*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2019, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
struct t_pbc;
-#define FLAG_DOTS 01
-#define FLAG_VOLUME 02
-#define FLAG_ATOM_AREA 04
+#define FLAG_DOTS 01
+#define FLAG_VOLUME 02
+#define FLAG_ATOM_AREA 04
namespace gmx
{
*/
class SurfaceAreaCalculator
{
- public:
- /*! \brief
- * Initializes a surface area calculator.
- *
- * \throws std::bad_alloc if out of memory.
- */
- SurfaceAreaCalculator();
- ~SurfaceAreaCalculator();
+public:
+ /*! \brief
+ * Initializes a surface area calculator.
+ *
+ * \throws std::bad_alloc if out of memory.
+ */
+ SurfaceAreaCalculator();
+ ~SurfaceAreaCalculator();
- /*! \brief
- * Sets the number of surface dots per sphere to use.
- *
- * This function must be called before calculate() to set the desired
- * accuracy/computational cost.
- */
- void setDotCount(int dotCount);
- /*! \brief
- * Sets the radii of spheres to use in the calculation.
- *
- * \param[in] radius Radius for each atom/sphere.
- *
- * This function must be called before calculate() to set the radii for
- * the spheres. All calculations must use the same set of radii to
- * share the same grid search.
- * These radii are used as-is, without adding any probe radius.
- * The passed array must remain valid for the lifetime of this object.
- *
- * Does not throw.
- */
- void setRadii(const ArrayRef<const real> &radius);
+ /*! \brief
+ * Sets the number of surface dots per sphere to use.
+ *
+ * This function must be called before calculate() to set the desired
+ * accuracy/computational cost.
+ */
+ void setDotCount(int dotCount);
+ /*! \brief
+ * Sets the radii of spheres to use in the calculation.
+ *
+ * \param[in] radius Radius for each atom/sphere.
+ *
+ * This function must be called before calculate() to set the radii for
+ * the spheres. All calculations must use the same set of radii to
+ * share the same grid search.
+ * These radii are used as-is, without adding any probe radius.
+ * The passed array must remain valid for the lifetime of this object.
+ *
+ * Does not throw.
+ */
+ void setRadii(const ArrayRef<const real>& radius);
- /*! \brief
- * Requests calculation of volume.
- *
- * If not called, and FLAG_VOLUME is not passed to calculate(), the
- * volume output is not produced.
- *
- * Does not throw.
- */
- void setCalculateVolume(bool bVolume);
- /*! \brief
- * Requests output of per-atom areas.
- *
- * If not called, and FLAG_ATOM_AREA is not passed to calculate(), the
- * atom area output is not produced.
- *
- * Does not throw.
- */
- void setCalculateAtomArea(bool bAtomArea);
- /*! \brief
- * Requests output of all surface dots.
- *
- * If not called, and FLAG_DOTS is not passed to calculate(), the
- * surface dot output is not produced.
- *
- * Does not throw.
- */
- void setCalculateSurfaceDots(bool bDots);
+ /*! \brief
+ * Requests calculation of volume.
+ *
+ * If not called, and FLAG_VOLUME is not passed to calculate(), the
+ * volume output is not produced.
+ *
+ * Does not throw.
+ */
+ void setCalculateVolume(bool bVolume);
+ /*! \brief
+ * Requests output of per-atom areas.
+ *
+ * If not called, and FLAG_ATOM_AREA is not passed to calculate(), the
+ * atom area output is not produced.
+ *
+ * Does not throw.
+ */
+ void setCalculateAtomArea(bool bAtomArea);
+ /*! \brief
+ * Requests output of all surface dots.
+ *
+ * If not called, and FLAG_DOTS is not passed to calculate(), the
+ * surface dot output is not produced.
+ *
+ * Does not throw.
+ */
+ void setCalculateSurfaceDots(bool bDots);
- /*! \brief
- * Calculates the surface area for a set of positions.
- *
- * \param[in] x Atom positions (sphere centers).
- * \param[in] pbc PBC information (if `NULL`, calculation is done
- * without PBC).
- * \param[in] nat Number of atoms to calculate.
- * \param[in] index Atom indices to include in the calculation.
- * \param[in] flags Additional flags for the calculation.
- * \param[out] area Total surface area (must be non-`NULL`).
- * \param[out] volume Total volume (can be `NULL`).
- * \param[out] at_area Surface area for each atom in \p index
- * (\p nat values) (can be `NULL`).
- * \param[out] lidots Surface dots as x,y,z triplets (`3*lidots` values)
- * (can be `NULL`).
- * \param[out] n_dots Number of surface dots in \p lidots
- * (can be `NULL`).
- *
- * Calculates the surface area of spheres centered at `x[index[0]]`,
- * ..., `x[index[nat-1]]`, with radii `radii[index[0]]`, ..., where
- * `radii` is the array passed to setRadii().
- *
- * If \p flags is 0, the calculation is done for the items specified
- * with setCalculateVolume(), setCalculateAtomArea(), and
- * setCalculateSurfaceDots(). Flags can specify FLAG_VOLUME,
- * FLAG_ATOM_AREA, and/or FLAG_DOTS to request additional output for
- * this particular calculation. If any output is `NULL`, that output
- * is not calculated, irrespective of the calculation mode set.
- *
- * \todo
- * Make the output options more C++-like, in particular for the array
- * outputs.
- */
- void calculate(const rvec *x, const t_pbc *pbc,
- int nat, int index[], int flags, real *area,
- real *volume, real **at_area,
- real **lidots, int *n_dots) const;
+ /*! \brief
+ * Calculates the surface area for a set of positions.
+ *
+ * \param[in] x Atom positions (sphere centers).
+ * \param[in] pbc PBC information (if `NULL`, calculation is done
+ * without PBC).
+ * \param[in] nat Number of atoms to calculate.
+ * \param[in] index Atom indices to include in the calculation.
+ * \param[in] flags Additional flags for the calculation.
+ * \param[out] area Total surface area (must be non-`NULL`).
+ * \param[out] volume Total volume (can be `NULL`).
+ * \param[out] at_area Surface area for each atom in \p index
+ * (\p nat values) (can be `NULL`).
+ * \param[out] lidots Surface dots as x,y,z triplets (`3*lidots` values)
+ * (can be `NULL`).
+ * \param[out] n_dots Number of surface dots in \p lidots
+ * (can be `NULL`).
+ *
+ * Calculates the surface area of spheres centered at `x[index[0]]`,
+ * ..., `x[index[nat-1]]`, with radii `radii[index[0]]`, ..., where
+ * `radii` is the array passed to setRadii().
+ *
+ * If \p flags is 0, the calculation is done for the items specified
+ * with setCalculateVolume(), setCalculateAtomArea(), and
+ * setCalculateSurfaceDots(). Flags can specify FLAG_VOLUME,
+ * FLAG_ATOM_AREA, and/or FLAG_DOTS to request additional output for
+ * this particular calculation. If any output is `NULL`, that output
+ * is not calculated, irrespective of the calculation mode set.
+ *
+ * \todo
+ * Make the output options more C++-like, in particular for the array
+ * outputs.
+ */
+ void calculate(const rvec* x,
+ const t_pbc* pbc,
+ int nat,
+ int index[],
+ int flags,
+ real* area,
+ real* volume,
+ real** at_area,
+ real** lidots,
+ int* n_dots) const;
- private:
- class Impl;
+private:
+ class Impl;
- PrivateImplPointer<Impl> impl_;
+ PrivateImplPointer<Impl> impl_;
};
} // namespace gmx
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff