src/gromacs/trajectoryanalysis/modules/surfacearea.h

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  37 #ifndef GMX_TRAJECTORYANALYSIS_SURFACEAREA_H
  38 #define GMX_TRAJECTORYANALYSIS_SURFACEAREA_H
  39
  40 #include "gromacs/math/vectypes.h"
  41 #include "gromacs/utility/arrayref.h"
  42 #include "gromacs/utility/classhelpers.h"
  43 #include "gromacs/utility/real.h"
  44
  45 struct t_pbc;
  46
  47 #define FLAG_DOTS       01
  48 #define FLAG_VOLUME     02
  49 #define FLAG_ATOM_AREA  04
  50
  51 namespace gmx
  52 {
  53
  54 /*! \internal
  55  * \brief
  56  * Computes surface areas for a group of atoms/spheres.
  57  *
  58  * This class provides a surface area/volume calculator.
  59  *
  60  * The algorithm is based on representing each atom/sphere surface as a set of
  61  * dots, and determining which dots are on the surface (not covered by any
  62  * other atom/sphere).  The dots are distributed evenly using an icosahedron- or
  63  * a dodecahedron-based method (see the original reference cited in the code).
  64  * The area is then estimated from the area represented by each dot.
  65  * The volume is calculated by selecting a fixed point and integrating over the
  66  * surface dots, summing up the cones whose tip is at the fixed point and base
  67  * at the surface points.
  68  *
  69  * The default dot density per sphere is 32, which gives quite inaccurate
  70  * areas and volumes, but a reasonable number of surface points.  According to
  71  * original documentation of the method, a density of 600-700 dots gives an
  72  * accuracy of 1.5 A^2 per atom.
  73  *
  74  * \ingroup module_trajectoryanalysis
  75  */
  76 class SurfaceAreaCalculator
  77 {
  78     public:
  79         /*! \brief
  80          * Initializes a surface area calculator.
  81          *
  82          * \throws std::bad_alloc if out of memory.
  83          */
  84         SurfaceAreaCalculator();
  85         ~SurfaceAreaCalculator();
  86
  87         /*! \brief
  88          * Sets the number of surface dots per sphere to use.
  89          *
  90          * This function must be called before calculate() to set the desired
  91          * accuracy/computational cost.
  92          */
  93         void setDotCount(int dotCount);
  94         /*! \brief
  95          * Sets the radii of spheres to use in the calculation.
  96          *
  97          * \param[in]  radius  Radius for each atom/sphere.
  98          *
  99          * This function must be called before calculate() to set the radii for
 100          * the spheres.  All calculations must use the same set of radii to
 101          * share the same grid search.
 102          * These radii are used as-is, without adding any probe radius.
 103          * The passed array must remain valid for the lifetime of this object.
 104          *
 105          * Does not throw.
 106          */
 107         void setRadii(const ArrayRef<const real> &radius);
 108
 109         /*! \brief
 110          * Requests calculation of volume.
 111          *
 112          * If not called, and FLAG_VOLUME is not passed to calculate(), the
 113          * volume output is not produced.
 114          *
 115          * Does not throw.
 116          */
 117         void setCalculateVolume(bool bVolume);
 118         /*! \brief
 119          * Requests output of per-atom areas.
 120          *
 121          * If not called, and FLAG_ATOM_AREA is not passed to calculate(), the
 122          * atom area output is not produced.
 123          *
 124          * Does not throw.
 125          */
 126         void setCalculateAtomArea(bool bAtomArea);
 127         /*! \brief
 128          * Requests output of all surface dots.
 129          *
 130          * If not called, and FLAG_DOTS is not passed to calculate(), the
 131          * surface dot output is not produced.
 132          *
 133          * Does not throw.
 134          */
 135         void setCalculateSurfaceDots(bool bDots);
 136
 137         /*! \brief
 138          * Calculates the surface area for a set of positions.
 139          *
 140          * \param[in]  x       Atom positions (sphere centers).
 141          * \param[in]  pbc     PBC information (if `NULL`, calculation is done
 142          *     without PBC).
 143          * \param[in]  nat     Number of atoms to calculate.
 144          * \param[in]  index   Atom indices to include in the calculation.
 145          * \param[in]  flags   Additional flags for the calculation.
 146          * \param[out] area    Total surface area (must be non-`NULL`).
 147          * \param[out] volume  Total volume (can be `NULL`).
 148          * \param[out] at_area Surface area for each atom in \p index
 149          *     (\p nat values) (can be `NULL`).
 150          * \param[out] lidots  Surface dots as x,y,z triplets (`3*lidots` values)
 151          *     (can be `NULL`).
 152          * \param[out] n_dots Number of surface dots in \p lidots
 153          *     (can be `NULL`).
 154          *
 155          * Calculates the surface area of spheres centered at `x[index[0]]`,
 156          * ..., `x[index[nat-1]]`, with radii `radii[index[0]]`, ..., where
 157          * `radii` is the array passed to setRadii().
 158          *
 159          * If \p flags is 0, the calculation is done for the items specified
 160          * with setCalculateVolume(), setCalculateAtomArea(), and
 161          * setCalculateSurfaceDots().  Flags can specify FLAG_VOLUME,
 162          * FLAG_ATOM_AREA, and/or FLAG_DOTS to request additional output for
 163          * this particular calculation.  If any output is `NULL`, that output
 164          * is not calculated, irrespective of the calculation mode set.
 165          *
 166          * \todo
 167          * Make the output options more C++-like, in particular for the array
 168          * outputs.
 169          */
 170         void calculate(const rvec *x, const t_pbc *pbc,
 171                        int nat, int index[], int flags, real *area,
 172                        real *volume, real **at_area,
 173                        real **lidots, int *n_dots) const;
 174
 175     private:
 176         class Impl;
 177
 178         PrivateImplPointer<Impl> impl_;
 179 };
 180
 181 } // namespace gmx
 182
 183 #endif