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. PR: ports/146564 Submitted by: Gvozdikov Veniamin <g.veniamin@googlemail.com>
This commit is contained in:
Wen Heping
parent
59b8e8bcfa
commit
cc8da973ab
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=254638
@ -82,6 +82,7 @@
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SUBDIR += libsvm
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SUBDIR += libsvm-python
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SUBDIR += linsmith
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SUBDIR += massxpert
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SUBDIR += mayavi
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SUBDIR += mbdyn
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SUBDIR += mcstas
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28
science/massxpert/Makefile
Normal file
28
science/massxpert/Makefile
Normal file
@ -0,0 +1,28 @@
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# New ports collection makefile for: massxpert
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# Date created: 2010-05-14
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# Whom: Gvozdikov Veniamin <g.veniamin@googlemail.com>
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#
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# $FreeBSD$
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#
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PORTNAME= massxpert
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PORTVERSION= 2.3.6
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CATEGORIES= science
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MASTER_SITES= http://download.tuxfamily.org/massxpert/source/
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MAINTAINER= g.veniamin@googlemail.com
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COMMENT= The massXpert software for (bio)chemists
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USE_QT_VER= 4
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USE_CMAKE= yes
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USE_LDCONFIG= yes
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QT_COMPONENTS= gui xml rcc_build qmake_build uic_build moc_build \
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svg
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.include <bsd.port.pre.mk>
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.if ${OSVERSION} < 700000
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CMAKE_USE_PTHREAD= yes
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.endif
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.include <bsd.port.post.mk>
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3
science/massxpert/distinfo
Normal file
3
science/massxpert/distinfo
Normal file
@ -0,0 +1,3 @@
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MD5 (massxpert-2.3.6.tar.gz) = e51cf36f01e78cf07a71e33a8e0f8ad7
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SHA256 (massxpert-2.3.6.tar.gz) = 9c28de0eb45c027551b52b865bae4a9cdcc874869cefadb3fe61a71e391f49e4
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SIZE (massxpert-2.3.6.tar.gz) = 14197098
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20
science/massxpert/pkg-descr
Normal file
20
science/massxpert/pkg-descr
Normal file
@ -0,0 +1,20 @@
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The massXpert project aims at providing (bio)chemists with a software
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package allowing the following:
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* User-specific atom definitions and polymer chemistry definitions;
|
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* Powerful sequence editing with user-defined glyphs for each monomer
|
||||
and monomer chemical modification. Multi-region selections;
|
||||
* Polymer sequence chemical/enzymatic cleavage;
|
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* Intramolecular cross-linking, like disulfide bonds with total resolution
|
||||
of the peptides generated upon enzymatic cleavage;
|
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* 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
|
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number format 3) sort mass lists.
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WWW: http://massxpert.org/
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225
science/massxpert/pkg-plist
Normal file
225
science/massxpert/pkg-plist
Normal file
@ -0,0 +1,225 @@
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bin/massxpert
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lib/massxpert/plugins/libmassListSorterPlugin.so
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lib/massxpert/plugins/libseqToolsPlugin.so
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lib/massxpert/plugins/libnumeralsLocaleConverterPlugin.so
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%%DOCSDIR%%/COPYING
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share/applications/massxpert.desktop
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share/man/man1/massxpert.1
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share/man/man7/massxpert-data.7
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%%DATADIR%%/locales/massxpert_fr.qm
