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Commit 1329302c by Mustafa Tekpinar
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Updated docs/input-preparation.rst.

parent 037eb6d5
Showing with 52 additions and 44 deletions
docs/_build/html/_sources/input-preparation.rst.txt
...@@ -43,7 +43,7 @@ structure is to use Colabfold. Let's do this step by step: ...@@ -43,7 +43,7 @@ structure is to use Colabfold. Let's do this step by step:
.. code:: bash .. code:: bash
sudo docker run -ti --rm --mount type=bind,source=$PWD,target=/home/tekpinar/research/myexample \ sudo docker run -ti --rm --mount type=bind,source=$PWD,target=/home/tekpinar/research/myexample \
tekpinar/esgemme-docker:v1.3.0 tekpinar/prescott-docker:v1.5.0
9. Now, change the directory to myexample folder. 9. Now, change the directory to myexample folder.
...@@ -76,8 +76,9 @@ a3m and fasta files are too long. We have to shorten them. We can do that with ...@@ -76,8 +76,9 @@ a3m and fasta files are too long. We have to shorten them. We can do that with
Congratulations! Now, you have all the input files required for PRESCOTT: Congratulations! Now, you have all the input files required for PRESCOTT:
I. An input MSA: AKE_nogaps_short_names.fasta
II. An input PDB: myprotein.pdb #. An input MSA: AKE_nogaps_short_names.fasta
#. An input PDB: myprotein.pdb
......
docs/_build/html/input-preparation.html
...@@ -20,7 +20,7 @@ ...@@ -20,7 +20,7 @@
<link rel="index" title="Index" href="genindex.html" /> <link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" /> <link rel="search" title="Search" href="search.html" />
<link rel="next" title="Installation" href="installation.html" /> <link rel="next" title="Installation" href="installation.html" />
<link rel="prev" title="Analyzing and Modifying the PRESCOTT Output" href="analysis.html" /> <link rel="prev" title="Analyzing and Modifying the ESCOTT Output" href="analysis.html" />
</head> </head>
<body class="wy-body-for-nav"> <body class="wy-body-for-nav">
...@@ -44,8 +44,9 @@ ...@@ -44,8 +44,9 @@
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu"> </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
<p class="caption" role="heading"><span class="caption-text">Contents:</span></p> <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul class="current"> <ul class="current">
<li class="toctree-l1"><a class="reference internal" href="docker.html">Using PRESCOTT via Docker</a></li> <li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing and Modifying the PRESCOTT Output</a></li> <li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESCOTT via Docker</a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing and Modifying the ESCOTT Output</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Preparing Your Own Input</a><ul> <li class="toctree-l1 current"><a class="current reference internal" href="#">Preparing Your Own Input</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#preparing-your-input-msa-and-pdb-with-colabfold">Preparing Your Input MSA and PDB with Colabfold</a></li> <li class="toctree-l2"><a class="reference internal" href="#preparing-your-input-msa-and-pdb-with-colabfold">Preparing Your Input MSA and PDB with Colabfold</a></li>
</ul> </ul>
...@@ -109,7 +110,7 @@ or Jalview. However, it is a labor intensive procedure. Here, I will use a ...@@ -109,7 +110,7 @@ or Jalview. However, it is a labor intensive procedure. Here, I will use a
small tool that I developed and added to the PRESCOTT docker image that I created.</p></li> small tool that I developed and added to the PRESCOTT docker image that I created.</p></li>
<li><p>Start the docker image with the following command:</p> <li><p>Start the docker image with the following command:</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">$PWD</span>,target<span class="o">=</span>/home/tekpinar/research/myexample <span class="se">\</span> <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>sudo docker run -ti --rm --mount <span class="nv">type</span><span class="o">=</span>bind,source<span class="o">=</span><span class="nv">$PWD</span>,target<span class="o">=</span>/home/tekpinar/research/myexample <span class="se">\</span>
tekpinar/esgemme-docker:v1.3.0 tekpinar/prescott-docker:v1.5.0
</pre></div> </pre></div>
