Skip to content

P
PRESCOTT
Commit ae5d1c5f by Mustafa Tekpinar
Options

Created docs folder and its content with sphinx.

parent a46cad97
Showing with 3658 additions and 34 deletions
README.md
...@@ -54,42 +54,9 @@ JET is run in its iterative mode, iJET, 10 times and the final conservation leve ...@@ -54,42 +54,9 @@ JET is run in its iterative mode, iJET, 10 times and the final conservation leve
values obtained over the 10 iterations. values obtained over the 10 iterations.
JET2 configuration file is: default.conf. JET2 configuration file is: default.conf.
JET2 output file is: myProt_jet.res. JET2 output file is: myProt_jet.res.
### Analyzing the ESGEMME output
By default, ESGEMME will output the following files:
* myProt_normPred_evolEpi.txt
* myProt_normPred_evolInd.txt
* myProt_normPred_evolCombi.txt
The most important output file is **myProt_normPred_evolCombi.txt**.
The values of interest are the normalized predictions (normPred). Each file contains a 20 x n matrix,
where n is the number of positions in the query sequence.
If the user provides her/his own list of mutations, then only the global epistatic model will be run
and the output file will contain 2 columns, the first one with the mutations, the second one with the
normalized predicted effects.
## Installation ## Installation
ESGEMME is implemented in Python 3 and R. It has been tested only on Linux. Since ESGEMME has many dependencies, we recommend using our web site or our docker image. If you are a determined user, here comes the steps required to install it from the source. ESGEMME is implemented in Python 3 and R. It has been tested only on Linux. Since ESGEMME has many dependencies, we recommend using our web site or our docker image. If you are a determined user, you can find the steps required to install it from the source in the following link (or in the docs folder of this repository):
### Installation from the source:
#### Getting the source code and preparing the environment:
Download the ESGEMME source code from http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME.
Define and export the environment variable ESGEMME_PATH=/path-to-ESGEMME-directory/
```bash
export ESGEMME_PATH=/path-to-ESGEMME-directory/
```
#### Installing the dependencies:
ESGEMME has the following external dependencies:
* Joint Evolutionary Trees: http://www.lcqb.upmc.fr/JET2/ and its dependencies:
- naccess: http://www.bioinf.manchester.ac.uk/naccess/
- muscle: https://www.drive5.com/muscle/
**
* seqinr R package: https://cran.r-project.org/web/packages/seqinr/index.html
* dssp for secondary structure prediction.
These tools should be installed to be able to use ESGEMME.
# Cite # Cite
......
docs/Makefile 0 → 100644
# Minimal makefile for Sphinx documentation
#
# You can set these variables from the command line, and also
# from the environment for the first two.
SPHINXOPTS ?=
SPHINXBUILD ?= sphinx-build
SOURCEDIR = .
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)
docs/_build/.buildinfo 0 → 100644
# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: ee0c3cda5e96b708cc4747fb117bcc00
tags: 645f666f9bcd5a90fca523b33c5a78b7
docs/_build/LICRcyr2utf8.xdy 0 → 100644
;; -*- coding: utf-8; mode: Lisp; -*-
;; style file for xindy
;; filename: LICRcyr2utf8.xdy
;; description: style file for xindy which maps back LaTeX Internal
;; Character Representation of Cyrillic to utf-8
;; usage: for use with pdflatex produced .idx files.
;; Contributed by the Sphinx team, July 2018.
(merge-rule "\IeC {\'\CYRG }" "Ѓ" :string)
(merge-rule "\IeC {\'\CYRK }" "Ќ" :string)
(merge-rule "\IeC {\'\cyrg }" "ѓ" :string)
(merge-rule "\IeC {\'\cyrk }" "ќ" :string)
(merge-rule "\IeC {\CYRA }" "А" :string)
(merge-rule "\IeC {\CYRB }" "Б" :string)
(merge-rule "\IeC {\CYRC }" "Ц" :string)
(merge-rule "\IeC {\CYRCH }" "Ч" :string)
(merge-rule "\IeC {\CYRD }" "Д" :string)
(merge-rule "\IeC {\CYRDJE }" "Ђ" :string)
(merge-rule "\IeC {\CYRDZE }" "Ѕ" :string)
(merge-rule "\IeC {\CYRDZHE }" "Џ" :string)
(merge-rule "\IeC {\CYRE }" "Е" :string)
(merge-rule "\IeC {\CYREREV }" "Э" :string)
(merge-rule "\IeC {\CYRERY }" "Ы" :string)
(merge-rule "\IeC {\CYRF }" "Ф" :string)
(merge-rule "\IeC {\CYRG }" "Г" :string)
(merge-rule "\IeC {\CYRGUP }" "Ґ" :string)
(merge-rule "\IeC {\CYRH }" "Х" :string)
(merge-rule "\IeC {\CYRHRDSN }" "Ъ" :string)
(merge-rule "\IeC {\CYRI }" "И" :string)
(merge-rule "\IeC {\CYRIE }" "Є" :string)
(merge-rule "\IeC {\CYRII }" "І" :string)
(merge-rule "\IeC {\CYRISHRT }" "Й" :string)
(merge-rule "\IeC {\CYRJE }" "Ј" :string)
(merge-rule "\IeC {\CYRK }" "К" :string)
(merge-rule "\IeC {\CYRL }" "Л" :string)
(merge-rule "\IeC {\CYRLJE }" "Љ" :string)
(merge-rule "\IeC {\CYRM }" "М" :string)
(merge-rule "\IeC {\CYRN }" "Н" :string)
(merge-rule "\IeC {\CYRNJE }" "Њ" :string)
(merge-rule "\IeC {\CYRO }" "О" :string)
(merge-rule "\IeC {\CYRP }" "П" :string)
(merge-rule "\IeC {\CYRR }" "Р" :string)
(merge-rule "\IeC {\CYRS }" "С" :string)
(merge-rule "\IeC {\CYRSFTSN }" "Ь" :string)
(merge-rule "\IeC {\CYRSH }" "Ш" :string)
(merge-rule "\IeC {\CYRSHCH }" "Щ" :string)
(merge-rule "\IeC {\CYRT }" "Т" :string)
(merge-rule "\IeC {\CYRTSHE }" "Ћ" :string)
(merge-rule "\IeC {\CYRU }" "У" :string)
(merge-rule "\IeC {\CYRUSHRT }" "Ў" :string)
(merge-rule "\IeC {\CYRV }" "В" :string)
(merge-rule "\IeC {\CYRYA }" "Я" :string)
(merge-rule "\IeC {\CYRYI }" "Ї" :string)
(merge-rule "\IeC {\CYRYO }" "Ё" :string)
(merge-rule "\IeC {\CYRYU }" "Ю" :string)
(merge-rule "\IeC {\CYRZ }" "З" :string)
(merge-rule "\IeC {\CYRZH }" "Ж" :string)
(merge-rule "\IeC {\cyra }" "а" :string)
(merge-rule "\IeC {\cyrb }" "б" :string)
(merge-rule "\IeC {\cyrc }" "ц" :string)
(merge-rule "\IeC {\cyrch }" "ч" :string)
(merge-rule "\IeC {\cyrd }" "д" :string)
(merge-rule "\IeC {\cyrdje }" "ђ" :string)
(merge-rule "\IeC {\cyrdze }" "ѕ" :string)
(merge-rule "\IeC {\cyrdzhe }" "џ" :string)
(merge-rule "\IeC {\cyre }" "е" :string)
(merge-rule "\IeC {\cyrerev }" "э" :string)
(merge-rule "\IeC {\cyrery }" "ы" :string)
(merge-rule "\IeC {\cyrf }" "ф" :string)
(merge-rule "\IeC {\cyrg }" "г" :string)
(merge-rule "\IeC {\cyrgup }" "ґ" :string)
(merge-rule "\IeC {\cyrh }" "х" :string)
(merge-rule "\IeC {\cyrhrdsn }" "ъ" :string)
(merge-rule "\IeC {\cyri }" "и" :string)
(merge-rule "\IeC {\cyrie }" "є" :string)
(merge-rule "\IeC {\cyrii }" "і" :string)
(merge-rule "\IeC {\cyrishrt }" "й" :string)
(merge-rule "\IeC {\cyrje }" "ј" :string)
(merge-rule "\IeC {\cyrk }" "к" :string)
(merge-rule "\IeC {\cyrl }" "л" :string)
(merge-rule "\IeC {\cyrlje }" "љ" :string)
(merge-rule "\IeC {\cyrm }" "м" :string)
(merge-rule "\IeC {\cyrn }" "н" :string)
(merge-rule "\IeC {\cyrnje }" "њ" :string)
(merge-rule "\IeC {\cyro }" "о" :string)
(merge-rule "\IeC {\cyrp }" "п" :string)
(merge-rule "\IeC {\cyrr }" "р" :string)
(merge-rule "\IeC {\cyrs }" "с" :string)
(merge-rule "\IeC {\cyrsftsn }" "ь" :string)
(merge-rule "\IeC {\cyrsh }" "ш" :string)
(merge-rule "\IeC {\cyrshch }" "щ" :string)
(merge-rule "\IeC {\cyrt }" "т" :string)
(merge-rule "\IeC {\cyrtshe }" "ћ" :string)
(merge-rule "\IeC {\cyru }" "у" :string)
(merge-rule "\IeC {\cyrushrt }" "ў" :string)
(merge-rule "\IeC {\cyrv }" "в" :string)
(merge-rule "\IeC {\cyrya }" "я" :string)
(merge-rule "\IeC {\cyryi }" "ї" :string)
(merge-rule "\IeC {\cyryo }" "ё" :string)
(merge-rule "\IeC {\cyryu }" "ю" :string)
(merge-rule "\IeC {\cyrz }" "з" :string)
(merge-rule "\IeC {\cyrzh }" "ж" :string)
docs/_build/Makefile 0 → 100644
# Makefile for Sphinx LaTeX output
ALLDOCS = $(basename $(wildcard *.tex))
ALLPDF = $(addsuffix .pdf,$(ALLDOCS))
ALLDVI = $(addsuffix .dvi,$(ALLDOCS))
ALLXDV =
ALLPS = $(addsuffix .ps,$(ALLDOCS))
ALLIMGS = $(wildcard *.png *.gif *.jpg *.jpeg)
# Prefix for archive names
ARCHIVEPREFIX =
# Additional LaTeX options (passed via variables in latexmkrc/latexmkjarc file)
export LATEXOPTS ?=
# Additional latexmk options
LATEXMKOPTS ?=
# format: pdf or dvi (used only by archive targets)
FMT = pdf
LATEX = latexmk -dvi
PDFLATEX = latexmk -pdf -dvi- -ps-
%.png %.gif %.jpg %.jpeg: FORCE_MAKE
extractbb '$@'
%.dvi: %.tex FORCE_MAKE
$(LATEX) $(LATEXMKOPTS) '$<'
%.ps: %.dvi
dvips '$<'
%.pdf: %.tex FORCE_MAKE
$(PDFLATEX) $(LATEXMKOPTS) '$<'
all: $(ALLPDF)
all-dvi: $(ALLDVI)
all-ps: $(ALLPS)
all-pdf: $(ALLPDF)
zip: all-$(FMT)
mkdir $(ARCHIVEPREFIX)docs-$(FMT)
cp $(ALLPDF) $(ARCHIVEPREFIX)docs-$(FMT)
zip -q -r -9 $(ARCHIVEPREFIX)docs-$(FMT).zip $(ARCHIVEPREFIX)docs-$(FMT)
rm -r $(ARCHIVEPREFIX)docs-$(FMT)
tar: all-$(FMT)
mkdir $(ARCHIVEPREFIX)docs-$(FMT)
cp $(ALLPDF) $(ARCHIVEPREFIX)docs-$(FMT)
tar cf $(ARCHIVEPREFIX)docs-$(FMT).tar $(ARCHIVEPREFIX)docs-$(FMT)
rm -r $(ARCHIVEPREFIX)docs-$(FMT)
gz: tar
gzip -9 < $(ARCHIVEPREFIX)docs-$(FMT).tar > $(ARCHIVEPREFIX)docs-$(FMT).tar.gz
bz2: tar
bzip2 -9 -k $(ARCHIVEPREFIX)docs-$(FMT).tar
xz: tar
xz -9 -k $(ARCHIVEPREFIX)docs-$(FMT).tar
clean:
rm -f *.log *.ind *.aux *.toc *.syn *.idx *.out *.ilg *.pla *.ps *.tar *.tar.gz *.tar.bz2 *.tar.xz $(ALLPDF) $(ALLDVI) $(ALLXDV) *.fls *.fdb_latexmk
.PHONY: all all-pdf all-dvi all-ps clean zip tar gz bz2 xz
.PHONY: FORCE_MAKE
\ No newline at end of file
docs/_build/_sources/analysis.rst.txt 0 → 100644
Analyzing the ESGEMME output
----------------------------
By default, ESGEMME will output the following files: \*
myProt_normPred_evolEpi.txt \* myProt_normPred_evolInd.txt \*
myProt_normPred_evolCombi.txt
The most important output file is **myProt_normPred_evolCombi.txt**. The
values of interest are the normalized predictions (normPred). Each file
contains a 20 x n matrix, where n is the number of positions (columns) in the
query sequence. If the user provides her/his own list of mutations, then
only the global epistatic model will be run and the output file will
contain 2 columns, the first one with the mutations, the second one with
the normalized predicted effects.
docs/_build/_sources/docker.rst.txt 0 → 100644
Using ESGEMME via Docker
========================
Requirements
------------
You need to have docker installed on your machine. You can consult the
following page for this: https://docs.docker.com/get-docker/
I am assuming some basic familiarity with Linux/Unix/MacOS terminal
commands.
Let’s start our favorite terminal app.
You must to create a folder called docker-tutorial and go to that empty
folder:
.. code:: bash
mkdir docker-tutorial
cd docker-tutorial
Getting the input data
----------------------
Let’s download the sample data provided in the ESGEMME repository for
this exercise. First, we will download the multiple sequence alignment
file in fasta format:
.. code:: bash
wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/blob/master/data/aliBLAT.fasta
If you don’t have wget, you can try the same command with curl:
.. code:: bash
curl http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/blob/master/data/aliBLAT.fasta
Please verify that the aliBLAT.fasta file is in the folder.
Now, we will download the PDB (Protein Databank) file for BLAT:
.. code:: bash
wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/blob/master/data/blat-af2.pdb
Single point mutation calculations
----------------------------------
In order to make sure that the docker is installed:
.. code:: bash
sudo docker -h
If it shows you a list of options, you are on a good track. On MacOS,
you may not need ‘sudo’ word before the docker command at all.
.. code:: bash
sudo docker run -ti --rm --mount type=bind,source=$PWD,target=/home/tekpinar/research/myexample \
tekpinar/esgemme-docker:v1.3.0
You are in the container (your virtual operating system) now. You
created a folder called myexample in your container with the previous
command. Let’s change to that folder.
.. code:: bash
cd ../myexample/
When you check the data in that folder with ‘ls’ command, you are
supposed to see aliBLAT.fasta and blat-af2.pdb files. Basically, your
docker-tutorial folder on the host system and myexample folder on the
docker container are pointing to the same place.
Obtaining the entire single point mutation landscape
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
In this step, we will use only evolutionary information from an MSA file:
.. code:: bash
python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta
After a few minutes of calculation, you must see at least two files named
BLAT_normPred_evolCombi.txt and BLAT_normPred_evolCombi.png. You have
the entire single point mutational landscape of BLAT protein in these
files.
If you want to utilize structural information (highly recommended) as well as
evolutionary information:
.. code:: bash
python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta \
--pdbfile blat-af2.pdb \
--normweightmode sstjetormax
Obtaining the effect of a subset of single point mutations
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
If you are interested in only a bunch of single point mutations,
you have to prepare a mut file. The format is a simple text file and
each line contains a single point mutation such as D26A....
Fortunately, we have an example mut in data folder of ESGEMME repository.