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%%DATADIR%%/pol-chem-defs/dna/adenine.svg
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%%DATADIR%%/pol-chem-defs/dna/biotlink.svg
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||||
%%DATADIR%%/pol-chem-defs/dna/chem_pad.conf
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||||
%%DATADIR%%/pol-chem-defs/dna/cross_linker_dictionary
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%%DATADIR%%/pol-chem-defs/dna/cursor.svg
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||||
%%DATADIR%%/pol-chem-defs/dna/cytosine.svg
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||||
%%DATADIR%%/pol-chem-defs/dna/default-cross-link-vignette.svg
|
||||
%%DATADIR%%/pol-chem-defs/dna/default-modif-vignette.svg
|
||||
%%DATADIR%%/pol-chem-defs/dna/diphospho.svg
|
||||
%%DATADIR%%/pol-chem-defs/dna/dna.xml
|
||||
%%DATADIR%%/pol-chem-defs/dna/guanine.svg
|
||||
%%DATADIR%%/pol-chem-defs/dna/methyl.svg
|
||||
%%DATADIR%%/pol-chem-defs/dna/modification_dictionary
|
||||
%%DATADIR%%/pol-chem-defs/dna/monomer_dictionary
|
||||
%%DATADIR%%/pol-chem-defs/dna/oxidation.svg
|
||||
%%DATADIR%%/pol-chem-defs/dna/phospho.svg
|
||||
%%DATADIR%%/pol-chem-defs/dna/ps-adenine.svg
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||||
%%DATADIR%%/pol-chem-defs/dna/ps-cytosine.svg
|
||||
%%DATADIR%%/pol-chem-defs/dna/ps-guanine.svg
|
||||
%%DATADIR%%/pol-chem-defs/dna/ps-thymine.svg
|
||||
%%DATADIR%%/pol-chem-defs/dna/thymine-dimer.svg
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||||
%%DATADIR%%/pol-chem-defs/dna/thymine.svg
|
||||
%%DATADIR%%/pol-chem-defs/dna/uracile.svg
|
||||
%%DATADIR%%/pol-chem-defs/massxpert-pol-chem-defs-cat
|
||||
%%DATADIR%%/pol-chem-defs/nucac/biotlink.svg
|
||||
%%DATADIR%%/pol-chem-defs/nucac/chem_pad.conf
|
||||
%%DATADIR%%/pol-chem-defs/nucac/cross_linker_dictionary
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||||
%%DATADIR%%/pol-chem-defs/nucac/cursor.svg
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||||
%%DATADIR%%/pol-chem-defs/nucac/dadenine.svg
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||||
%%DATADIR%%/pol-chem-defs/nucac/dcytosine.svg
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||||
%%DATADIR%%/pol-chem-defs/nucac/default-cross-link-vignette.svg
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||||
%%DATADIR%%/pol-chem-defs/nucac/default-modif-vignette.svg
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||||
%%DATADIR%%/pol-chem-defs/nucac/dguanine.svg
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||||
%%DATADIR%%/pol-chem-defs/nucac/diphospho.svg
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||||
%%DATADIR%%/pol-chem-defs/nucac/dthymine.svg
|
||||
%%DATADIR%%/pol-chem-defs/nucac/methyl.svg
|
||||
%%DATADIR%%/pol-chem-defs/nucac/modification_dictionary
|
||||
%%DATADIR%%/pol-chem-defs/nucac/monomer_dictionary
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||||
%%DATADIR%%/pol-chem-defs/nucac/nucac.xml
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||||
%%DATADIR%%/pol-chem-defs/nucac/oxidation.svg
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||||
%%DATADIR%%/pol-chem-defs/nucac/phospho.svg
|
||||
%%DATADIR%%/pol-chem-defs/nucac/ps-dadenine.svg
|
||||
%%DATADIR%%/pol-chem-defs/nucac/ps-dguanine.svg
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||||
%%DATADIR%%/pol-chem-defs/nucac/ps-dcytosine.svg
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||||
%%DATADIR%%/pol-chem-defs/nucac/ps-dthymine.svg
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||||
%%DATADIR%%/pol-chem-defs/nucac/ps-radenine.svg
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||||
%%DATADIR%%/pol-chem-defs/nucac/ps-rcytosine.svg
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||||
%%DATADIR%%/pol-chem-defs/nucac/ps-rguanine.svg
|
||||
%%DATADIR%%/pol-chem-defs/nucac/ps-ruracile.svg
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||||
%%DATADIR%%/pol-chem-defs/nucac/radenine.svg
|
||||
%%DATADIR%%/pol-chem-defs/nucac/rcytosine.svg
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||||
%%DATADIR%%/pol-chem-defs/nucac/rguanine.svg
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||||
%%DATADIR%%/pol-chem-defs/nucac/ruracile.svg
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||||
%%DATADIR%%/pol-chem-defs/nucac/thymine-dimer.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/acetyl.svg
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||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/alanine.svg
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||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/arginine.svg
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||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/asparagine.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/aspartate.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/cfp-chromophore.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/chem_pad.conf
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/cross_linker_dictionary
