Commit 8aa1b417 authored by Nicolas  MAILLET's avatar Nicolas MAILLET
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CHANGELOG
=========
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User Guide
==========
Todo
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# 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)
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.. include:: ../../CHANGELOG.rst
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# -*- 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 -------------------------------------------------
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===================
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.