< effective charge
79 double V1; //!< sp3 torsional barrier parameter
80 double U1; //!< torsional contribution for sp2-sp3 bonds
81 double GMP_Xi; //!< GMP Electronegativity;
82 double GMP_Hardness; //!< GMP Hardness
83 double GMP_Radius; //!< GMP Radius value
84 };
85
86 namespace Params {
87 const double lambda = 0.1332; //!< scaling factor for rBO correction
88 const double G = 332.06; //!< bond force constant prefactor
89 const double amideBondOrder =
90 1.41; //!< special case bond order for amide C-N bonds.
91 };
92
93 //! singleton class for retrieving UFF AtomParams
94 /*!
95 Use the singleton like this:
96
97 \verbatim
98 ParamCollection *params=ParamCollection::getParams();
99 const AtomParams *ap=params("C_3");
100 \endverbatim
101
102 If you have your own parameter data, it can be supplied as a string:
103 \verbatim
104 ParamCollection *params=ParamCollection::getParams(myParamData);
105 const AtomParams *ap=params("C_3");
106 \endverbatim
107 You are responsible for making sure that the data is in the correct
108 format (see Params.cpp for an example).
109
110 */
111 class ParamCollection {
112 public:
113 //! gets a pointer to the singleton ParamCollection
114 /*!
115 \param paramData (optional) a string with parameter data. See
116 below for more information about this argument
117
118 \return a pointer to the singleton ParamCollection
119
120 <b>Notes:</b>
121 - do <b>not</b> delete the pointer returned here
122 - if the singleton ParamCollection has already been instantiated and
123 \c paramData is empty, the singleton will be returned.
124 - if \c paramData is empty and the singleton ParamCollection has
125 not yet been instantiated, the default UFF parameters (from Params.cpp)
126 will be used.
127 - if \c paramData is supplied, a new singleton will be instantiated.
128 The current instantiation (if there is one) will be deleted.
129 */
130 static ParamCollection *getParams(const std::string &paramData = "");
131 //! Looks up the parameters for a particular UFF key and returns them.
132 /*!
133 \return a pointer to the AtomicParams object, NULL on failure.
134 */
135 const AtomicParams *operator()(const std::string &symbol) const {
136 std::map<std::string, AtomicParams>::const_iterator res;
137 res = d_params.find(symbol);
138 if (res != d_params.end()) {
139 return &((*res).second);
140 }
141 return 0;
142 }
143
144 private:
145 //! to force this to be a singleton, the constructor must be private
146 ParamCollection(std::string paramData);
147 static class ParamCollection *ds_instance; //!< the singleton
148 std::map<std::string, AtomicParams> d_params; //!< the parameter map
149 };
150 }
151 }
152 #endif
ForceFields::UFF::AtomicParams
class to store atomic parameters for the Universal Force Field
Definition: UFF/Params.h:71
ForceFields::UFF::UFFVdW::D_ij
double D_ij
Definition: UFF/Params.h:67
ForceFields::UFF::AtomicParams::theta0
double theta0
valence angle
Definition: UFF/Params.h:74
ForceFields::UFF::DEG2RAD
const double DEG2RAD
Definition: UFF/Params.h:24
ForceFields::UFF::Params::G
const double G
bond force constant prefactor
Definition: UFF/Params.h:88
ForceFields::UFF::AtomicParams::r1
double r1
valence bond radius
Definition: UFF/Params.h:73
ForceFields::UFF::Params::amideBondOrder
const double amideBondOrder
special case bond order for amide C-N bonds.
Definition: UFF/Params.h:89
ForceFields::UFF::Params::lambda
const double lambda
scaling factor for rBO correction
Definition: UFF/Params.h:87
ForceFields::UFF::isDoubleZero
bool isDoubleZero(const double x)
Definition: UFF/Params.h:26
ForceFields::UFF::RAD2DEG
const double RAD2DEG
Definition: UFF/Params.h:25
ForceFields::UFF::AtomicParams::U1
double U1
torsional contribution for sp2-sp3 bonds
Definition: UFF/Params.h:80
M_PI
#define M_PI
Definition: UFF/Params.h:18
ForceFields::UFF::UFFInv::K
double K
Definition: UFF/Params.h:60
RDKit::paramData
std::string paramData
ForceFields::UFF::ParamCollection
singleton class for retrieving UFF AtomParams
Definition: UFF/Params.h:111
ForceFields
Definition: TorsionAngleM6.h:23
ForceFields::UFF::UFFAngle::ka
double ka
Definition: UFF/Params.h:47
ForceFields::UFF::AtomicParams::V1
double V1
sp3 torsional barrier parameter
Definition: UFF/Params.h:79
ForceFields::UFF::ParamCollection::operator()
const AtomicParams * operator()(const std::string &symbol) const
Looks up the parameters for a particular UFF key and returns them.
Definition: UFF/Params.h:135
ForceFields::UFF::UFFVdW
class to store UFF parameters for van der Waals interactions
Definition: UFF/Params.h:64
ForceFields::UFF::AtomicParams::GMP_Xi
double GMP_Xi
GMP Electronegativity;.
Definition: UFF/Params.h:81
ForceFields::UFF::UFFBond
class to store UFF parameters for bond stretching
Definition: UFF/Params.h:38
ForceFields::UFF::UFFAngle
class to store UFF parameters for angle bending
Definition: UFF/Params.h:45
ForceFields::UFF::UFFInv
class to store UFF parameters for inversions
Definition: UFF/Params.h:58
ForceFields::UFF::UFFAngle::theta0
double theta0
Definition: UFF/Params.h:48
ForceFields::UFF::AtomicParams::x1
double x1
vdW characteristic length
Definition: UFF/Params.h:75
ForceFields::UFF::UFFVdW::x_ij
double x_ij
Definition: UFF/Params.h:66
ForceFields::UFF::AtomicParams::GMP_Hardness
double GMP_Hardness
GMP Hardness.
Definition: UFF/Params.h:82
ForceFields::UFF::UFFBond::r0
double r0
Definition: UFF/Params.h:41
ForceFields::UFF::AtomicParams::Z1
double Z1
effective charge
Definition: UFF/Params.h:78
ForceFields::UFF::UFFTor
class to store UFF parameters for torsions
Definition: UFF/Params.h:52
ForceFields::UFF::UFFTor::V
double V
Definition: UFF/Params.h:54
ForceFields::UFF::UFFBond::kb
double kb
Definition: UFF/Params.h:40
ForceFields::UFF::AtomicParams::GMP_Radius
double GMP_Radius
GMP Radius value.
Definition: UFF/Params.h:83
ForceFields::UFF::AtomicParams::D1
double D1
vdW atomic energy
Definition: UFF/Params.h:76
ForceFields::UFF::clipToOne
void clipToOne(double &x)
Definition: UFF/Params.h:29
ForceFields::UFF::AtomicParams::zeta
double zeta
vdW scaling term
Definition: UFF/Params.h:77