BSD Ports

science/massxpert 6.0.3_1 FreeBSD

Software suite for (bio)chemists

System
FreeBSD
Repository
FreeBSD ports
Maintainer
[email protected]
License
GPLv3
Categories
science
Package size
1120.7 KiB, 4348.1 KiB installed

Description

The massXpert project aims at providing (bio)chemists with a software package allowing the following:

* User-specific atom definitions and polymer chemistry definitions; * Powerful sequence editing with user-defined glyphs for each monomer and monomer chemical modification. Multi-region selections; * Polymer sequence chemical/enzymatic cleavage; * Intramolecular cross-linking, like disulfide bonds with total resolution of the peptides generated upon enzymatic cleavage; * Gas-phase fragmentation of oligomers; * Mass-to-charge ratio calculations with inline change of ionization agent; * Calculation of net electrical charge and of isoelectric point (even by taking into account monomer modifications if polymer is a protein); * Simulation of isotopic patterns for any chemical formula and z charge; * A number of plugins allow 1) translation of the sequence from one format to another (using a dictionary, like between the 1-letter code and the 3-letter code of proteins) 2) conversion of number format according to any localized number format 3) sort mass lists.

In the other systems

SystemPortVersion
FreeBSDscience/massxpert6.0.3_1
HardenedBSDscience/massxpert6.0.3_1
GhostBSDscience/massxpert6.0.3_1

Install

Binary package:

pkg install massxpert

From the ports tree:

cd /usr/ports/science/massxpert/ && make install clean

To depend on this port in another port's Makefile:

RUN_DEPENDS=	massxpert>0:science/massxpert

Packages

The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.

Repositoryaarch64amd64armv6armv7i386
FreeBSD:14:latest6.0.3_16.0.3_1-6.0.3_16.0.3_1
FreeBSD:14:quarterly6.0.3_16.0.3_1n/a6.0.3_16.0.3_1
FreeBSD:15:latest6.0.3_16.0.3_1n/a6.0.3_16.0.3_1
FreeBSD:15:quarterly6.0.3_16.0.3_1n/an/an/a
FreeBSD:16:latest6.0.3_16.0.3_1n/an/an/a
FreeBSD:16:quarterlyn/an/an/an/an/a

Dependencies

As this port's Makefile names them.

Library 4

The full lists below include those, and their dependencies in turn.

Build dependencies 92
Run dependencies 82

No port depends on this one.

Configuration

No options to configure.

USES
cmake compiler:c++17-lang gnome qt:5 xorg
Service scripts
none

Message after installing

===>   NOTICE:

The massxpert port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:

https://bugs.freebsd.org/bugzilla

More information about port maintainership is available at:

