Linux Manuals

NAME openbox — A minimalistic, highly configurable, next generation window manager with extensive standards support. SYNOPSIS openbox [–help] [–display DISPLAY] [–id ID] [–root] [–] [PROPERTY …] DESCRIPTION obxprop is a tool for displaying the properties on an x window. This tool has a similar functionality to xprop, but obxprop allows you to see UTF-8 strings…

NAME obspectrophore – SPECTROPHORE calculator SYNOPSIS [options ] –i input_file [-u | h ] DESCRIPTION can be used to generate Spectrophores, which are one-dimensional descriptors generated from the property fields surrounding the molecules. This technology allows the accurate description of molecules in terms of their surface properties or fields. Comparison of molecules property fields provides…

NAME observations2map – Transforms a set of pairs <pose,observation> into metric maps. SYNOPSIS observations2map config_file.ini observations.simplemap output_maps_prefix DESCRIPTION observations2map reads a multi metric map description from the config file and insert all the observations into it. Then it saves all the metric maps to independent files. It can be used to generate point maps, occupancy…

NAME obrotate – batch-rotate dihedral angles matching SMARTS patterns SYNOPSIS ‘SMARTS-pattern’ filename atom1 atom2 atom3 atom4 angle DESCRIPTION The obrotate program rotates the torsional (dihedral) angle of a specified bond in molecules to that defined by the user. In other words, it does the same as a user setting an angle in a molecular modelling…

NAME obrotamer – generate conformer/rotamer coordinates SYNOPSIS filename DESCRIPTION The obrotamer tool can be used as part of a conformational search by generating random isomers based on rotating dihedral angles. These rotamers are not conformers — that is, obrotamer does not perform geometry optimization after generating the rotamer structure. The obminimize tool can do geometry…

NAME obprop – print standard molecular properties SYNOPSIS filename DESCRIPTION The obprop program is a tool to print a set of standard molecular properties for all molecules in a file. It also serves as example code for using the Open Babel library (libopenbabel). Output format includes: name [Name ] formula [Formula ] mol_weight [Molecular Weight…

NAME obprobe – create electrostatic probe grid SYNOPSIS [OPTIONS ] type pchg filename DESCRIPTION The obprobe tool creates a grid around a molecule, placing a probe atom with a specified atom type and partial charge at each point to calculate the MMFF94 energy. This can be used for docking experiments to test hydrogen-bond affinity, electrostatic…

NAME obminimize – optimize the geometry, minimize the energy for a molecule SYNOPSIS [OPTIONS ] filename DESCRIPTION The obminimize tool can be used to minimize the energy for molecules inside (multi-)molecule files (e.g., MOL2, etc.) OPTIONS If no filename is given, obminimize will give all options including the available forcefields. -n steps Specify the maximum…

NAME objdump – display information from object files SYNOPSIS objdump [-a|–archive-headers]         [-b bfdname|–target=bfdname]         [-C|–demangle[=style] ]         [-d|–disassemble[=symbol]]         [-D|–disassemble-all]         [-z|–disassemble-zeroes]         [-EB|-EL|–endian={big | little }]         [-f|–file-headers]         [-F|–file-offsets]         [–file-start-context]         [-g|–debugging]         [-e|–debugging-tags]         [-h|–section-headers|–headers]         [-i|–info]         [-j section|–section=section]         [-l|–line-numbers]         [-S|–source]         [–source-comment[=text]]         [-m machine|–architecture=machine]         [-M options|–disassembler-options=options]         [-p|–private-headers]         [-P options|–private=options]         [-r|–reloc]         [-R|–dynamic-reloc]         [-s|–full-contents]         [-W[lLiaprmfFsoORtUuTgAck]|          –dwarf[=rawline,=decodedline,=info,=abbrev,=pubnames,=aranges,=macro,=frames,=frames-interp,=str,=str-offsets,=loc,=Ranges,=pubtypes,=trace_info,=trace_abbrev,=trace_aranges,=gdb_index,=addr,=cu_index,=links]]         [-WK|–dwarf=follow-links]         [-WN|–dwarf=no-follow-links]         [-L|–process-links]         [–ctf=section]         [-G|–stabs]         [-t|–syms]         [-T|–dynamic-syms]         [-x|–all-headers]         [-w|–wide]         [–start-address=address]         [–stop-address=address]         [–no-addresses]         [–prefix-addresses]         [–[no-]show-raw-insn]         [–adjust-vma=offset]         [–dwarf-depth=n]…