.. code:: bash
wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/raw/master/data/Stiffler_2015_BLAT_ECOLX.mut
Similar to the previous step, there are two possible ways to do the calculations: with or without
structural information. First, without structural information:
.. code:: bash
python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta \
-m Stiffler_2015_BLAT_ECOLX.mut
You can include structural information in the following way:
.. code:: bash
python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta \
--pdbfile blat-af2.pdb \
--normweightmode sstjetormax \
-m Stiffler_2015_BLAT_ECOLX.mut
You will have BLAT_normPred_evolCombi.txt file in your folder. However, the output
format is completely different from the entire mutational landscape scanning file.
Each line of this file is a mutation and its predicted effect separated by a space.
In addition, you won't have a png file like in the previous case.
Multiple point mutation calculations
------------------------------------
Sometimes, we need to see effects of double or triple mutations. ESGEMME can
perform calculations if you provide a mut file. In this case, the mut file must
have the following format:
.. code:: bash
E26D:Y44R
E56N:A77F:H94V
The first line of the text file is impact of a double mutations and the second
line is the impact of the triple mutations. As you can see, the mutations are
separated by a colon(:) character.
The output file will be in a similar format. Each line will contain the multiple
mutation and its predicted effect, separated by a space.
Running several jobs using docker
---------------------------------
docs/_build/_sources/index.rst.txt 0 → 100644
.. esgemme documentation master file, created by
sphinx-quickstart on Fri May 5 13:52:13 2023.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
Welcome to esgemme's documentation!
===================================
.. toctree::
:maxdepth: 2
:caption: Contents:
docker.rst
analysis.rst
installation.rst
Indices and tables
==================
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
docs/_build/_sources/installation.rst.txt 0 → 100644
Installation
------------
ESGEMME is implemented in Python 3 and R. It has been tested only on
Linux. Since ESGEMME has many dependencies, we recommend using our web
site or our docker image. If you are a determined user, here comes the
steps required to install it from the source.
Installing the dependencies:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ESGEMME has the following external dependencies: \* Joint Evolutionary
Trees: http://www.lcqb.upmc.fr/JET2/ and its dependencies: - naccess:
http://www.bioinf.manchester.ac.uk/naccess/ - muscle:
https://www.drive5.com/muscle/ \*\* \* seqinr R package:
https://cran.r-project.org/web/packages/seqinr/index.html \* dssp for
secondary structure prediction.
These tools should be installed to be able to use ESGEMME.
Getting the source code and preparing the environment:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Download the ESGEMME source code from
http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME. Define and export the
environment variable ESGEMME_PATH=/path-to-ESGEMME-directory/
.. code:: bash
export ESGEMME_PATH=/path-to-ESGEMME-directory/
Configuring default.conf file
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Inside ESGEMME folder, there is an important file called default.conf.
This file contains essential parameters of ESGEMME, such as paths of
external parts, default internal parameters. etc. You have to correct the Software section of this
file according to your system.
\ No newline at end of file
docs/_build/_static/css/badge_only.css 0 → 100644
.clearfix{*zoom:1}.clearfix:after,.clearfix:before{display:table;content:""}.clearfix:after{clear:both}@font-face{font-family:FontAwesome;font-style:normal;font-weight:400;src:url(fonts/fontawesome-webfont.eot?674f50d287a8c48dc19ba404d20fe713?#iefix) format("embedded-opentype"),url(fonts/fontawesome-webfont.woff2?af7ae505a9eed503f8b8e6982036873e) format("woff2"),url(fonts/fontawesome-webfont.woff?fee66e712a8a08eef5805a46892932ad) format("woff"),url(fonts/fontawesome-webfont.ttf?b06871f281fee6b241d60582ae9369b9) format("truetype"),url(fonts/fontawesome-webfont.svg?912ec66d7572ff821749319396470bde#FontAwesome) format("svg")}.fa:before{font-family:FontAwesome;font-style:normal;font-weight:400;line-height:1}.fa:before,a .fa{text-decoration:inherit}.fa:before,a .fa,li .fa{display:inline-block}li .fa-large:before{width:1.875em}ul.fas{list-style-type:none;margin-left:2em;text-indent:-.8em}ul.fas li .fa{width:.8em}ul.fas li .fa-large:before{vertical-align:baseline}.fa-book:before,.icon-book:before{content:"\f02d"}.fa-caret-down:before,.icon-caret-down:before{content:"\f0d7"}.fa-caret-up:before,.icon-caret-up:before{content:"\f0d8"}.fa-caret-left:before,.icon-caret-left:before{content:"\f0d9"}.fa-caret-right:before,.icon-caret-right:before{content:"\f0da"}.rst-versions{position:fixed;bottom:0;left:0;width:300px;color:#fcfcfc;background:#1f1d1d;font-family:Lato,proxima-nova,Helvetica Neue,Arial,sans-serif;z-index:400}.rst-versions a{color:#2980b9;text-decoration:none}.rst-versions .rst-badge-small{display:none}.rst-versions .rst-current-version{padding:12px;background-color:#272525;display:block;text-align:right;font-size:90%;cursor:pointer;color:#27ae60}.rst-versions .rst-current-version:after{clear:both;content:"";display:block}.rst-versions .rst-current-version .fa{color:#fcfcfc}.rst-versions .rst-current-version .fa-book,.rst-versions .rst-current-version .icon-book{float:left}.rst-versions .rst-current-version.rst-out-of-date{background-color:#e74c3c;color:#fff}.rst-versions .rst-current-version.rst-active-old-version{background-color:#f1c40f;color:#000}.rst-versions.shift-up{height:auto;max-height:100%;overflow-y:scroll}.rst-versions.shift-up .rst-other-versions{display:block}.rst-versions .rst-other-versions{font-size:90%;padding:12px;color:grey;display:none}.rst-versions .rst-other-versions hr{display:block;height:1px;border:0;margin:20px 0;padding:0;border-top:1px solid #413d3d}.rst-versions .rst-other-versions dd{display:inline-block;margin:0}.rst-versions .rst-other-versions dd a{display:inline-block;padding:6px;color:#fcfcfc}.rst-versions.rst-badge{width:auto;bottom:20px;right:20px;left:auto;border:none;max-width:300px;max-height:90%}.rst-versions.rst-badge .fa-book,.rst-versions.rst-badge .icon-book{float:none;line-height:30px}.rst-versions.rst-badge.shift-up .rst-current-version{text-align:right}.rst-versions.rst-badge.shift-up .rst-current-version .fa-book,.rst-versions.rst-badge.shift-up .rst-current-version .icon-book{float:left}.rst-versions.rst-badge>.rst-current-version{width:auto;height:30px;line-height:30px;padding:0 6px;display:block;text-align:center}@media screen and (max-width:768px){.rst-versions{width:85%;display:none}.rst-versions.shift{display:block}}
\ No newline at end of file
docs/_build/_static/css/fonts/fontawesome-webfont.svg 0 → 100644
This source diff could not be displayed because it is too large. You can view the blob instead.
docs/_build/_static/css/theme.css 0 → 100644
This source diff could not be displayed because it is too large. You can view the blob instead.
docs/_build/_static/custom.css 0 → 100644
/* This file intentionally left blank. */
docs/_build/_static/doctools.js 0 → 100644
/*
* doctools.js
* ~~~~~~~~~~~
*
* Sphinx JavaScript utilities for all documentation.
*
* :copyright: Copyright 2007-2020 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
/**
* select a different prefix for underscore
*/
$u = _.noConflict();
/**
* make the code below compatible with browsers without
* an installed firebug like debugger
if (!window.console || !console.firebug) {
var names = ["log", "debug", "info", "warn", "error", "assert", "dir",
"dirxml", "group", "groupEnd", "time", "timeEnd", "count", "trace",
"profile", "profileEnd"];
window.console = {};
for (var i = 0; i < names.length; ++i)
window.console[names[i]] = function() {};
}
*/
/**
* small helper function to urldecode strings
*/
jQuery.urldecode = function(x) {
return decodeURIComponent(x).replace(/\+/g, ' ');
};
/**
* small helper function to urlencode strings
*/
jQuery.urlencode = encodeURIComponent;
/**
* This function returns the parsed url parameters of the
* current request. Multiple values per key are supported,
* it will always return arrays of strings for the value parts.
*/
jQuery.getQueryParameters = function(s) {
if (typeof s === 'undefined')
s = document.location.search;
var parts = s.substr(s.indexOf('?') + 1).split('&');
var result = {};
for (var i = 0; i < parts.length; i++) {
var tmp = parts[i].split('=', 2);
var key = jQuery.urldecode(tmp[0]);
var value = jQuery.urldecode(tmp[1]);
if (key in result)
result[key].push(value);
else
result[key] = [value];
}
return result;
};
/**
* highlight a given string on a jquery object by wrapping it in
* span elements with the given class name.
*/
jQuery.fn.highlightText = function(text, className) {
function highlight(node, addItems) {
if (node.nodeType === 3) {
var val = node.nodeValue;
var pos = val.toLowerCase().indexOf(text);
if (pos >= 0 &&
!jQuery(node.parentNode).hasClass(className) &&
!jQuery(node.parentNode).hasClass("nohighlight")) {
var span;
var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
if (isInSVG) {
span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
} else {
span = document.createElement("span");
span.className = className;
}
span.appendChild(document.createTextNode(val.substr(pos, text.length)));
node.parentNode.insertBefore(span, node.parentNode.insertBefore(
document.createTextNode(val.substr(pos + text.length)),
node.nextSibling));
node.nodeValue = val.substr(0, pos);
if (isInSVG) {
var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
var bbox = node.parentElement.getBBox();
rect.x.baseVal.value = bbox.x;
rect.y.baseVal.value = bbox.y;
rect.width.baseVal.value = bbox.width;
rect.height.baseVal.value = bbox.height;
rect.setAttribute('class', className);
addItems.push({
"parent": node.parentNode,
"target": rect});
}
}
}
else if (!jQuery(node).is("button, select, textarea")) {
jQuery.each(node.childNodes, function() {
highlight(this, addItems);
});
}
}
var addItems = [];
var result = this.each(function() {
highlight(this, addItems);
});
for (var i = 0; i < addItems.length; ++i) {
jQuery(addItems[i].parent).before(addItems[i].target);
}
return result;
};
/*
* backward compatibility for jQuery.browser
* This will be supported until firefox bug is fixed.
*/
if (!jQuery.browser) {
jQuery.uaMatch = function(ua) {
ua = ua.toLowerCase();
var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
/(webkit)[ \/]([\w.]+)/.exec(ua) ||
/(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
/(msie) ([\w.]+)/.exec(ua) ||
ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
[];
return {
browser: match[ 1 ] || "",
version: match[ 2 ] || "0"
};
};
jQuery.browser = {};
jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
}
/**
* Small JavaScript module for the documentation.
*/
var Documentation = {
init : function() {
this.fixFirefoxAnchorBug();
this.highlightSearchWords();
this.initIndexTable();
if (DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) {
this.initOnKeyListeners();
}
},
/**
* i18n support
*/
TRANSLATIONS : {},
PLURAL_EXPR : function(n) { return n === 1 ? 0 : 1; },
LOCALE : 'unknown',
// gettext and ngettext don't access this so that the functions
// can safely bound to a different name (_ = Documentation.gettext)
gettext : function(string) {
var translated = Documentation.TRANSLATIONS[string];
if (typeof translated === 'undefined')
return string;
return (typeof translated === 'string') ? translated : translated[0];
},
ngettext : function(singular, plural, n) {
var translated = Documentation.TRANSLATIONS[singular];
if (typeof translated === 'undefined')
return (n == 1) ? singular : plural;
return translated[Documentation.PLURALEXPR(n)];
},
addTranslations : function(catalog) {
for (var key in catalog.messages)
this.TRANSLATIONS[key] = catalog.messages[key];
this.PLURAL_EXPR = new Function('n', 'return +(' + catalog.plural_expr + ')');
this.LOCALE = catalog.locale;
},
/**
* add context elements like header anchor links
*/
addContextElements : function() {
$('div[id] > :header:first').each(function() {
$('<a class="headerlink">\u00B6</a>').
attr('href', '#' + this.id).
attr('title', _('Permalink to this headline')).
appendTo(this);
});
$('dt[id]').each(function() {
$('<a class="headerlink">\u00B6</a>').
attr('href', '#' + this.id).
attr('title', _('Permalink to this definition')).
appendTo(this);
});
},
/**
* workaround a firefox stupidity
* see: https://bugzilla.mozilla.org/show_bug.cgi?id=645075
*/
fixFirefoxAnchorBug : function() {
if (document.location.hash && $.browser.mozilla)
window.setTimeout(function() {
document.location.href += '';
}, 10);
},
/**
* highlight the search words provided in the url in the text
*/
highlightSearchWords : function() {
var params = $.getQueryParameters();
var terms = (params.highlight) ? params.highlight[0].split(/\s+/) : [];
if (terms.length) {
var body = $('div.body');
if (!body.length) {
body = $('body');
}
window.setTimeout(function() {
$.each(terms, function() {
body.highlightText(this.toLowerCase(), 'highlighted');
});
}, 10);
$('<p class="highlight-link"><a href="javascript:Documentation.' +
'hideSearchWords()">' + _('Hide Search Matches') + '</a></p>')
.appendTo($('#searchbox'));
}
},
/**
* init the domain index toggle buttons
*/
initIndexTable : function() {
var togglers = $('img.toggler').click(function() {
var src = $(this).attr('src');
var idnum = $(this).attr('id').substr(7);
$('tr.cg-' + idnum).toggle();
if (src.substr(-9) === 'minus.png')
$(this).attr('src', src.substr(0, src.length-9) + 'plus.png');
else
$(this).attr('src', src.substr(0, src.length-8) + 'minus.png');
}).css('display', '');
if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) {
togglers.click();
}
},
/**
* helper function to hide the search marks again
*/
hideSearchWords : function() {
$('#searchbox .highlight-link').fadeOut(300);
$('span.highlighted').removeClass('highlighted');
},
/**
* make the url absolute
*/
makeURL : function(relativeURL) {
return DOCUMENTATION_OPTIONS.URL_ROOT + '/' + relativeURL;
},
/**
* get the current relative url
*/
getCurrentURL : function() {
var path = document.location.pathname;
var parts = path.split(/\//);
$.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() {
if (this === '..')
parts.pop();
});
var url = parts.join('/');
return path.substring(url.lastIndexOf('/') + 1, path.length - 1);
},
initOnKeyListeners: function() {
$(document).keydown(function(event) {
var activeElementType = document.activeElement.tagName;
// don't navigate when in search box or textarea
if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT'
&& !event.altKey && !event.ctrlKey && !event.metaKey && !event.shiftKey) {
switch (event.keyCode) {
case 37: // left
var prevHref = $('link[rel="prev"]').prop('href');
if (prevHref) {
window.location.href = prevHref;
return false;
}
case 39: // right
var nextHref = $('link[rel="next"]').prop('href');
if (nextHref) {
window.location.href = nextHref;
return false;
}
}
}
});
}
};
// quick alias for translations
_ = Documentation.gettext;
$(document).ready(function() {
Documentation.init();
});
docs/_build/_static/documentation_options.js 0 → 100644
var DOCUMENTATION_OPTIONS = {
URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
VERSION: '1.3.0',
LANGUAGE: 'None',
COLLAPSE_INDEX: false,
BUILDER: 'html',
FILE_SUFFIX: '.html',
HAS_SOURCE: true,
SOURCELINK_SUFFIX: '.txt',
NAVIGATION_WITH_KEYS: false
};
\ No newline at end of file
docs/_build/_static/jquery-3.4.1.js 0 → 100644
This source diff could not be displayed because it is too large. You can view the blob instead.
docs/_build/_static/js/badge_only.js 0 → 100644
!function(e){var t={};function r(n){if(t[n])return t[n].exports;var o=t[n]={i:n,l:!1,exports:{}};return e[n].call(o.exports,o,o.exports,r),o.l=!0,o.exports}r.m=e,r.c=t,r.d=function(e,t,n){r.o(e,t)||Object.defineProperty(e,t,{enumerable:!0,get:n})},r.r=function(e){"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.defineProperty(e,Symbol.toStringTag,{value:"Module"}),Object.defineProperty(e,"__esModule",{value:!0})},r.t=function(e,t){if(1&t&&(e=r(e)),8&t)return e;if(4&t&&"object"==typeof e&&e&&e.__esModule)return e;var n=Object.create(null);if(r.r(n),Object.defineProperty(n,"default",{enumerable:!0,value:e}),2&t&&"string"!=typeof e)for(var o in e)r.d(n,o,function(t){return e[t]}.bind(null,o));return n},r.n=function(e){var t=e&&e.__esModule?function(){return e.default}:function(){return e};return r.d(t,"a",t),t},r.o=function(e,t){return Object.prototype.hasOwnProperty.call(e,t)},r.p="",r(r.s=4)}({4:function(e,t,r){}});
\ No newline at end of file
docs/_build/_static/js/html5shiv-printshiv.min.js 0 → 100644
/**
* @preserve HTML5 Shiv 3.7.3-pre | @afarkas @jdalton @jon_neal @rem | MIT/GPL2 Licensed
*/
!function(a,b){function c(a,b){var c=a.createElement("p"),d=a.getElementsByTagName("head")[0]||a.documentElement;return c.innerHTML="x<style>"+b+"</style>",d.insertBefore(c.lastChild,d.firstChild)}function d(){var a=y.elements;return"string"==typeof a?a.split(" "):a}function e(a,b){var c=y.elements;"string"!=typeof c&&(c=c.join(" ")),"string"!=typeof a&&(a=a.join(" ")),y.elements=c+" "+a,j(b)}function f(a){var b=x[a[v]];return b||(b={},w++,a[v]=w,x[w]=b),b}function g(a,c,d){if(c||(c=b),q)return c.createElement(a);d||(d=f(c));var e;return e=d.cache[a]?d.cache[a].cloneNode():u.test(a)?(d.cache[a]=d.createElem(a)).cloneNode():d.createElem(a),!e.canHaveChildren||t.test(a)||e.tagUrn?e:d.frag.appendChild(e)}function h(a,c){if(a||(a=b),q)return a.createDocumentFragment();c=c||f(a);for(var e=c.frag.cloneNode(),g=0,h=d(),i=h.length;i>g;g++)e.createElement(h[g]);return e}function i(a,b){b.cache||(b.cache={},b.createElem=a.createElement,b.createFrag=a.createDocumentFragment,b.frag=b.createFrag()),a.createElement=function(c){return y.shivMethods?g(c,a,b):b.createElem(c)},a.createDocumentFragment=Function("h,f","return function(){var n=f.cloneNode(),c=n.createElement;h.shivMethods&&("+d().join().replace(/[\w\-:]+/g,function(a){return b.createElem(a),b.frag.createElement(a),'c("'+a+'")'})+");return n}")(y,b.frag)}function j(a){a||(a=b);var d=f(a);return!y.shivCSS||p||d.hasCSS||(d.hasCSS=!!c(a,"article,aside,dialog,figcaption,figure,footer,header,hgroup,main,nav,section{display:block}mark{background:#FF0;color:#000}template{display:none}")),q||i(a,d),a}function k(a){for(var b,c=a.getElementsByTagName("*"),e=c.length,f=RegExp("^(?:"+d().join("|")+")$","i"),g=[];e--;)b=c[e],f.test(b.nodeName)&&g.push(b.applyElement(l(b)));return g}function l(a){for(var b,c=a.attributes,d=c.length,e=a.ownerDocument.createElement(A+":"+a.nodeName);d--;)b=c[d],b.specified&&e.setAttribute(b.nodeName,b.nodeValue);return e.style.cssText=a.style.cssText,e}function m(a){for(var b,c=a.split("{"),e=c.length,f=RegExp("(^|[\\s,>+~])("+d().join("|")+")(?=[[\\s,>+~#.:]|$)","gi"),g="$1"+A+"\\:$2";e--;)b=c[e]=c[e].split("}"),b[b.length-1]=b[b.length-1].replace(f,g),c[e]=b.join("}");return c.join("{")}function n(a){for(var b=a.length;b--;)a[b].removeNode()}function o(a){function b(){clearTimeout(g._removeSheetTimer),d&&d.removeNode(!0),d=null}var d,e,g=f(a),h=a.namespaces,i=a.parentWindow;return!B||a.printShived?a:("undefined"==typeof h[A]&&h.add(A),i.attachEvent("onbeforeprint",function(){b();for(var f,g,h,i=a.styleSheets,j=[],l=i.length,n=Array(l);l--;)n[l]=i[l];for(;h=n.pop();)if(!h.disabled&&z.test(h.media)){try{f=h.imports,g=f.length}catch(o){g=0}for(l=0;g>l;l++)n.push(f[l]);try{j.push(h.cssText)}catch(o){}}j=m(j.reverse().join("")),e=k(a),d=c(a,j)}),i.attachEvent("onafterprint",function(){n(e),clearTimeout(g._removeSheetTimer),g._removeSheetTimer=setTimeout(b,500)}),a.printShived=!0,a)}var p,q,r="3.7.3",s=a.html5||{},t=/^<|^(?:button|map|select|textarea|object|iframe|option|optgroup)$/i,u=/^(?:a|b|code|div|fieldset|h1|h2|h3|h4|h5|h6|i|label|li|ol|p|q|span|strong|style|table|tbody|td|th|tr|ul)$/i,v="_html5shiv",w=0,x={};!function(){try{var a=b.createElement("a");a.innerHTML="<xyz></xyz>",p="hidden"in a,q=1==a.childNodes.length||function(){b.createElement("a");var a=b.createDocumentFragment();return"undefined"==typeof a.cloneNode||"undefined"==typeof a.createDocumentFragment||"undefined"==typeof a.createElement}()}catch(c){p=!0,q=!0}}();var y={elements:s.elements||"abbr article aside audio bdi canvas data datalist details dialog figcaption figure footer header hgroup main mark meter nav output picture progress section summary template time video",version:r,shivCSS:s.shivCSS!==!1,supportsUnknownElements:q,shivMethods:s.shivMethods!==!1,type:"default",shivDocument:j,createElement:g,createDocumentFragment:h,addElements:e};a.html5=y,j(b);var z=/^$|\b(?:all|print)\b/,A="html5shiv",B=!q&&function(){var c=b.documentElement;return!("undefined"==typeof b.namespaces||"undefined"==typeof b.parentWindow||"undefined"==typeof c.applyElement||"undefined"==typeof c.removeNode||"undefined"==typeof a.attachEvent)}();y.type+=" print",y.shivPrint=o,o(b),"object"==typeof module&&module.exports&&(module.exports=y)}("undefined"!=typeof window?window:this,document);
\ No newline at end of file
docs/_build/_static/js/html5shiv.min.js 0 → 100644
/**
* @preserve HTML5 Shiv 3.7.3 | @afarkas @jdalton @jon_neal @rem | MIT/GPL2 Licensed
*/
!function(a,b){function c(a,b){var c=a.createElement("p"),d=a.getElementsByTagName("head")[0]||a.documentElement;return c.innerHTML="x<style>"+b+"</style>",d.insertBefore(c.lastChild,d.firstChild)}function d(){var a=t.elements;return"string"==typeof a?a.split(" "):a}function e(a,b){var c=t.elements;"string"!=typeof c&&(c=c.join(" ")),"string"!=typeof a&&(a=a.join(" ")),t.elements=c+" "+a,j(b)}function f(a){var b=s[a[q]];return b||(b={},r++,a[q]=r,s[r]=b),b}function g(a,c,d){if(c||(c=b),l)return c.createElement(a);d||(d=f(c));var e;return e=d.cache[a]?d.cache[a].cloneNode():p.test(a)?(d.cache[a]=d.createElem(a)).cloneNode():d.createElem(a),!e.canHaveChildren||o.test(a)||e.tagUrn?e:d.frag.appendChild(e)}function h(a,c){if(a||(a=b),l)return a.createDocumentFragment();c=c||f(a);for(var e=c.frag.cloneNode(),g=0,h=d(),i=h.length;i>g;g++)e.createElement(h[g]);return e}function i(a,b){b.cache||(b.cache={},b.createElem=a.createElement,b.createFrag=a.createDocumentFragment,b.frag=b.createFrag()),a.createElement=function(c){return t.shivMethods?g(c,a,b):b.createElem(c)},a.createDocumentFragment=Function("h,f","return function(){var n=f.cloneNode(),c=n.createElement;h.shivMethods&&("+d().join().replace(/[\w\-:]+/g,function(a){return b.createElem(a),b.frag.createElement(a),'c("'+a+'")'})+");return n}")(t,b.frag)}function j(a){a||(a=b);var d=f(a);return!t.shivCSS||k||d.hasCSS||(d.hasCSS=!!c(a,"article,aside,dialog,figcaption,figure,footer,header,hgroup,main,nav,section{display:block}mark{background:#FF0;color:#000}template{display:none}")),l||i(a,d),a}var k,l,m="3.7.3-pre",n=a.html5||{},o=/^<|^(?:button|map|select|textarea|object|iframe|option|optgroup)$/i,p=/^(?:a|b|code|div|fieldset|h1|h2|h3|h4|h5|h6|i|label|li|ol|p|q|span|strong|style|table|tbody|td|th|tr|ul)$/i,q="_html5shiv",r=0,s={};!function(){try{var a=b.createElement("a");a.innerHTML="<xyz></xyz>",k="hidden"in a,l=1==a.childNodes.length||function(){b.createElement("a");var a=b.createDocumentFragment();return"undefined"==typeof a.cloneNode||"undefined"==typeof a.createDocumentFragment||"undefined"==typeof a.createElement}()}catch(c){k=!0,l=!0}}();var t={elements:n.elements||"abbr article aside audio bdi canvas data datalist details dialog figcaption figure footer header hgroup main mark meter nav output picture progress section summary template time video",version:m,shivCSS:n.shivCSS!==!1,supportsUnknownElements:l,shivMethods:n.shivMethods!==!1,type:"default",shivDocument:j,createElement:g,createDocumentFragment:h,addElements:e};a.html5=t,j(b),"object"==typeof module&&module.exports&&(module.exports=t)}("undefined"!=typeof window?window:this,document);
\ No newline at end of file
docs/_build/_static/js/theme.js 0 → 100644
!function(n){var e={};function t(i){if(e[i])return e[i].exports;var o=e[i]={i:i,l:!1,exports:{}};return n[i].call(o.exports,o,o.exports,t),o.l=!0,o.exports}t.m=n,t.c=e,t.d=function(n,e,i){t.o(n,e)||Object.defineProperty(n,e,{enumerable:!0,get:i})},t.r=function(n){"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.defineProperty(n,Symbol.toStringTag,{value:"Module"}),Object.defineProperty(n,"__esModule",{value:!0})},t.t=function(n,e){if(1&e&&(n=t(n)),8&e)return n;if(4&e&&"object"==typeof n&&n&&n.__esModule)return n;var i=Object.create(null);if(t.r(i),Object.defineProperty(i,"default",{enumerable:!0,value:n}),2&e&&"string"!=typeof n)for(var o in n)t.d(i,o,function(e){return n[e]}.bind(null,o));return i},t.n=function(n){var e=n&&n.__esModule?function(){return n.default}:function(){return n};return t.d(e,"a",e),e},t.o=function(n,e){return Object.prototype.hasOwnProperty.call(n,e)},t.p="",t(t.s=0)}([function(n,e,t){t(1),n.exports=t(3)},function(n,e,t){(function(){var e="undefined"!=typeof window?window.jQuery:t(2);n.exports.ThemeNav={navBar:null,win:null,winScroll:!1,winResize:!1,linkScroll:!1,winPosition:0,winHeight:null,docHeight:null,isRunning:!1,enable:function(n){var t=this;void 0===n&&(n=!0),t.isRunning||(t.isRunning=!0,e((function(e){t.init(e),t.reset(),t.win.on("hashchange",t.reset),n&&t.win.on("scroll",(function(){t.linkScroll||t.winScroll||(t.winScroll=!0,requestAnimationFrame((function(){t.onScroll()})))})),t.win.on("resize",(function(){t.winResize||(t.winResize=!0,requestAnimationFrame((function(){t.onResize()})))})),t.onResize()})))},enableSticky:function(){this.enable(!0)},init:function(n){n(document);var e=this;this.navBar=n("div.wy-side-scroll:first"),this.win=n(window),n(document).on("click","[data-toggle='wy-nav-top']",(function(){n("[data-toggle='wy-nav-shift']").toggleClass("shift"),n("[data-toggle='rst-versions']").toggleClass("shift")})).on("click",".wy-menu-vertical .current ul li a",(function(){var t=n(this);n("[data-toggle='wy-nav-shift']").removeClass("shift"),n("[data-toggle='rst-versions']").toggleClass("shift"),e.toggleCurrent(t),e.hashChange()})).on("click","[data-toggle='rst-current-version']",(function(){n("[data-toggle='rst-versions']").toggleClass("shift-up")})),n("table.docutils:not(.field-list,.footnote,.citation)").wrap("<div class='wy-table-responsive'></div>"),n("table.docutils.footnote").wrap("<div class='wy-table-responsive footnote'></div>"),n("table.docutils.citation").wrap("<div class='wy-table-responsive citation'></div>"),n(".wy-menu-vertical ul").not(".simple").siblings("a").each((function(){var t=n(this);expand=n('<button class="toctree-expand" title="Open/close menu"></button>'),expand.on("click",(function(n){return e.toggleCurrent(t),n.stopPropagation(),!1})),t.prepend(expand)}))},reset:function(){var n=encodeURI(window.location.hash)||"#";try{var e=$(".wy-menu-vertical"),t=e.find('[href="'+n+'"]');if(0===t.length){var i=$('.document [id="'+n.substring(1)+'"]').closest("div.section");0===(t=e.find('[href="#'+i.attr("id")+'"]')).length&&(t=e.find('[href="#"]'))}if(t.length>0){$(".wy-menu-vertical .current").removeClass("current").attr("aria-expanded","false"),t.addClass("current").attr("aria-expanded","true"),t.closest("li.toctree-l1").parent().addClass("current").attr("aria-expanded","true");for(let n=1;n<=10;n++)t.closest("li.toctree-l"+n).addClass("current").attr("aria-expanded","true");t[0].scrollIntoView()}}catch(n){console.log("Error expanding nav for anchor",n)}},onScroll:function(){this.winScroll=!1;var n=this.win.scrollTop(),e=n+this.winHeight,t=this.navBar.scrollTop()+(n-this.winPosition);n<0||e>this.docHeight||(this.navBar.scrollTop(t),this.winPosition=n)},onResize:function(){this.winResize=!1,this.winHeight=this.win.height(),this.docHeight=$(document).height()},hashChange:function(){this.linkScroll=!0,this.win.one("hashchange",(function(){this.linkScroll=!1}))},toggleCurrent:function(n){var e=n.closest("li");e.siblings("li.current").removeClass("current").attr("aria-expanded","false"),e.siblings().find("li.current").removeClass("current").attr("aria-expanded","false");var t=e.find("> ul li");t.length&&(t.removeClass("current").attr("aria-expanded","false"),e.toggleClass("current").attr("aria-expanded",(function(n,e){return"true"==e?"false":"true"})))}},"undefined"!=typeof window&&(window.SphinxRtdTheme={Navigation:n.exports.ThemeNav,StickyNav:n.exports.ThemeNav}),function(){for(var n=0,e=["ms","moz","webkit","o"],t=0;t<e.length&&!window.requestAnimationFrame;++t)window.requestAnimationFrame=window[e[t]+"RequestAnimationFrame"],window.cancelAnimationFrame=window[e[t]+"CancelAnimationFrame"]||window[e[t]+"CancelRequestAnimationFrame"];window.requestAnimationFrame||(window.requestAnimationFrame=function(e,t){var i=(new Date).getTime(),o=Math.max(0,16-(i-n)),r=window.setTimeout((function(){e(i+o)}),o);return n=i+o,r}),window.cancelAnimationFrame||(window.cancelAnimationFrame=function(n){clearTimeout(n)})}()}).call(window)},function(n,e){n.exports=jQuery},function(n,e,t){}]);
\ No newline at end of file
docs/_build/_static/pygments.css 0 → 100644
.highlight .hll { background-color: #ffffcc }
.highlight { background: #f8f8f8; }
.highlight .c { color: #408080; font-style: italic } /* Comment */
.highlight .err { border: 1px solid #FF0000 } /* Error */
.highlight .k { color: #008000; font-weight: bold } /* Keyword */
.highlight .o { color: #666666 } /* Operator */
.highlight .ch { color: #408080; font-style: italic } /* Comment.Hashbang */
.highlight .cm { color: #408080; font-style: italic } /* Comment.Multiline */
.highlight .cp { color: #BC7A00 } /* Comment.Preproc */
.highlight .cpf { color: #408080; font-style: italic } /* Comment.PreprocFile */
.highlight .c1 { color: #408080; font-style: italic } /* Comment.Single */
.highlight .cs { color: #408080; font-style: italic } /* Comment.Special */
.highlight .gd { color: #A00000 } /* Generic.Deleted */
.highlight .ge { font-style: italic } /* Generic.Emph */
.highlight .gr { color: #FF0000 } /* Generic.Error */
.highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
.highlight .gi { color: #00A000 } /* Generic.Inserted */
.highlight .go { color: #888888 } /* Generic.Output */
.highlight .gp { color: #000080; font-weight: bold } /* Generic.Prompt */
.highlight .gs { font-weight: bold } /* Generic.Strong */
.highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */
.highlight .gt { color: #0044DD } /* Generic.Traceback */
.highlight .kc { color: #008000; font-weight: bold } /* Keyword.Constant */
.highlight .kd { color: #008000; font-weight: bold } /* Keyword.Declaration */
.highlight .kn { color: #008000; font-weight: bold } /* Keyword.Namespace */
.highlight .kp { color: #008000 } /* Keyword.Pseudo */
.highlight .kr { color: #008000; font-weight: bold } /* Keyword.Reserved */
.highlight .kt { color: #B00040 } /* Keyword.Type */
.highlight .m { color: #666666 } /* Literal.Number */
.highlight .s { color: #BA2121 } /* Literal.String */
.highlight .na { color: #7D9029 } /* Name.Attribute */
.highlight .nb { color: #008000 } /* Name.Builtin */
.highlight .nc { color: #0000FF; font-weight: bold } /* Name.Class */
.highlight .no { color: #880000 } /* Name.Constant */
.highlight .nd { color: #AA22FF } /* Name.Decorator */
.highlight .ni { color: #999999; font-weight: bold } /* Name.Entity */
.highlight .ne { color: #D2413A; font-weight: bold } /* Name.Exception */
.highlight .nf { color: #0000FF } /* Name.Function */
.highlight .nl { color: #A0A000 } /* Name.Label */
.highlight .nn { color: #0000FF; font-weight: bold } /* Name.Namespace */
.highlight .nt { color: #008000; font-weight: bold } /* Name.Tag */
.highlight .nv { color: #19177C } /* Name.Variable */
.highlight .ow { color: #AA22FF; font-weight: bold } /* Operator.Word */
.highlight .w { color: #bbbbbb } /* Text.Whitespace */
.highlight .mb { color: #666666 } /* Literal.Number.Bin */
.highlight .mf { color: #666666 } /* Literal.Number.Float */
.highlight .mh { color: #666666 } /* Literal.Number.Hex */
.highlight .mi { color: #666666 } /* Literal.Number.Integer */
.highlight .mo { color: #666666 } /* Literal.Number.Oct */
.highlight .sa { color: #BA2121 } /* Literal.String.Affix */
.highlight .sb { color: #BA2121 } /* Literal.String.Backtick */
.highlight .sc { color: #BA2121 } /* Literal.String.Char */
.highlight .dl { color: #BA2121 } /* Literal.String.Delimiter */
.highlight .sd { color: #BA2121; font-style: italic } /* Literal.String.Doc */
.highlight .s2 { color: #BA2121 } /* Literal.String.Double */
.highlight .se { color: #BB6622; font-weight: bold } /* Literal.String.Escape */
.highlight .sh { color: #BA2121 } /* Literal.String.Heredoc */
.highlight .si { color: #BB6688; font-weight: bold } /* Literal.String.Interpol */
.highlight .sx { color: #008000 } /* Literal.String.Other */
.highlight .sr { color: #BB6688 } /* Literal.String.Regex */
.highlight .s1 { color: #BA2121 } /* Literal.String.Single */
.highlight .ss { color: #19177C } /* Literal.String.Symbol */
.highlight .bp { color: #008000 } /* Name.Builtin.Pseudo */
.highlight .fm { color: #0000FF } /* Name.Function.Magic */
.highlight .vc { color: #19177C } /* Name.Variable.Class */
.highlight .vg { color: #19177C } /* Name.Variable.Global */
.highlight .vi { color: #19177C } /* Name.Variable.Instance */
.highlight .vm { color: #19177C } /* Name.Variable.Magic */
.highlight .il { color: #666666 } /* Literal.Number.Integer.Long */
\ No newline at end of file
docs/_build/analysis.html 0 → 100644
<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Analyzing the ESGEMME output &mdash; esgemme 1.3.0 documentation</title><link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<!--[if lt IE 9]>
<script src="_static/js/html5shiv.min.js"></script>
<![endif]-->
<script id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/doctools.js"></script>
<script src="_static/language_data.js"></script>
<script src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="prev" title="Using ESGEMME via Docker" href="docker.html" />
</head>
<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
<div class="wy-side-nav-search" >
<a href="index.html" class="icon icon-home">
esgemme
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
<input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
</div>
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
<p class="caption"><span class="caption-text">Contents:</span></p>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESGEMME via Docker</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Analyzing the ESGEMME output</a></li>
</ul>
</div>
</div>
</nav>
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="index.html">esgemme</a>
</nav>
<div class="wy-nav-content">
<div class="rst-content">
<div role="navigation" aria-label="Page navigation">
<ul class="wy-breadcrumbs">
<li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
<li class="breadcrumb-item active">Analyzing the ESGEMME output</li>
<li class="wy-breadcrumbs-aside">
<a href="_sources/analysis.rst.txt" rel="nofollow"> View page source</a>
</li>
</ul>
<hr/>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<div class="section" id="analyzing-the-esgemme-output">
<h1>Analyzing the ESGEMME output<a class="headerlink" href="#analyzing-the-esgemme-output" title="Permalink to this headline"></a></h1>
<p>By default, ESGEMME will output the following files: *
myProt_normPred_evolEpi.txt * myProt_normPred_evolInd.txt *
myProt_normPred_evolCombi.txt</p>
<p>The most important output file is <strong>myProt_normPred_evolCombi.txt</strong>. The
values of interest are the normalized predictions (normPred). Each file
contains a 20 x n matrix, where n is the number of positions (columns) in the
query sequence. If the user provides her/his own list of mutations, then
only the global epistatic model will be run and the output file will
contain 2 columns, the first one with the mutations, the second one with
the normalized predicted effects.</p>
</div>
</div>
</div>
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
<a href="docker.html" class="btn btn-neutral float-left" title="Using ESGEMME via Docker" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
</div>
<hr/>
<div role="contentinfo">
<p>&#169; Copyright 2023, Mustafa Tekpinar.</p>
</div>
Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
<a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
</footer>
</div>
</div>
</section>
</div>
<script>
jQuery(function () {
SphinxRtdTheme.Navigation.enable(true);
});
</script>
</body>
</html>
\ No newline at end of file
docs/_build/footnotehyper-sphinx.sty 0 → 100644
\NeedsTeXFormat{LaTeX2e}
\ProvidesPackage{footnotehyper-sphinx}%
[2017/10/27 v1.7 hyperref aware footnote.sty for sphinx (JFB)]
%%
%% Package: footnotehyper-sphinx
%% Version: based on footnotehyper.sty 2017/03/07 v1.0
%% as available at https://www.ctan.org/pkg/footnotehyper
%% License: the one applying to Sphinx
%%
%% Refer to the PDF documentation at https://www.ctan.org/pkg/footnotehyper for
%% the code comments.
%%
%% Differences:
%% 1. a partial tabulary compatibility layer added (enough for Sphinx mark-up),
%% 2. use of \spx@opt@BeforeFootnote from sphinx.sty,
%% 3. use of \sphinxunactivateextrasandspace from sphinx.sty,
%% 4. macro definition \sphinxfootnotemark,
%% 5. macro definition \sphinxlongtablepatch
%% 6. replaced an \undefined by \@undefined
\DeclareOption*{\PackageWarning{footnotehyper-sphinx}{Option `\CurrentOption' is unknown}}%
\ProcessOptions\relax
\newbox\FNH@notes
\newdimen\FNH@width
\let\FNH@colwidth\columnwidth
\newif\ifFNH@savingnotes
\AtBeginDocument {%
\let\FNH@latex@footnote \footnote
\let\FNH@latex@footnotetext\footnotetext
\let\FNH@H@@footnotetext \@footnotetext
\newenvironment{savenotes}
{\FNH@savenotes\ignorespaces}{\FNH@spewnotes\ignorespacesafterend}%
\let\spewnotes \FNH@spewnotes
\let\footnote \FNH@footnote
\let\footnotetext \FNH@footnotetext
\let\endfootnote \FNH@endfntext
\let\endfootnotetext\FNH@endfntext
\@ifpackageloaded{hyperref}
{\ifHy@hyperfootnotes
\let\FNH@H@@footnotetext\H@@footnotetext
\else
\let\FNH@hyper@fntext\FNH@nohyp@fntext
\fi}%
{\let\FNH@hyper@fntext\FNH@nohyp@fntext}%
}%
\def\FNH@hyper@fntext{\FNH@fntext\FNH@hyper@fntext@i}%
\def\FNH@nohyp@fntext{\FNH@fntext\FNH@nohyp@fntext@i}%
\def\FNH@fntext #1{%
\ifx\ifmeasuring@\@undefined
\expandafter\@secondoftwo\else\expandafter\@firstofone\fi
% these two lines modified for Sphinx (tabulary compatibility):
{\ifmeasuring@\expandafter\@gobbletwo\else\expandafter\@firstofone\fi}%
{\ifx\equation$\expandafter\@gobbletwo\fi #1}%$
}%
\long\def\FNH@hyper@fntext@i#1{%
\global\setbox\FNH@notes\vbox
{\unvbox\FNH@notes
\FNH@startnote
\@makefntext
{\rule\z@\footnotesep\ignorespaces
\ifHy@nesting\expandafter\ltx@firstoftwo
\else\expandafter\ltx@secondoftwo
\fi
{\expandafter\hyper@@anchor\expandafter{\Hy@footnote@currentHref}{#1}}%
{\Hy@raisedlink
{\expandafter\hyper@@anchor\expandafter{\Hy@footnote@currentHref}%
{\relax}}%
\let\@currentHref\Hy@footnote@currentHref
\let\@currentlabelname\@empty
#1}%
\@finalstrut\strutbox
}%
\FNH@endnote
}%
}%
\long\def\FNH@nohyp@fntext@i#1{%
\global\setbox\FNH@notes\vbox
{\unvbox\FNH@notes
\FNH@startnote
\@makefntext{\rule\z@\footnotesep\ignorespaces#1\@finalstrut\strutbox}%
\FNH@endnote
}%
}%
\def\FNH@startnote{%
\hsize\FNH@colwidth
\interlinepenalty\interfootnotelinepenalty
\reset@font\footnotesize
\floatingpenalty\@MM
\@parboxrestore
\protected@edef\@currentlabel{\csname p@\@mpfn\endcsname\@thefnmark}%
\color@begingroup
}%
\def\FNH@endnote{\color@endgroup}%
\def\FNH@savenotes{%
\begingroup
\ifFNH@savingnotes\else
\FNH@savingnotestrue
\let\@footnotetext \FNH@hyper@fntext
\let\@mpfootnotetext \FNH@hyper@fntext
\let\H@@mpfootnotetext\FNH@nohyp@fntext
\FNH@width\columnwidth
\let\FNH@colwidth\FNH@width
\global\setbox\FNH@notes\box\voidb@x
\let\FNH@thempfn\thempfn
\let\FNH@mpfn\@mpfn
\ifx\@minipagerestore\relax\let\@minipagerestore\@empty\fi
\expandafter\def\expandafter\@minipagerestore\expandafter{%
\@minipagerestore
\let\thempfn\FNH@thempfn
\let\@mpfn\FNH@mpfn
}%
\fi
}%
\def\FNH@spewnotes {%
\endgroup
\ifFNH@savingnotes\else
\ifvoid\FNH@notes\else
\begingroup
\let\@makefntext\@empty
\let\@finalstrut\@gobble
\let\rule\@gobbletwo
\FNH@H@@footnotetext{\unvbox\FNH@notes}%
\endgroup
\fi
\fi
}%
\def\FNH@footnote@envname {footnote}%
\def\FNH@footnotetext@envname{footnotetext}%
\def\FNH@footnote{%
% this line added for Sphinx:
\spx@opt@BeforeFootnote
\ifx\@currenvir\FNH@footnote@envname
\expandafter\FNH@footnoteenv
\else
\expandafter\FNH@latex@footnote
\fi
}%
\def\FNH@footnoteenv{%
% this line added for Sphinx (footnotes in parsed literal blocks):
\catcode13=5 \sphinxunactivateextrasandspace
\@ifnextchar[%
\FNH@footnoteenv@i %]
{\stepcounter\@mpfn
\protected@xdef\@thefnmark{\thempfn}%
\@footnotemark
\def\FNH@endfntext@fntext{\@footnotetext}%
\FNH@startfntext}%
}%
\def\FNH@footnoteenv@i[#1]{%
\begingroup
\csname c@\@mpfn\endcsname #1\relax
\unrestored@protected@xdef\@thefnmark{\thempfn}%
\endgroup
\@footnotemark
\def\FNH@endfntext@fntext{\@footnotetext}%
\FNH@startfntext
}%
\def\FNH@footnotetext{%
\ifx\@currenvir\FNH@footnotetext@envname
\expandafter\FNH@footnotetextenv
\else
\expandafter\FNH@latex@footnotetext
\fi
}%
\def\FNH@footnotetextenv{%
\@ifnextchar[%
\FNH@footnotetextenv@i %]
{\protected@xdef\@thefnmark{\thempfn}%
\def\FNH@endfntext@fntext{\@footnotetext}%
\FNH@startfntext}%
}%
\def\FNH@footnotetextenv@i[#1]{%
\begingroup
\csname c@\@mpfn\endcsname #1\relax
\unrestored@protected@xdef\@thefnmark{\thempfn}%
\endgroup
\ifFNH@savingnotes
\def\FNH@endfntext@fntext{\FNH@nohyp@fntext}%
\else
\def\FNH@endfntext@fntext{\FNH@H@@footnotetext}%
\fi
\FNH@startfntext
}%
\def\FNH@startfntext{%
\setbox\z@\vbox\bgroup
\FNH@startnote
\FNH@prefntext
\rule\z@\footnotesep\ignorespaces
}%
\def\FNH@endfntext {%
\@finalstrut\strutbox
\FNH@postfntext
\FNH@endnote
\egroup
\begingroup
\let\@makefntext\@empty\let\@finalstrut\@gobble\let\rule\@gobbletwo
\FNH@endfntext@fntext {\unvbox\z@}%
\endgroup
}%
\AtBeginDocument{%
\let\FNH@@makefntext\@makefntext
\ifx\@makefntextFB\@undefined
\expandafter\@gobble\else\expandafter\@firstofone\fi
{\ifFBFrenchFootnotes \let\FNH@@makefntext\@makefntextFB \else
\let\FNH@@makefntext\@makefntextORI\fi}%
\expandafter\FNH@check@a\FNH@@makefntext{1.2!3?4,}%
\FNH@@@1.2!3?4,\FNH@@@\relax
}%
\long\def\FNH@check@a #11.2!3?4,#2\FNH@@@#3{%
\ifx\relax#3\expandafter\@firstoftwo\else\expandafter\@secondoftwo\fi
\FNH@bad@makefntext@alert
{\def\FNH@prefntext{#1}\def\FNH@postfntext{#2}\FNH@check@b}%
}%
\def\FNH@check@b #1\relax{%
\expandafter\expandafter\expandafter\FNH@check@c
\expandafter\meaning\expandafter\FNH@prefntext
\meaning\FNH@postfntext1.2!3?4,\FNH@check@c\relax
}%
\def\FNH@check@c #11.2!3?4,#2#3\relax{%
\ifx\FNH@check@c#2\expandafter\@gobble\fi\FNH@bad@makefntext@alert
}%
% slight reformulation for Sphinx
\def\FNH@bad@makefntext@alert{%
\PackageWarningNoLine{footnotehyper-sphinx}%
{Footnotes will be sub-optimal, sorry. This is due to the document class or^^J
some package modifying macro \string\@makefntext.^^J
You can try to report this incompatibility at^^J
https://github.com/sphinx-doc/sphinx with this info:}%
\typeout{\meaning\@makefntext}%
\let\FNH@prefntext\@empty\let\FNH@postfntext\@empty
}%
% this macro from original footnote.sty is not used anymore by Sphinx
% but for simplicity sake let's just keep it as is
\def\makesavenoteenv{\@ifnextchar[\FNH@msne@ii\FNH@msne@i}%]
\def\FNH@msne@i #1{%
\expandafter\let\csname FNH$#1\expandafter\endcsname %$
\csname #1\endcsname
\expandafter\let\csname endFNH$#1\expandafter\endcsname %$
\csname end#1\endcsname
\FNH@msne@ii[#1]{FNH$#1}%$
}%
\def\FNH@msne@ii[#1]#2{%
\expandafter\edef\csname#1\endcsname{%
\noexpand\savenotes
\expandafter\noexpand\csname#2\endcsname
}%
\expandafter\edef\csname end#1\endcsname{%
\expandafter\noexpand\csname end#2\endcsname
\noexpand\expandafter
\noexpand\spewnotes
\noexpand\if@endpe\noexpand\@endpetrue\noexpand\fi
}%
}%
% end of footnotehyper 2017/02/16 v0.99
% some extras for Sphinx :
% \sphinxfootnotemark: usable in section titles and silently removed from TOCs.
\def\sphinxfootnotemark [#1]%
{\ifx\thepage\relax\else\protect\spx@opt@BeforeFootnote
\protect\footnotemark[#1]\fi}%
\AtBeginDocument{%
% let hyperref less complain
\pdfstringdefDisableCommands{\def\sphinxfootnotemark [#1]{}}%
% to obtain hyperlinked footnotes in longtable environment we must replace
% hyperref's patch of longtable's patch of \@footnotetext by our own
\let\LT@p@ftntext\FNH@hyper@fntext
% this *requires* longtable to be used always wrapped in savenotes environment
}%
\endinput
%%
%% End of file `footnotehyper-sphinx.sty'.
docs/_build/genindex.html 0 → 100644
<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Index &mdash; esgemme 1.3.0 documentation</title><link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<!--[if lt IE 9]>
<script src="_static/js/html5shiv.min.js"></script>
<![endif]-->
<script id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/doctools.js"></script>
<script src="_static/language_data.js"></script>
<script src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="#" />
<link rel="search" title="Search" href="search.html" />
</head>
<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
<div class="wy-side-nav-search" >
<a href="index.html" class="icon icon-home">
esgemme
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
<input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
</div>
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
<p class="caption"><span class="caption-text">Contents:</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESGEMME via Docker</a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing the ESGEMME output</a></li>
<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
</ul>
</div>
</div>
</nav>
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="index.html">esgemme</a>
</nav>
<div class="wy-nav-content">
<div class="rst-content">
<div role="navigation" aria-label="Page navigation">
<ul class="wy-breadcrumbs">
<li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
<li class="breadcrumb-item active">Index</li>
<li class="wy-breadcrumbs-aside">
</li>
</ul>
<hr/>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<h1 id="index">Index</h1>
<div class="genindex-jumpbox">
</div>
</div>
</div>
<footer>
<hr/>
<div role="contentinfo">
<p>&#169; Copyright 2023, Mustafa Tekpinar.</p>
</div>
Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
<a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
</footer>
</div>
</div>
</section>
</div>
<script>
jQuery(function () {
SphinxRtdTheme.Navigation.enable(true);
});
</script>
</body>
</html>
\ No newline at end of file
docs/_build/html/.buildinfo 0 → 100644
# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 2b63f8059aa2ad903c52bf6ea56d7c9d
tags: 645f666f9bcd5a90fca523b33c5a78b7
docs/_build/html/_sources/docker.rst.txt 0 → 100644
Using ESGEMME via Docker
========================
Requirements
------------
You need to have docker installed on your machine. You can consult the
following page for this: https://docs.docker.com/get-docker/
I am assuming some basic familiarity with Linux/Unix/MacOS terminal
commands.
Let’s start our favorite terminal app.
You must to create a folder called docker-tutorial and go to that empty
folder:
.. code:: bash
mkdir docker-tutorial
cd docker-tutorial
Getting the input data
----------------------
Let’s download the sample data provided in the ESGEMME repository for
this exercise. First, we will download the multiple sequence alignment
file in fasta format:
.. code:: bash
wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/blob/master/data/aliBLAT.fasta
If you don’t have wget, you can try the same command with curl:
.. code:: bash
curl http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/blob/master/data/aliBLAT.fasta
Please verify that the aliBLAT.fasta file is in the folder.
Now, we will download the PDB (Protein Databank) file for BLAT:
.. code:: bash
wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/blob/master/data/blat-af2.pdb
Running a calculation for a single sequence/protein
---------------------------------------------------
In order to make sure that the docker is installed:
.. code:: bash
docker -h
If it shows you a list of options, you are on a good track. On MacOS,
you may not need ‘sudo’ word before the docker command at all.
.. code:: bash
sudo docker run -ti --rm --mount type=bind,source=$PWD,target=/home/tekpinar/research/myexample tekpinar/esgemme-docker:v1.3.0
You are in the container (your virtual operating system) now. You
created a folder called myexample in your container with the previous
command. Let’s change to that folder.
.. code:: bash
cd ../myexample/
When you check the data in that folder with ‘ls’ command, you are
supposed to see aliBLAT.fasta and blat-af2.pdb files. Basically, your
docker-tutorial folder on the host system and myexample folder on the
docker container are pointing to the same place.
One last step and we are done:
.. code:: bash
python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta --pdbfile blat-af2.pdb
After a few minutes of calculation, you must see two files named
BLAT_normPred_evolCombi.txt and BLAT_normPred_evolCombi.png. You have
the entire single point mutational landscape of BLAT protein in these
files.
Running several jobs using docker
---------------------------------
docs/_build/html/_sources/index.rst.txt 0 → 100644
.. esgemme documentation master file, created by
sphinx-quickstart on Fri May 5 13:52:13 2023.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
Welcome to esgemme's documentation!
===================================
.. toctree::
:maxdepth: 2
:caption: Contents:
docker.rst
Indices and tables
==================
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
docs/_build/html/_static/custom.css 0 → 100644
/* This file intentionally left blank. */
docs/_build/html/_static/doctools.js 0 → 100644
/*
* doctools.js
* ~~~~~~~~~~~
*
* Sphinx JavaScript utilities for all documentation.
*
* :copyright: Copyright 2007-2020 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
/**
* select a different prefix for underscore
*/
$u = _.noConflict();
/**
* make the code below compatible with browsers without
* an installed firebug like debugger
if (!window.console || !console.firebug) {
var names = ["log", "debug", "info", "warn", "error", "assert", "dir",
"dirxml", "group", "groupEnd", "time", "timeEnd", "count", "trace",
"profile", "profileEnd"];
window.console = {};
for (var i = 0; i < names.length; ++i)
window.console[names[i]] = function() {};
}
*/
/**
* small helper function to urldecode strings
*/
jQuery.urldecode = function(x) {
return decodeURIComponent(x).replace(/\+/g, ' ');
};
/**
* small helper function to urlencode strings
*/
jQuery.urlencode = encodeURIComponent;
/**
* This function returns the parsed url parameters of the
* current request. Multiple values per key are supported,
* it will always return arrays of strings for the value parts.
*/
jQuery.getQueryParameters = function(s) {
if (typeof s === 'undefined')
s = document.location.search;
var parts = s.substr(s.indexOf('?') + 1).split('&');
var result = {};
for (var i = 0; i < parts.length; i++) {
var tmp = parts[i].split('=', 2);
var key = jQuery.urldecode(tmp[0]);
var value = jQuery.urldecode(tmp[1]);
if (key in result)
result[key].push(value);
else
result[key] = [value];
}
return result;
};
/**
* highlight a given string on a jquery object by wrapping it in
* span elements with the given class name.
*/
jQuery.fn.highlightText = function(text, className) {
function highlight(node, addItems) {
if (node.nodeType === 3) {
var val = node.nodeValue;
var pos = val.toLowerCase().indexOf(text);
if (pos >= 0 &&
!jQuery(node.parentNode).hasClass(className) &&
!jQuery(node.parentNode).hasClass("nohighlight")) {
var span;
var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
if (isInSVG) {
span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
} else {
span = document.createElement("span");
span.className = className;
}
span.appendChild(document.createTextNode(val.substr(pos, text.length)));
node.parentNode.insertBefore(span, node.parentNode.insertBefore(
document.createTextNode(val.substr(pos + text.length)),
node.nextSibling));
node.nodeValue = val.substr(0, pos);
if (isInSVG) {
var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
var bbox = node.parentElement.getBBox();
rect.x.baseVal.value = bbox.x;
rect.y.baseVal.value = bbox.y;
rect.width.baseVal.value = bbox.width;
rect.height.baseVal.value = bbox.height;
rect.setAttribute('class', className);
addItems.push({
"parent": node.parentNode,
"target": rect});
}
}
}
else if (!jQuery(node).is("button, select, textarea")) {
jQuery.each(node.childNodes, function() {
highlight(this, addItems);
});
}
}
var addItems = [];
var result = this.each(function() {
highlight(this, addItems);
});
for (var i = 0; i < addItems.length; ++i) {
jQuery(addItems[i].parent).before(addItems[i].target);
}
return result;
};
/*
* backward compatibility for jQuery.browser
* This will be supported until firefox bug is fixed.
*/
if (!jQuery.browser) {
jQuery.uaMatch = function(ua) {
ua = ua.toLowerCase();
var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
/(webkit)[ \/]([\w.]+)/.exec(ua) ||
/(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
/(msie) ([\w.]+)/.exec(ua) ||
ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
[];
return {
browser: match[ 1 ] || "",
version: match[ 2 ] || "0"
};
};
jQuery.browser = {};
jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
}
/**
* Small JavaScript module for the documentation.
*/
var Documentation = {
init : function() {
this.fixFirefoxAnchorBug();
this.highlightSearchWords();
this.initIndexTable();
if (DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) {
this.initOnKeyListeners();
}
},
/**
* i18n support
*/
TRANSLATIONS : {},
PLURAL_EXPR : function(n) { return n === 1 ? 0 : 1; },
LOCALE : 'unknown',
// gettext and ngettext don't access this so that the functions
// can safely bound to a different name (_ = Documentation.gettext)
gettext : function(string) {
var translated = Documentation.TRANSLATIONS[string];
if (typeof translated === 'undefined')
return string;
return (typeof translated === 'string') ? translated : translated[0];
},
ngettext : function(singular, plural, n) {
var translated = Documentation.TRANSLATIONS[singular];
if (typeof translated === 'undefined')
return (n == 1) ? singular : plural;
return translated[Documentation.PLURALEXPR(n)];
},
addTranslations : function(catalog) {
for (var key in catalog.messages)
this.TRANSLATIONS[key] = catalog.messages[key];
this.PLURAL_EXPR = new Function('n', 'return +(' + catalog.plural_expr + ')');
this.LOCALE = catalog.locale;
},
/**
* add context elements like header anchor links
*/
addContextElements : function() {
$('div[id] > :header:first').each(function() {
$('<a class="headerlink">\u00B6</a>').
attr('href', '#' + this.id).
attr('title', _('Permalink to this headline')).
appendTo(this);
});
$('dt[id]').each(function() {
$('<a class="headerlink">\u00B6</a>').
attr('href', '#' + this.id).
attr('title', _('Permalink to this definition')).
appendTo(this);
});
},
/**
* workaround a firefox stupidity
* see: https://bugzilla.mozilla.org/show_bug.cgi?id=645075
*/
fixFirefoxAnchorBug : function() {
if (document.location.hash && $.browser.mozilla)
window.setTimeout(function() {
document.location.href += '';
}, 10);
},
/**
* highlight the search words provided in the url in the text
*/
highlightSearchWords : function() {
var params = $.getQueryParameters();
var terms = (params.highlight) ? params.highlight[0].split(/\s+/) : [];
if (terms.length) {
var body = $('div.body');
if (!body.length) {
body = $('body');
}
window.setTimeout(function() {
$.each(terms, function() {
body.highlightText(this.toLowerCase(), 'highlighted');
});
}, 10);
$('<p class="highlight-link"><a href="javascript:Documentation.' +
'hideSearchWords()">' + _('Hide Search Matches') + '</a></p>')
.appendTo($('#searchbox'));
}
},
/**
* init the domain index toggle buttons
*/
initIndexTable : function() {
var togglers = $('img.toggler').click(function() {
var src = $(this).attr('src');
var idnum = $(this).attr('id').substr(7);
$('tr.cg-' + idnum).toggle();
if (src.substr(-9) === 'minus.png')
$(this).attr('src', src.substr(0, src.length-9) + 'plus.png');
else
$(this).attr('src', src.substr(0, src.length-8) + 'minus.png');
}).css('display', '');
if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) {
togglers.click();
}
},
/**
* helper function to hide the search marks again
*/
hideSearchWords : function() {
$('#searchbox .highlight-link').fadeOut(300);
$('span.highlighted').removeClass('highlighted');
},
/**
* make the url absolute
*/
makeURL : function(relativeURL) {
return DOCUMENTATION_OPTIONS.URL_ROOT + '/' + relativeURL;
},
/**
* get the current relative url
*/
getCurrentURL : function() {
var path = document.location.pathname;
var parts = path.split(/\//);
$.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() {
if (this === '..')
parts.pop();
});
var url = parts.join('/');
return path.substring(url.lastIndexOf('/') + 1, path.length - 1);
},
initOnKeyListeners: function() {
$(document).keydown(function(event) {
var activeElementType = document.activeElement.tagName;
// don't navigate when in search box or textarea
if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT'
&& !event.altKey && !event.ctrlKey && !event.metaKey && !event.shiftKey) {
switch (event.keyCode) {
case 37: // left
var prevHref = $('link[rel="prev"]').prop('href');
if (prevHref) {
window.location.href = prevHref;
return false;
}
case 39: // right
var nextHref = $('link[rel="next"]').prop('href');
if (nextHref) {
window.location.href = nextHref;
return false;
}
}
}
});
}
};
// quick alias for translations
_ = Documentation.gettext;
$(document).ready(function() {
Documentation.init();
});
docs/_build/html/_static/documentation_options.js 0 → 100644
var DOCUMENTATION_OPTIONS = {
URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
VERSION: '1.3.0',
LANGUAGE: 'None',
COLLAPSE_INDEX: false,
BUILDER: 'html',
FILE_SUFFIX: '.html',
HAS_SOURCE: true,
SOURCELINK_SUFFIX: '.txt',
NAVIGATION_WITH_KEYS: false
};
\ No newline at end of file
docs/_build/html/_static/jquery-3.4.1.js 0 → 100644
This source diff could not be displayed because it is too large. You can view the blob instead.