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/cursor.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/cysteine.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/default-cross-link-vignette.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/default-modif-vignette.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/disulfidebond-cross-link.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/glutamate.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/glutamine.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/glycine.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/histidine.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/isoleucine.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/leucine.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/lysine.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/methionine.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/modification_dictionary
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/monomer_dictionary
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/oxidation.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/pdb-code-conversion.dic
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/phenylalanine.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/phospho.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/pka_ph_pi.xml
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/proline.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/protein-1-letter.xml
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/protonloss.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/serine.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/sulfbond.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/sulpho.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/threonine.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/tryptophan.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/tyrosine.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-1-letter/valine.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/acetyl.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/alanine.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/arginine.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/asparagine.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/aspartate.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/chem_pad.conf
|
||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/cross_linker_dictionary
|
||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/cursor.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/cysteine.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/default-cross-link-vignette.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/default-modif-vignette.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/glutamate.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/glutamine.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/glycine.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/histidine.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/isoleucine.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/leucine.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/lysine.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/methionine.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/phospho.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/modification_dictionary
|
||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/monomer_dictionary
|
||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/oxidation.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/pdb-code-conversion.dic
|
||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/phenylalanine.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/proline.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/protein-3-letters.xml
|
||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/protonloss.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/serine.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/sulfbond.svg
|
||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/sulpho.svg
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||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/threonine.svg
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||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/tryptophan.svg
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||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/tyrosine.svg
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||||
%%DATADIR%%/pol-chem-defs/protein-3-letters/valine.svg
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||||
%%DATADIR%%/pol-chem-defs/saccharide/allose-text.svg
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||||
%%DATADIR%%/pol-chem-defs/saccharide/allose.svg
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||||
%%DATADIR%%/pol-chem-defs/saccharide/altrose-text.svg
|
||||
%%DATADIR%%/pol-chem-defs/saccharide/altrose.svg
|
||||
%%DATADIR%%/pol-chem-defs/saccharide/arabinose-text.svg
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||||
%%DATADIR%%/pol-chem-defs/saccharide/arabinose.svg
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||||
%%DATADIR%%/pol-chem-defs/saccharide/chem_pad.conf
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||||
%%DATADIR%%/pol-chem-defs/saccharide/cross_linker_dictionary
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||||
%%DATADIR%%/pol-chem-defs/saccharide/cursor.svg
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||||
