ocamldebug – the OCaml source-level replay debugger. Synopsisocamldebug [ options ] program [ arguments ] Descriptionocamldebug 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 they must be…
ocamlcp, ocamloptp – The OCaml profiling compilers Synopsisocamlcp [ ocamlc options ] [ -P flags ] filename … ocamloptp [ ocamlopt options ] [ -P flags ] filename … DescriptionThe 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 called, branches of…
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)…
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)…
ocamlbuild – The OCaml project compilation tool Synopsisocamlbuild [ -Is dir1,… ] [ -libs lib1,… ] [ -lflags flag1,… ] [ -pp flags ] [ -tags tag1,… ] [ -j parallel-jobs ] target.native [ — arg1 arg2 … ] (same options) Descriptionocamlbuild(1) orchestrates the compilation process of your OCaml project. It is similar in function to make(1) except that…
ocaml – The OCaml interactive toplevel Synopsisocaml [ options ] [ object-files ] [ script-file ] DescriptionThe 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 and evaluates them,…
openbox — A minimalistic, highly configurable, next generation window manager with extensive standards support. Synopsisopenbox [–help] [–display DISPLAY] [–id ID] [–root] [–] [PROPERTY …] Descriptionobxprop 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 as text. You…
obspectrophore – SPECTROPHORE calculator Synopsis[options ] –i input_file [-u | h ] Descriptioncan 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 a robust structure-independent…
observations2map – Transforms a set of pairs <pose,observation> into metric maps. Synopsisobservations2map config_file.ini observations.simplemap output_maps_prefix Descriptionobservations2map 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 grid maps, or…
obrotate – batch-rotate dihedral angles matching SMARTS patterns Synopsis‘SMARTS-pattern’ filename atom1 atom2 atom3 atom4 angle DescriptionThe 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 package, but much…
obrotamer – generate conformer/rotamer coordinates Synopsisfilename DescriptionThe 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 optimization using molecular…
obprop – print standard molecular properties Synopsisfilename DescriptionThe 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 ] exact_mass [Isotopic…
obprobe – create electrostatic probe grid Synopsis[OPTIONS ] type pchg filename DescriptionThe 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 potential, etc. Output…
obminimize – optimize the geometry, minimize the energy for a molecule Synopsis[OPTIONS ] filename DescriptionThe obminimize tool can be used to minimize the energy for molecules inside (multi-)molecule files (e.g., MOL2, etc.) OptionsIf no filename is given, obminimize will give all options including the available forcefields. -n steps Specify the maximum number of steps (default=2500)…
objdump – display information from object files Synopsisobjdump [-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] [–dwarf-start=n] [–ctf-parent=section]…
objcopy – copy and translate object files Synopsisobjcopy [-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] [–dump-section sectionname=filename] [–update-section sectionname=filename]…
obgui – Open Babel graphical user interface SynopsisOptionsThere are no command line options. Descriptionis the Open Babel graphical user interface, an alternative to using the command line with the same capabilities. See Alsoobabel(1). The web pages for Open Babel can be found at: <http://openbabel.org/> AuthorsAn -nosplit Open Babel is developed by a cast of many,…
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…