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utilities.C File Reference

#include <string.h>
#include <ctype.h>
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <unistd.h>
#include <sys/time.h>
#include <errno.h>
#include "utilities.h"

Go to the source code of this file.

Functions

char * combine_arguments (int argc, const char **argv, int n)

given an argc, argv pair, take all the arguments from the Nth one on and combine them into a single string with spaces separating words. This allocates space for the string, which must be freed by the user. More...

char * stringdup (const char *s)

make a copy of a string using c++ new routine for memory alloc. More...

char * stringtoupper (char *s)

convert the given string to upper case. More...

void stripslashes (char *str)

strip trailing '/' characters from a string. More...

int strupcmp (const char *a, const char *b)

do case-insensitive string comparisons. More...

int strupncmp (const char *a, const char *b, int n)

do case-insensitive string comparisons. More...

void breakup_filename (const char *full, char **path, char **name)

break a file name up into path + name, returning both in the specified character pointers. This creates storage for the new strings by allocating space for them. More...

char * str_tokenize (const char *newcmd, int *argc, char *argv[])

double time_of_day (void)

get the time of day from the system clock, and return it (in seconds) (This is supposedly accurate to within about 1 millisecond. More...

int vmd_check_stdin (void)

check for input on stdin. More...

char * vmd_username (void)

return the username of the currently logged-on user. More...

int vmd_getuid (void)

return the uid of the currently logged-on user. More...

float * cross_prod (float *x1, const float *x2, const float *x3)

compute the cross product, assumes that x1 memory is _different_ than both x2 and x3, and returns the pointer to x1. More...

float * vec_normalize (float *vect)

normalizes the 3-vector to length one and returns the pointer note that this changes the vector. More...

float norm (const float *vect)

find and return the norm of a 3-vector. More...

int tri_degenerate (const float *v0, const float *v1, const float *v2)

determine if a triangle is degenerate or not. More...

float angle (const float *a, const float *b)

compute the angle between two vectors a & b (0 to 180 deg). More...

float dihedral (const float *a1, const float *a2, const float *a3, const float *a4)

Compute the dihedral angle for the given atoms, returning a value between -180 and 180. More...

float distance (const float *a, const float *b)

compute the distance between two points a & b. More...

char * vmd_tempfile (const char *s)

VMD temp file (portable) given a string, return a new one with the temp dir name prepended. The returned string must be deleted. More...

int vmd_delete_file (const char *path)

VMD file deletion function (portable). More...

void vmd_sleep (int secs)

VMD process sleep functions (portable). More...

void vmd_msleep (int msecs)

int vmd_system (const char *cmd)

a buffer function to system() call to be replaced by a different implementation in console-free Win32 applications. More...

long vmd_random (void)

portable random number generation, NOT thread-safe however XXX we should replace these with our own thread-safe random number generator implementation at some point. More...

void vmd_srandom (unsigned int seed)

portable random number generation, NOT thread-safe however. More...

float vmd_random_gaussian ()

Slow but accurate standard distribution random number generator (variance = 1). More...

long vmd_get_total_physmem_mb (void)

return the number of MB of physical memory installed in the system. More...

long vmd_get_avail_physmem_mb (void)

return the number of MB of physical memory "free" (no VM/swap counted...). More...

long vmd_get_avail_physmem_percent (void)

return the percentage of physical memory available. More...

float correction (int nrays)

void print_xyz (float *population, int nrays)

float arcdistance (float lambda1, float lambda2, float phi1, float phi2)

int k_candidates (int k, int nrays, int idx, int testpt, float minD, float *candidates, float *population)

int poisson_sample_on_sphere (float *population, int N, int k, int verbose)

Function Documentation

float angle ( const float * a,

const float * b

)

compute the angle between two vectors a & b (0 to 180 deg).

Definition at line 395 of file utilities.C.
References cross_prod, and dot_prod.

float arcdistance ( float lambda1,

float lambda2,

float phi1,

float phi2

)

Definition at line 719 of file utilities.C.

void breakup_filename ( const char * full,

char ** path,

char ** name

)

break a file name up into path + name, returning both in the specified character pointers. This creates storage for the new strings by allocating space for them.

Definition at line 158 of file utilities.C.
References NULL, and stringdup.

char* combine_arguments ( int argc,

const char ** argv,

int n

)

given an argc, argv pair, take all the arguments from the Nth one on and combine them into a single string with spaces separating words. This allocates space for the string, which must be freed by the user.

Definition at line 63 of file utilities.C.
References n, and NULL.

float correction ( int nrays )

Definition at line 693 of file utilities.C.
References VMD_PIF.

float* cross_prod ( float * x1,

const float * x2,

const float * x3

)

compute the cross product, assumes that x1 memory is _different_ than both x2 and x3, and returns the pointer to x1.

