g_bond – calculates distances between atoms VERSION 4.0.1 Synopsisg_bond -f traj.xtc -n index.ndx -s topol.tpr -o bonds.xvg -l bonds.log -d distance.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -blen real -tol real -[no]aver -[no]averdist Descriptiong_bond makes a distribution of bond lengths. If all is well a gaussian distribution should be made…
g_angle – calculates distributions and correlations for angles and dihedrals VERSION 4.0.1 Synopsisg_angle -f traj.xtc -n angle.ndx -od angdist.xvg -ov angaver.xvg -of dihfrac.xvg -ot dihtrans.xvg -oh trhisto.xvg -oc dihcorr.xvg -or traj.trr -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -type enum -[no]all -binwidth real -[no]periodic -[no]chandler -[no]avercorr -acflen int -[no]normalize -P enum…
g_angle – calculates distributions and correlations for angles and dihedrals VERSION 4.0.1 Synopsisg_angle -f traj.xtc -n angle.ndx -od angdist.xvg -ov angaver.xvg -of dihfrac.xvg -ot dihtrans.xvg -oh trhisto.xvg -oc dihcorr.xvg -or traj.trr -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -type enum -[no]all -binwidth real -[no]periodic -[no]chandler -[no]avercorr -acflen int -[no]normalize -P enum…
g_analyze – analyzes data sets VERSION 4.0.1 Synopsisg_analyze -f graph.xvg -ac autocorr.xvg -msd msd.xvg -cc coscont.xvg -dist distr.xvg -av average.xvg -ee errest.xvg -g fitlog.log -[no]h -nice int -[no]w -[no]xvgr -[no]time -b real -e real -n int -[no]d -bw real -errbar enum -[no]integrate -aver_start real -[no]xydy -[no]regression -[no]luzar -temp real -fitstart real -smooth real -filter real…
g_analyze – analyzes data sets VERSION 4.0.1 Synopsisg_analyze -f graph.xvg -ac autocorr.xvg -msd msd.xvg -cc coscont.xvg -dist distr.xvg -av average.xvg -ee errest.xvg -g fitlog.log -[no]h -nice int -[no]w -[no]xvgr -[no]time -b real -e real -n int -[no]d -bw real -errbar enum -[no]integrate -aver_start real -[no]xydy -[no]regression -[no]luzar -temp real -fitstart real -smooth real -filter real…
g_anaeig – analyzes the eigenvectors VERSION 4.0.1 Synopsisg_anaeig -v eigenvec.trr -v2 eigenvec2.trr -f traj.xtc -s topol.tpr -n index.ndx -eig eigenval.xvg -eig2 eigenval2.xvg -comp eigcomp.xvg -rmsf eigrmsf.xvg -proj proj.xvg -2d 2dproj.xvg -3d 3dproj.pdb -filt filtered.xtc -extr extreme.pdb -over overlap.xvg -inpr inprod.xpm -[no]h -nice int -b time -e time -dt time -tu enum -[no]w -[no]xvgr -first int…
g_anaeig – analyzes the eigenvectors VERSION 4.0.1 Synopsisg_anaeig -v eigenvec.trr -v2 eigenvec2.trr -f traj.xtc -s topol.tpr -n index.ndx -eig eigenval.xvg -eig2 eigenval2.xvg -comp eigcomp.xvg -rmsf eigrmsf.xvg -proj proj.xvg -2d 2dproj.xvg -3d 3dproj.pdb -filt filtered.xtc -extr extreme.pdb -over overlap.xvg -inpr inprod.xpm -[no]h -nice int -b time -e time -dt time -tu enum -[no]w -[no]xvgr -first int…
anadock – cluster structures from Autodock runs VERSION 4.0.1 Synopsisanadock -f eiwit.pdb -ox cluster.pdb -od edocked.xvg -of efree.xvg -g anadock.log -[no]h -nice int -[no]xvgr -[no]free -[no]rms -cutoff real Descriptionanadock analyses the results of an Autodock run and clusters the structures together, based on distance or RMSD. The docked energy and free energy estimates are analysed,…
anadock – cluster structures from Autodock runs VERSION 4.0.1 Synopsisanadock -f eiwit.pdb -ox cluster.pdb -od edocked.xvg -of efree.xvg -g anadock.log -[no]h -nice int -[no]xvgr -[no]free -[no]rms -cutoff real Descriptionanadock analyses the results of an Autodock run and clusters the structures together, based on distance or RMSD. The docked energy and free energy estimates are analysed,…
g3topbm – convert a Group 3 fax file into a portable bitmap Synopsisg3topbm [-kludge] [-reversebits] [-stretch] [g3file] DescriptionReads a Group 3 fax file as input. Produces a portable bitmap as output. Options-kludge Tells g3topbm to ignore the first few lines of the file; sometimes fax files have some junk at the beginning. -reversebits Tells g3topbm…