https://docs.freebsd.org/en/articles/contributing/#ports-contributing

Files

Manual pages 1
  • massxpert(1)
pkg-plist 340
  • bin/massxpert
  • share/applications/org.msxpertsuite.massxpert.desktop
  • share/icons/hicolor/16x16/apps/massxpert.png
  • share/icons/hicolor/32x32/apps/massxpert.png
  • share/icons/hicolor/48x48/apps/massxpert.png
  • share/icons/hicolor/64x64/apps/massxpert.png
  • share/man/man1/massxpert.1.gz
  • share/massxpert/data/chemPad.conf
  • share/massxpert/data/dictionaries/codon-to-protein-1.dic
  • share/massxpert/data/dictionaries/codon-to-protein-3.dic
  • share/massxpert/data/dictionaries/pdb-protein-to-mxp.dic
  • share/massxpert/data/dictionaries/protein-1-to-3.dic
  • share/massxpert/data/dictionaries/protein-3-to-1.dic
  • share/massxpert/data/polChemDefs/dna/adenine.svg
  • share/massxpert/data/polChemDefs/dna/biotlink.svg
  • share/massxpert/data/polChemDefs/dna/chemPad.conf
  • share/massxpert/data/polChemDefs/dna/cross_linker_dictionary
  • share/massxpert/data/polChemDefs/dna/cursor.svg
  • share/massxpert/data/polChemDefs/dna/cytosine.svg
  • share/massxpert/data/polChemDefs/dna/default-cross-link-vignette.svg
  • share/massxpert/data/polChemDefs/dna/default-modif-vignette.svg
  • share/massxpert/data/polChemDefs/dna/diphospho.svg
  • share/massxpert/data/polChemDefs/dna/dna.xml
  • share/massxpert/data/polChemDefs/dna/guanine.svg
  • share/massxpert/data/polChemDefs/dna/methyl.svg
  • share/massxpert/data/polChemDefs/dna/modification_dictionary
  • share/massxpert/data/polChemDefs/dna/monomer_dictionary
  • share/massxpert/data/polChemDefs/dna/oxidation.svg
  • share/massxpert/data/polChemDefs/dna/phospho.svg
  • share/massxpert/data/polChemDefs/dna/ps-adenine.svg
  • share/massxpert/data/polChemDefs/dna/ps-cytosine.svg
  • share/massxpert/data/polChemDefs/dna/ps-guanine.svg
  • share/massxpert/data/polChemDefs/dna/ps-thymine.svg
  • share/massxpert/data/polChemDefs/dna/thymine-dimer.svg
  • share/massxpert/data/polChemDefs/dna/thymine.svg
  • share/massxpert/data/polChemDefs/dna/uracile.svg
  • share/massxpert/data/polChemDefs/massxpert-polChemDefsCat
  • share/massxpert/data/polChemDefs/nucac/biotlink.svg
  • share/massxpert/data/polChemDefs/nucac/chemPad.conf
  • share/massxpert/data/polChemDefs/nucac/cross_linker_dictionary
  • share/massxpert/data/polChemDefs/nucac/cursor.svg
  • share/massxpert/data/polChemDefs/nucac/dadenine.svg
  • share/massxpert/data/polChemDefs/nucac/dcytosine.svg
  • share/massxpert/data/polChemDefs/nucac/default-cross-link-vignette.svg
  • share/massxpert/data/polChemDefs/nucac/default-modif-vignette.svg
  • share/massxpert/data/polChemDefs/nucac/dguanine.svg
  • share/massxpert/data/polChemDefs/nucac/diphospho.svg
  • share/massxpert/data/polChemDefs/nucac/dthymine.svg
  • share/massxpert/data/polChemDefs/nucac/methyl.svg
  • share/massxpert/data/polChemDefs/nucac/modification_dictionary
  • share/massxpert/data/polChemDefs/nucac/monomer_dictionary
  • share/massxpert/data/polChemDefs/nucac/nucac.xml
  • share/massxpert/data/polChemDefs/nucac/oxidation.svg
  • share/massxpert/data/polChemDefs/nucac/phospho.svg
  • share/massxpert/data/polChemDefs/nucac/ps-dadenine.svg
  • share/massxpert/data/polChemDefs/nucac/ps-dcytosine.svg
  • share/massxpert/data/polChemDefs/nucac/ps-dguanine.svg
  • share/massxpert/data/polChemDefs/nucac/ps-dthymine.svg
  • share/massxpert/data/polChemDefs/nucac/ps-radenine.svg
  • share/massxpert/data/polChemDefs/nucac/ps-rcytosine.svg
  • share/massxpert/data/polChemDefs/nucac/ps-rguanine.svg
  • share/massxpert/data/polChemDefs/nucac/ps-ruracile.svg
  • share/massxpert/data/polChemDefs/nucac/radenine.svg
  • share/massxpert/data/polChemDefs/nucac/rcytosine.svg
  • share/massxpert/data/polChemDefs/nucac/rguanine.svg
  • share/massxpert/data/polChemDefs/nucac/ruracile.svg
  • share/massxpert/data/polChemDefs/nucac/thymine-dimer.svg
  • share/massxpert/data/polChemDefs/protein-1-letter-c13-n15/acetyl.svg
  • share/massxpert/data/polChemDefs/protein-1-letter-c13-n15/alanine.svg
  • share/massxpert/data/polChemDefs/protein-1-letter-c13-n15/arginine.svg
  • share/massxpert/data/polChemDefs/protein-1-letter-c13-n15/asparagine.svg
  • share/massxpert/data/polChemDefs/protein-1-letter-c13-n15/aspartate.svg
  • share/massxpert/data/polChemDefs/protein-1-letter-c13-n15/cfp-chromophore.svg
  • share/massxpert/data/polChemDefs/protein-1-letter-c13-n15/chemPad.conf
  • share/massxpert/data/polChemDefs/protein-1-letter-c13-n15/cross_linker_dictionary
  • share/massxpert/data/polChemDefs/protein-1-letter-c13-n15/cursor.svg
  • share/massxpert/data/polChemDefs/protein-1-letter-c13-n15/cysteine.svg
  • share/massxpert/data/polChemDefs/protein-1-letter-c13-n15/default-cross-link-vignette.svg
  • share/massxpert/data/polChemDefs/protein-1-letter-c13-n15/default-modif-vignette.svg
  • share/massxpert/data/polChemDefs/protein-1-letter-c13-n15/diaminopimelic.svg
  • share/massxpert/data/polChemDefs/protein-1-letter-c13-n15/disulfidebond-cross-link.svg
  • share/massxpert/data/polChemDefs/protein-1-letter-c13-n15/glutamate.svg
  • share/massxpert/data/polChemDefs/protein-1-letter-c13-n15/glutamine.svg
  • share/massxpert/data/polChemDefs/protein-1-letter-c13-n15/glutamylation.svg
  • share/massxpert/data/polChemDefs/protein-1-letter-c13-n15/glycine.svg
  • share/massxpert/data/polChemDefs/protein-1-letter-c13-n15/glycylation.svg
  • share/massxpert/data/polChemDefs/protein-1-letter-c13-n15/histidine.svg
  • share/massxpert/data/polChemDefs/protein-1-letter-c13-n15/hydroxylation.svg
  • share/massxpert/data/polChemDefs/protein-1-letter-c13-n15/isoleucine.svg
  • share/massxpert/data/polChemDefs/protein-1-letter-c13-n15/leucine.svg
  • share/massxpert/data/polChemDefs/protein-1-letter-c13-n15/lysine.svg
  • share/massxpert/data/polChemDefs/protein-1-letter-c13-n15/methionine.svg
  • share/massxpert/data/polChemDefs/protein-1-letter-c13-n15/modification_dictionary
  • share/massxpert/data/polChemDefs/protein-1-letter-c13-n15/monomer_dictionary
  • share/massxpert/data/polChemDefs/protein-1-letter-c13-n15/oxidation.svg
  • share/massxpert/data/polChemDefs/protein-1-letter-c13-n15/pdb-code-conversion.dic
  • share/massxpert/data/polChemDefs/protein-1-letter-c13-n15/phenylalanine.svg
  • share/massxpert/data/polChemDefs/protein-1-letter-c13-n15/phospho.svg
  • share/massxpert/data/polChemDefs/protein-1-letter-c13-n15/pka_ph_pi.xml
  • share/massxpert/data/polChemDefs/protein-1-letter-c13-n15/proline.svg

The first 100 are listed.

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