docs/_build/html/_static/pygments.css 0 → 100644
.highlight .hll { background-color: #ffffcc }
.highlight { background: #f8f8f8; }
.highlight .c { color: #8f5902; font-style: italic } /* Comment */
.highlight .err { color: #a40000; border: 1px solid #ef2929 } /* Error */
.highlight .g { color: #000000 } /* Generic */
.highlight .k { color: #004461; font-weight: bold } /* Keyword */
.highlight .l { color: #000000 } /* Literal */
.highlight .n { color: #000000 } /* Name */
.highlight .o { color: #582800 } /* Operator */
.highlight .x { color: #000000 } /* Other */
.highlight .p { color: #000000; font-weight: bold } /* Punctuation */
.highlight .ch { color: #8f5902; font-style: italic } /* Comment.Hashbang */
.highlight .cm { color: #8f5902; font-style: italic } /* Comment.Multiline */
.highlight .cp { color: #8f5902 } /* Comment.Preproc */
.highlight .cpf { color: #8f5902; font-style: italic } /* Comment.PreprocFile */
.highlight .c1 { color: #8f5902; font-style: italic } /* Comment.Single */
.highlight .cs { color: #8f5902; font-style: italic } /* Comment.Special */
.highlight .gd { color: #a40000 } /* Generic.Deleted */
.highlight .ge { color: #000000; font-style: italic } /* Generic.Emph */
.highlight .gr { color: #ef2929 } /* Generic.Error */
.highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
.highlight .gi { color: #00A000 } /* Generic.Inserted */
.highlight .go { color: #888888 } /* Generic.Output */
.highlight .gp { color: #745334 } /* Generic.Prompt */
.highlight .gs { color: #000000; font-weight: bold } /* Generic.Strong */
.highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */
.highlight .gt { color: #a40000; font-weight: bold } /* Generic.Traceback */
.highlight .kc { color: #004461; font-weight: bold } /* Keyword.Constant */
.highlight .kd { color: #004461; font-weight: bold } /* Keyword.Declaration */
.highlight .kn { color: #004461; font-weight: bold } /* Keyword.Namespace */
.highlight .kp { color: #004461; font-weight: bold } /* Keyword.Pseudo */
.highlight .kr { color: #004461; font-weight: bold } /* Keyword.Reserved */
.highlight .kt { color: #004461; font-weight: bold } /* Keyword.Type */
.highlight .ld { color: #000000 } /* Literal.Date */
.highlight .m { color: #990000 } /* Literal.Number */
.highlight .s { color: #4e9a06 } /* Literal.String */
.highlight .na { color: #c4a000 } /* Name.Attribute */
.highlight .nb { color: #004461 } /* Name.Builtin */
.highlight .nc { color: #000000 } /* Name.Class */
.highlight .no { color: #000000 } /* Name.Constant */
.highlight .nd { color: #888888 } /* Name.Decorator */
.highlight .ni { color: #ce5c00 } /* Name.Entity */
.highlight .ne { color: #cc0000; font-weight: bold } /* Name.Exception */
.highlight .nf { color: #000000 } /* Name.Function */
.highlight .nl { color: #f57900 } /* Name.Label */
.highlight .nn { color: #000000 } /* Name.Namespace */
.highlight .nx { color: #000000 } /* Name.Other */
.highlight .py { color: #000000 } /* Name.Property */
.highlight .nt { color: #004461; font-weight: bold } /* Name.Tag */
.highlight .nv { color: #000000 } /* Name.Variable */
.highlight .ow { color: #004461; font-weight: bold } /* Operator.Word */
.highlight .w { color: #f8f8f8; text-decoration: underline } /* Text.Whitespace */
.highlight .mb { color: #990000 } /* Literal.Number.Bin */
.highlight .mf { color: #990000 } /* Literal.Number.Float */
.highlight .mh { color: #990000 } /* Literal.Number.Hex */
.highlight .mi { color: #990000 } /* Literal.Number.Integer */
.highlight .mo { color: #990000 } /* Literal.Number.Oct */
.highlight .sa { color: #4e9a06 } /* Literal.String.Affix */
.highlight .sb { color: #4e9a06 } /* Literal.String.Backtick */
.highlight .sc { color: #4e9a06 } /* Literal.String.Char */
.highlight .dl { color: #4e9a06 } /* Literal.String.Delimiter */
.highlight .sd { color: #8f5902; font-style: italic } /* Literal.String.Doc */
.highlight .s2 { color: #4e9a06 } /* Literal.String.Double */
.highlight .se { color: #4e9a06 } /* Literal.String.Escape */
.highlight .sh { color: #4e9a06 } /* Literal.String.Heredoc */
.highlight .si { color: #4e9a06 } /* Literal.String.Interpol */
.highlight .sx { color: #4e9a06 } /* Literal.String.Other */
.highlight .sr { color: #4e9a06 } /* Literal.String.Regex */
.highlight .s1 { color: #4e9a06 } /* Literal.String.Single */
.highlight .ss { color: #4e9a06 } /* Literal.String.Symbol */
.highlight .bp { color: #3465a4 } /* Name.Builtin.Pseudo */
.highlight .fm { color: #000000 } /* Name.Function.Magic */
.highlight .vc { color: #000000 } /* Name.Variable.Class */
.highlight .vg { color: #000000 } /* Name.Variable.Global */
.highlight .vi { color: #000000 } /* Name.Variable.Instance */
.highlight .vm { color: #000000 } /* Name.Variable.Magic */
.highlight .il { color: #990000 } /* Literal.Number.Integer.Long */
\ No newline at end of file
docs/_build/html/docker.html 0 → 100644
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
<title>Using ESGEMME via Docker &#8212; esgemme 1.3.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/doctools.js"></script>
<script src="_static/language_data.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="prev" title="Welcome to esgemme’s documentation!" href="index.html" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
<div class="body" role="main">
<div class="section" id="using-esgemme-via-docker">
<h1>Using ESGEMME via Docker<a class="headerlink" href="#using-esgemme-via-docker" title="Permalink to this headline"></a></h1>
<div class="section" id="requirements">
<h2>Requirements<a class="headerlink" href="#requirements" title="Permalink to this headline"></a></h2>
<p>You need to have docker installed on your machine. You can consult the
following page for this: <a class="reference external" href="https://docs.docker.com/get-docker/">https://docs.docker.com/get-docker/</a></p>
<p>I am assuming some basic familiarity with Linux/Unix/MacOS terminal
commands.</p>
<p>Let’s start our favorite terminal app.</p>
<p>You must to create a folder called docker-tutorial and go to that empty
folder:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>mkdir docker-tutorial
<span class="nb">cd</span> docker-tutorial
</pre></div>
</div>
</div>
<div class="section" id="getting-the-input-data">
<h2>Getting the input data<a class="headerlink" href="#getting-the-input-data" title="Permalink to this headline"></a></h2>
<p>Let’s download the sample data provided in the ESGEMME repository for
this exercise. First, we will download the multiple sequence alignment
file in fasta format:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/blob/master/data/aliBLAT.fasta
</pre></div>
</div>
<p>If you don’t have wget, you can try the same command with curl:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>curl http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/blob/master/data/aliBLAT.fasta
</pre></div>
</div>
<p>Please verify that the aliBLAT.fasta file is in the folder.</p>
<p>Now, we will download the PDB (Protein Databank) file for BLAT:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/blob/master/data/blat-af2.pdb
</pre></div>
</div>
</div>
<div class="section" id="running-a-calculation-for-a-single-sequence-protein">
<h2>Running a calculation for a single sequence/protein<a class="headerlink" href="#running-a-calculation-for-a-single-sequence-protein" title="Permalink to this headline"></a></h2>
<p>In order to make sure that the docker is installed:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>docker -h
</pre></div>
</div>
<p>If it shows you a list of options, you are on a good track. On MacOS,
you may not need ‘sudo’ word before the docker command at all.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>sudo docker run -ti --rm --mount <span class="nv">type</span><span class="o">=</span>bind,source<span class="o">=</span><span class="nv">$PWD</span>,target<span class="o">=</span>/home/tekpinar/research/myexample tekpinar/esgemme-docker:v1.3.0
</pre></div>
</div>
<p>You are in the container (your virtual operating system) now. You
created a folder called myexample in your container with the previous
command. Let’s change to that folder.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span> ../myexample/
</pre></div>
</div>
<p>When you check the data in that folder with ‘ls’ command, you are
supposed to see aliBLAT.fasta and blat-af2.pdb files. Basically, your
docker-tutorial folder on the host system and myexample folder on the
docker container are pointing to the same place.</p>
<p>One last step and we are done:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>python <span class="nv">$ESGEMME_PATH</span>/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta --pdbfile blat-af2.pdb
</pre></div>
</div>
<p>After a few minutes of calculation, you must see two files named
BLAT_normPred_evolCombi.txt and BLAT_normPred_evolCombi.png. You have
the entire single point mutational landscape of BLAT protein in these
files.</p>
</div>
<div class="section" id="running-several-jobs-using-docker">
<h2>Running several jobs using docker<a class="headerlink" href="#running-several-jobs-using-docker" title="Permalink to this headline"></a></h2>
</div>
</div>
</div>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
<h1 class="logo"><a href="index.html">esgemme</a></h1>
<h3>Navigation</h3>
<p class="caption"><span class="caption-text">Contents:</span></p>
<ul class="current">
<li class="toctree-l1 current"><a class="current reference internal" href="#">Using ESGEMME via Docker</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#requirements">Requirements</a></li>
<li class="toctree-l2"><a class="reference internal" href="#getting-the-input-data">Getting the input data</a></li>
<li class="toctree-l2"><a class="reference internal" href="#running-a-calculation-for-a-single-sequence-protein">Running a calculation for a single sequence/protein</a></li>
<li class="toctree-l2"><a class="reference internal" href="#running-several-jobs-using-docker">Running several jobs using docker</a></li>
</ul>
</li>
</ul>
<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="index.html">Documentation overview</a><ul>
<li>Previous: <a href="index.html" title="previous chapter">Welcome to esgemme’s documentation!</a></li>
</ul></li>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
<h3 id="searchlabel">Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="search.html" method="get">
<input type="text" name="q" aria-labelledby="searchlabel" />
<input type="submit" value="Go" />
</form>
</div>
</div>
<script>$('#searchbox').show(0);</script>
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
&copy;2023, Mustafa Tekpinar.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 2.4.0</a>
&amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
<a href="_sources/docker.rst.txt"
rel="nofollow">Page source</a>
</div>
</body>
</html>
\ No newline at end of file
docs/_build/html/genindex.html 0 → 100644
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
<title>Index &#8212; esgemme 1.3.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/doctools.js"></script>
<script src="_static/language_data.js"></script>
<link rel="index" title="Index" href="#" />
<link rel="search" title="Search" href="search.html" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
<div class="body" role="main">
<h1 id="index">Index</h1>
<div class="genindex-jumpbox">
</div>
</div>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
<h1 class="logo"><a href="index.html">esgemme</a></h1>
<h3>Navigation</h3>
<p class="caption"><span class="caption-text">Contents:</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESGEMME via Docker</a></li>
</ul>
<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="index.html">Documentation overview</a><ul>
</ul></li>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
<h3 id="searchlabel">Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="search.html" method="get">
<input type="text" name="q" aria-labelledby="searchlabel" />
<input type="submit" value="Go" />
</form>
</div>
</div>
<script>$('#searchbox').show(0);</script>
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
&copy;2023, Mustafa Tekpinar.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 2.4.0</a>
&amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
</div>
</body>
</html>
\ No newline at end of file
docs/_build/html/index.html 0 → 100644
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
<title>Welcome to esgemme’s documentation! &#8212; esgemme 1.3.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/doctools.js"></script>
<script src="_static/language_data.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Using ESGEMME via Docker" href="docker.html" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
<div class="body" role="main">
<div class="section" id="welcome-to-esgemme-s-documentation">
<h1>Welcome to esgemme’s documentation!<a class="headerlink" href="#welcome-to-esgemme-s-documentation" title="Permalink to this headline"></a></h1>
<div class="toctree-wrapper compound">
<p class="caption"><span class="caption-text">Contents:</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESGEMME via Docker</a><ul>
<li class="toctree-l2"><a class="reference internal" href="docker.html#requirements">Requirements</a></li>
<li class="toctree-l2"><a class="reference internal" href="docker.html#getting-the-input-data">Getting the input data</a></li>
<li class="toctree-l2"><a class="reference internal" href="docker.html#running-a-calculation-for-a-single-sequence-protein">Running a calculation for a single sequence/protein</a></li>
<li class="toctree-l2"><a class="reference internal" href="docker.html#running-several-jobs-using-docker">Running several jobs using docker</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div class="section" id="indices-and-tables">
<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline"></a></h1>
<ul class="simple">
<li><p><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></p></li>
<li><p><a class="reference internal" href="py-modindex.html"><span class="std std-ref">Module Index</span></a></p></li>
<li><p><a class="reference internal" href="search.html"><span class="std std-ref">Search Page</span></a></p></li>
</ul>
</div>
</div>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
<h1 class="logo"><a href="#">esgemme</a></h1>
<h3>Navigation</h3>
<p class="caption"><span class="caption-text">Contents:</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESGEMME via Docker</a></li>
</ul>
<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="#">Documentation overview</a><ul>
<li>Next: <a href="docker.html" title="next chapter">Using ESGEMME via Docker</a></li>
</ul></li>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
<h3 id="searchlabel">Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="search.html" method="get">
<input type="text" name="q" aria-labelledby="searchlabel" />
<input type="submit" value="Go" />
</form>
</div>
</div>
<script>$('#searchbox').show(0);</script>
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
&copy;2023, Mustafa Tekpinar.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 2.4.0</a>
&amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
<a href="_sources/index.rst.txt"
rel="nofollow">Page source</a>
</div>
</body>
</html>
\ No newline at end of file
docs/_build/html/search.html 0 → 100644
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
<title>Search &#8212; esgemme 1.3.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/doctools.js"></script>
<script src="_static/language_data.js"></script>
<script src="_static/searchtools.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="#" />
<script src="searchindex.js" defer></script>
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
<div class="body" role="main">
<h1 id="search-documentation">Search</h1>
<div id="fallback" class="admonition warning">
<script>$('#fallback').hide();</script>
<p>
Please activate JavaScript to enable the search
functionality.
</p>
</div>
<p>
From here you can search these documents. Enter your search
words into the box below and click "search". Note that the search
function will automatically search for all of the words. Pages
containing fewer words won't appear in the result list.
