1 User commands

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ch

ch-build Build an image and place it in the builder's back-end storage
ch-build2dir Build a Charliecloud image from Dockerfile and unpack it into a directory
ch-builder2squash Flatten a builder image into a Charliecloud SquashFS file
ch-builder2tar Flatten a builder image into a Charliecloud image tarball
ch-checkns Check "ch-run" prerequisites, e.g., namespaces and "pivot_root(2)"
ch-convert Convert an image from one format to another
ch-dir2squash Create a SquashFS file from an image directory
ch-docker2tar Flatten a Docker image into a Charliecloud image tarball
ch-fromhost Inject files from the host into an image directory, with various magic
ch-grow Deprecated name for "ch-image"; will be removed in version 0.23.
ch-image Build and manage images; completely unprivileged
ch-mount Mount a SquashFS image file using FUSE
ch-pull2dir Pull image from a Docker Hub and unpack into directory
ch-pull2tar Pull image from a Docker Hub and flatten into tarball
ch-run Run a command in a Charliecloud container
ch-run-oci OCI wrapper for "ch-run"
ch-ssh Run a remote command in a Charliecloud container
ch-tar2dir Unpack an image tarball into a directory
ch-test Run some or all of the Charliecloud test suite
ch-umount Unmount a FUSE mounted squash filesystem and remove the mount point
ch_lab change/copy label files
ch_track change/copy track file
ch_utt change/copy utterance file
ch_wave change/copy/combine waveform files
cha the Chawan text-mode browser
chacl change the access control list of a file or directory
chafa Character art facsimile generator
chage change user password expiry information
chain2dim two-dimensional match chaining
chainsaw Cut a gene tree based on a reconciliation
chake serverless configuration management tool
chameleon put an image or color in the root window
chamo.byte OCaml code editor.
change-po-charset change the charset value in content-type header of a gettext po file
change_aspect_16_9 variety of tools that transform between various MPEG stream formats
change_aspect_1_1 variety of tools that transform between various MPEG stream formats
change_aspect_221_1 variety of tools that transform between various MPEG stream formats
change_aspect_4_3 variety of tools that transform between various MPEG stream formats
change_paired_read_orientation Reverses the orientation of each paired-end FASTA sequence
changeDictionary part of OpenFOAM (The Open Source CFD Toolbox).
changelogd Changelogs without conflicts
changeme Default Credential Scanner
changeotheruserpwd launch ukui-control-center program
changestool verify, dump, modify, create or fix Debian .changes files
changetrack track changes to files
changeuserpwd launch ukui-control-center program
chaosread read raw noise source from chaoskey
chaosreader trace network sessions and export it to html format
char2sp AME
charactermanaj program to edit character avatars
chardet universal character encoding detector
chardet3 universal character encoding detector
chardetect universal character encoding detector
chardetect3 universal character encoding detector
charisma Utility to generate an index of package's maintainers
charliecloud Lightweight user-defined software stacks for high-performance computing
charm Do Charm stuff
Charmap a character map
charmap Unicode character picker and font browser
charpick_applet Character Picker Applet for the GNOME panel.
charset Set an ACM for use in one of the G0/G1 charset slots.
chartread Read Target Test Chart.
chase chase symbolic links
chasen Japanese Morphological Analysis System
chasen-config Japanese Morphological Analysis System
chasquid SMTP (email) server
chasquid-util chasquid management tool
chat write to another user
chatplus_client a simple LAN chat program (client)
chatplus_server a simple LAN chat program (server)
chattr change file attributes on a Linux file system
chatty SMS/MMS and Matrix messaging
chaussette Chaussette Documentation [image] Chaussette is a WSGI server you can use to run your Python WSGI applications. The particularity of Chaussette is that it can either bind a socket on a port like any other server does or run against already opened sockets. That makes Chaussette the best companion to run a WSGI or Django stack under a process and socket manager, such as Circus or Supervisor. Build StatusCoverage Status on master You can run a plain WSGI application, a Django application, or a Paste application. To get all options, just run chaussette --help.