g3data – A tool for extracting data from graphs. Synopsisg3data [ -max x y ] [ -scale factor ] [ -coords llx lly rux ruy ] [ -errors ] [ -lnx ] [ -lny ] [ filename(s) … ] Descriptiong3data is a tool for extracting data from scanned graphs. For graphs published in scientific articles…
g3cat – concatenate multiple g3 documents Synopsisg3cat [-l] [-a] g3-file1 … Descriptiong3cat concatenates g3 files. These can either be ‘raw’, that is, bitmaps packed according to the CCITT T.4 standard for one-dimensional bitmap encoding, or ‘digifax’ files, created by GNU’s GhostScript package with the digifax drivers. Its output is a concatenation of all the input…
g32pbm – convert a Group 3 fax file into a portable bitmap Synopsisg32pbm [-reversebits] [-stretch] [g3file] DescriptionReads a Group 3 fax file (raw or digifax) as input. If no filename is given, stdin is used. Produces a portable bitmap as output. Options-r Tells g32pbm to interpret bits least-significant first, instead of the default most-significant first…
g2root – convert GEANT geometry files to ROOT files Synopsisg2rootd [-f map_name] geant_name macro_name DescriptionYou can convert a GEANT (see http://geant.cern.ch/ fore more on GEANT) geometry to ROOT geometry with the following steps 1 Run the interactive version of GEANT and produce a Zebra RZ file detector.geom, by typing the command: Geant > rz/file 21…
g-ir-scanner – extracting C metadata from sources and headers Synopsisg-ir-scanner [OPTION…] FILES… Descriptiong-ir-scanner is a tool which generates GIR XML files by parsing headers and introspecting GObject based libraries. It is usually invoked during the normal build step for a project and the information is saved to disk and later installed, so that language bindings…
g-ir-generate – typelib generator Synopsisg-ir-generate [OPTION…] FILES… Descriptiong-ir-generate is an GIR generator, using the repository API. It generates GIR files from a raw typelib or in a shared library (–shlib). The output will be written to standard output unless the –output is specified. Options, –help Show help options , –shlib=FILENAME The shared library to read…
g-ir-compiler – typelib compiler. Synopsisg-ir-compiler [OPTION…] GIRFILE Descriptiong-ir-compiler converts one or more GIR files into one or more typelib. The output will be written to standard output unless the –output is specified. Options–help Show help options –output=FILENAME Save the resulting output in FILENAME. –verbose Show verbose messages –debug Show debug messages –includedir=DIRECTORY Adds a directory…
gcc – GNU project C and C++ compiler Synopsisgcc [-c|-S|-E] [-std=standard] [-g] [-pg] [-Olevel] [-Wwarn…] [-pedantic] [-Idir…] [-Ldir…] [-Dmacro[=defn]…] [-Umacro] [-foption…] [-mmachine-option…] [-o outfile] [@file] infile… Only the most useful options are listed here; see below for the remainder. g++ accepts mostly the same options as gcc. DescriptionWhen you invoke GCC, it normally does preprocessing, compilation, assembly and linking. The “overall options” allow you…
g.version – Displays version and copyright information. Keywordsgeneral Synopsisg.version g.version help g.version [-cb] [–verbose] [–quiet] Flags:-c Print the copyright message -b Print the GRASS build information –verbose Verbose module output –quiet Quiet module outputDescriptiong.version prints to standard output the GRASS version number, date, the GRASS copyright and GRASS build information. NotesThis program requires no command…
gcc – GNU project C and C++ compiler Synopsisgcc [-c|-S|-E] [-std=standard] [-g] [-pg] [-Olevel] [-Wwarn…] [-Wpedantic] [-Idir…] [-Ldir…] [-Dmacro[=defn]…] [-Umacro] [-foption…] [-mmachine-option…] [-o outfile] [@file] infile… Only the most useful options are listed here; see below for the remainder. g++ accepts mostly the same options as gcc. DescriptionWhen you invoke GCC, it normally does preprocessing, compilation, assembly and linking. The “overall options” allow you…