</p>
<form action="" method="get">
<input type="text" name="q" aria-labelledby="search-documentation" value="" />
<input type="submit" value="search" />
<span id="search-progress" style="padding-left: 10px"></span>
</form>
<div id="search-results">
</div>
</div>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
<h1 class="logo"><a href="index.html">esgemme</a></h1>
<h3>Navigation</h3>
<p class="caption"><span class="caption-text">Contents:</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESGEMME via Docker</a></li>
</ul>
<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="index.html">Documentation overview</a><ul>
</ul></li>
</ul>
</div>
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
&copy;2023, Mustafa Tekpinar.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 2.4.0</a>
&amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
</div>
</body>
</html>
\ No newline at end of file
docs/_build/html/searchindex.js 0 → 100644
Search.setIndex({docnames:["docker","index"],envversion:{"sphinx.domains.c":1,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":1,"sphinx.domains.index":1,"sphinx.domains.javascript":1,"sphinx.domains.math":2,"sphinx.domains.python":1,"sphinx.domains.rst":1,"sphinx.domains.std":1,sphinx:56},filenames:["docker.rst","index.rst"],objects:{},objnames:{},objtypes:{},terms:{"try":0,One:0,Using:1,af2:0,after:0,aliblat:0,align:0,all:0,app:0,assum:0,basic:0,befor:0,bind:0,blat:0,blat_normpred_evolcombi:0,blob:0,calcul:1,call:0,can:0,chang:0,check:0,com:0,command:0,consult:0,contain:0,content:1,creat:0,curl:0,data:1,databank:0,doc:0,docker:1,don:0,done:0,download:0,empti:0,entir:0,esgemme_path:0,exercis:0,familiar:0,fasta:0,favorit:0,few:0,file:0,first:0,folder:0,follow:0,format:0,get:1,gitlab:0,good:0,have:0,home:0,host:0,http:0,index:1,input:1,instal:0,job:1,landscap:0,last:0,lcqb:0,let:0,linux:0,list:0,machin:0,maco:0,mai:0,make:0,master:0,minut:0,mkdir:0,modul:1,mount:0,multipl:0,must:0,mutat:0,myexampl:0,name:0,need:0,now:0,oper:0,option:0,order:0,our:0,page:[0,1],pdb:0,pdbfile:0,place:0,pleas:0,png:0,point:0,previou:0,protein:1,provid:0,pwd:0,python:0,repositori:0,requir:1,research:0,run:1,same:0,sampl:0,search:1,see:0,sequenc:1,sever:1,show:0,singl:1,some:0,sourc:0,start:0,step:0,sudo:0,suppos:0,sure:0,system:0,target:0,tekpinar:0,termin:0,thi:0,track:0,tutori:0,two:0,txt:0,type:0,unix:0,upmc:0,using:1,verifi:0,via:1,virtual:0,wget:0,when:0,word:0,you:0,your:0},titles:["Using ESGEMME via Docker","Welcome to esgemme\u2019s documentation!"],titleterms:{Using:0,calcul:0,data:0,docker:0,document:1,esgemm:[0,1],get:0,indic:1,input:0,job:0,protein:0,requir:0,run:0,sequenc:0,sever:0,singl:0,tabl:1,using:0,via:0,welcom:1}})
\ No newline at end of file
docs/_build/index.html 0 → 100644
<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Welcome to esgemme’s documentation! &mdash; esgemme 1.3.0 documentation</title><link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<!--[if lt IE 9]>
<script src="_static/js/html5shiv.min.js"></script>
<![endif]-->
<script id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/doctools.js"></script>
<script src="_static/language_data.js"></script>
<script src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Using ESGEMME via Docker" href="docker.html" />
</head>
<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
<div class="wy-side-nav-search" >
<a href="#" class="icon icon-home">
esgemme
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
<input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
</div>
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
<p class="caption"><span class="caption-text">Contents:</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESGEMME via Docker</a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing the ESGEMME output</a></li>
<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
</ul>
</div>
</div>
</nav>
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="#">esgemme</a>
</nav>
<div class="wy-nav-content">
<div class="rst-content">
<div role="navigation" aria-label="Page navigation">
<ul class="wy-breadcrumbs">
<li><a href="#" class="icon icon-home" aria-label="Home"></a></li>
<li class="breadcrumb-item active">Welcome to esgemme’s documentation!</li>
<li class="wy-breadcrumbs-aside">
<a href="_sources/index.rst.txt" rel="nofollow"> View page source</a>
</li>
</ul>
<hr/>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<div class="section" id="welcome-to-esgemme-s-documentation">
<h1>Welcome to esgemme’s documentation!<a class="headerlink" href="#welcome-to-esgemme-s-documentation" title="Permalink to this headline"></a></h1>
<div class="toctree-wrapper compound">
<p class="caption"><span class="caption-text">Contents:</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESGEMME via Docker</a><ul>
<li class="toctree-l2"><a class="reference internal" href="docker.html#requirements">Requirements</a></li>
<li class="toctree-l2"><a class="reference internal" href="docker.html#getting-the-input-data">Getting the input data</a></li>
<li class="toctree-l2"><a class="reference internal" href="docker.html#single-point-mutation-calculations">Single point mutation calculations</a></li>
<li class="toctree-l2"><a class="reference internal" href="docker.html#multiple-point-mutation-calculations">Multiple point mutation calculations</a></li>
<li class="toctree-l2"><a class="reference internal" href="docker.html#running-several-jobs-using-docker">Running several jobs using docker</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing the ESGEMME output</a></li>
<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a><ul>
<li class="toctree-l2"><a class="reference internal" href="installation.html#installing-the-dependencies">Installing the dependencies:</a></li>
<li class="toctree-l2"><a class="reference internal" href="installation.html#getting-the-source-code-and-preparing-the-environment">Getting the source code and preparing the environment:</a></li>
<li class="toctree-l2"><a class="reference internal" href="installation.html#configuring-default-conf-file">Configuring default.conf file</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div class="section" id="indices-and-tables">
<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline"></a></h1>
<ul class="simple">
<li><p><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></p></li>
<li><p><a class="reference internal" href="py-modindex.html"><span class="std std-ref">Module Index</span></a></p></li>
<li><p><a class="reference internal" href="search.html"><span class="std std-ref">Search Page</span></a></p></li>
</ul>
</div>
</div>
</div>
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
<a href="docker.html" class="btn btn-neutral float-right" title="Using ESGEMME via Docker" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
</div>
<hr/>
<div role="contentinfo">
<p>&#169; Copyright 2023, Mustafa Tekpinar.</p>
</div>
Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
<a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
</footer>
</div>
</div>
</section>
</div>
<script>
jQuery(function () {
SphinxRtdTheme.Navigation.enable(true);
});
</script>
</body>
</html>
\ No newline at end of file
docs/_build/installation.html 0 → 100644
<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Installation &mdash; esgemme 1.3.0 documentation</title><link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<!--[if lt IE 9]>
<script src="_static/js/html5shiv.min.js"></script>
<![endif]-->
<script id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/doctools.js"></script>
<script src="_static/language_data.js"></script>
<script src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="prev" title="Analyzing the ESGEMME output" href="analysis.html" />
</head>
<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
<div class="wy-side-nav-search" >
<a href="index.html" class="icon icon-home">
esgemme
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
<input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
</div>
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
<p class="caption"><span class="caption-text">Contents:</span></p>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESGEMME via Docker</a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing the ESGEMME output</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Installation</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#installing-the-dependencies">Installing the dependencies:</a></li>
<li class="toctree-l2"><a class="reference internal" href="#getting-the-source-code-and-preparing-the-environment">Getting the source code and preparing the environment:</a></li>
<li class="toctree-l2"><a class="reference internal" href="#configuring-default-conf-file">Configuring default.conf file</a></li>
</ul>
</li>
</ul>
</div>
</div>
</nav>
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="index.html">esgemme</a>
</nav>
<div class="wy-nav-content">
<div class="rst-content">
<div role="navigation" aria-label="Page navigation">
<ul class="wy-breadcrumbs">
<li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
<li class="breadcrumb-item active">Installation</li>
<li class="wy-breadcrumbs-aside">
<a href="_sources/installation.rst.txt" rel="nofollow"> View page source</a>
</li>
</ul>
<hr/>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<div class="section" id="installation">
<h1>Installation<a class="headerlink" href="#installation" title="Permalink to this headline"></a></h1>
<p>ESGEMME is implemented in Python 3 and R. It has been tested only on
Linux. Since ESGEMME has many dependencies, we recommend using our web
site or our docker image. If you are a determined user, here comes the
steps required to install it from the source.</p>
<div class="section" id="installing-the-dependencies">
<h2>Installing the dependencies:<a class="headerlink" href="#installing-the-dependencies" title="Permalink to this headline"></a></h2>
<p>ESGEMME has the following external dependencies: * Joint Evolutionary
Trees: <a class="reference external" href="http://www.lcqb.upmc.fr/JET2/">http://www.lcqb.upmc.fr/JET2/</a> and its dependencies: - naccess:
<a class="reference external" href="http://www.bioinf.manchester.ac.uk/naccess/">http://www.bioinf.manchester.ac.uk/naccess/</a> - muscle:
<a class="reference external" href="https://www.drive5.com/muscle/">https://www.drive5.com/muscle/</a> ** * seqinr R package:
<a class="reference external" href="https://cran.r-project.org/web/packages/seqinr/index.html">https://cran.r-project.org/web/packages/seqinr/index.html</a> * dssp for
secondary structure prediction.</p>
<p>These tools should be installed to be able to use ESGEMME.</p>
</div>
<div class="section" id="getting-the-source-code-and-preparing-the-environment">
<h2>Getting the source code and preparing the environment:<a class="headerlink" href="#getting-the-source-code-and-preparing-the-environment" title="Permalink to this headline"></a></h2>
<p>Download the ESGEMME source code from
<a class="reference external" href="http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME">http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME</a>. Define and export the
environment variable ESGEMME_PATH=/path-to-ESGEMME-directory/</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">export</span> <span class="nv">ESGEMME_PATH</span><span class="o">=</span>/path-to-ESGEMME-directory/
</pre></div>
</div>
</div>
<div class="section" id="configuring-default-conf-file">
<h2>Configuring default.conf file<a class="headerlink" href="#configuring-default-conf-file" title="Permalink to this headline"></a></h2>
<p>Inside ESGEMME folder, there is an important file called default.conf.
This file contains essential parameters of ESGEMME, such as paths of
external parts, default internal parameters. etc. You have to correct the Software section of this
file according to your system.</p>
</div>
</div>
</div>
</div>
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
<a href="analysis.html" class="btn btn-neutral float-left" title="Analyzing the ESGEMME output" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
</div>
<hr/>
<div role="contentinfo">
<p>&#169; Copyright 2023, Mustafa Tekpinar.</p>
</div>
Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
<a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
</footer>
</div>
</div>
</section>
</div>
<script>
jQuery(function () {
SphinxRtdTheme.Navigation.enable(true);
});
</script>
</body>
</html>
\ No newline at end of file
docs/_build/latex/LICRcyr2utf8.xdy 0 → 100644
;; -*- coding: utf-8; mode: Lisp; -*-
;; style file for xindy
;; filename: LICRcyr2utf8.xdy
;; description: style file for xindy which maps back LaTeX Internal
;; Character Representation of Cyrillic to utf-8
;; usage: for use with pdflatex produced .idx files.
;; Contributed by the Sphinx team, July 2018.
(merge-rule "\IeC {\'\CYRG }" "Ѓ" :string)
(merge-rule "\IeC {\'\CYRK }" "Ќ" :string)
(merge-rule "\IeC {\'\cyrg }" "ѓ" :string)
(merge-rule "\IeC {\'\cyrk }" "ќ" :string)
(merge-rule "\IeC {\CYRA }" "А" :string)
(merge-rule "\IeC {\CYRB }" "Б" :string)
(merge-rule "\IeC {\CYRC }" "Ц" :string)
(merge-rule "\IeC {\CYRCH }" "Ч" :string)
(merge-rule "\IeC {\CYRD }" "Д" :string)
(merge-rule "\IeC {\CYRDJE }" "Ђ" :string)
(merge-rule "\IeC {\CYRDZE }" "Ѕ" :string)
(merge-rule "\IeC {\CYRDZHE }" "Џ" :string)
(merge-rule "\IeC {\CYRE }" "Е" :string)
(merge-rule "\IeC {\CYREREV }" "Э" :string)
(merge-rule "\IeC {\CYRERY }" "Ы" :string)
(merge-rule "\IeC {\CYRF }" "Ф" :string)
(merge-rule "\IeC {\CYRG }" "Г" :string)
(merge-rule "\IeC {\CYRGUP }" "Ґ" :string)
(merge-rule "\IeC {\CYRH }" "Х" :string)
(merge-rule "\IeC {\CYRHRDSN }" "Ъ" :string)
(merge-rule "\IeC {\CYRI }" "И" :string)
(merge-rule "\IeC {\CYRIE }" "Є" :string)
(merge-rule "\IeC {\CYRII }" "І" :string)
(merge-rule "\IeC {\CYRISHRT }" "Й" :string)
(merge-rule "\IeC {\CYRJE }" "Ј" :string)
(merge-rule "\IeC {\CYRK }" "К" :string)
(merge-rule "\IeC {\CYRL }" "Л" :string)
(merge-rule "\IeC {\CYRLJE }" "Љ" :string)
(merge-rule "\IeC {\CYRM }" "М" :string)
(merge-rule "\IeC {\CYRN }" "Н" :string)
(merge-rule "\IeC {\CYRNJE }" "Њ" :string)
(merge-rule "\IeC {\CYRO }" "О" :string)
(merge-rule "\IeC {\CYRP }" "П" :string)
(merge-rule "\IeC {\CYRR }" "Р" :string)
(merge-rule "\IeC {\CYRS }" "С" :string)
(merge-rule "\IeC {\CYRSFTSN }" "Ь" :string)
(merge-rule "\IeC {\CYRSH }" "Ш" :string)
(merge-rule "\IeC {\CYRSHCH }" "Щ" :string)
(merge-rule "\IeC {\CYRT }" "Т" :string)
(merge-rule "\IeC {\CYRTSHE }" "Ћ" :string)
(merge-rule "\IeC {\CYRU }" "У" :string)
(merge-rule "\IeC {\CYRUSHRT }" "Ў" :string)
(merge-rule "\IeC {\CYRV }" "В" :string)
(merge-rule "\IeC {\CYRYA }" "Я" :string)
(merge-rule "\IeC {\CYRYI }" "Ї" :string)
(merge-rule "\IeC {\CYRYO }" "Ё" :string)
(merge-rule "\IeC {\CYRYU }" "Ю" :string)
(merge-rule "\IeC {\CYRZ }" "З" :string)
(merge-rule "\IeC {\CYRZH }" "Ж" :string)
(merge-rule "\IeC {\cyra }" "а" :string)
(merge-rule "\IeC {\cyrb }" "б" :string)
(merge-rule "\IeC {\cyrc }" "ц" :string)
(merge-rule "\IeC {\cyrch }" "ч" :string)
(merge-rule "\IeC {\cyrd }" "д" :string)
(merge-rule "\IeC {\cyrdje }" "ђ" :string)
(merge-rule "\IeC {\cyrdze }" "ѕ" :string)
(merge-rule "\IeC {\cyrdzhe }" "џ" :string)
(merge-rule "\IeC {\cyre }" "е" :string)
(merge-rule "\IeC {\cyrerev }" "э" :string)
(merge-rule "\IeC {\cyrery }" "ы" :string)
(merge-rule "\IeC {\cyrf }" "ф" :string)
(merge-rule "\IeC {\cyrg }" "г" :string)
(merge-rule "\IeC {\cyrgup }" "ґ" :string)
(merge-rule "\IeC {\cyrh }" "х" :string)
(merge-rule "\IeC {\cyrhrdsn }" "ъ" :string)
(merge-rule "\IeC {\cyri }" "и" :string)
(merge-rule "\IeC {\cyrie }" "є" :string)
(merge-rule "\IeC {\cyrii }" "і" :string)
(merge-rule "\IeC {\cyrishrt }" "й" :string)
(merge-rule "\IeC {\cyrje }" "ј" :string)
(merge-rule "\IeC {\cyrk }" "к" :string)
(merge-rule "\IeC {\cyrl }" "л" :string)
(merge-rule "\IeC {\cyrlje }" "љ" :string)
(merge-rule "\IeC {\cyrm }" "м" :string)
(merge-rule "\IeC {\cyrn }" "н" :string)
(merge-rule "\IeC {\cyrnje }" "њ" :string)
(merge-rule "\IeC {\cyro }" "о" :string)
(merge-rule "\IeC {\cyrp }" "п" :string)
(merge-rule "\IeC {\cyrr }" "р" :string)
(merge-rule "\IeC {\cyrs }" "с" :string)
(merge-rule "\IeC {\cyrsftsn }" "ь" :string)
(merge-rule "\IeC {\cyrsh }" "ш" :string)
(merge-rule "\IeC {\cyrshch }" "щ" :string)
(merge-rule "\IeC {\cyrt }" "т" :string)
(merge-rule "\IeC {\cyrtshe }" "ћ" :string)
(merge-rule "\IeC {\cyru }" "у" :string)
(merge-rule "\IeC {\cyrushrt }" "ў" :string)
(merge-rule "\IeC {\cyrv }" "в" :string)
(merge-rule "\IeC {\cyrya }" "я" :string)
(merge-rule "\IeC {\cyryi }" "ї" :string)
(merge-rule "\IeC {\cyryo }" "ё" :string)
(merge-rule "\IeC {\cyryu }" "ю" :string)
(merge-rule "\IeC {\cyrz }" "з" :string)
(merge-rule "\IeC {\cyrzh }" "ж" :string)
docs/_build/latex/Makefile 0 → 100644
# Makefile for Sphinx LaTeX output
ALLDOCS = $(basename $(wildcard *.tex))
ALLPDF = $(addsuffix .pdf,$(ALLDOCS))
ALLDVI = $(addsuffix .dvi,$(ALLDOCS))
ALLXDV =
ALLPS = $(addsuffix .ps,$(ALLDOCS))
ALLIMGS = $(wildcard *.png *.gif *.jpg *.jpeg)
# Prefix for archive names
ARCHIVEPREFIX =
# Additional LaTeX options (passed via variables in latexmkrc/latexmkjarc file)
export LATEXOPTS ?=
# Additional latexmk options
LATEXMKOPTS ?=
# format: pdf or dvi (used only by archive targets)
FMT = pdf
LATEX = latexmk -dvi
PDFLATEX = latexmk -pdf -dvi- -ps-
%.png %.gif %.jpg %.jpeg: FORCE_MAKE
extractbb '$@'
%.dvi: %.tex FORCE_MAKE
$(LATEX) $(LATEXMKOPTS) '$<'
%.ps: %.dvi
dvips '$<'
%.pdf: %.tex FORCE_MAKE
$(PDFLATEX) $(LATEXMKOPTS) '$<'
all: $(ALLPDF)
all-dvi: $(ALLDVI)
all-ps: $(ALLPS)
all-pdf: $(ALLPDF)
zip: all-$(FMT)
mkdir $(ARCHIVEPREFIX)docs-$(FMT)
cp $(ALLPDF) $(ARCHIVEPREFIX)docs-$(FMT)
zip -q -r -9 $(ARCHIVEPREFIX)docs-$(FMT).zip $(ARCHIVEPREFIX)docs-$(FMT)
rm -r $(ARCHIVEPREFIX)docs-$(FMT)
tar: all-$(FMT)
mkdir $(ARCHIVEPREFIX)docs-$(FMT)
cp $(ALLPDF) $(ARCHIVEPREFIX)docs-$(FMT)
tar cf $(ARCHIVEPREFIX)docs-$(FMT).tar $(ARCHIVEPREFIX)docs-$(FMT)
rm -r $(ARCHIVEPREFIX)docs-$(FMT)
gz: tar
gzip -9 < $(ARCHIVEPREFIX)docs-$(FMT).tar > $(ARCHIVEPREFIX)docs-$(FMT).tar.gz
bz2: tar
bzip2 -9 -k $(ARCHIVEPREFIX)docs-$(FMT).tar
xz: tar
xz -9 -k $(ARCHIVEPREFIX)docs-$(FMT).tar
clean:
rm -f *.log *.ind *.aux *.toc *.syn *.idx *.out *.ilg *.pla *.ps *.tar *.tar.gz *.tar.bz2 *.tar.xz $(ALLPDF) $(ALLDVI) $(ALLXDV) *.fls *.fdb_latexmk
.PHONY: all all-pdf all-dvi all-ps clean zip tar gz bz2 xz
.PHONY: FORCE_MAKE
\ No newline at end of file
docs/_build/latex/footnotehyper-sphinx.sty 0 → 100644
\NeedsTeXFormat{LaTeX2e}
\ProvidesPackage{footnotehyper-sphinx}%
[2017/10/27 v1.7 hyperref aware footnote.sty for sphinx (JFB)]
%%
%% Package: footnotehyper-sphinx
%% Version: based on footnotehyper.sty 2017/03/07 v1.0
%% as available at https://www.ctan.org/pkg/footnotehyper
%% License: the one applying to Sphinx
%%
%% Refer to the PDF documentation at https://www.ctan.org/pkg/footnotehyper for
%% the code comments.