chbg root background image changer & manager for X
chcon change file security context
chdir index of FreeBSD shell built-in commands
chdist script to easily play with several distributions
chdman MAME Compressed Hunks of Data (CHD) manager
chdosattr change DOS file attributes
chdrv A Chinese console with input capability
cheatmake fool make into not rebuilding certain files
check a unit testing framework for C
check-bios-nx determine if BIOS has blocked CPU's NX capabilities
check-cdcontrol-codes No manpage for this program, utility or function.
check-dfsg-status report of installed non-free software
check-enhancements show enhancement packages
check-foreground-console A tool to check if the current console is owned by the calling user
check-ifupdown-scripts-zg2.d-symlinks preliminary manpage dump-ifupdown-scripts-zg2.d-symlinks kill-ifupdown-scripts-zg2.d-symlinks check-ifupdown-scripts-zg2.d-symlinks
check-lib-depends scan port for shared libraries
check-manifest Check a Python MANIFEST.in file for completeness
check-mir check support status of dependencies
check-module program to check gnulib modules.
check-openstack-debian-image check if a Debian image is up-to-date
check-pyproject Validate the given 'pyproject.toml' file
check-regexp test regular expressions from the command line
check-sendfile Check if some files have arrived
check-sieve Syntax checker for mail sieves.
check-sort-order programs for use in ggd
check-support-status check installed packages for security support (debian-security-support)
check-symbols verify symbols exported by a new library version
check-trac-subtickets Checks consistency of subtickets in Trac.
check_calib DEPRECATED tool that checks a calibratation at the sub-pixel level
check_driver Linux 2.6(.16+) userspace device rebinding helper.
check_driver_cpad Linux 2.6(.16+) userspace device rebinding helper.
check_hd
check_het Reversible jump MCMC linkage analysis in general pedigrees
check_patroni Nagios plugin to check on patroni
check_pgactivity PostgreSQL plugin for Nagios
check_pgbackrest pgBackRest backup check plugin for Nagios
check_ssl_cert checks the validity of X.509 certificates
check_tang A Nagios plugin for Tang
check_tradis_tags bio-tradis: check for the existence of tradis tags in a bam
check_urdf try parsing a URDF file to validate it
checkalias check to see if an alias is defined.
checkbash Check for bashisms in maintainer scripts
checkbashisms check for bashisms in /bin/sh scripts
checkbox CheckboxNG Documentation CheckboxNG is a hardware testing tool useful for certifying laptops, desktops and servers with Ubuntu. It is a new version of Checkbox <http://plainbox.readthedocs.org/en/latest/glossary.html#term-checkbox> that is built directly on top of PlainBox <http://plainbox.readthedocs.org/en/latest/glossary.html#term-plainbox> CheckboxNG replaces Checkbox, where applicable. WARNING:
checkbox-cli CheckboxNG Documentation CheckboxNG is a hardware testing tool useful for certifying laptops, desktops and servers with Ubuntu. It is a new version of Checkbox <http://plainbox.readthedocs.org/en/latest/glossary.html#term-checkbox> that is built directly on top of PlainBox <http://plainbox.readthedocs.org/en/latest/glossary.html#term-plainbox> CheckboxNG replaces Checkbox, where applicable. WARNING:
checkbox_ng CheckboxNG Documentation CheckboxNG is a hardware testing tool useful for certifying laptops, desktops and servers with Ubuntu. It is a new version of Checkbox <http://plainbox.readthedocs.org/en/latest/glossary.html#term-checkbox> that is built directly on top of PlainBox <http://plainbox.readthedocs.org/en/latest/glossary.html#term-plainbox> CheckboxNG replaces Checkbox, where applicable. WARNING:
checkbrack check parenthesis and bracket count
checkdigits verify and compute checkdigits
checkdirfile verify Dirfile database metadata
checkdotdin This program's purpose is to be an audio synthesizer of a 3rd kind.
checker SPARK Proof Checker
checkerg++ compiler interface to Checker
checkergcc compiler interface to Checker
checkFaMesh part of OpenFOAM (The Open Source CFD Toolbox).
checkflac A tagger for whole album FLACs using data from the MusicBrainz service
checkgmail system tray applet to check a Gmail account for new mail
checkinstall generate packages by tracking installation scripts
checkint Show active network interfaces
checkisomd5 check an MD5 checksum implanted by implantisomd5
checkit_tiff is a conformance checker for baseline TIFFs'
checklink check the validity of links in an HTML or XHTML document
checkLocalKDC checks a LocalKDC
checkMesh part of OpenFOAM (The Open Source CFD Toolbox).