</div> </div>
</li> </li>
...@@ -139,9 +140,11 @@ a3m and fasta files are too long. We have to shorten them. We can do that with</ ...@@ -139,9 +140,11 @@ a3m and fasta files are too long. We have to shorten them. We can do that with</
</pre></div> </pre></div>
</div> </div>
</div></blockquote> </div></blockquote>
<p>Congratulations! Now, you have all the input files required for PRESCOTT: <p>Congratulations! Now, you have all the input files required for PRESCOTT:</p>
I. An input MSA: AKE_nogaps_short_names.fasta <ol class="arabic simple">
II. An input PDB: myprotein.pdb</p> <li><p>An input MSA: AKE_nogaps_short_names.fasta</p></li>
<li><p>An input PDB: myprotein.pdb</p></li>
</ol>
</section> </section>
</section> </section>
...@@ -149,7 +152,7 @@ II. An input PDB: myprotein.pdb</p> ...@@ -149,7 +152,7 @@ II. An input PDB: myprotein.pdb</p>
</div> </div>
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\ No newline at end of file \ No newline at end of file
docs/_build/latex/prescott.fdb_latexmk
# Fdb version 3 # Fdb version 3
["makeindex prescott.idx"] 1691770116 "prescott.idx" "prescott.ind" "prescott" 1698162636 ["makeindex prescott.idx"] 1691770116 "prescott.idx" "prescott.ind" "prescott" 1698222132
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(generated) (generated)
"prescott.ilg" "prescott.ilg"
"prescott.ind" "prescott.ind"
["pdflatex"] 1698162636 "prescott.tex" "prescott.pdf" "prescott" 1698162636 ["pdflatex"] 1698222131 "prescott.tex" "prescott.pdf" "prescott" 1698222132
"/etc/texmf/web2c/texmf.cnf" 1686915816 475 c0e671620eb5563b2130f56340a5fde8 "" "/etc/texmf/web2c/texmf.cnf" 1686915816 475 c0e671620eb5563b2130f56340a5fde8 ""
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"/usr/share/texlive/texmf-dist/fonts/tfm/jknappen/ec/ecrm1000.tfm" 1136768653 3584 adb004a0c8e7c46ee66cad73671f37b4 "" "/usr/share/texlive/texmf-dist/fonts/tfm/jknappen/ec/ecrm1000.tfm" 1136768653 3584 adb004a0c8e7c46ee66cad73671f37b4 ""
...@@ -140,13 +140,13 @@ ...@@ -140,13 +140,13 @@
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"/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map" 1692610720 128028 f533b797fba58d231669ea19e894e23e "" "/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map" 1692610720 128028 f533b797fba58d231669ea19e894e23e ""
"/var/lib/texmf/web2c/pdftex/pdflatex.fmt" 1692610730 1455466 cf5d347cc06e6f91065ccb2619b82e95 "" "/var/lib/texmf/web2c/pdftex/pdflatex.fmt" 1692610730 1455466 cf5d347cc06e6f91065ccb2619b82e95 ""
"prescott.aux" 1698162636 8757 49bd9be15e4a1990a75c401ccac48f11 "pdflatex" "prescott.aux" 1698222131 8757 49bd9be15e4a1990a75c401ccac48f11 "pdflatex"
"prescott.ind" 1694694190 0 d41d8cd98f00b204e9800998ecf8427e "makeindex prescott.idx" "prescott.ind" 1694694190 0 d41d8cd98f00b204e9800998ecf8427e "makeindex prescott.idx"
"prescott.out" 1698162636 6307 8119393c8f110ffbb217a1e7b2c390de "pdflatex" "prescott.out" 1698222132 6307 8119393c8f110ffbb217a1e7b2c390de "pdflatex"
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"prescott.toc" 1698162636 2706 6a2a8c488f73b27e9fedb6cddefdfa53 "pdflatex" "prescott.toc" 1698222132 2706 6a2a8c488f73b27e9fedb6cddefdfa53 "pdflatex"
"sphinx.sty" 1691571542 12780 919e6ba449302e2597e7722681a087c6 "" "sphinx.sty" 1691571542 12780 919e6ba449302e2597e7722681a087c6 ""
"sphinxhighlight.sty" 1698162635 6679 76d10c62e0f0661410b46f5db6118e26 "" "sphinxhighlight.sty" 1698222131 6679 76d10c62e0f0661410b46f5db6118e26 ""
"sphinxlatexadmonitions.sty" 1691571543 6238 2d867d769abf3f72abc17ef52adff78b "" "sphinxlatexadmonitions.sty" 1691571543 6238 2d867d769abf3f72abc17ef52adff78b ""
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...@@ -161,7 +161,7 @@ ...@@ -161,7 +161,7 @@
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"sphinxoptionsgeometry.sty" 1691571542 2061 47bb34b8ed8a78823eb0c886abfb9f4d "" "sphinxoptionsgeometry.sty" 1691571542 2061 47bb34b8ed8a78823eb0c886abfb9f4d ""
"sphinxoptionshyperref.sty" 1691571543 1094 79beb8b8a3f10784f8cce804e0f9d3aa "" "sphinxoptionshyperref.sty" 1691571543 1094 79beb8b8a3f10784f8cce804e0f9d3aa ""
"sphinxpackagefootnote.sty" 1691571543 15217 dd26fe418b6fb1b26b18f042a7f43d40 "" "sphinxpackagefootnote.sty" 1691571543 15217 dd26fe418b6fb1b26b18f042a7f43d40 ""
......
