/usr/include/avogadro/zmatrix.h is in libavogadro-dev 1.1.1-0ubuntu7.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 | /**********************************************************************
ZMatrix - Class to store a z matrix
Copyright (C) 2009 Marcus D. Hanwell
This file is part of the Avogadro molecular editor project.
For more information, see <http://avogadro.openmolecules.net/>
Avogadro is free software; you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
the Free Software Foundation; either version 2.1 of the License, or
(at your option) any later version.
Avogadro 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 General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
02110-1301, USA.
**********************************************************************/
#ifndef ZMATRIX_H
#define ZMATRIX_H
#include "global.h"
#include <QObject>
#include <QList>
namespace Avogadro {
class Molecule;
/**
* @class ZMatrix zmatrix.h <avogadro/zmatrix.h>
* @brief Z-matrix internal coordinates for a molecule.
* @author Marcus D. Hanwell
*
* The ZMatrix class is a Primitive subclass that provides a ZMatrix object.
* All z matrices must be owned by a Molecule. It should also be removed by
* the Molecule that owns it.
*/
class A_EXPORT ZMatrix : public QObject
{
Q_OBJECT
public:
/**
* Constructor. Parent should always be a Molecule.
*/
explicit ZMatrix(QObject *parent = 0);
/**
* Destructor.
*/
~ZMatrix();
/**
* Add a new line to the z-matrix.
* @param row Row to add, default to adding a new row at the end.
*/
void addRow(int row = -1);
/**
* @return The number of rows in the z-matrix.
*/
int rows();
/**
* Set the atom that the z matrix item is bonded to.
* @param atom1 The first atom in the bond
* @param atom2 The second atom in the bond
*/
void setBond(int atom1, int atom2);
/**
* Update the atoms of the z matrix according to the z matrix
*/
void update();
// private:
/**
* Struct storing a z-matrix
*/
struct zItem
{
unsigned int atomIndex; // Unique ID of the atom
short atomicNumber; // The atomic number of the entry
double lengths[3]; // Length, angle, dihedral
short indices[3]; // z-matrix reference to other atoms in the matrix
};
QList<zItem> m_items;
Molecule *m_molecule;
Q_SIGNALS:
void rowAdded(int row);
};
inline int ZMatrix::rows()
{
return m_items.size();
}
} // End namespace Avogadro
#endif // ZMATRIX_H
|