checkmk Awk script for generating C unit tests for use with the Check unit testing framework.
checkmp3 identify MP3s that do not follow the MP3 format
checkndx a collection of tools for xbase database files
checkpkg Compare the current build package with the repository version
checkproof manual page for checkproof 3.2.5
checkpto Helper program for Hugin's assistant
checkrebuild
checkrestart check which processes need to be restarted after an upgrade
checksctp check if kernel supports SCTP
checksec check executable and kernel security properties
checkservice checks the status of services on (remote) hosts
checkstyle static code analysis tool to check if Java source code complies with coding rules
checksub a validator for NCBI ASN.1 Seq-submit data
checkTargetSortedness check BAM file for sortedness
checkUserPwd launch ukui-control-center program
checkuserpwd launch ukui-control-center program
checkXML An XML lint tool for KDE DocBook XML documents.
checkXML5 An XML lint tool for KDE DocBook XML documents
checkXML6 An XML lint tool for KDE DocBook XML documents
cheese tool to take pictures and videos from your webcam
cheesetracker sound-module tracking program
cheetah Python template command-line tool
cheetah-analyze Python template command-line tool
cheetah-analyze3 Python template command-line tool
cheetah-compile Python template command-line tool
cheetah-compile-python2.2 Python template command-line tool
cheetah-compile-python2.3 Python template command-line tool
cheetah-compile-python2.4 Python template command-line tool
cheetah-compile3 Python template command-line tool
cheetah-python2.2 Python template command-line tool
cheetah-python2.3 Python template command-line tool
cheetah-python2.4 Python template command-line tool
cheetah3 Python template command-line tool
chef-shell The man page for the chef-shell command line tool. chef-shell is a recipe debugging tool that allows the use of breakpoints within recipes. chef-shell runs as an Interactive Ruby (IRb) session. chef-shell supports both recipe and attribute file syntax, as well as interactive debugging features. NOTE: The chef-shell executable is run as a command-line tool.
chelonia Client for the Chelonia storage system
chem embed chemical structure diagrams in groff documents
chemdiff finding duplications and visual comparison of two files containing multiple structures
chemeq Chemical Equation Parser and Renderer
chemFoam part of OpenFOAM (The Open Source CFD Toolbox).
chemkinToFoam part of OpenFOAM (The Open Source CFD Toolbox).
chemps2 spin-adapted DMRG for ab initio quantum chemistry
chemstruc calls a browser to view molecular structures
chemtool chemical structures editor
cheops-ng network monitor tools for system administration
cherokee Cherokee Web Server
cherokee-admin Runs Cherokee's administrative interface
cherokee-config script to get information about the installed version of Cherokee
cherokee-guardian Cherokee web server safe invoker
cherokee-tweak Command-line interface to the Cherokee administrative interface
cherokee-worker Cherokee Web Server internal worker
cherokee_logrotate Cherokee on-the-fly log rotation tool
cherryd Starts the CherryPy HTTP server as a daemon
cherryd3 Starts the CherryPy HTTP server as a daemon
cherryhotreload sends a hotReload signal to a cherrypy process
cherrypy Python-based tool for developing dynamic web sites
cherrytree a hierarchical note taking application
Chess Chess for GNUstep ported from OPENSTEP
chewing-cli Tools of the Chewing (酷音) intelligent Zhuyin input method.
chewing-cli-dump Dump the dictionary entries into tsi.src formatted stream
chewing-cli-info Display information about the dictionary
chewing-cli-init-database Create a new dictionary file
chewing-editor chewing userphrase editor
chewmail mail archiver
chezdav simple WebDAV server
chezscheme Chez Scheme petite - Petite Chez Scheme
chezscheme9.5 Chez Scheme petite9.5 - Petite Chez Scheme
chflags change file flags
chfn change your finger information
chg a fast client for Mercurial command server
chgrp change group ownership
chi2mcrl2 convert a Chi (v1.0) model to an mCRL2 specification
chiaki PlayStation remote play client
chicken A Scheme-to-C translator
chicken-bug generates a bug report from user input
chicken-config script that emits suitable options for the host systems C compiler
chicken-csc driver program for the CHICKEN Scheme compiler
chicken-csi The CHICKEN Scheme interpreter
chicken-do run a shell command unless the target exists and any dependency is not newer than the target
chicken-install download and install extension libraries for CHICKEN Scheme
chicken-profile generate a report from profile-information
chicken-setup install extension libraries for Chicken Scheme
chicken-status list information about installed libraries
chicken-uninstall uninstall extension library
childCheckpwdwithPAM launch ukui-control-center program
chilight highlight a C source file
chill No manpage for this program, utility or function.