docs/_build/latex/prescott.log
This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex 2023.8.21) 24 OCT 2023 17:50 This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex 2023.8.21) 25 OCT 2023 10:22
entering extended mode entering extended mode
restricted \write18 enabled. restricted \write18 enabled.
%&-line parsing enabled. %&-line parsing enabled.
...@@ -810,18 +810,12 @@ File: ts1txtt.fd 2000/12/15 v3.1 ...@@ -810,18 +810,12 @@ File: ts1txtt.fd 2000/12/15 v3.1
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(Font) Font shape `T1/txtt/m/sl' tried instead on input line 614. (Font) Font shape `T1/txtt/m/sl' tried instead on input line 614.
[12]
Underfull \hbox (badness 10000) in paragraph at lines 618--622
[]\T1/qtm/m/n/10 Con-grat-u-la-tions! Now, you have all the in-put files re-qui
red for PRESCOTT: I. An in-put MSA:
[]
[12]
Chapter 5. Chapter 5.
[13 [13
] [14] ] [14]
Underfull \hbox (badness 7981) in paragraph at lines 789--792 Underfull \hbox (badness 7981) in paragraph at lines 798--801
[]\T1/qtm/m/n/10 #Down-load PRESCOTT from [][]$http : / / gitlab . lcqb . upmc []\T1/qtm/m/n/10 #Down-load PRESCOTT from [][]$http : / / gitlab . lcqb . upmc
. fr / tekpinar / PRESCOTT$[][] repos-i-tory and go in-side the . fr / tekpinar / PRESCOTT$[][] repos-i-tory and go in-side the
[] []
...@@ -835,8 +829,8 @@ Package rerunfilecheck Info: File `prescott.out' has not changed. ...@@ -835,8 +829,8 @@ Package rerunfilecheck Info: File `prescott.out' has not changed.
(rerunfilecheck) Checksum: 8119393C8F110FFBB217A1E7B2C390DE;6307. (rerunfilecheck) Checksum: 8119393C8F110FFBB217A1E7B2C390DE;6307.
) )
Here is how much of TeX's memory you used: Here is how much of TeX's memory you used:
14690 strings out of 480204 14692 strings out of 480204
234039 string characters out of 5895010 234053 string characters out of 5895010
598445 words of memory out of 5000000 598445 words of memory out of 5000000
32211 multiletter control sequences out of 15000+600000 32211 multiletter control sequences out of 15000+600000
520869 words of font info for 70 fonts, out of 8000000 for 9000 520869 words of font info for 70 fonts, out of 8000000 for 9000
...@@ -852,10 +846,10 @@ usr/share/texlive/texmf-dist/fonts/type1/public/txfonts/t1xbtt.pfb></usr/share/ ...@@ -852,10 +846,10 @@ usr/share/texlive/texmf-dist/fonts/type1/public/txfonts/t1xbtt.pfb></usr/share/
texlive/texmf-dist/fonts/type1/public/txfonts/t1xtt.pfb></usr/share/texlive/tex texlive/texmf-dist/fonts/type1/public/txfonts/t1xtt.pfb></usr/share/texlive/tex
mf-dist/fonts/type1/public/txfonts/t1xtt.pfb></usr/share/texlive/texmf-dist/fon mf-dist/fonts/type1/public/txfonts/t1xtt.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/txfonts/tcxtt.pfb> ts/type1/public/txfonts/tcxtt.pfb>
Output written on prescott.pdf (21 pages, 171998 bytes). Output written on prescott.pdf (21 pages, 172069 bytes).
