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diff --git a/python-glypy.spec b/python-glypy.spec new file mode 100644 index 0000000..e75911f --- /dev/null +++ b/python-glypy.spec @@ -0,0 +1,216 @@ +%global _empty_manifest_terminate_build 0 +Name: python-glypy +Version: 1.0.8 +Release: 1 +Summary: A Glycoinformatics Toolkit +License: Apache Software License +URL: https://github.com/mobiusklein/glypy +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/96/44/c3146665f579c7cf33cd125dc2a8318c585ce1fd3bd3da060f7c1d26613b/glypy-1.0.8.tar.gz + +Requires: python3-hjson +Requires: python3-six +Requires: python3-requests +Requires: python3-SPARQLWrapper +Requires: python3-matplotlib +Requires: python3-rdflib +Requires: python3-requests +Requires: python3-rdflib +Requires: python3-SPARQLWrapper +Requires: python3-matplotlib + +%description +|https://img.shields.io/travis/mobiusklein/glypy.svg| |Documentation +Status| +Glycobiology is the study of the biological functions, properties, and +structures of carbohydrate biomolecules, also called *glycans*. These +large, tree-like molecules are complex, having a wide variety of +building blocks as well as modifications and substitutions on those +building blocks. +`glypy` is a Python library providing code for reading, writing, and +manipulating glycan structures, glycan compositions, monosaccharides, and +their substituents. It also includes interfaces to popular glycan structure +databases, `GlyTouCan <https://glytoucan.org/>`_ and `UnicarbKB <http://www.unicarbkb.org/>`_ +using `SPARQL` queries and an RDF-object mapper. +Example Use Cases +~~~~~~~~~~~~~~~~~ +1. Traverse structures using either canonical or residue-level rule + ordering. +2. Operate on monosaccharide and substituents as nodes and bonds as + edges. +3. Add, remove, and modify these structures to alter glycan properties. +4. Identify substructures and motifs, classifying glycans. +5. Evaluate structural similarities with one of several ordering and + comparator methods. +6. Plot tree structures with MatPlotLib, rendering using a configurable + symbol nomenclature, such as SNFG, CFG, or IUPAC. Layout using vector + graphics for lossless scaling. +7. Calculate the mass of a native or derivatized glycan. +8. Generate glycosidic and cross ring cleavage fragments for a + collection of glycan structures for performing MS/MS database search. +9. Perform substructure similarity searches with exact ordering or + topological comparison and exact or fuzzy per-residue matching to + classify a structure as an N-linked glycan. +10. Annotate MS spectra with glycan structures, labeling which peaks + matched a database entry. +11. Download all N-Glycans from `GlyTouCan <https://glytoucan.org/>`__ +12. Find all glycans in a list which contain a particular subtree, or + find common subtrees in a database of glycans, performing treelet + enrichment analysis. +13. Synthesize all possible glycans using a set of enzymes starting from + a set of seed structures. +Citing +~~~~~~ +If you use `glypy` in a publication please cite: + Klein, J., & Zaia, J. (2019). glypy - An open source glycoinformatics library. + Journal of Proteome Research. + https://doi.org/10.1021/acs.jproteome.9b00367 + +%package -n python3-glypy +Summary: A Glycoinformatics Toolkit +Provides: python-glypy +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +BuildRequires: python3-cffi +BuildRequires: gcc +BuildRequires: gdb +%description -n python3-glypy +|https://img.shields.io/travis/mobiusklein/glypy.svg| |Documentation +Status| +Glycobiology is the study of the biological functions, properties, and +structures of carbohydrate biomolecules, also called *glycans*. These +large, tree-like molecules are complex, having a wide variety of +building blocks as well as modifications and substitutions on those +building blocks. +`glypy` is a Python library providing code for reading, writing, and +manipulating glycan structures, glycan compositions, monosaccharides, and +their substituents. It also includes interfaces to popular glycan structure +databases, `GlyTouCan <https://glytoucan.org/>`_ and `UnicarbKB <http://www.unicarbkb.org/>`_ +using `SPARQL` queries and an RDF-object mapper. +Example Use Cases +~~~~~~~~~~~~~~~~~ +1. Traverse structures using either canonical or residue-level rule + ordering. +2. Operate on monosaccharide and substituents as nodes and bonds as + edges. +3. Add, remove, and modify these structures to alter glycan properties. +4. Identify substructures and motifs, classifying glycans. +5. Evaluate structural similarities with one of several ordering and + comparator methods. +6. Plot tree structures with MatPlotLib, rendering using a configurable + symbol nomenclature, such as SNFG, CFG, or IUPAC. Layout using vector + graphics for lossless scaling. +7. Calculate the mass of a native or derivatized glycan. +8. Generate glycosidic and cross ring cleavage fragments for a + collection of glycan structures for performing MS/MS database search. +9. Perform substructure similarity searches with exact ordering or + topological comparison and exact or fuzzy per-residue matching to + classify a structure as an N-linked glycan. +10. Annotate MS spectra with glycan structures, labeling which peaks + matched a database entry. +11. Download all N-Glycans from `GlyTouCan <https://glytoucan.org/>`__ +12. Find all glycans in a list which contain a particular subtree, or + find common subtrees in a database of glycans, performing treelet + enrichment analysis. +13. Synthesize all possible glycans using a set of enzymes starting from + a set of seed structures. +Citing +~~~~~~ +If you use `glypy` in a publication please cite: + Klein, J., & Zaia, J. (2019). glypy - An open source glycoinformatics library. + Journal of Proteome Research. + https://doi.org/10.1021/acs.jproteome.9b00367 + +%package help +Summary: Development documents and examples for glypy +Provides: python3-glypy-doc +%description help +|https://img.shields.io/travis/mobiusklein/glypy.svg| |Documentation +Status| +Glycobiology is the study of the biological functions, properties, and +structures of carbohydrate biomolecules, also called *glycans*. These +large, tree-like molecules are complex, having a wide variety of +building blocks as well as modifications and substitutions on those +building blocks. +`glypy` is a Python library providing code for reading, writing, and +manipulating glycan structures, glycan compositions, monosaccharides, and +their substituents. It also includes interfaces to popular glycan structure +databases, `GlyTouCan <https://glytoucan.org/>`_ and `UnicarbKB <http://www.unicarbkb.org/>`_ +using `SPARQL` queries and an RDF-object mapper. +Example Use Cases +~~~~~~~~~~~~~~~~~ +1. Traverse structures using either canonical or residue-level rule + ordering. +2. Operate on monosaccharide and substituents as nodes and bonds as + edges. +3. Add, remove, and modify these structures to alter glycan properties. +4. Identify substructures and motifs, classifying glycans. +5. Evaluate structural similarities with one of several ordering and + comparator methods. +6. Plot tree structures with MatPlotLib, rendering using a configurable + symbol nomenclature, such as SNFG, CFG, or IUPAC. Layout using vector + graphics for lossless scaling. +7. Calculate the mass of a native or derivatized glycan. +8. Generate glycosidic and cross ring cleavage fragments for a + collection of glycan structures for performing MS/MS database search. +9. Perform substructure similarity searches with exact ordering or + topological comparison and exact or fuzzy per-residue matching to + classify a structure as an N-linked glycan. +10. Annotate MS spectra with glycan structures, labeling which peaks + matched a database entry. +11. Download all N-Glycans from `GlyTouCan <https://glytoucan.org/>`__ +12. Find all glycans in a list which contain a particular subtree, or + find common subtrees in a database of glycans, performing treelet + enrichment analysis. +13. Synthesize all possible glycans using a set of enzymes starting from + a set of seed structures. +Citing +~~~~~~ +If you use `glypy` in a publication please cite: + Klein, J., & Zaia, J. (2019). glypy - An open source glycoinformatics library. + Journal of Proteome Research. + https://doi.org/10.1021/acs.jproteome.9b00367 + +%prep +%autosetup -n glypy-1.0.8 + +%build +%py3_build + +%install +%py3_install +install -d -m755 %{buildroot}/%{_pkgdocdir} +if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi +if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi +if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi +if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi +pushd %{buildroot} +if [ -d usr/lib ]; then + find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/lib64 ]; then + find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/bin ]; then + find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/sbin ]; then + find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst +fi +touch doclist.lst +if [ -d usr/share/man ]; then + find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst +fi +popd +mv %{buildroot}/filelist.lst . +mv %{buildroot}/doclist.lst . + +%files -n python3-glypy -f filelist.lst +%dir %{python3_sitearch}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Wed May 10 2023 Python_Bot <Python_Bot@openeuler.org> - 1.0.8-1 +- Package Spec generated |