Initial commit

CHANGELOG.rst

+=========
+CHANGELOG
+=========
\ No newline at end of file

README.rst

+==========
+User Guide
+==========
+
+Todo
\ No newline at end of file

docs/Makefile

+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = RapidPeptidesGenerator
+SOURCEDIR     = ./source
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
\ No newline at end of file

docs/source/changelog.rst

+.. include:: ../../CHANGELOG.rst
\ No newline at end of file

docs/source/conf.py

+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/stable/config
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__),
+                                                '../../rpg')))
+
+# -- Project information -----------------------------------------------------
+
+project = 'RapidPeptidesGenerator'
+copyright = '2018, Nicolas Maillet'
+author = 'Nicolas Maillet'
+
+# The short X.Y version
+version = ''
+# The full version, including alpha/beta/rc tags
+release = '0.5.1'
+
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.coverage',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.githubpages',
+    'sphinx.ext.napoleon',
+]
+napoleon_google_docstring = False
+napoleon_use_param = False
+napoleon_use_ivar = True
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path .
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  Major themes that come with
+# Sphinx are currently 'default' and 'sphinxdoc'.
+    
+html_theme = 'sphinx_rtd_theme'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+# html_static_path = ['_static']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'RapidPeptidesGeneratordoc'
+html_short_title = 'RPG'
+
+
+# -- Options for LaTeX output ------------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'RapidPeptidesGenerator.tex', 'RapidPeptidesGenerator Documentation',
+     'Nicolas Maillet', 'manual'),
+]
+
+
+# -- Options for manual page output ------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'rapidpeptidesgenerator', 'RapidPeptidesGenerator Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output ----------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'RapidPeptidesGenerator', 'RapidPeptidesGenerator Documentation',
+     author, 'RapidPeptidesGenerator', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+# -- Extension configuration -------------------------------------------------
\ No newline at end of file

docs/source/enzymes.rst

+===================
+Enzymes definitions
+===================
+All default available enzymes (`enzymes_definition.py`) are listed bellow.
+
+For each of them, there is the equivalent in `RPG` grammar.
+
+-----------------
+Available enzymes
+-----------------
+
+==================  ==================  ==================
+0: :ref:`arg-c`     1: :ref:`asp-n`     2: :ref:`bnps`
+3: :ref:`casp1`     4: :ref:`casp2`     5: :ref:`casp3`
+6: :ref:`casp4`     7: :ref:`casp5`     8: :ref:`casp6`
+9: :ref:`casp7`     10: :ref:`casp8`    11: :ref:`casp9`
+12: :ref:`casp10`   13: :ref:`chymh`    14: :ref:`chyml`
+15: :ref:`clost`    16: :ref:`cnbr`     17: :ref:`enter`
+18: :ref:`fxa`      19: :ref:`gluc`     20: :ref:`lysc`
+21: :ref:`lysn`     22: :ref:`ntcb`     23: :ref:`peps13`
+24: :ref:`peps2`    25: :ref:`throm`    26: :ref:`thromsg`
+27: :ref:`tryps`
+==================  ==================  ==================
+
+.. _arg-c:
+
+Arg-C
+.....
+
+Arg-C proteinase proteinase preferentially cleaves after R
+
+**RPG definition:**
+
+cleaving rule:
+
+* ``(R,)``
+
+More informations:
+https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#ArgC
+
+
+
+.. _asp-n:
+
+Asp-N
+.....
+
+Asp-N Sequencing Grade preferentially cleaves before C or D
+
+**RPG definition:**
+
+cleaving rule:
+
+* ``(,C or D)``
+
+More informations:
+https://france.promega.com/resources/pubhub/using-endoproteinases-asp-n-and-glu-c-to-improve-protein-characterization/
+
+
+
+.. _bnps:
+
+BNPS-Skatole
+............
+
+BNPS-Skatole preferentially cleaves after W
+
+**RPG definition:**
+
+cleaving rule:
+
+* ``(W,)``
+
+More informations:
+https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#BNPS
+
+
+
+.. _casp1:
+
+Caspase 1
+.........
+
+Caspase 1 preferentially cleaves after D preceded by H, A or T in `P2` and preceded by F, W, Y or L in `P4`. It will not cleave if D is followed by P, E, D, Q ,K or R
+
+**RPG definition:**
+
+cleaving rule:
+
+* ``(F or W or Y or L)()(H or A or T)(D,)``
+
+exception rule:
+
+* ``(F or W or Y or L)()(H or A or T)(D,)(P or E or D or Q or K or R)``
+
+More informations:
+https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp1
+
+
+
+.. _casp2:
+
+Caspase 2
+.........
+
+Caspase 2 preferentially cleaves after D preceded by DVA or DEH. It will not cleave if D is followed by P, E, D, Q ,K or R. 
+
+**RPG definition:**
+
+cleaving rules:
+
+* ``(D)(V)(A)(D,)``
+* ``(D)(E)(H)(D,)``
+
+exception rules:
+
+* ``(D)(V)(A)(D,)(P or E or D or Q or K or R)``
+* ``(D)(E)(H)(D,)(P or E or D or Q or K or R)``
+
+More informations:
+https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp2
+
+
+
+.. _casp3:
+
+Caspase 3
+.........
+
+Caspase 3 preferentially cleaves after D preceded by DMQ or DEV. It will not cleave if D is followed by P, E, D, Q ,K or R. 
+
+**RPG definition:**
+
+cleaving rules:
+
+* ``(D)(M)(Q)(D,)``
+* ``(D)(E)(V)(D,)``
+
+exception rules:
+
+* ``(D)(M)(Q)(D,)(P or E or D or Q or K or R)``
+* ``(D)(E)(V)(D,)(P or E or D or Q or K or R)``
+
+More informations:
+https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp3
+
+
+
+.. _casp4:
+
+Caspase 4
+.........
+
+Caspase 4 preferentially cleaves after D preceded by LEV or (W/L)EH. It will not cleave if D is followed by P, E, D, Q ,K or R. 
+
+**RPG definition:**
+
+cleaving rules:
+
+* ``(L)(E)(V)(D,)``
+* ``(W or L)(E)(H)(D,)``
+
+exception rules:
+
+* ``(L)(E)(V)(D,)(P or E or D or Q or K or R)``
+* ``(W or L)(E)(H)(D,)(P or E or D or Q or K or R)``
+
+More informations:
+https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp4
+
+
+
+.. _casp5:
+
+Caspase 5
+.........
+
+Caspase 5 preferentially cleaves after D preceded by (W/L)EH.
+
+**RPG definition:**
+
+cleaving rule:
+
+* ``(W or L)(E)(H)(D,)``
+
+More informations:
+https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp5
+
+
+
+.. _casp6:
+
+Caspase 6
+.........
+
+Caspase 6 preferentially cleaves after D preceded by VEI or VEH. It will not cleave if D is followed by P, E, D, Q ,K or R. 
+
+**RPG definition:**
+
+cleaving rule:
+
+* ``(V)(E)(I or H)(D,)``
+
+exception rule:
+
+* ``(V)(E)(I or H)(D,)(P or E or D or Q or K or R)``
+
+More informations:
+https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp6
+
+
+
+.. _casp7:
+
+Caspase 7
+.........
+
+Caspase 7 preferentially cleaves after D preceded by DEV. It will not cleave if D is followed by P, E, D, Q ,K or R. 
+
+**RPG definition:**
+
+cleaving rule:
+
+* ``(D)(E)(V)(D,)``
+
+exception rule:
+
+* ``(D)(E)(V)(D,)(P or E or D or Q or K or R)``
+
+More informations:
+https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp7
+
+
+
+.. _casp8:
+
+Caspase 8
+.........
+
+Caspase 8 preferentially cleaves after D preceded by (I/L)ET. It will not cleave if D is followed by P, E, D, Q ,K or R. 
+
+**RPG definition:**
+
+cleaving rule:
+
+* ``(I or L)(E)(T)(D,)``
+
+exception rule:
+
+* ``(I or L)(E)(T)(D,)(P or E or D or Q or K or R)``
+
+More informations:
+https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp8
+
+
+
+.. _casp9:
+
+Caspase 9
+.........
+
+Caspase 9 preferentially cleaves after D preceded by LEH.
+
+**RPG definition:**
+
+cleaving rule:
+
+* ``(L)(E)(H)(D,)``
+
+More informations:
+https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp9
+
+
+
+.. _casp10:
+
+Caspase 10
+..........
+
+Caspase 10 preferentially cleaves after D preceded by IEA.
+
+**RPG definition:**
+
+cleaving rule:
+
+* ``(I)(E)(A)(D,)``
+
+More informations:
+https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp10
+
+
+
+.. _chymh:
+
+Chymotrypsin high specificity
+.............................
+
+This chymotrypsin preferentially cleaves after F, Y or W if not followed by P. It will not cleave after W followed by M.
+
+**RPG definition:**
+
+cleaving rule:
+
+* ``(F or Y or W,)``
+
+exception rules:
+
+* ``(F or Y or W,)(P)``
+* ``(W,)(M)``
+
+More informations:
+https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Chym
+
+
+
+.. _chyml:
+
+Chymotrypsin low specificity
+.............................
+
+This chymotrypsin preferentially cleaves after F, L, Y, W, M or H if not followed by P. It will not cleave after W followed by M. It will not cleave after M followed by Y. It will not cleave after H followed by D/M/W.
+
+**RPG definition:**
+
+cleaving rule:
+
+* ``(F or L or Y or W or M or H,)``
+
+exception rules:
+
+* ``(F or L or Y or W or M or H,)(P)``
+* ``(W,)(M)``
+* ``(M,)(Y)``
+* ``(H,)(D or M or W)``
+
+More informations:
+https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Chym
+
+
+
+.. _clost:
+
+Clostripain
+...........
+
+Clostripain (Clostridiopeptidase B) preferentially cleaves after R.
+
+**RPG definition:**
+
+cleaving rule:
+
+* ``(R,)``
+
+More informations:
+https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Clost
+
+
+
+.. _cnbr:
+
+CNBr
+....
+
+CNBr preferentially cleaves after M.
+
+**RPG definition:**
+
+cleaving rule:
+
+* ``(M,)``
+
+More informations:
+https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#CNBr
+
+
+
+.. _enter:
+
+Enterokinase
+............
+
+Enterokinase preferentially cleaves after K preceded by D/E in `P2`, `P3`, `P4` and `P5`.
+
+**RPG definition:**
+
+cleaving rule:
+
+* ``(D or E)(D or E)(D or E)(D or E)(K,)``
+
+More informations:
+https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Enter
+
+
+
+.. _fxa:
+
+Factor Xa
+.........
+
+Factor Xa preferentially cleaves after R preceded by G in `P2`, D/E in `P3` and A/F/I/L/V/W/G/T in `P4`.
+
+**RPG definition:**
+
+cleaving rule:
+
+* ``(A or F or I or L or V or W or G or T)(D or E)(G)(R,)``
+
+More informations:
+https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Xa
+
+
+
+.. _gluc:
+
+Glu-C
+.....
+
+Glu-C Sequencing Grade preferentially cleaves after D or E.
+
+**RPG definition:**
+
+cleaving rule:
+
+* ``(D or E,)``
+
+More informations:
+https://france.promega.com/resources/pubhub/using-endoproteinases-asp-n-and-glu-c-to-improve-protein-characterization/
+
+
+
+.. _lysc:
+
+Lys-C
+.....
+
+LysC Lysyl endopeptidase (Achromobacter proteinase I) preferentially cleaves after K.