chill-2.95 No manpage for this program, utility or function.
chime2jmol convert chime into jmol scripts
chimera2 X/Athena World-Wide Web Client
ChimeraSlayer detects likely chimeras in PCR amplified DNA
chimeraslayer detects likely chimeras in PCR amplified DNA
chio medium changer control utility
ChiPass
ChiPass-cli
chipcard-config A little program to output installation paths
chipcard-tool a commandline client to access smart cards via libchipcard
chipcardd LibChipCard's card reader daemon
chipcenter Feature Centering Tool for ChIP-seq data analysis
chipcor Feature Correlation Tool for ChIP-seq data analysis
chipextract Feature Correlation and Extraction Tool for ChIP-seq data analysis
chippart Partitioning Tool for ChIP-seq data analysis
chippeak Locates signal peaks within a set of tags positions produced by a ChIP-Seq experiment
chipscore Feature Extraction Tool for ChIP-seq data analysis
chipw Editor for Chip's Challenge??? and Tile World.
chirp command line tool providing explicit control of a Chirp server.
chirp_audit_cluster share resources in a heterogeneous, and unreliable computing environment
chirp_benchmark do micro-performance tests on a Chirp server
chirp_distribute copy a directory from one Chirp server to one or more Chirp server(s).
chirp_fuse create a FCFUSEFT mount point with virtual access to remote chirp servers
chirp_get get a single file from a Chirp server to local machine
chirp_md5sum share resources in a heterogeneous, and unreliable computing environment
chirp_put copy a single file from local machine to a Chirp server
chirp_server create a Chirp user-level filesystem
chirp_server_hdfs run a chirp server with HDFS client setup
chirp_status get current status of a one or more Chirp server(s)
chirp_stream_files move data to/from chirp servers in parallel
chirpw A tool for programming two-way radio equipment
chkalias check to see if an alias is defined.
chkconc list concatenation for hinshi
chkdupexe find duplicate executables
chkdvifont CHecK DVI/tfm/font file and report information of FONTs
chkhelp check performance metrics help text files
chklastlog check lastlog-file for deleted entries
chklref manual page for chklref 3.1.2
chkmail check for new mail
chkmpqcval run the mpqc validation suite chkmpqcval - check the .out files for correctness
chknvm Qualcomm Atheros PLC Image File Validator
chknvm2 Qualcomm Atheros PLC Image File Validator
chkpib Qualcomm Atheros PLC Parameter File Inspector
chkpib2 Qualcomm Atheros PLC Parameter File Inspector
chkrootkit Determine whether the system is infected with a rootkit
chktex finds typographic errors in LaTeX.
chktri check for trigraphs in C source code
chktrust Check the trust of a PE executable.
chkuser Slash user utility tool
chkweb runs the LaTeX parts of a CWEB file through chktex
chkwtmp check wtmp-file for deleted entries
chm2pdf A tool convert chm to pdf format
chm_http Simplistic web server to allow browsing of chm files without extracting them.
chmcmd The FPC Pascal htmlhelp (CHM) compiler
chmcmd-2.6.0 The FPC Pascal htmlhelp (CHM) compiler
chmcmd-2.6.4 The FPC Pascal htmlhelp (CHM) compiler
chmcmd-3.0.0 The FPC Pascal htmlhelp (CHM) compiler
chmcmd-3.0.4 The FPC Pascal htmlhelp (CHM) compiler
chmcmd-3.2.0 The FPC Pascal htmlhelp (CHM) compiler
chmcmd-3.2.2 The FPC Pascal htmlhelp (CHM) compiler
chmls The FPC Pascal CHM utility
chmls-2.6.0 The FPC Pascal CHM utility
chmls-2.6.4 The FPC Pascal CHM utility
chmls-3.0.0 The FPC Pascal CHM utility
chmls-3.0.4 The FPC Pascal CHM utility
chmls-3.2.0 The FPC Pascal CHM utility
chmls-3.2.2 The FPC Pascal CHM utility
chmod change file mode bits
chmoddic change access rights for a directory
chmsee A chm file viewer written in GTK
choom display or adjust OOM-killer score
chooseLines Randomly choose k lines from a file of n lines, for 0 < k < n.
