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|
/* Copyright (C) 2000-2006 Damir Zucic */
/*=============================================================================
print_help.c
Purpose:
Print brief help: short introduction and list of options. This is not
the true (on-line) help for garlic!
Input:
No input.
Output:
Introductory information written to stdout.
Return value:
No return value.
========includes:============================================================*/
#include <stdio.h>
/*======print brief help:====================================================*/
void PrintHelp_ (void)
{
fprintf (stdout, "\n");
fprintf (stdout,
"=========================================================================\n");
fprintf (stdout,
" Garlic - free molecular viewer and editor\n");
fprintf (stdout,
"=========================================================================\n");
fprintf (stdout, "\n");
fprintf (stdout,
"Garlic was written by Damir Zucic (zucic@mefos.hr) as a complement to\n");
fprintf (stdout,
"other molecular visualization programs, like rasmol (by Roger Sayle).\n");
fprintf (stdout,
"It was written to simplify the analysis of membrane proteins, but it can\n");
fprintf (stdout,
"be used as general purpose molecular visualization program, provided that\n");
fprintf (stdout,
"molecular coordinates are available in PDB format, version 2.1 or older.\n");
fprintf (stdout,
"Garlic may also be used to analyze protein sequences.\n");
fprintf (stdout, "\n");
fprintf (stdout,
"Some of the features, which distinguish this program from others, are:\n");
fprintf (stdout,
"(1) Coordinates, labels and other data are automatically displayed for\n");
fprintf (stdout,
" the atom nearest to the current pointer (mouse) position.\n");
fprintf (stdout,
"(2) Additional numeric data, like hydrophobicity, may be associated to\n");
fprintf (stdout,
" each amino acid. The whole structure may be colored according to\n");
fprintf (stdout,
" these values.\n");
fprintf (stdout,
"(3) Selection mechanism is different.\n");
fprintf (stdout,
"(4) Two bonds at different distance from observer have different colors.\n");
fprintf (stdout,
"-------------------------------------------------------------------------\n");
fprintf (stdout,
"Usage: garlic [true_garlic_options] [X11_options] [filename]\n");
fprintf (stdout,
"-------------------------------------------------------------------------\n");
fprintf (stdout,
"Command line options may be divided in two groups: true (specific) garlic\n");
fprintf (stdout,
"options and X11 options. Options may be given in any order. All options\n");
fprintf (stdout,
"and hard-coded default values are listed in the table below. For each\n");
fprintf (stdout,
"parameter, the value defined through command line is used, if available.\n");
fprintf (stdout,
"If not, the value defined in .garlicrc file is used. If .garlicrc file is\n");
fprintf (stdout,
"not available, or there is no corresponding entry in this file, the\n");
fprintf (stdout,
"hard-coded default value is used. The sample .garlicrc file included in\n");
fprintf (stdout,
"the original package contains the values equal to hard-coded defaults.\n");
fprintf (stdout,
"-------------------------------------------------------------------------\n");
fprintf (stdout,
"garlic option: Description:\n");
fprintf (stdout,
"-------------------------------------------------------------------------\n");
fprintf (stdout,
"-h, --help Print help and exit.\n");
fprintf (stdout,
"-v, --version Print version and exit.\n");
fprintf (stdout,
"-r, --register Register garlic: inform author that your site has\n");
fprintf (stdout,
" garlic installed and that someone is going to use\n");
fprintf (stdout,
" this program. By registering, you are encouraging\n");
fprintf (stdout,
" author to continue development of garlic. You can\n");
