src/gromacs/gmxana/princ.h

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  38 #ifndef GMX_GMXANA_PRINC_H
  39 #define GMX_GMXANA_PRINC_H
  40
  41 #include "gromacs/math/vectypes.h"
  42 #include "gromacs/topology/idef.h"
  43 #include "gromacs/utility/basedefinitions.h"
  44
  45 struct t_atom;
  46 struct t_atoms;
  47
  48 void rotate_atoms(int gnx, const int index[], rvec x[], matrix trans);
  49 /* Rotate all atoms in index using matrix trans */
  50
  51 void principal_comp(int n, const int index[], t_atom atom[], rvec x[], matrix trans, rvec d);
  52 /* Calculate the principal components of atoms in index. Atoms are
  53  * mass weighted. It is assumed that the center of mass is in the origin!
  54  */
  55
  56 void orient_princ(const t_atoms* atoms, int isize, const int* index, int natoms, rvec x[], rvec* v, rvec d);
  57 /* rotates molecule to align principal axes with coordinate axes */
  58
  59 real calc_xcm(const rvec x[], int gnx, const int* index, const t_atom* atom, rvec xcm, gmx_bool bQ);
  60 /* Calculate the center of mass of the atoms in index. if bQ then the atoms
  61  * will be charge weighted rather than mass weighted.
  62  * Returns the total mass/charge.
  63  */
  64
  65 real sub_xcm(rvec x[], int gnx, const int* index, const t_atom atom[], rvec xcm, gmx_bool bQ);
  66 /* Calc. the center of mass and subtract it from all coordinates.
  67  * Returns the original center of mass in xcm
  68  * Returns the total mass
  69  */
  70
  71 void add_xcm(rvec x[], int gnx, const int* index, rvec xcm);
  72 /* Increment all atoms in index with xcm */
  73
  74 #endif