The Linux Manuals (man pages) document is an important part of Linux documents. Linux Manuals are organized as several sections. Each section has a group of commands for a specific area in Linux usage, administration or development.
obgrep – an advanced molecular search program using SMARTS Synopsis[OPTIONS ] ‘SMARTS-pattern’ filename DescriptionThe obgrep tool can be used to search for molecules inside multi-molecule database files (e.g., SMILES, SDF, etc.) or across multiple files. OptionsIf only a filename is given, obgrep will attempt to guess the file type from the filename extension. -c Print…
obgen – generate 3D coordinates for a molecule Synopsis[OPTIONS ] filename DescriptionThe obgen tool will generate 3D coordinates for molecules in a file (e.g. multi-molecule SMILES files). The resulting structure will be optimized using the given forcefield and checked for the lowest-energy conformer using a Monte Carlo search. Output will be sent to standard output…
obfit – superimpose two molecules based on a pattern SynopsisSMARTS-pattern fixed-file outfile DescriptionSuperimpose two molecules using a quaternion fit. The atoms used to fit the two molecules are defined by the SMARTS pattern given by the user. It is useful to align congeneric series of molecules on a common structural scaffold for 3D-QSAR studies. It…
obexftpd – Mobile Equipment file transfer server Synopsisobexftpd [OPTIONS] [TRANSPORT] DescriptionWith obexftpd you can set up an obex server on any computers using IrDA, Bluetooth or TCP/IP. Use e.g. obexftp or the ObexFS to access the files on this server. OptionsThe ordering of options is important. The first transport option will start the server. Use…
obexftp – Mobile Equipment file transfer tool Synopsisobexftp [OPTION] [COMMANDS] Descriptionobexftp is used to access files on mobile equipment, i.e. cell phones. With obexftpd you can transfer files between any computers using IrDA, Bluetooth and TCP/IP. This tool lets you access the ObexFTP library by the means of a command line interface. You might consider…
obexctl – A command-line interface of BlueZ for OBEX (file transfer) Usage: obexctl [options]Options–timeout Timeout in seconds for non-interactive mode –version Display version –help Display help
obex_push – Push and Receive Files over the Bluetooth OBEX Push Channel Synopsisobex_push [<channel>] [<bdaddr> <filename>] Descriptionobex_push can send and receive files over the Bluetooth OBEX Push Channel. Link your bluetooth device with your computer. You can see the SDP services with: $ sdptool browse <bdaddr> OptionsIf no options are given, any files sent over…
obex-data-server – D-Bus service providing OBEX functionality Synopsisobex-data-server [OPTIONS] Descriptionobex-data-server is D-Bus service providing high-level OBEX client and server side functionality. It currently supports OPP (Object Push Profile), FTP (File Transfer profile) and partially BIP (Basic Imaging profile). Supported transports are Bluetooth, USB (client only) or TTY. obex-data-server exposes it’s functionality through ‘org.openobex’ namespace in…
obenergy – calculate the energy for a molecule Synopsis[OPTIONS ] filename DescriptionThe obenergy tool can be used to calculate the energy for molecules inside (multi-)molecule files (e.g., MOL2, etc.) OptionsIf no filename is given, obenergy will give all options including the available forcefields. -v Verbose: print out all individual energy interactions -ff forcefield Select the…
obconformer – generate conformer coordinates Synopsis# of conformers # of optimization steps filename DescriptionThe obconformer tool can be used as part of a conformational study by generating random conformers using a Monte Carlo search. The best conformer out of the batch of conformers will be output, after taking the supplied number of geometry optimization steps….
