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
|
#include "bind_valist.hpp"
void Valist_load(Valist *self,
int size,
std::vector<double> x,
std::vector<double> y,
std::vector<double> z,
std::vector<double> chg,
std::vector<double> rad)
{
int i, j;
double pos[3];
Vatom *atom;
VASSERT(self != VNULL);
self->atoms = static_cast<Vatom*>(Vmem_malloc(self->vmem, size, sizeof(Vatom)));
self->number = size;
for (i = 0; i < size; i++) {
pos[0] = x[i];
pos[1] = y[i];
pos[2] = z[i];
Vatom_setCharge(&(self->atoms[i]), chg[i]);
Vatom_setRadius(&(self->atoms[i]), rad[i]);
Vatom_setPosition(&(self->atoms[i]), pos);
Vatom_setAtomID(&(self->atoms[i]), i);
}
self->center[0] = 0.0;
self->center[1] = 0.0;
self->center[2] = 0.0;
self->maxrad = 0.0;
self->charge = 0.0;
/* Reset stat variables */
atom = &(self->atoms[0]);
for (i = 0; i < 3; i++) {
self->maxcrd[i] = self->mincrd[i] = atom->position[i];
}
self->maxrad = atom->radius;
for (i = 0; i < self->number; i++) {
atom = &(self->atoms[i]);
for (j = 0; j < 3; j++) {
if (atom->position[j] < self->mincrd[j])
self->mincrd[j] = atom->position[j];
if (atom->position[j] > self->maxcrd[j])
self->maxcrd[j] = atom->position[j];
}
if (atom->radius > self->maxrad) self->maxrad = atom->radius;
self->charge = self->charge + atom->charge;
}
self->center[0] = 0.5 * (self->maxcrd[0] + self->mincrd[0]);
self->center[1] = 0.5 * (self->maxcrd[1] + self->mincrd[1]);
self->center[2] = 0.5 * (self->maxcrd[2] + self->mincrd[2]);
}
/**
* @brief Class to bind sValist to C++ STL types for better interfacing
* with python.
*/
struct Valist_glue : public Valist
{
std::array<double, 3> center; /**< Molecule center (xmin - xmax)/2, etc.*/
std::array<double, 3> mincrd; /**< Minimum coordinates */
std::array<double, 3> maxcrd; /**< Maximum coordinates */
std::vector<Vatom> vatoms; /**< Atom list */
};
void bind_valist(py::module &m)
{
py::class_<Valist_glue>(m, "Valist")
.def(py::init<>())
.def("__del__", [](Valist* self) { Valist_dtor(&self); })
.def("load", &Valist_load)
.def("getAtomList" , &Valist_getAtomList)
.def("getCenterX" , &Valist_getCenterX)
.def("getCenterY" , &Valist_getCenterY)
.def("getCenterZ" , &Valist_getCenterZ)
.def("getNumberAtoms" , &Valist_getNumberAtoms)
.def("getAtom" , &Valist_getAtom)
.def("memChk" , &Valist_memChk)
.def("readPQR" , &Valist_readPQR)
.def("readPDB" , &Valist_readPDB)
.def("readXML" , &Valist_readXML)
.def_readwrite("number" , &Valist::number)
.def_readwrite("center" , &Valist_glue::center)
.def_readwrite("mincrd" , &Valist_glue::mincrd)
.def_readwrite("maxcrd" , &Valist_glue::maxcrd)
.def_readwrite("maxrad" , &Valist::maxrad)
.def_readwrite("charge" , &Valist::charge)
.def_readwrite("vatoms" , &Valist_glue::vatoms)
.def_readwrite("vmem" , &Valist::vmem);
}
|