choosewm Select a window manager to be used.
choqok Blogging client for KDE4
chordata Analyzes chords on audio files
chordii A text file to music sheet converter
choreonoid an integrated robotics GUI environment
chown change file owner and group
chp4_servs Starts the P4 secure servers on machines known to MPICH
chpass add or change user database information
chpl Change header of SWI-Prolog saved-states
chpmnk-analog A circuit schematic capture tool and simulation environment
chpmnk-diglog A circuit schematic capture tool and simulation environment
chpmnk-loged A circuit schematic capture tool and simulation environment
chpp text preprocessor
chprop change file properties on the Rio Karma
chr chr is a terminal based editor
chroma general purpose syntax highlighting program
chroma-v2 general purpose syntax highlighting program
ChromHMM Learning and analysis chromatin states using a multivariate Hidden Markov Model
ChromImpute Large-scale systematic epigenome imputation
chromium the web browser from Google
chromium-browser the web browser from Google
chromostitch.pl Makes stitch files for feeding to geneparse.pl to allow feeding of multiple chromosomes to programs like murasaki
chronic runs a command quietly unless it fails
chronicle A simple blog compiler.
chronicle-entry-filter Convert blog files to HTML, if required.
chronicle-ping Send outgoing PING requests for new pages.
chronicle-rss-importer Import entries from an RSS feed to chronicle
chronicle-spooler Automatically post pre-written entries.
chrony programs for keeping computer clocks accurate
chronyc command-line interface for chrony daemon
chronyd a daemon that sets your clock from the Net.
chroot run command or interactive shell with special root directory
chroot_package_run repeat a program within the package with the help of FCchrootFT
chrootuid run command in restricted environment
chrpath change the rpath or runpath in binaries
chrt manipulate the real-time attributes of a process
chsh change your login shell
chsh.ldap change login shell in LDAP
cht chemtool drawings analyzer
cht.sh The only cheat sheet you need (command line client for cheat.sh)
chtMultiRegionFoam part of OpenFOAM (The Open Source CFD Toolbox).
chtMultiRegionSimpleFoam part of OpenFOAM (The Open Source CFD Toolbox).
chtMultiRegionTwoPhaseEulerFoam part of OpenFOAM (The Open Source CFD Toolbox).
chts Cahn-Hilliard Timestepping Demo
chuck audio programming language for real-time synthesis, composition, and performance
chuck.alsa audio programming language for real-time synthesis, composition, and performance
chuck.oss audio programming language for real-time synthesis, composition, and performance
chuck.pulse audio programming language for real-time synthesis, composition, and performance
chui Cahn-Hilliard User Interface
chvt change foreground virtual terminal

ci

ci check in RCS revisions
cicqconv
cicqsync
cif-diff A tool to compare two mmCIF files
cif-drop A tool to drop columns from mmCIF files
cif-grep A tool like grep to print fields in mmCIF files that match patterns
cif-merge Merge the content of a modified PDB file into a mmCIF file
cif-to-utf8 convert CIF escape sequences into Unicode characters.
cif-validate Validate the content of a mmCIF file
cif2cbf convert a CIF to a CBF file
cif2cell prepare CIF files for electronic structure calculations
cif2cod parse a CIF file, prepare a COD database table entry from it.
cif2csv convert a CIF file into a CSV file.
cif2hkl cif2hkl
cif2json parse CIF file and print out the structure generated by CIF parser.
cif2pdb Convert the contents of a mmCIF file into PDB format
cif2qg parse CIF file and print out the quotient graph.
cif2rdf parse a CIF file and describe its properties in RDF format.