%%DATADIR%%/pol-chem-defs/saccharide/default-cross-link-vignette.svg
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||||
%%DATADIR%%/pol-chem-defs/saccharide/default-modif-vignette.svg
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||||
%%DATADIR%%/pol-chem-defs/saccharide/erythrose-text.svg
|
||||
%%DATADIR%%/pol-chem-defs/saccharide/erythrose.svg
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||||
%%DATADIR%%/pol-chem-defs/saccharide/erythrulose-text.svg
|
||||
%%DATADIR%%/pol-chem-defs/saccharide/erythrulose.svg
|
||||
%%DATADIR%%/pol-chem-defs/saccharide/fructose-text.svg
|
||||
%%DATADIR%%/pol-chem-defs/saccharide/fructose.svg
|
||||
%%DATADIR%%/pol-chem-defs/saccharide/galactose-text.svg
|
||||
%%DATADIR%%/pol-chem-defs/saccharide/galactose.svg
|
||||
%%DATADIR%%/pol-chem-defs/saccharide/glucose-text.svg
|
||||
%%DATADIR%%/pol-chem-defs/saccharide/glucose.svg
|
||||
%%DATADIR%%/pol-chem-defs/saccharide/gulose-text.svg
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||||
%%DATADIR%%/pol-chem-defs/saccharide/gulose.svg
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||||
%%DATADIR%%/pol-chem-defs/saccharide/idose-text.svg
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||||
%%DATADIR%%/pol-chem-defs/saccharide/idose.svg
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||||
%%DATADIR%%/pol-chem-defs/saccharide/lyxose-text.svg
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||||
%%DATADIR%%/pol-chem-defs/saccharide/lyxose.svg
|
||||
%%DATADIR%%/pol-chem-defs/saccharide/mannose-text.svg
|
||||
%%DATADIR%%/pol-chem-defs/saccharide/mannose.svg
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||||
%%DATADIR%%/pol-chem-defs/saccharide/methyl.svg
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||||
%%DATADIR%%/pol-chem-defs/saccharide/modification_dictionary
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||||
%%DATADIR%%/pol-chem-defs/saccharide/monomer_dictionary
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||||
%%DATADIR%%/pol-chem-defs/saccharide/psicose-text.svg
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||||
%%DATADIR%%/pol-chem-defs/saccharide/psicose.svg
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||||
%%DATADIR%%/pol-chem-defs/saccharide/ribose-text.svg
|
||||
%%DATADIR%%/pol-chem-defs/saccharide/ribose.svg
|
||||
%%DATADIR%%/pol-chem-defs/saccharide/ribulose-text.svg
|
||||
%%DATADIR%%/pol-chem-defs/saccharide/ribulose.svg
|
||||
%%DATADIR%%/pol-chem-defs/saccharide/saccharide.xml
|
||||
%%DATADIR%%/pol-chem-defs/saccharide/sorbose-text.svg
|
||||
%%DATADIR%%/pol-chem-defs/saccharide/sorbose.svg
|
||||
%%DATADIR%%/pol-chem-defs/saccharide/tagatose-text.svg
|
||||
%%DATADIR%%/pol-chem-defs/saccharide/tagatose.svg
|
||||
%%DATADIR%%/pol-chem-defs/saccharide/talose-text.svg
|
||||
%%DATADIR%%/pol-chem-defs/saccharide/talose.svg
|
||||
%%DATADIR%%/pol-chem-defs/saccharide/template-text.svg
|
||||
%%DATADIR%%/pol-chem-defs/saccharide/threose-text.svg
|
||||
%%DATADIR%%/pol-chem-defs/saccharide/threose.svg
|
||||
%%DATADIR%%/pol-chem-defs/saccharide/xylose-text.svg
|
||||
%%DATADIR%%/pol-chem-defs/saccharide/xylose.svg
|
||||
%%DATADIR%%/pol-chem-defs/saccharide/xylulose-text.svg
|
||||
%%DATADIR%%/pol-chem-defs/saccharide/xylulose.svg
|
||||
%%DATADIR%%/pol-seqs/17-mer-ps-po-dna-chimera.mxp
|
||||
%%DATADIR%%/pol-seqs/centrin-2-human.mxp
|
||||
%%DATADIR%%/pol-seqs/cerulean-histag.mxp
|
||||
%%DATADIR%%/pol-seqs/chicken-telokin.mxp
|
||||
%%DATADIR%%/pol-seqs/citrin-fluorescent-protein.mxp
|
||||
%%DATADIR%%/pol-seqs/cyan-fluorescent-protein-h148d-histag.mxp
|
||||
%%DATADIR%%/pol-seqs/cyan-fluorescent-protein.mxp
|
||||
%%DATADIR%%/pol-seqs/horse-myoglobin.mxp
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||||
%%DATADIR%%/pol-seqs/kunitz-inhibitor-human.mxp
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||||
%%DATADIR%%/pol-seqs/leu-enkephalin.mxp
|
||||
%%DATADIR%%/pol-seqs/protein-1-letter.mxp
|
||||
%%DATADIR%%/pol-seqs/protein-3-letters.mxp
|
||||
%%DATADIR%%/pol-seqs/tev-protease-his-tag.mxp
|
||||
%%DATADIR%%/pol-seqs/yellow-fluorescent-protein.mxp
|
||||
%%DATADIR%%/dictionaries/codon-to-protein-1.dic
|
||||
%%DATADIR%%/dictionaries/codon-to-protein-3.dic
|
||||
%%DATADIR%%/dictionaries/pdb-protein-to-mxp.dic
|
||||
%%DATADIR%%/dictionaries/protein-1-to-3.dic
|
||||
%%DATADIR%%/dictionaries/protein-3-to-1.dic
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||||
%%DATADIR%%/chem_pad.conf
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||||
@dirrmtry %%DATADIR%%/pol-seqs
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||||
@dirrmtry %%DATADIR%%/pol-chem-defs/saccharide
|
||||
@dirrmtry %%DATADIR%%/pol-chem-defs/protein-3-letters
|
||||
@dirrmtry %%DATADIR%%/pol-chem-defs/protein-1-letter
|
||||
@dirrmtry %%DATADIR%%/pol-chem-defs/nucac
|
||||
@dirrmtry %%DATADIR%%/pol-chem-defs/dna
|
||||
@dirrmtry %%DATADIR%%/pol-chem-defs
|
||||
@dirrmtry %%DATADIR%%/locales
|
||||
@dirrmtry %%DATADIR%%/dictionaries
|
||||
@dirrmtry share/applications
|
||||
@dirrmtry %%DATADIR%%
|
||||
@dirrmtry share/man/man7
|
||||
@dirrmtry share/man/man1
|
||||
@dirrmtry share/man
|
||||
@dirrm %%DOCSDIR%%
|
||||
@dirrm lib/massxpert/plugins
|
||||
@dirrm lib/massxpert
|
||||
Loading…
Reference in New Issue
Block a user