NAME objcopy – copy and translate object files SYNOPSIS objcopy [-F bfdname|–target=bfdname]         [-I bfdname|–input-target=bfdname]         [-O bfdname|–output-target=bfdname]         [-B bfdarch|–binary-architecture=bfdarch]         [-S|–strip-all]         [-g|–strip-debug]         [–strip-unneeded]         [-K symbolname|–keep-symbol=symbolname]         [–keep-file-symbols]         [–keep-section-symbols]         [-N symbolname|–strip-symbol=symbolname]         [–strip-unneeded-symbol=symbolname]         [-G symbolname|–keep-global-symbol=symbolname]         [–localize-hidden]         [-L symbolname|–localize-symbol=symbolname]         [–globalize-symbol=symbolname]         [–globalize-symbols=filename]         [-W symbolname|–weaken-symbol=symbolname]         [-w|–wildcard]         [-x|–discard-all]         [-X|–discard-locals]         [-b byte|–byte=byte]         [-i [breadth]|–interleave[=breadth]]         [–interleave-width=width]         [-j sectionpattern|–only-section=sectionpattern]         [-R sectionpattern|–remove-section=sectionpattern]         [–keep-section=sectionpattern]         [–remove-relocations=sectionpattern]         [-p|–preserve-dates]         [-D|–enable-deterministic-archives]         [-U|–disable-deterministic-archives]         [–debugging]         [–gap-fill=val]         [–pad-to=address]         [–set-start=val]         [–adjust-start=incr]         [–change-addresses=incr]         [–change-section-address sectionpattern{=,+,-}val]         [–change-section-lma sectionpattern{=,+,-}val]         [–change-section-vma sectionpattern{=,+,-}val]         [–change-warnings] [–no-change-warnings]         [–set-section-flags sectionpattern=flags]         [–set-section-alignment sectionpattern=align]         [–add-section sectionname=filename]…

NAME obgui – Open Babel graphical user interface SYNOPSIS OPTIONS There are no command line options. DESCRIPTION is the Open Babel graphical user interface, an alternative to using the command line with the same capabilities. SEE ALSO obabel(1). The web pages for Open Babel can be found at: <http://openbabel.org/> AUTHORS An -nosplit Open Babel is…

NAME obgrep – an advanced molecular search program using SMARTS SYNOPSIS [OPTIONS ] ‘SMARTS-pattern’ filename DESCRIPTION The obgrep tool can be used to search for molecules inside multi-molecule database files (e.g., SMILES, SDF, etc.) or across multiple files. OPTIONS If only a filename is given, obgrep will attempt to guess the file type from the…

NAME obgen – generate 3D coordinates for a molecule SYNOPSIS [OPTIONS ] filename DESCRIPTION The 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…

NAME obfit – superimpose two molecules based on a pattern SYNOPSIS SMARTS-pattern fixed-file outfile DESCRIPTION Superimpose 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…

NAME obexftpd – Mobile Equipment file transfer server SYNOPSIS obexftpd [OPTIONS] [TRANSPORT] DESCRIPTION With 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. OPTIONS The ordering of options is important. The first transport option will…

NAME obexftp – Mobile Equipment file transfer tool SYNOPSIS obexftp [OPTION] [COMMANDS] DESCRIPTION obexftp 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….

NAME 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 Index

NAME obex_push – Push and Receive Files over the Bluetooth OBEX Push Channel SYNOPSIS obex_push [<channel>] [<bdaddr> <filename>] DESCRIPTION obex_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> OPTIONS If no options are given,…

NAME obex-data-server – D-Bus service providing OBEX functionality SYNOPSIS obex-data-server [OPTIONS] DESCRIPTION obex-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…

NAME obenergy – calculate the energy for a molecule SYNOPSIS [OPTIONS ] filename DESCRIPTION The obenergy tool can be used to calculate the energy for molecules inside (multi-)molecule files (e.g., MOL2, etc.) OPTIONS If no filename is given, obenergy will give all options including the available forcefields. -v Verbose: print out all individual energy interactions…