mirror of
https://github.com/schrodinger/pymol-open-source.git
synced 2026-06-07 20:44:23 +08:00
f3c0419654
- Add `pbc` argument to cmd.rebond() - Refactor ObjectMoleculeConnect - Add support for OpenMP
86 lines
2.4 KiB
C++
86 lines
2.4 KiB
C++
|
|
/*
|
|
A* -------------------------------------------------------------------
|
|
B* This file contains source code for the PyMOL computer program
|
|
C* Copyright (c) Schrodinger, LLC.
|
|
D* -------------------------------------------------------------------
|
|
E* It is unlawful to modify or remove this copyright notice.
|
|
F* -------------------------------------------------------------------
|
|
G* Please see the accompanying LICENSE file for further information.
|
|
H* -------------------------------------------------------------------
|
|
I* Additional authors of this source file include:
|
|
-*
|
|
-*
|
|
-*
|
|
Z* -------------------------------------------------------------------
|
|
*/
|
|
#ifndef _H_Crystal
|
|
#define _H_Crystal
|
|
|
|
#include "os_python.h"
|
|
|
|
class CGO;
|
|
|
|
/**
|
|
* Representation of a unit cell.
|
|
*
|
|
* Calling setDims() or setAngles() will define an x-axis and xy-plane aligned
|
|
* coordinate system. Calling setFracToReal() can define an arbitrarily oriented
|
|
* coordinate system.
|
|
*/
|
|
struct CCrystal {
|
|
PyMOLGlobals* G;
|
|
|
|
private:
|
|
float Dim[3] = {1.0, 1.0, 1.0};
|
|
float Angle[3] = {90.0, 90.0, 90.0}; /* stored in degrees for convenience */
|
|
float RealToFrac[9];
|
|
float FracToReal[9];
|
|
|
|
bool m_RealToFracValid = false;
|
|
bool m_FracToRealValid = false;
|
|
|
|
void invalidateMatrices()
|
|
{
|
|
m_RealToFracValid = false;
|
|
m_FracToRealValid = false;
|
|
}
|
|
|
|
public:
|
|
/// Cell edge lengths in Angstroms (a, b, c)
|
|
const float* dims() const { return Dim; }
|
|
void setDims(const float*);
|
|
void setDims(float, float, float);
|
|
|
|
/// Cell angles in degrees (alpha, beta, gamma)
|
|
const float* angles() const { return Angle; }
|
|
void setAngles(const float*);
|
|
void setAngles(float, float, float);
|
|
|
|
/// 3x3 transformation matrix from cartesian space to fractional space
|
|
const float* realToFrac() const;
|
|
|
|
/// 3x3 transformation matrix from fractional space to cartesian space
|
|
const float* fracToReal() const;
|
|
|
|
/// Set the fracToReal() matrix. Also updates all other parameters
|
|
/// (realToFrac(), dims(), angles()).
|
|
void setFracToReal(const float*);
|
|
|
|
/// Unit cell volume in Angstrom^3
|
|
float unitCellVolume() const;
|
|
|
|
/// True if this cell is an orthogonal 1x1x1 or is singular
|
|
bool isSuspicious() const;
|
|
|
|
CCrystal(PyMOLGlobals* GParam);
|
|
|
|
friend void CrystalDump(const CCrystal*);
|
|
friend int CrystalFromPyList(CCrystal*, PyObject*);
|
|
friend PyObject* CrystalAsPyList(const CCrystal*);
|
|
};
|
|
|
|
CGO* CrystalGetUnitCellCGO(const CCrystal* I);
|
|
|
|
#endif
|