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
|
/*****************************************************************************
* $CAMITK_LICENCE_BEGIN$
*
* CamiTK - Computer Assisted Medical Intervention ToolKit
* (c) 2001-2025 Univ. Grenoble Alpes, CNRS, Grenoble INP - UGA, TIMC, 38000 Grenoble, France
*
* Visit http://camitk.imag.fr for more information
*
* This file is part of CamiTK.
*
* CamiTK is free software: you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License version 3
* only, as published by the Free Software Foundation.
*
* CamiTK is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License version 3 for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* version 3 along with CamiTK. If not, see <http://www.gnu.org/licenses/>.
*
* $CAMITK_LICENCE_END$
****************************************************************************/
#include "Atom.h"
#include "StructuralComponent.h"
#include "PhysicalModel.h"
// pmlschema includes
#include <Atom.hxx>
//----------------------- Constructors -----------------------
Atom::Atom(PhysicalModel* p) {
properties = new AtomProperties(p);
}
Atom::Atom(PhysicalModel* p, physicalModel::Atom node, unsigned int id) {
properties = new AtomProperties(p, node.atomProperties());
indexInAtoms = id;
}
Atom::Atom(PhysicalModel* p, const double pos[3]) {
properties = new AtomProperties(p, pos);
}
Atom::Atom(PhysicalModel* p, const unsigned int ind) {
properties = new AtomProperties(p, ind);
}
Atom::Atom(PhysicalModel* p, const unsigned int ind, const double pos[3]) {
properties = new AtomProperties(p, ind, pos);
}
//----------------------- Destructor -----------------------
Atom::~Atom() {
delete (AtomProperties*) properties;
properties = nullptr;
}
//----------------------- setIndex -----------------------
bool Atom::setIndex(const unsigned int index) {
// set the property
Structure::setIndex(index);
// tell the physical model about the change (and return true if insertion was ok)
return properties->getPhysicalModel()->addGlobalIndexAtomPair(std::GlobalIndexStructurePair(index, this));
}
//----------------------- getIndexInAtoms -----------------------
unsigned int Atom::getIndexInAtoms() const {
return indexInAtoms;
}
// --------------- xmlPrint ---------------
void Atom::xmlPrint(std::ostream& o, const StructuralComponent* sc) {
// nothing is to be done in particular with sc, but it is here
// because of the Structure::xmlPrint method has to be overriden
// depending on the structure who do the calls, two cases:
if (properties->getPhysicalModel() != nullptr && sc == properties->getPhysicalModel()->getAtoms()) {
// - if it is the physical model atom list: the atom print its properties
// print the atom and its properties
o << "<atom>" << std::endl;
((AtomProperties*) properties)->xmlPrint(o);
o << "</atom>" << std::endl;
}
else {
// - if it is any other structural component: the atom print its ref
o << "<atomRef index=\"" << getIndex() << "\"/>" << std::endl;
}
}
|