%%
%% Differences:
%% 1. a partial tabulary compatibility layer added (enough for Sphinx mark-up),
%% 2. use of \spx@opt@BeforeFootnote from sphinx.sty,
%% 3. use of \sphinxunactivateextrasandspace from sphinx.sty,
%% 4. macro definition \sphinxfootnotemark,
%% 5. macro definition \sphinxlongtablepatch
%% 6. replaced an \undefined by \@undefined
\DeclareOption*{\PackageWarning{footnotehyper-sphinx}{Option `\CurrentOption' is unknown}}%
\ProcessOptions\relax
\newbox\FNH@notes
\newdimen\FNH@width
\let\FNH@colwidth\columnwidth
\newif\ifFNH@savingnotes
\AtBeginDocument {%
\let\FNH@latex@footnote \footnote
\let\FNH@latex@footnotetext\footnotetext
\let\FNH@H@@footnotetext \@footnotetext
\newenvironment{savenotes}
{\FNH@savenotes\ignorespaces}{\FNH@spewnotes\ignorespacesafterend}%
\let\spewnotes \FNH@spewnotes
\let\footnote \FNH@footnote
\let\footnotetext \FNH@footnotetext
\let\endfootnote \FNH@endfntext
\let\endfootnotetext\FNH@endfntext
\@ifpackageloaded{hyperref}
{\ifHy@hyperfootnotes
\let\FNH@H@@footnotetext\H@@footnotetext
\else
\let\FNH@hyper@fntext\FNH@nohyp@fntext
\fi}%
{\let\FNH@hyper@fntext\FNH@nohyp@fntext}%
}%
\def\FNH@hyper@fntext{\FNH@fntext\FNH@hyper@fntext@i}%
\def\FNH@nohyp@fntext{\FNH@fntext\FNH@nohyp@fntext@i}%
\def\FNH@fntext #1{%
\ifx\ifmeasuring@\@undefined
\expandafter\@secondoftwo\else\expandafter\@firstofone\fi
% these two lines modified for Sphinx (tabulary compatibility):
{\ifmeasuring@\expandafter\@gobbletwo\else\expandafter\@firstofone\fi}%
{\ifx\equation$\expandafter\@gobbletwo\fi #1}%$
}%
\long\def\FNH@hyper@fntext@i#1{%
\global\setbox\FNH@notes\vbox
{\unvbox\FNH@notes
\FNH@startnote
\@makefntext
{\rule\z@\footnotesep\ignorespaces
\ifHy@nesting\expandafter\ltx@firstoftwo
\else\expandafter\ltx@secondoftwo
\fi
{\expandafter\hyper@@anchor\expandafter{\Hy@footnote@currentHref}{#1}}%
{\Hy@raisedlink
{\expandafter\hyper@@anchor\expandafter{\Hy@footnote@currentHref}%
{\relax}}%
\let\@currentHref\Hy@footnote@currentHref
\let\@currentlabelname\@empty
#1}%
\@finalstrut\strutbox
}%
\FNH@endnote
}%
}%
\long\def\FNH@nohyp@fntext@i#1{%
\global\setbox\FNH@notes\vbox
{\unvbox\FNH@notes
\FNH@startnote
\@makefntext{\rule\z@\footnotesep\ignorespaces#1\@finalstrut\strutbox}%
\FNH@endnote
}%
}%
\def\FNH@startnote{%
\hsize\FNH@colwidth
\interlinepenalty\interfootnotelinepenalty
\reset@font\footnotesize
\floatingpenalty\@MM
\@parboxrestore
\protected@edef\@currentlabel{\csname p@\@mpfn\endcsname\@thefnmark}%
\color@begingroup
}%
\def\FNH@endnote{\color@endgroup}%
\def\FNH@savenotes{%
\begingroup
\ifFNH@savingnotes\else
\FNH@savingnotestrue
\let\@footnotetext \FNH@hyper@fntext
\let\@mpfootnotetext \FNH@hyper@fntext
\let\H@@mpfootnotetext\FNH@nohyp@fntext
\FNH@width\columnwidth
\let\FNH@colwidth\FNH@width
\global\setbox\FNH@notes\box\voidb@x
\let\FNH@thempfn\thempfn
\let\FNH@mpfn\@mpfn
\ifx\@minipagerestore\relax\let\@minipagerestore\@empty\fi
\expandafter\def\expandafter\@minipagerestore\expandafter{%
\@minipagerestore
\let\thempfn\FNH@thempfn
\let\@mpfn\FNH@mpfn
}%
\fi
}%
\def\FNH@spewnotes {%
\endgroup
\ifFNH@savingnotes\else
\ifvoid\FNH@notes\else
\begingroup
\let\@makefntext\@empty
\let\@finalstrut\@gobble
\let\rule\@gobbletwo
\FNH@H@@footnotetext{\unvbox\FNH@notes}%
\endgroup
\fi
\fi
}%
\def\FNH@footnote@envname {footnote}%
\def\FNH@footnotetext@envname{footnotetext}%
\def\FNH@footnote{%
% this line added for Sphinx:
\spx@opt@BeforeFootnote
\ifx\@currenvir\FNH@footnote@envname
\expandafter\FNH@footnoteenv
\else
\expandafter\FNH@latex@footnote
\fi
}%
\def\FNH@footnoteenv{%
% this line added for Sphinx (footnotes in parsed literal blocks):
\catcode13=5 \sphinxunactivateextrasandspace
\@ifnextchar[%
\FNH@footnoteenv@i %]
{\stepcounter\@mpfn
\protected@xdef\@thefnmark{\thempfn}%
\@footnotemark
\def\FNH@endfntext@fntext{\@footnotetext}%
\FNH@startfntext}%
}%
\def\FNH@footnoteenv@i[#1]{%
\begingroup
\csname c@\@mpfn\endcsname #1\relax
\unrestored@protected@xdef\@thefnmark{\thempfn}%
\endgroup
\@footnotemark
\def\FNH@endfntext@fntext{\@footnotetext}%
\FNH@startfntext
}%
\def\FNH@footnotetext{%
\ifx\@currenvir\FNH@footnotetext@envname
\expandafter\FNH@footnotetextenv
\else
\expandafter\FNH@latex@footnotetext
\fi
}%
\def\FNH@footnotetextenv{%
\@ifnextchar[%
\FNH@footnotetextenv@i %]
{\protected@xdef\@thefnmark{\thempfn}%
\def\FNH@endfntext@fntext{\@footnotetext}%
\FNH@startfntext}%
}%
\def\FNH@footnotetextenv@i[#1]{%
\begingroup
\csname c@\@mpfn\endcsname #1\relax
\unrestored@protected@xdef\@thefnmark{\thempfn}%
\endgroup
\ifFNH@savingnotes
\def\FNH@endfntext@fntext{\FNH@nohyp@fntext}%
\else
\def\FNH@endfntext@fntext{\FNH@H@@footnotetext}%
\fi
\FNH@startfntext
}%
\def\FNH@startfntext{%
\setbox\z@\vbox\bgroup
\FNH@startnote
\FNH@prefntext
\rule\z@\footnotesep\ignorespaces
}%
\def\FNH@endfntext {%
\@finalstrut\strutbox
\FNH@postfntext
\FNH@endnote
\egroup
\begingroup
\let\@makefntext\@empty\let\@finalstrut\@gobble\let\rule\@gobbletwo
\FNH@endfntext@fntext {\unvbox\z@}%
\endgroup
}%
\AtBeginDocument{%
\let\FNH@@makefntext\@makefntext
\ifx\@makefntextFB\@undefined
\expandafter\@gobble\else\expandafter\@firstofone\fi
{\ifFBFrenchFootnotes \let\FNH@@makefntext\@makefntextFB \else
\let\FNH@@makefntext\@makefntextORI\fi}%
\expandafter\FNH@check@a\FNH@@makefntext{1.2!3?4,}%
\FNH@@@1.2!3?4,\FNH@@@\relax
}%
\long\def\FNH@check@a #11.2!3?4,#2\FNH@@@#3{%
\ifx\relax#3\expandafter\@firstoftwo\else\expandafter\@secondoftwo\fi
\FNH@bad@makefntext@alert
{\def\FNH@prefntext{#1}\def\FNH@postfntext{#2}\FNH@check@b}%
}%
\def\FNH@check@b #1\relax{%
\expandafter\expandafter\expandafter\FNH@check@c
\expandafter\meaning\expandafter\FNH@prefntext
\meaning\FNH@postfntext1.2!3?4,\FNH@check@c\relax
}%
\def\FNH@check@c #11.2!3?4,#2#3\relax{%
\ifx\FNH@check@c#2\expandafter\@gobble\fi\FNH@bad@makefntext@alert
}%
% slight reformulation for Sphinx
\def\FNH@bad@makefntext@alert{%
\PackageWarningNoLine{footnotehyper-sphinx}%
{Footnotes will be sub-optimal, sorry. This is due to the document class or^^J
some package modifying macro \string\@makefntext.^^J
You can try to report this incompatibility at^^J
https://github.com/sphinx-doc/sphinx with this info:}%
\typeout{\meaning\@makefntext}%
\let\FNH@prefntext\@empty\let\FNH@postfntext\@empty
}%
% this macro from original footnote.sty is not used anymore by Sphinx
% but for simplicity sake let's just keep it as is
\def\makesavenoteenv{\@ifnextchar[\FNH@msne@ii\FNH@msne@i}%]
\def\FNH@msne@i #1{%
\expandafter\let\csname FNH$#1\expandafter\endcsname %$
\csname #1\endcsname
\expandafter\let\csname endFNH$#1\expandafter\endcsname %$
\csname end#1\endcsname
\FNH@msne@ii[#1]{FNH$#1}%$
}%
\def\FNH@msne@ii[#1]#2{%
\expandafter\edef\csname#1\endcsname{%
\noexpand\savenotes
\expandafter\noexpand\csname#2\endcsname
}%
\expandafter\edef\csname end#1\endcsname{%
\expandafter\noexpand\csname end#2\endcsname
\noexpand\expandafter
\noexpand\spewnotes
\noexpand\if@endpe\noexpand\@endpetrue\noexpand\fi
}%
}%
% end of footnotehyper 2017/02/16 v0.99
% some extras for Sphinx :
% \sphinxfootnotemark: usable in section titles and silently removed from TOCs.
\def\sphinxfootnotemark [#1]%
{\ifx\thepage\relax\else\protect\spx@opt@BeforeFootnote
\protect\footnotemark[#1]\fi}%
\AtBeginDocument{%
% let hyperref less complain
\pdfstringdefDisableCommands{\def\sphinxfootnotemark [#1]{}}%
% to obtain hyperlinked footnotes in longtable environment we must replace
% hyperref's patch of longtable's patch of \@footnotetext by our own
\let\LT@p@ftntext\FNH@hyper@fntext
% this *requires* longtable to be used always wrapped in savenotes environment
}%
\endinput
%%
%% End of file `footnotehyper-sphinx.sty'.
docs/_build/latex/latexmkjarc 0 → 100644
$latex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' -kanji=utf8 %O %S';
$dvipdf = 'dvipdfmx %O -o %D %S';
$makeindex = 'internal mendex %S %B %D';
sub mendex {
my ($source, $basename, $destination) = @_;
my $dictfile = $basename . ".dic";
unlink($destination);
system("mendex", "-U", "-f", "-d", $dictfile, "-s", "python.ist", $source);
if ($? > 0) {
print("mendex exited with error code $? (ignored)\n");
}
if (!-e $destination) {
# create an empty .ind file if nothing
open(FH, ">" . $destination);
close(FH);
}
return 0;
}
add_cus_dep( "glo", "gls", 0, "makeglo" );
sub makeglo {
return system( "mendex -J -f -s gglo.ist -o '$_[0].gls' '$_[0].glo'" );
}
\ No newline at end of file
docs/_build/latex/latexmkrc 0 → 100644
$latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S';
$xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S';
$makeindex = 'makeindex -s python.ist %O -o %D %S';
add_cus_dep( "glo", "gls", 0, "makeglo" );
sub makeglo {
return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" );
}
\ No newline at end of file
docs/_build/latex/make.bat 0 → 100644
@ECHO OFF
REM Command file for Sphinx documentation
pushd %~dp0
set PDFLATEX=latexmk -pdf -dvi- -ps-
set "LATEXOPTS= "
if "%1" == "" goto all-pdf
if "%1" == "all-pdf" (
:all-pdf
for %%i in (*.tex) do (
%PDFLATEX% %LATEXMKOPTS% %%i
)
goto end
)
if "%1" == "all-pdf-ja" (
goto all-pdf
)
if "%1" == "clean" (
del /q /s *.dvi *.log *.ind *.aux *.toc *.syn *.idx *.out *.ilg *.pla *.ps *.tar *.tar.gz *.tar.bz2 *.tar.xz *.fls *.fdb_latexmk
goto end
)
:end
popd
\ No newline at end of file
docs/_build/latex/python.ist 0 → 100644
line_max 100
headings_flag 1
heading_prefix " \\bigletter "
preamble "\\begin{sphinxtheindex}
\\let\\bigletter\\sphinxstyleindexlettergroup
\\let\\spxpagem \\sphinxstyleindexpagemain
\\let\\spxentry \\sphinxstyleindexentry
\\let\\spxextra \\sphinxstyleindexextra
"
postamble "\n\n\\end{sphinxtheindex}\n"
symhead_positive "{\\sphinxsymbolsname}"
numhead_positive "{\\sphinxnumbersname}"
docs/conf.py 0 → 100644
This diff is collapsed. Click to expand it.
docs/docker.rst 0 → 100644
This diff is collapsed. Click to expand it.
docs/index.rst 0 → 100644
This diff is collapsed. Click to expand it.
docs/make.bat 0 → 100644
This diff is collapsed. Click to expand it.
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment