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>

4 files changed, 276 insertions, 0 deletions

diff --git a/science/massxpert/Makefile b/science/massxpert/Makefile
new file mode 100644
index 000000000000..869fa6cb7c50
--- /dev/null
+++ b/science/massxpert/Makefile
@@ -0,0 +1,28 @@
+# New ports collection makefile for:	massxpert
+# Date created:		2010-05-14
+# Whom:			Gvozdikov Veniamin <g.veniamin@googlemail.com>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	massxpert
+PORTVERSION=	2.3.6
+CATEGORIES=	science
+MASTER_SITES=	http://download.tuxfamily.org/massxpert/source/
+
+MAINTAINER=	g.veniamin@googlemail.com
+COMMENT=	The massXpert software for (bio)chemists
+
+USE_QT_VER=	4
+USE_CMAKE=	yes
+USE_LDCONFIG=	yes
+QT_COMPONENTS=	gui xml rcc_build qmake_build uic_build moc_build \
+		svg
+
+.include <bsd.port.pre.mk>
+
+.if ${OSVERSION} < 700000
+CMAKE_USE_PTHREAD=	yes
+.endif
+
+.include <bsd.port.post.mk>
diff --git a/science/massxpert/distinfo b/science/massxpert/distinfo
new file mode 100644
index 000000000000..7778af9beea3
--- /dev/null
+++ b/science/massxpert/distinfo
@@ -0,0 +1,3 @@
+MD5 (massxpert-2.3.6.tar.gz) = e51cf36f01e78cf07a71e33a8e0f8ad7
+SHA256 (massxpert-2.3.6.tar.gz) = 9c28de0eb45c027551b52b865bae4a9cdcc874869cefadb3fe61a71e391f49e4
+SIZE (massxpert-2.3.6.tar.gz) = 14197098
diff --git a/science/massxpert/pkg-descr b/science/massxpert/pkg-descr
new file mode 100644
index 000000000000..061168528c02
--- /dev/null
+++ b/science/massxpert/pkg-descr
@@ -0,0 +1,20 @@
+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.
+
+WWW:	http://massxpert.org/
diff --git a/science/massxpert/pkg-plist b/science/massxpert/pkg-plist
new file mode 100644
index 000000000000..63d560a0f924
--- /dev/null
+++ b/science/massxpert/pkg-plist
@@ -0,0 +1,225 @@
+bin/massxpert
+lib/massxpert/plugins/libmassListSorterPlugin.so
+lib/massxpert/plugins/libseqToolsPlugin.so
+lib/massxpert/plugins/libnumeralsLocaleConverterPlugin.so
+%%DOCSDIR%%/COPYING
+share/applications/massxpert.desktop
+share/man/man1/massxpert.1
+share/man/man7/massxpert-data.7
+%%DATADIR%%/locales/massxpert_fr.qm
+%%DATADIR%%/pol-chem-defs/dna/adenine.svg
+%%DATADIR%%/pol-chem-defs/dna/biotlink.svg
+%%DATADIR%%/pol-chem-defs/dna/chem_pad.conf
+%%DATADIR%%/pol-chem-defs/dna/cross_linker_dictionary
+%%DATADIR%%/pol-chem-defs/dna/cursor.svg
+%%DATADIR%%/pol-chem-defs/dna/cytosine.svg
+%%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
+%%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
+%%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
+%%DATADIR%%/pol-chem-defs/nucac/cursor.svg
+%%DATADIR%%/pol-chem-defs/nucac/dadenine.svg
+%%DATADIR%%/pol-chem-defs/nucac/dcytosine.svg
+%%DATADIR%%/pol-chem-defs/nucac/default-cross-link-vignette.svg
+%%DATADIR%%/pol-chem-defs/nucac/default-modif-vignette.svg
+%%DATADIR%%/pol-chem-defs/nucac/dguanine.svg
+%%DATADIR%%/pol-chem-defs/nucac/diphospho.svg
+%%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
+%%DATADIR%%/pol-chem-defs/nucac/nucac.xml
+%%DATADIR%%/pol-chem-defs/nucac/oxidation.svg
+%%DATADIR%%/pol-chem-defs/nucac/phospho.svg
+%%DATADIR%%/pol-chem-defs/nucac/ps-dadenine.svg
+%%DATADIR%%/pol-chem-defs/nucac/ps-dguanine.svg
+%%DATADIR%%/pol-chem-defs/nucac/ps-dcytosine.svg
+%%DATADIR%%/pol-chem-defs/nucac/ps-dthymine.svg
+%%DATADIR%%/pol-chem-defs/nucac/ps-radenine.svg
+%%DATADIR%%/pol-chem-defs/nucac/ps-rcytosine.svg
+%%DATADIR%%/pol-chem-defs/nucac/ps-rguanine.svg
+%%DATADIR%%/pol-chem-defs/nucac/ps-ruracile.svg
+%%DATADIR%%/pol-chem-defs/nucac/radenine.svg
+%%DATADIR%%/pol-chem-defs/nucac/rcytosine.svg
+%%DATADIR%%/pol-chem-defs/nucac/rguanine.svg
+%%DATADIR%%/pol-chem-defs/nucac/ruracile.svg
+%%DATADIR%%/pol-chem-defs/nucac/thymine-dimer.svg
+%%DATADIR%%/pol-chem-defs/protein-1-letter/acetyl.svg
+%%DATADIR%%/pol-chem-defs/protein-1-letter/alanine.svg
+%%DATADIR%%/pol-chem-defs/protein-1-letter/arginine.svg
+%%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
+%%DATADIR%%/pol-chem-defs/protein-3-letters/threonine.svg
+%%DATADIR%%/pol-chem-defs/protein-3-letters/tryptophan.svg
+%%DATADIR%%/pol-chem-defs/protein-3-letters/tyrosine.svg
+%%DATADIR%%/pol-chem-defs/protein-3-letters/valine.svg
+%%DATADIR%%/pol-chem-defs/saccharide/allose-text.svg
+%%DATADIR%%/pol-chem-defs/saccharide/allose.svg
+%%DATADIR%%/pol-chem-defs/saccharide/altrose-text.svg
+%%DATADIR%%/pol-chem-defs/saccharide/altrose.svg
+%%DATADIR%%/pol-chem-defs/saccharide/arabinose-text.svg
+%%DATADIR%%/pol-chem-defs/saccharide/arabinose.svg
+%%DATADIR%%/pol-chem-defs/saccharide/chem_pad.conf
+%%DATADIR%%/pol-chem-defs/saccharide/cross_linker_dictionary
+%%DATADIR%%/pol-chem-defs/saccharide/cursor.svg
+%%DATADIR%%/pol-chem-defs/saccharide/default-cross-link-vignette.svg
+%%DATADIR%%/pol-chem-defs/saccharide/default-modif-vignette.svg
+%%DATADIR%%/pol-chem-defs/saccharide/erythrose-text.svg
+%%DATADIR%%/pol-chem-defs/saccharide/erythrose.svg
+%%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
+%%DATADIR%%/pol-chem-defs/saccharide/gulose.svg
+%%DATADIR%%/pol-chem-defs/saccharide/idose-text.svg
+%%DATADIR%%/pol-chem-defs/saccharide/idose.svg
+%%DATADIR%%/pol-chem-defs/saccharide/lyxose-text.svg
+%%DATADIR%%/pol-chem-defs/saccharide/lyxose.svg
+%%DATADIR%%/pol-chem-defs/saccharide/mannose-text.svg
+%%DATADIR%%/pol-chem-defs/saccharide/mannose.svg
+%%DATADIR%%/pol-chem-defs/saccharide/methyl.svg
+%%DATADIR%%/pol-chem-defs/saccharide/modification_dictionary
+%%DATADIR%%/pol-chem-defs/saccharide/monomer_dictionary
+%%DATADIR%%/pol-chem-defs/saccharide/psicose-text.svg
+%%DATADIR%%/pol-chem-defs/saccharide/psicose.svg
+%%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
+%%DATADIR%%/pol-seqs/kunitz-inhibitor-human.mxp
+%%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
+%%DATADIR%%/chem_pad.conf
+@dirrmtry %%DATADIR%%/pol-seqs
+@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