Definition at line 317 of file utilities.C.

float dihedral ( const float * a1,

const float * a2,

const float * a3,

const float * a4

)

Compute the dihedral angle for the given atoms, returning a value between -180 and 180.

Definition at line 407 of file utilities.C.
References cross_prod, dot_prod, and vec_sub.

float distance ( const float * a,

const float * b

)

compute the distance between two points a & b.

Definition at line 426 of file utilities.C.
References distance2.

int k_candidates ( int k,

int nrays,

int idx,

int testpt,

float minD,

float * candidates,

float * population

)

Definition at line 735 of file utilities.C.
References arcdistance, VMD_PIF, VMD_RAND_MAX, vmd_random, and VMD_TWOPIF.

float norm ( const float * vect )

find and return the norm of a 3-vector.

Definition at line 343 of file utilities.C.

int poisson_sample_on_sphere ( float * population,

int N,

int k,

int verbose

)

Definition at line 785 of file utilities.C.
References correction, k_candidates, NULL, result, VMD_PI, VMD_RAND_MAX, vmd_random, vmd_srandom, and VMD_TWOPI.

void print_xyz ( float * population,

int nrays

)

Definition at line 704 of file utilities.C.
References z.

char* str_tokenize ( const char * newcmd,

int * argc,

char * argv[]

)

Definition at line 190 of file utilities.C.
References NULL, and stringdup.

char* stringdup ( const char * s )

make a copy of a string using c++ new routine for memory alloc.

Definition at line 90 of file utilities.C.
References NULL.

char* stringtoupper ( char * s )

convert the given string to upper case.

Definition at line 104 of file utilities.C.
References NULL.

void stripslashes ( char * str )

strip trailing '/' characters from a string.

Definition at line 115 of file utilities.C.

int strupcmp ( const char * a,

const char * b

)

do case-insensitive string comparisons.

Definition at line 122 of file utilities.C.
References stringdup, and stringtoupper.

int strupncmp ( const char * a,

const char * b,

int n

)

do case-insensitive string comparisons.

Definition at line 139 of file utilities.C.
References n.

double time_of_day ( void )

get the time of day from the system clock, and return it (in seconds) (This is supposedly accurate to within about 1 millisecond.

Definition at line 231 of file utilities.C.
Referenced by Animation::Animation, Animation::check_event, TclTextInterp::done_waiting, AtomColor::find, FPS::FPS, VMDTitle::prepare, FPS::prepare, VMDTitle::VMDTitle, and TclTextInterp::wait.

int tri_degenerate ( const float * v0,

const float * v1,

const float * v2

)

determine if a triangle is degenerate or not.

Definition at line 349 of file utilities.C.

float* vec_normalize ( float * vect )

normalizes the 3-vector to length one and returns the pointer note that this changes the vector.

Definition at line 327 of file utilities.C.

int vmd_check_stdin ( void )

check for input on stdin.

Definition at line 249 of file utilities.C.
References NULL.
Referenced by TclTextInterp::doEvent, PythonTextInterp::doEvent, and main.

int vmd_delete_file ( const char * path )

VMD file deletion function (portable).

Definition at line 474 of file utilities.C.

long vmd_get_avail_physmem_mb ( void )

return the number of MB of physical memory "free" (no VM/swap counted...).

Definition at line 609 of file utilities.C.
References NULL.
Referenced by vmd_gaussdensity_threaded, vmd_get_avail_physmem_percent, vmdinfo_tcl, VMDApp::VMDinit, volin_threaded, and volin_threaded_prob.

long vmd_get_avail_physmem_percent ( void )

return the percentage of physical memory available.

Definition at line 681 of file utilities.C.
References vmd_get_avail_physmem_mb, and vmd_get_total_physmem_mb.
Referenced by VMDApp::VMDinit.

long vmd_get_total_physmem_mb ( void )

return the number of MB of physical memory installed in the system.

Definition at line 554 of file utilities.C.
References NULL.
Referenced by vmd_get_avail_physmem_percent.

int vmd_getuid ( void )

return the uid of the currently logged-on user.

Definition at line 305 of file utilities.C.
Referenced by Surf::compute, NanoShaperInterface::compute_from_file, and MSMSInterface::compute_from_file.

void vmd_msleep ( int msecs )

Definition at line 493 of file utilities.C.
References NULL.

long vmd_random ( void )

portable random number generation, NOT thread-safe however XXX we should replace these with our own thread-safe random number generator implementation at some point.

Definition at line 512 of file utilities.C.
Referenced by Surf::compute, NanoShaperInterface::compute_from_file, MSMSInterface::compute_from_file, k_candidates, measure_sasa, measure_sasa_perresidue, measure_sasalist, poisson_sample_on_sphere, vmd_measure_volinterior, and vmd_random_gaussian.

float vmd_random_gaussian ( )

Slow but accurate standard distribution random number generator (variance = 1).