cif2ref parse a CIF file and print out the essential information in the COD REF format. Accepts optional bibliography file in ref, xrf or plaintext format as the second command line argument.
cif2tsv get specified data values from a CIF file(s).
cif2xyz read CIF files and print atom coordinates in XYZ format. The default output format is as described in https://en.wikipedia.org/wiki/XYZ_file_format.
cif_adjust_journal_name_volume parse a CIF file, update the journal name and journal volume based on heuristics and output the updated file to STDOUT. The following heuristic is applied: if journal volume starts with a letter, add this letter to the journal name, and leave journal volume purely numeric.
cif_automorphism find automorphism orbits in CIF files.
cif_bounding_box transform non-crystal CIF file (missing cell parameters and symmetry information, Cartesian coordinates are given instead of fractional) into a crystal description.
cif_cell_contents calculate cell contents from atom coordinates and symmetry information.
cif_classify classify a CIF structure -- find out if it is organic compound, inorganic, mineral, etc.
cif_cod_check parse a CIF file, check if certain data values match COD requirements and IUCr data validation criteria (Version: 2000.06.09, https://www.iucr.org/__data/iucr/ftp/pub/dvntests or ftp://ftp.iucr.org/pub/dvntests)
cif_cod_deposit deposit CIFs into COD database using CGI deposition interface.
cif_cod_numbers find COD numbers for the CIF files in given directories of file lists.
cif_CODify extract essential data from the input CIF file and format it using the rules of the Crystallography Open Database (COD).
cif_compare_dics checks a pair of DDL1/DDLm dictionaries for compatibility breaking differences. Discrepancies between corresponding enumeration sets, default values, permitted ranges as well as data items unique to one of the dictionaries are reported.
cif_correct_tags correct misspelt tags in a CIF file and output made changes into the standard I/O streams. By default, only tags from CIF Core and CIF COD dictionaries with extra '^_+' prefixes are corrected. Additionally, a replacement list file can be provided for the correction of misspelt tags.
cif_create_AMCSD_pressure_temp_tags parse a CIF file, determine pressure and temperature tag values from the values of other tags. Designed for CIFs from AMCSD.
cif_ddl1_dic_check check DDL1 dictionaries against a set of best practice rules.
cif_ddlm_dic_check check DDLm dictionaries against a set of best practice rules.
cif_ddlm_dic_print pretty-print a DDLm dictionary file.
cif_dictionary_tags generate a list of all tags in a CIF dictionary.
cif_diff parse two CIF files and compare their content
cif_distances calculate minimal distance between atoms read from a CIF file.
cif_estimate_Z calculate Z value (i.e. the number of "chemical formula units" in the unit cell) using the provided cell volume, crystal density and molecular weight.
cif_eval_numbers read a CIF file and convert those number values that are written as simple fractions (e.g. "1/4") into a single floating point number.
cif_Fcalc compute the structure factors from CIF files.
cif_fillcell generate symmetric atoms from a CIF file.
cif_filter parse a CIF file and print out essential data values in the CIF format, the COD CIF style. This script has also many capabilities -- it can restore space group symbols from symmetry operators (consulting predefined tables), parse and tidy-up _chemical_formula_sum, compute cell volume, exclude unknown or "empty" tags, and add specified bibliography data.
cif_find_duplicates find COD numbers for the .cif files in given directories of file lists.
cif_find_symmetry find the symmetry of the atoms in the unit cell of a CIF crystal structure. In order to obtain correct results most of the time, all atoms of the unit cell should be present in the input. This can be achieved by using cif_p1 or similar programs.
cif_fix_AMCSD_aniso_labels read the CIF file, assuming that it follows AMCSD atom naming conventions, and correct the _atom_site_aniso_label values using some heuristics.
cif_fix_AMCSD_atom_labels read the CIF file, assuming that it follows AMCSD atom naming conventions, and correct duplicated _atom_site_label and _atom_site_aniso_label values.
cif_fix_values correct various CIF file values and output the made changes into the standard I/O streams. The script is capable of making these corrections: - Converting temperature from degrees Celsius to kelvins, removing temperature units of measurement, processing other undefined temperature values; - Fixing misspelled values by using the provided replacement value file; - Fixing enumeration values in CIF file against CIF dictionaries; - Correcting values of '_exptl_crystal_density_meas' data item. All described corrections are enabled by default, but can be disabled by prefixing the corresponding options by '--do-not', '--dont' or '--no' (for example, '--no-fix-temperature').
