Package: nef-pipelines
NEF-PipelinesTools for Manipulating NEF [NMR Exchange Format] Files and Foreign File AccessNEF-Pipelines is a set of command line (currently... there maybe a gui later!) tools for maniulating [NEF] or NMR
Exchange Format files which can be used to move NMR meta data [peaks, shifts, sequences etc] between NMR data processing
programs.The progrmas provide basic tools for manipulating nef files:Please note NEF-Pipelines is beta software and is quite new so if you do find problems put in an issue on theissue tracker. Even better if you can help improve the software do get in touch, there is much to do!molecular chains: listing, renaming and cloning molecular chainssave-frames [tables]: deleting, inserting, listing and pretty printing (tabulate)headerscreation / updating NEF headers with correct UUIDs and historystreaming: NEF files into a pipelinetesting: self testing of NEF pipelinesIt also provides tools for importing and exporing non NEF files from the following programs [transcoding / translators]fastasequence [read and write]marsshifts [write]nmrpipesequences [read]shifts [read]peaks [read]nmrview/nmrfxpeaks [read and write]sequence [read]shifts [read]palesrdc restraints [write]rdc restraints template [write]pdbxsequence [read]xplorsequence [read]dihedral restraints [read]distance restraints 'single atom selections [read]InstallationNEF-Pipelines can be installed using pip and pipxFirstly install pipx if you need to, using the commands for your OS ...OSXpython3-mpipinstall--userpipx
python3-mpipxensurepathWindows using WSL2follow the instruction for linux distro of choice inside WSL2...Ubuntu / Mintsudoaptinstallpipxpython3-venvFedora / RHEL / Centos/ ROCKY Linux / AlmaLinuxsudodnfinstallpipxopenSUSEsudozypperinstallpython3-pipxThen to install NEF-Pipelinespython3-mpipxinstallnef-pipelinesafter the install has completed you can typenefand should see output that startsUsage: nef [OPTIONS] COMMAND [ARGS]...                                                                                                                                                                                        ✔ ╱ took 14s  ╱ nef_pipelines  ╱ at 23:29:36 

Options:
...Updating NEF-Pipelinespython3-mpipinstall--user-UpipxPipelines and Standalone UseAll commands also have a
help options triggered using--helpor when no input is detected. So for example thenefcommand on its own producesUsage: nef [OPTIONS] COMMAND [ARGS]...

Options:
  --install-completion [bash|zsh|fish|powershell|pwsh]
                                  Install completion for the specified shell.
  --show-completion [bash|zsh|fish|powershell|pwsh]
                                  Show completion for the specified shell, to
                                  copy it or customize the installation.

  --help                          Show this message and exit.

Commands:
  chains   - carry out operations on chains
  fasta    - read and write fasta sequences
  frames   - carry out operations on frames in nef frames
  header   - add a header to the stream
  mars     - export mars [shifts and sequences]
  nmrpipe  - read nmrpipe [peaks shifts & sequencess]
  nmrview  - read and write nmrview [peaks, sequences & shifts]
  pales    - read and write pales/dc [rdcs]
  pdb      - read pdb [sequences]
  stream   - stream a nef file
  test     - run the test suiteIndividual nef pipeline componenets can be used standalone by using the--inor--pipeparameter which will either
read a foreign file for translators or read a NEF file for commands that manipulate NEF files. So for example to lists
the frames in NEF frame you can typenefframeslist--intest_data/pales_test_1.nefthis will produceentrypales_test

nef_molecular_systemnef_rdc_restraint_list_test_1which shows  the entry name followed by the frames in the filetest_data/pales_test_1.nef. However,  the real
power in NEF-Pipelines comes from combining pipeline commands together or with command line tools. For examplenefheader\|neffastaimportsequencetailin1.fasta\|src/nefnmrviewimportshiftstailin1.out\|src/nefnmrviewimportpeakstailin1.out\>tailin1.nefwill create a valid NEF header followed by the tailin1 sequence as a molecular system and then import shifts and peaks
for talin1 before writing a new NEF filetailin1.nefThe commands provided by NEF-Pipelines are hierarchical in nature. All commands are call by the NEF command but there
are sub commands so for example to import a sequence froma pdb file tou would typenef psb import sequencefollowed
by the name of the PDB file and relevant options. This can look lomng winded bu NEF-Pipelines support command completion
so typing a double tab will list all availabe sub commands.For examplenef<tab><tab>showschains   fasta    frames   header   mars     nmrpipe  nmrview  pales    pdb      stream   testandnefnmrviewimport<tab<tab>showspeaks sequence shiftsMore information on NEFThe origionalNEF paperis not a good description of the format more an outline of ideals and needs. TheCCPNwebsite has a goodguide to nefand development takes place ongithubvia theNEF consortium repositorywhich
includes anannotated NEF exampleand adictionary defining the format. NEF is aSTAR formatwhich means it has
similarities toNMRStarfiles used by theBMRBandPDBx / mmCIFused by theRCSB / PDBbecause its uses the same
underling format. However, its is not directly interchangeable with these file formats as it has a different syntax and
intention / underlying use easy and accurate NMR data interchange] as opposed to archiving for example.