fprintf (stdout,
" also help author to ensure support for further\n");
fprintf (stdout,
" development. This option sends an e-mail message,\n");
fprintf (stdout,
" containing only the e-mail message header and the\n");
fprintf (stdout,
" word 'Hi!', to zucic@garlic.mefos.hr. Please type\n");
fprintf (stdout,
" garlic -r if you are going to use this program.\n");
fprintf (stdout,
" If your system is not connected to the Internet,\n");
fprintf (stdout,
" you can send short e-mail from some other system.\n");
fprintf (stdout,
"-nosys Hide the coordinate system icon (top left corner).\n");
fprintf (stdout,
"-no-control Hide the control window (upper right corner).\n");
fprintf (stdout,
"-stereo Display stereo image.\n");
fprintf (stdout,
"-slab mode Default slab mode. Available slab modes are: off,\n");
fprintf (stdout,
" planar (default), sphere, half-sphere, cylinder\n");
fprintf (stdout,
" and half cylinder.\n");
fprintf (stdout,
"-fading mode Default color fading mode. Available modes: off,\n");
fprintf (stdout,
" planar (default), sphere, half-sphere, cylinder\n");
fprintf (stdout,
" and half cylinder.\n");
fprintf (stdout,
"-as number Default atom drawing style (hard-coded default: 2).\n");
fprintf (stdout,
"-bs number Default bond drawing style (hard-coded default: 3).\n");
fprintf (stdout,
"-fs number Default number of color fading surfaces. Parallel\n");
fprintf (stdout,
" planes, concentric spheres or conc. cylinders may\n");
fprintf (stdout,
" be used as fading surfaces. Three RGB triplets\n");
fprintf (stdout,
" are assigned to each surface. Surfaces are evenly\n");
fprintf (stdout,
" spaced; at least one and at most eight should be\n");
fprintf (stdout,
" defined. At least three colors (left, middle and\n");
fprintf (stdout,
" right) are assigned to each visible atom. These\n");
fprintf (stdout,
" three colors are based on the position of a given\n");
fprintf (stdout,
" atom relative to the nearest fading surface(s)\n");
fprintf (stdout,
" and on colors assigned to these surfaces. Colors\n");
fprintf (stdout,
" are combined using linear weighting.\n");
fprintf (stdout,
"-lc<i> color Left color at the i-th surface; i is between zero\n");
fprintf (stdout,
" and seven. The color string should be compliant\n");
fprintf (stdout,
" with X11R5. Blue, for example, may be specified\n");
fprintf (stdout,
" as blue or as RGB:0000/0000/FFFF etc. For example\n");
fprintf (stdout,
" -lc4 RGB:BBBB/8888/4444 defines the left color\n");
fprintf (stdout,
" at the surface whose index is equal to four.\n");
fprintf (stdout,
"-mc<i> color Middle color at the i-th surface.\n");
fprintf (stdout,
"-rc<i> color Right color at the i-th surface.\n");
fprintf (stdout,
"-pc, --print-config Print configuration data and exit.\n");
fprintf (stdout,
"-pcn Print cursor names to stdout and exit.\n");
fprintf (stdout,
"-log logfile Write commands and messages to log file. The file\n");
fprintf (stdout,
" will be created in the current working directory.\n");
fprintf (stdout,
" If this is not possible, log file will be created\n");
fprintf (stdout,
" in users home directory.\n");
fprintf (stdout,
"-------------------------------------------------------------------------\n");
fprintf (stdout,
"X11 option: Description:\n");
fprintf (stdout,
"-------------------------------------------------------------------------\n");
fprintf (stdout,
"-display displayname X server to contact.\n");
fprintf (stdout,
"-geometry geom Window geometry (default: almost the whole screen).\n");
fprintf (stdout,
"-bg color Main window background color (default is black).\n");
fprintf (stdout,
"-fg color Main window foreground color (default: white).\n");
fprintf (stdout,
"-fn fontname Text font; (default is 10x20).\n");
fprintf (stdout,
"-tbg color Text background color (default is black).\n");