cif_guess_AMCSD_atom_types read the CIF file, assuming that it follows AMCSD atom naming conventions, and assign atom types and attached hydrogen counts as follows: - for 'Wat' atoms (with or without a number) assign atom type 'O' and hydrogen count 2. - for 'O-H' atoms assign atom type 'O' and hydrogen count 1. - for 'OH' atoms assign atom type 'O' and hydrogen count 0 (hydrogen atoms are usually given explicitly in such cases). - For other 'O[a-rt-z]' matching atoms, assign type 'O' and no attached hydrogens.
cif_hkl_check check the correspondence between CIF and diffraction data files, taking data block names, cell parameters, author lists and symmetry group names into account.
cif_hkl_COD_number parse a CIF file and print out the essential information in the COD CIF format
cif_list_tags parse CIF file(s) and output a list of CIF data items.
cif_mark_disorder mark disorder in CIF files judging by distance and occupancy.
cif_merge merge data values in identical data blocks of multiple CIFs. Unique data items are combined into a single data block of the output CIF; data items with equivalent values are silently merged into one. When a value differs for the same data item and the same data block in two files, a warning (error) is issued.
cif_molecule restore molecules from a CIF file.
cif_mpod_v1_to_v2 convert MPOD structures from MPOD dictionary V1 to MPOD dict. V2 based data names.
cif_mpod_v1_to_v3 convert MPOD structures from MPOD dictionary V1 to MPOD dict. V3 based data names.
cif_mpod_v2_to_v1 convert MPOD structures from MPOD dictionary V2 to MPOD dict. V1 based data names.
cif_mpod_v3_to_v1 convert MPOD structures from MPOD dictionary V1 to MPOD dict. V3 based data names.
cif_overlay overlay atoms from each pair of CIFs given on the command line.
cif_p1 expand atoms in CIF to the P1 space group, preserving molecules (i.e. outputting atoms that are bonded at bond distances from each other).
cif_parse parse CIF file and print out the structure generated by CIF parser.
cif_polymer_multiplicity parse CIF file and print out multiplicity and dimensionality per each molecule. Requires TOPOCIF data items for representation of labeled quotient graphs: _topol_net.id, _topol_atom.atom_label, _topol_atom.node_id, _topol_link.node_id_1, _topol_link.node_id_2, _topol_link.translation_2_x, _topol_link.translation_2_y, _topol_link.translation_2_z.
cif_printout Parse CIF file and print out the structure generated by CIF parser.
cif_printout_Python Parse CIF file and print out the structure generated by CIF parser.
cif_reduce_cell perform reductions of the unit cell using different algorithms.
cif_reduce_Niggli perform Niggli cell reduction of CIF files.
cif_reformat_AMCSD_author_names parse a CIF file, reformat author names in AMCSD convention into COD format.
cif_reformat_pubmed_author_names parse a CIF file, reformat author names in PubMed convention into COD format.
cif_reformat_uppercase_author_names parse a CIF file, reformat author names in AMCSD convention into COD format.
cif_select read CIFs and print out selected tags with their values.
cif_set_value set specified CIF data items to the given values.
cif_sort_atoms sort atoms in a CIF file in given order. Accepts more than one sorting criterion.
cif_split split CIF files into separate files with one data_ section each. This script parses given CIF files to separate the data blocks, so is capable of splitting non-correctly formatted and nested CIF files.
cif_split_primitive split CIF files into separate files with one data_ section each. This is a very naive and primitive version of the splitter, which expects each data_... section to start on a new line. It may fail on some CIF files that do not follow such convention. For splitting of any correctly formatted CIF files, one must do full CIF parsing using CIF grammar and tokenisation of the file.
cif_symop_apply apply symmetry operator(s) to all atoms in a CIF.
cif_tags_in_list parse a DDL1 CIF dictionary file and generate a list of tags with additional information about their loop constraints. The first column signals whether the tag must be declared in a looped list ( '0' -- no, '1' -- 'yes', 2 -- 'both'), the second column signals whether the tag must be present in the loop structure containing other items of the designated _category, ( '0' -- no, '1' -- yes) and the third column is the tag name itself.
cif_tcod_tree prepare a calculation tree from descriptions in TCOD CIF file.
cif_validate validate CIF files against CIF dictionaries (DDL1 or DDLm).
cif_values read CIFs and print out requested tag values in a tabular form.
cifparse parse CIF file(s), check syntax, and optionally output pretty-printed data.
cifscreds manage NTLM credentials in kernel keyring
cifsiostat Report CIFS statistics.
cifvalues get specified data values from a CIF file(s).