Definition at line 530 of file utilities.C.
References VMD_RAND_MAX, and vmd_random.
Referenced by colvarproxy_vmd::rand_gaussian.

void vmd_sleep ( int secs )

VMD process sleep functions (portable).

Definition at line 485 of file utilities.C.

void vmd_srandom ( unsigned int seed )

portable random number generation, NOT thread-safe however.

Definition at line 520 of file utilities.C.

int vmd_system ( const char * cmd )

a buffer function to system() call to be replaced by a different implementation in console-free Win32 applications.

Definition at line 504 of file utilities.C.

char* vmd_tempfile ( const char * s )

VMD temp file (portable) given a string, return a new one with the temp dir name prepended. The returned string must be deleted.

Definition at line 430 of file utilities.C.
References NULL, stringdup, and stripslashes.

char* vmd_username ( void )

return the username of the currently logged-on user.

Definition at line 285 of file utilities.C.
References NULL, size, and stringdup.

Generated on Fri Oct 24 02:46:07 2025 for VMD (current) by

Functions
char *	combine_arguments (int argc, const char **argv, int n)
	given an argc, argv pair, take all the arguments from the Nth one on and combine them into a single string with spaces separating words. This allocates space for the string, which must be freed by the user. More...
char *	stringdup (const char *s)
	make a copy of a string using c++ new routine for memory alloc. More...
char *	stringtoupper (char *s)
	convert the given string to upper case. More...
void	stripslashes (char *str)
	strip trailing '/' characters from a string. More...
int	strupcmp (const char a, const char b)
	do case-insensitive string comparisons. More...
int	strupncmp (const char a, const char b, int n)
	do case-insensitive string comparisons. More...
void	breakup_filename (const char full, char path, char *name)
	break a file name up into path + name, returning both in the specified character pointers. This creates storage for the new strings by allocating space for them. More...
char *	str_tokenize (const char newcmd, int argc, char *argv[])
double	time_of_day (void)
	get the time of day from the system clock, and return it (in seconds) (This is supposedly accurate to within about 1 millisecond. More...
int	vmd_check_stdin (void)
	check for input on stdin. More...
char *	vmd_username (void)
	return the username of the currently logged-on user. More...
int	vmd_getuid (void)
	return the uid of the currently logged-on user. More...
float *	cross_prod (float x1, const float x2, const float *x3)
	compute the cross product, assumes that x1 memory is _different_ than both x2 and x3, and returns the pointer to x1. More...
float *	vec_normalize (float *vect)
	normalizes the 3-vector to length one and returns the pointer note that this changes the vector. More...
float	norm (const float *vect)
	find and return the norm of a 3-vector. More...
int	tri_degenerate (const float v0, const float v1, const float *v2)
	determine if a triangle is degenerate or not. More...
float	angle (const float a, const float b)
	compute the angle between two vectors a & b (0 to 180 deg). More...
float	dihedral (const float a1, const float a2, const float a3, const float a4)
	Compute the dihedral angle for the given atoms, returning a value between -180 and 180. More...
float	distance (const float a, const float b)
	compute the distance between two points a & b. More...
char *	vmd_tempfile (const char *s)
	VMD temp file (portable) given a string, return a new one with the temp dir name prepended. The returned string must be deleted. More...
int	vmd_delete_file (const char *path)
	VMD file deletion function (portable). More...
void	vmd_sleep (int secs)
	VMD process sleep functions (portable). More...
void	vmd_msleep (int msecs)
int	vmd_system (const char *cmd)
	a buffer function to system() call to be replaced by a different implementation in console-free Win32 applications. More...
long	vmd_random (void)
	portable random number generation, NOT thread-safe however XXX we should replace these with our own thread-safe random number generator implementation at some point. More...
void	vmd_srandom (unsigned int seed)
	portable random number generation, NOT thread-safe however. More...
float	vmd_random_gaussian ()
	Slow but accurate standard distribution random number generator (variance = 1). More...
long	vmd_get_total_physmem_mb (void)
	return the number of MB of physical memory installed in the system. More...
long	vmd_get_avail_physmem_mb (void)
	return the number of MB of physical memory "free" (no VM/swap counted...). More...
long	vmd_get_avail_physmem_percent (void)
	return the percentage of physical memory available. More...
float	correction (int nrays)
void	print_xyz (float *population, int nrays)
float	arcdistance (float lambda1, float lambda2, float phi1, float phi2)
int	k_candidates (int k, int nrays, int idx, int testpt, float minD, float candidates, float population)
int	poisson_sample_on_sphere (float *population, int N, int k, int verbose)