Measure.C File Reference

 {
  "no atom selection",                                  
  "no atoms in selection",                              
  "incorrect number of weights for selection",          
  "internal error: NULL pointer given",                 
  "bad weight sum, would cause divide by zero",         
  "molecule was deleted(?)",                            
  "cannot understand weight parameter",                 
  "non-number given as parameter",                      
  "two selections don't have the same number of atoms", 
  "internal error: out of range",                       
  "no coordinates in selection",                        
  "couldn't compute eigenvalue/vectors",                
  "unknown Tcl problem",                                
  "no atom radii",                                      
  "order parameter contains out-of-range atom index",   
  "order parameter not supported in old RMS fit mode",  
  "specified frames are out of range",                  
  "both selections must reference the same molecule",   
  "one atom appears twice in list",                     
  "molecule contains no frames",                        
  "invalid atom id",                                    
  "cutoff must be smaller than cell dimension",         
  "Zero volmap gridsize"                                
}

Compounds
struct	gofrparms_t
struct	sasathreadparms
Defines
#define	ROTATE(a, i, j, k, l)
#define	SWAP(qq, ww)
#define	NPTS 500
#define	SWAP(qq, ww)
Functions
const char *	measure_error (int errnum)
int	measure_move (const AtomSel sel, float framepos, const Matrix4 &mat)
int	measure_sumweights (const AtomSel sel, int numweights, const float weights, float *weightsum)
int	measure_center_perresidue (MoleculeList mlist, const AtomSel sel, const float framepos, const float weight, float *com)
int	measure_center (const AtomSel sel, const float framepos, const float weight, float com)
int	measure_minmax (int num, const int on, const float framepos, const float radii, float min_coord, float *max_coord)
int	measure_avpos_perresidue (const AtomSel sel, MoleculeList mlist, int start, int end, int step, float *avpos)
int	measure_avpos (const AtomSel sel, MoleculeList mlist, int start, int end, int step, float *avpos)
int	measure_dipole (const AtomSel sel, MoleculeList mlist, float *dipole, int unitsdebye, int usecenter)
int	measure_hbonds (Molecule mol, AtomSel sel1, AtomSel sel2, double cutoff, double maxangle, int donlist, int hydlist, int acclist, int maxsize)
int	measure_rmsf_perresidue (const AtomSel sel, MoleculeList mlist, int start, int end, int step, float *rmsf)
int	measure_rmsf (const AtomSel sel, MoleculeList mlist, int start, int end, int step, float *rmsf)
int	measure_rgyr (const AtomSel sel, MoleculeList mlist, const float weight, float rgyr)
	measure the radius of gyration, including the given weights. More...
int	measure_rmsd_perresidue (const AtomSel sel1, const AtomSel sel2, MoleculeList mlist, int num, float weight, float *rmsd)
int	measure_rmsd (const AtomSel sel1, const AtomSel sel2, int num, const float framepos1, const float framepos2, float weight, float rmsd)
	measure the rmsd given a selection and weight term. More...
int	jacobi (float a[4][4], float d[3], float v[3][3])
int	transvecinv (const double *v, Matrix4 &res)
int	transvec (const double *v, Matrix4 &res)
Matrix4	myfit2 (const float x, const float y, const float comx, const float comy)
Matrix4	myfit3 (const float x1, const float x2, const float y1, const float y2, const float comx, const float comy)
int	measure_fit (const AtomSel sel1, const AtomSel sel2, const float x, const float y, const float weight, const int order, Matrix4 *mat)
int	measure_sasa_perresidue (const AtomSel sel, const float framepos, const float radius, float srad, float sasa, ResizeArray< float > sasapts, const AtomSel restrictsel, const int nsamples, int rescount, MoleculeList *mlist)
int	measure_sasa (const AtomSel sel, const float framepos, const float radius, float srad, float sasa, ResizeArray< float > sasapts, const AtomSel restrictsel, const int *nsamples)
void *	measure_sasa_thread (void *voidparms)
int	measure_sasalist (MoleculeList mlist, const AtomSel sellist, int numsels, float srad, float sasalist, const int *nsamples)
float	fix_pbc_n_sqr (float delta, const float boxby2)
float	min_dist_with_pbc (const float a, const float b, const float *boxby2)
double	spherical_cap (const double &radius, const double &boxby2)
	the volume of a sperical cap. More...
void *	measure_gofr_orth (void *voidparms)
int	measure_gofr (AtomSel sel1, AtomSel sel2, MoleculeList mlist, const int count_h, double gofr, double numint, double histog, const float delta, int first, int last, int step, int *framecntr, int usepbc, int selupdate)
int	measure_geom (MoleculeList mlist, int molid, int atmid, ResizeArray< float > gValues, int frame, int first, int last, int defmolid, int geomtype)
int	calculate_bond (MoleculeList mlist, int molid, int atmid, float value)
int	calculate_angle (MoleculeList mlist, int molid, int atmid, float value)
int	calculate_dihed (MoleculeList mlist, int molid, int atmid, float value)
int	normal_atom_coord (Molecule mol, int a, float pos)
int	check_mol (Molecule *mol, int a)
int	measure_energy (MoleculeList mlist, int molid, int atmid, int natoms, ResizeArray< float > gValues, int frame, int first, int last, int defmolid, double *params, int geomtype)
int	compute_bond_energy (MoleculeList mlist, int molid, int atmid, float energy, float k, float x0)
int	compute_angle_energy (MoleculeList mlist, int molid, int atmid, float energy, float k, float x0, float kub, float s0)
int	compute_dihed_energy (MoleculeList mlist, int molid, int atmid, float energy, float k, int n, float delta)
int	compute_imprp_energy (MoleculeList mlist, int molid, int atmid, float energy, float k, float x0)
int	compute_vdw_energy (MoleculeList mlist, int molid, int atmid, float energy, float eps1, float rmin1, float eps2, float rmin2, float cutoff, float switchdist)
int	compute_elect_energy (MoleculeList mlist, int molid, int atmid, float energy, float q1, float q2, bool flag1, bool flag2, float cutoff)
void	center_of_mass (AtomSel sel, MoleculeList mlist, float *rcom)
int	measure_inertia (AtomSel sel, MoleculeList mlist, const float *coor, float rcom[3], float priaxes[3][3], float itensor[4][4], float evalue[3])
Variables
const char *	measure_error_messages []

Measure.C File Reference

Compounds

Defines

Functions

Variables

Define Documentation

Function Documentation

Variable Documentation