CigiDummyIG Sample CIGI Image Generator
CigiMiniHost Sample CIGI Host
cil the command-line issue list
cilc Mono CIL-to-C binding generator
cim Compile Simula programs into C
cimconv tool to convert contact lists and history from other IM clients
cin2gtab converts text input method table to hime's .gtab format
cin2tab The input-method table converter for xcin system.
cin2tab-gb The input-method table converter for xcin system.
cindex prepares the trigram index for csearch(1)
cindy Utility to alter or display the contents of a suite
cineoob search movies and persons around cinema
cinepaint 32-bit image painting and retouching
cinepaint-remote 32-bit image painting and retouching
cinepainttool script to perform various Gimpy functions
cinfo C programming language documentation tool
cinfoc cinfo database compiler
cinfodc cinfo database de-compiler
cinnamon desktop
cinnamon-extension-tool extension management program
cinnamon-launcher Start or restart a cinnamon session
cinnamon-looking-glass Debugging interface for Cinnamon
cinnamon-menu-editor Editor for the panel menu
cinnamon-screensaver screen saver and locker
cinnamon-screensaver-command controls Cinnamon screensaver
cinnamon-screensaver-lock-dialog message setting for cinnamon screensaver
cinnamon-session Start the GNOME desktop environment
cinnamon-session-cinnamon Start the GNOME desktop environment
cinnamon-session-cinnamon2d Start the GNOME desktop environment
cinnamon-session-properties Configure applications to start on login
cinnamon-session-quit End the current GNOME session
cinnamon-settings Configuration panel for cinnamon
cinnamon-settings-daemon Cinnamon settings daemon
cinnamon2d desktop
cint.root C/C++ interpreter
cints
ciptool Bluetooth Common ISDN Access Profile (CIP)
circlator circularize genome assemblies
circlepack manipulate and display circle packings
circo filter for drawing directed graphs neato - filter for drawing undirected graphs twopi - filter for radial layouts of graphs circo - filter for circular layout of graphs fdp - filter for drawing undirected graphs sfdp - filter for drawing large undirected graphs patchwork - filter for squarified tree maps osage - filter for array-based layouts
circos generate circular data visualizations
circuits.bench simple benchmaking of the circuits library
circuits.bench3 simple benchmaking of the circuits library
circuits.web Web Server and testing tool
circuits.web3 Web Server and testing tool
circus Circus Documentation [image] Circus is a Python program which can be used to monitor and control processes and sockets. Circus can be driven via a command-line interface, a web interface or programmatically through its python API. To install it and try its features check out the examples, or read the rest of this page for a quick introduction.
circus-plugin execute a Circus plugin
circus-top display Circus processes
circusctl circus daemon control insterface
circusd the circus daemon
circusd-stats circus daemon stats aggregator
cisco-decrypt decrypts an obfuscated Cisco vpn client pre-shared key
cisco7crack Crypt and decrypt the cisco type 7 passwords
cisco_ios2dlf convert cisco logs to dlf format
ciscodump Provide interfaces to capture from a remote Cisco device through SSH.
ciso PSP ISO compression tool
cistopbm convert Compuserve RLE image to PBM
cit2pmid find candidate NCBI PubMed identifiers for a citation
cite a fast unix command line interface to WWW services
citeproc-lua make CSL citations and bibliography for LaTeX
citmail Citadel /usr/sbin/sendmail replacement
citnames Deduce command semantic
citygml2vrml Convert citygml files to vrml
citygmltest Parsing CityGML file
civetweb embeddable web server with optional CGI, SSL and Lua support
ciwiki simple wiki implementation with built-in webserver

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