1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
|
// $Id$
//
// Copyright (C) 2005-2006 Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <ForceField/ForceField.h>
#include <GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h>
#include <boost/shared_ptr.hpp>
#include <vector>
#include <algorithm>
#include <Geometry/point.h>
namespace ForceFields {
class PyForceField {
public:
PyForceField( ForceField *f) : field(f) {};
~PyForceField() {
//std::cerr << " *** destroy PyForce field " << std::endl;
field.reset();
//std::cerr << " *** reset DONE" << std::endl;
extraPoints.clear();
//std::cerr << " *** destroy PyForce field DONE" << std::endl;
}
int addExtraPoint(double x,double y,double z,bool fixed=true){
RDGeom::Point3D *pt=new RDGeom::Point3D(x,y,z);
PRECONDITION(this->field,"no force field");
this->extraPoints.push_back(boost::shared_ptr<RDGeom::Point3D>(pt));
unsigned int ptIdx = this->extraPoints.size()-1;
RDGeom::Point3D *ptr=this->extraPoints[ptIdx].get();
this->field->positions().push_back(ptr);
int idx=this->field->positions().size();
if(fixed){
this->field->fixedPoints().push_back(idx-1);
}
return idx;
}
double calcEnergy() {
PRECONDITION(this->field,"no force field");
return this->field->calcEnergy();
}
int minimize(int maxIts,double forceTol,double energyTol){
PRECONDITION(this->field,"no force field");
return this->field->minimize(maxIts,forceTol,energyTol);
}
void initialize() {
PRECONDITION(this->field,"no force field");
this->field->initialize();
}
//private:
std::vector< boost::shared_ptr<RDGeom::Point3D> > extraPoints;
boost::shared_ptr<ForceField> field;
};
class PyMMFFMolProperties {
public:
PyMMFFMolProperties(RDKit::MMFF::MMFFMolProperties *mp) : mmffMolProperties(mp) {};
~PyMMFFMolProperties() {};
unsigned int getMMFFAtomType(unsigned int idx) {
return (unsigned int)(mmffMolProperties->getMMFFAtomType(idx));
};
double getMMFFFormalCharge(unsigned int idx) {
return mmffMolProperties->getMMFFFormalCharge(idx);
};
double getMMFFPartialCharge(unsigned int idx) {
return mmffMolProperties->getMMFFPartialCharge(idx);
};
void setMMFFDielectricModel(boost::uint8_t dielModel)
{
mmffMolProperties->setMMFFDielectricModel(dielModel);
};
void setMMFFDielectricConstant(double dielConst)
{
mmffMolProperties->setMMFFDielectricConstant(dielConst);
};
void setMMFFBondTerm(bool state)
{
mmffMolProperties->setMMFFBondTerm(state);
};
void setMMFFAngleTerm(const bool state)
{
mmffMolProperties->setMMFFAngleTerm(state);
};
void setMMFFStretchBendTerm(const bool state)
{
mmffMolProperties->setMMFFStretchBendTerm(state);
};
void setMMFFOopTerm(const bool state)
{
mmffMolProperties->setMMFFOopTerm(state);
};
void setMMFFTorsionTerm(const bool state)
{
mmffMolProperties->setMMFFTorsionTerm(state);
};
void setMMFFVdWTerm(const bool state)
{
mmffMolProperties->setMMFFVdWTerm(state);
};
void setMMFFEleTerm(const bool state)
{
mmffMolProperties->setMMFFEleTerm(state);
};
void setMMFFVariant(std::string mmffVariant)
{
mmffMolProperties->setMMFFVariant(mmffVariant);
};
void setMMFFVerbosity(unsigned int verbosity)
{
mmffMolProperties->setMMFFVerbosity(verbosity);
};
boost::shared_ptr<RDKit::MMFF::MMFFMolProperties> mmffMolProperties;
};
}
|