fprintf (stdout,
"-tfg color Text color (default is white).\n");
fprintf (stdout,
"-cursor cursorname Cursor name; see /usr/include/X11/cursorfont.h for\n");
fprintf (stdout,
" names; remove the XC_ prefix.\n");
fprintf (stdout,
"-------------------------------------------------------------------------\n");
fprintf (stdout,
"filename: The input file name. Full pathname may be used. If\n");
fprintf (stdout,
" filename does not contain the path, garlic will try\n");
fprintf (stdout,
" to find the specified file in the current working\n");
fprintf (stdout,
" directory. If the first attempt to open the file\n");
fprintf (stdout,
" fails, the filename is appended to the content of\n");
fprintf (stdout,
" the environment variable MOL_DIR for the second\n");
fprintf (stdout,
" attempt. If this fails too, garlic will search all\n");
fprintf (stdout,
" directories specified in the environment variable\n");
fprintf (stdout,
" MOL_PATH.\n");
fprintf (stdout,
"-------------------------------------------------------------------------\n");
fprintf (stdout,
"Personal initializations may be written to .garlicrc file. Normally, this\n");
fprintf (stdout,
"file should be kept in users home directory. Note that this is not the\n");
fprintf (stdout,
"first directory to be searched for .garlicrc file! Up to seven pathnames\n");
fprintf (stdout,
"are tryed in the following order:\n");
fprintf (stdout, "\n");
fprintf (stdout,
".garlicrc .garlicrc in current working directory.\n");
fprintf (stdout,
"$HOME/.garlicrc .garlicrc in home directory. This is the\n");
fprintf (stdout,
" recommended location.\n");
fprintf (stdout,
"$HOME/garlic/.garlicrc ./garlicrc, subdirectory garlic of users\n");
fprintf (stdout,
" home directory.\n");
fprintf (stdout,
"/usr/share/garlic/.garlicrc ./garlicrc in /usr/share/garlic (Linux).\n");
fprintf (stdout,
"/etc/garlicrc garlicrc in /etc, Debian Linux; note that\n");
fprintf (stdout,
" file name is garlicrc in this case!\n");
fprintf (stdout,
"/usr/local/lib/garlic/.garlicrc .garlicrc in /usr/local/lib/garlic dir.\n");
fprintf (stdout,
"/usr/lib/garlic/.garlicrc .garlicrc in /usr/lib/garlic; this is the\n");
fprintf (stdout,
" last attempt; if it failes, hard-coded\n");
fprintf (stdout,
" default values will be used.\n");
fprintf (stdout,
"-------------------------------------------------------------------------\n");
fprintf (stdout,
"Environment variables:\n");
fprintf (stdout,
"-------------------------------------------------------------------------\n");
fprintf (stdout,
"MOL_DIR Defines where to look for the specified file if not\n");
fprintf (stdout,
" found in the current working directory.\n");
fprintf (stdout,
"MOL_PATH The list of directories to be searched. It is used\n");
fprintf (stdout,
" if attempt with MOL_DIR failes or if MOL_DIR is\n");
fprintf (stdout,
" not defined. Use space or colon (:) to separate\n");
fprintf (stdout,
" directory names. MOL_PATH is quite useful; it is\n");
fprintf (stdout,
" recommended to define this environment variable\n");
fprintf (stdout,
" through .login, .bashrc or some other script.\n");
fprintf (stdout,
" MOL_PATH is more useful than MOL_DIR so it is\n");
fprintf (stdout,
" recommended to define only MOL_PATH variable.\n");
fprintf (stdout,
"DISPLAY X server to which the program should be connected.\n");
fprintf (stdout,
"-------------------------------------------------------------------------\n");
fprintf (stdout,
"garlic home page: http://garlic.mefos.hr/garlic\n");
fprintf (stdout,
"Damir Zucic home page: http://garlic.mefos.hr/zucic\n");
fprintf (stdout,
"E-mail: zucic@mefos.hr\n");
fprintf (stdout,
"=========================================================================\n");
fprintf (stdout, "\n");
}
/*===========================================================================*/
|
