Linux Manuals

NAME ocamldoc – The OCaml documentation generator SYNOPSIS ocamldoc [ options ] filename … DESCRIPTION The OCaml documentation generator ocamldoc(1) generates documentation from special comments embedded in source files. The comments used by ocamldoc are of the form (** … *) and follow the format described in the The OCaml user’s manual. ocamldoc can produce documentation…

NAME ocamldep – Dependency generator for OCaml SYNOPSIS ocamldep [ options ] filename … DESCRIPTION The ocamldep(1) command scans a set of OCaml source files (.ml and .mli files) for references to external compilation units, and outputs dependency lines in a format suitable for the make(1) utility. This ensures that make will compile the source…

NAME ocamldebug – the OCaml source-level replay debugger. SYNOPSIS ocamldebug [ options ] program [ arguments ] DESCRIPTION ocamldebug is the OCaml source-level replay debugger. Before the debugger can be used, the program must be compiled and linked with the -g option: all .cmo and .cma files that are part of the program should have been created with ocamlc -g, and…

NAME ocamlcp, ocamloptp – The OCaml profiling compilers SYNOPSIS ocamlcp [ ocamlc options ] [ -P flags ] filename … ocamloptp [ ocamlopt options ] [ -P flags ] filename … DESCRIPTION The ocamlcp and ocamloptp commands are front-ends to ocamlc(1) and ocamlopt(1) that instrument the source code, adding code to record how many times functions are…

NAME ocamlc – The OCaml bytecode compiler SYNOPSIS ocamlc [ options ] filename … ocamlc.opt [ options ] filename … DESCRIPTION The OCaml bytecode compiler ocamlc(1) compiles OCaml source files to bytecode object files and links these object files to produce standalone bytecode executable files. These executable files are then run by the bytecode interpreter…

ocamlc – The OCaml bytecode compiler Synopsisocamlc [ options ] filename … ocamlc.opt [ options ] filename … DescriptionThe OCaml bytecode compiler ocamlc(1) compiles OCaml source files to bytecode object files and links these object files to produce standalone bytecode executable files. These executable files are then run by the bytecode interpreter ocamlrun(1). The ocamlc(1)…

NAME ocamlbuild – The OCaml project compilation tool SYNOPSIS ocamlbuild [ -Is  dir1,… ] [ -libs lib1,… ] [ -lflags flag1,… ] [ -pp flags ] [ -tags tag1,… ] [ -j  parallel-jobs ] target.native [ — arg1 arg2 … ] (same options) DESCRIPTION ocamlbuild(1) orchestrates the compilation process of your OCaml project. It is similar in function to…

NAME ocaml – The OCaml interactive toplevel SYNOPSIS ocaml [ options ] [ object-files ] [ script-file ] DESCRIPTION The ocaml(1) command is the toplevel system for OCaml, that permits interactive use of the OCaml system through a read-eval-print loop. In this mode, the system repeatedly reads OCaml phrases from the input, then typechecks, compiles…

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…