obchiral – print molecular chirality information Synopsisfilename DescriptionThe obchiral program is a tool to print the chirality information for all molecules in a file. It also serves as example code for using the Open Babel library (libopenbabel). Examples"obchiral pyridines.sdf"See Alsobabel(1), obfit(1), obgrep(1), obprop(1), obrotate(1). The web pages for Open Babel can be found at: <http://openbabel.org/>…
babel , obabel – a converter for chemistry and molecular modeling data files Synopsis[-H help-options ] [OPTIONS ] [-i input-type ] infile [-o output-type ] outfile obabel [-H help-options ] obabel [OPTIONS ] [-i input-type | –: Qo SMILES-string Qc infile ] [-o output-type ] –O outfile Descriptionis a cross-platform program designed to interconvert between…
oathtool – OATH one-time password tool Synopsisoathtool [OPTIONS]… [KEY [OTP]]… Descriptionoathtool 2.4.1 Generate and validate OATH one-time passwords. -h, –help Print help and exit -V, –version Print version and exit –hotp use event-based HOTP mode (default=on) –totp use time-variant TOTP mode (default=off) -b, –base32 use base32 encoding of KEY instead of hex (default=off) -c, –counter=COUNTER…
oLschema2ldif – Converts LDAP schema’s to LDB-compatible LDIF Synopsis oLschema2ldif [-I INPUT-FILE] [-O OUTPUT-FILE]DescriptionoLschema2ldif is a simple tool that converts standard OpenLDAP schema files to a LDIF format that is understood by LDB. Options-I input-file OpenLDAP schema to read. If none are specified, the schema file will be read from standard input. -O output-file File…
nycli – New Korving CLI Synopsisnyxmms2 [command] [arguments] Descriptionnycli is the new official CLI XMMS2 client, replacing xmms2(1). InvocationInline ModeIf nycli is passed a command as an argument, that command will be interpreted and nycli will exit after it is finished. Interactive Modenycli features a powerful shell-like environment via readline that allows the user to…
nytprofpf – Generate a report for plat_forms (< http://www.plat-forms.org/>) from Devel::NYTProf data SynopsisTypical usage: $ perl -d:NYTProf some_perl_app.pl $ nytprofpfOptions synopsis: –file <file>, -f <file> Read profile data from the specified file [default: nytprof.out] –delete, -d Delete any old report files first –lib <lib>, -l <lib> Add <lib> to the beginning of \@INC –no-mergeevals Disable…
nytprofmerge – Reads multiple NYTProf profiles and outputs a merged one Synopsis $ nytprofmerge –out=nytprof-merged.out nytprof.out.* $ nytprofmerge nytprof.out.*DescriptionReads multiple profile data files generated by Devel::NYTProf and writes out a new profile data file containing data merged from the original files. "nytprofmerge" is likely to produce garbage if the input profiles aren’t all profiles of…
nytprofhtml – Generate reports from Devel::NYTProf data SynopsisTypical usage: $ perl -d:NYTProf some_perl_app.pl $ nytprofhtml –openOptions synopsis: $ nytprofhtml [-h] [-d] [-m] [-o <output directory>] [-f <input file>] [–open]DescriptionDevel::NYTProf is a powerful feature-rich Perl source code profiler. See Devel::NYTProf for details. "nytprofhtml" generates a set of html reports from a single data file generated by…
nytprofcsv – (DEPRECATED) Devel::NYTProf::Reader CSV format implementation Synopsis $ nytprofcsv [-h] [-d] [-o <output directory>] [-f <input file>] perl -d:NYTProf some_perl_app.pl nytprofcsv Generating CSV Output…Notenytprofcsv is deprecated and will be removed in a future release. Description"nytprofcsv" is a script that implements Devel::NYTProf::Reader to create comma-seperated value formatted reports from Devel::NYTProf databases. See the Devel::NYTProf Perl…
nytprofcg – Convert an NYTProf profile into Callgrind format Synopsis $ nytprofcg –file=nytprof.out –out=nytprof.callgrind $ nytprofcg # same as aboveDescriptionReads a profile data file generated by Devel::NYTProf and writes out the subroutine call graph information it contains in Callgrind format. The output Callgrind file can be loaded into the "kcachegrind" GUI for interactive exploration. For…