PDF statistics: PDF statistics:
329 PDF objects out of 1000 (max. 8388607) 332 PDF objects out of 1000 (max. 8388607)
286 compressed objects within 3 object streams 289 compressed objects within 3 object streams
65 named destinations out of 1000 (max. 500000) 67 named destinations out of 1000 (max. 500000)
253 words of extra memory for PDF output out of 10000 (max. 10000000) 253 words of extra memory for PDF output out of 10000 (max. 10000000)
docs/_build/latex/prescott.tex
...@@ -61,7 +61,7 @@ ...@@ -61,7 +61,7 @@
\title{prescott} \title{prescott}
\date{Oct 24, 2023} \date{Oct 25, 2023}
\release{1.5.0} \release{1.5.0}
\author{Mustafa Tekpinar} \author{Mustafa Tekpinar}
\newcommand{\sphinxlogo}{\vbox{}} \newcommand{\sphinxlogo}{\vbox{}}
...@@ -571,7 +571,7 @@ Start the docker image with the following command: ...@@ -571,7 +571,7 @@ Start the docker image with the following command:
\begin{sphinxVerbatim}[commandchars=\\\{\}] \begin{sphinxVerbatim}[commandchars=\\\{\}]
sudo docker run \PYGZhy{}ti \PYGZhy{}\PYGZhy{}rm \PYGZhy{}\PYGZhy{}mount \PYG{n+nv}{type}\PYG{o}{=}bind,source\PYG{o}{=}\PYG{n+nv}{\PYGZdl{}PWD},target\PYG{o}{=}/home/tekpinar/research/myexample \PYG{l+s+se}{\PYGZbs{}} sudo docker run \PYGZhy{}ti \PYGZhy{}\PYGZhy{}rm \PYGZhy{}\PYGZhy{}mount \PYG{n+nv}{type}\PYG{o}{=}bind,source\PYG{o}{=}\PYG{n+nv}{\PYGZdl{}PWD},target\PYG{o}{=}/home/tekpinar/research/myexample \PYG{l+s+se}{\PYGZbs{}}
tekpinar/esgemme\PYGZhy{}docker:v1.3.0 tekpinar/prescott\PYGZhy{}docker:v1.5.0
\end{sphinxVerbatim} \end{sphinxVerbatim}
\item {} \item {}
...@@ -617,8 +617,17 @@ awk \PYG{l+s+s1}{\PYGZsq{}BEGIN\PYGZob{}FS=\PYGZdq{} \PYGZdq{}\PYGZcb{}\PYGZob{} ...@@ -617,8 +617,17 @@ awk \PYG{l+s+s1}{\PYGZsq{}BEGIN\PYGZob{}FS=\PYGZdq{} \PYGZdq{}\PYGZcb{}\PYGZob{}
\sphinxAtStartPar \sphinxAtStartPar
Congratulations! Now, you have all the input files required for PRESCOTT: Congratulations! Now, you have all the input files required for PRESCOTT:
I. An input MSA: AKE\_nogaps\_short\_names.fasta \begin{enumerate}
II. An input PDB: myprotein.pdb \sphinxsetlistlabels{\arabic}{enumi}{enumii}{}{.}%
\item {}
\sphinxAtStartPar
An input MSA: AKE\_nogaps\_short\_names.fasta
\item {}
\sphinxAtStartPar
An input PDB: myprotein.pdb
\end{enumerate}
\sphinxstepscope \sphinxstepscope
......
docs/input-preparation.rst
...@@ -43,7 +43,7 @@ structure is to use Colabfold. Let's do this step by step: ...@@ -43,7 +43,7 @@ structure is to use Colabfold. Let's do this step by step:
.. code:: bash .. code:: bash
sudo docker run -ti --rm --mount type=bind,source=$PWD,target=/home/tekpinar/research/myexample \ sudo docker run -ti --rm --mount type=bind,source=$PWD,target=/home/tekpinar/research/myexample \
tekpinar/esgemme-docker:v1.3.0 tekpinar/prescott-docker:v1.5.0
9. Now, change the directory to myexample folder. 9. Now, change the directory to myexample folder.
...@@ -76,8 +76,9 @@ a3m and fasta files are too long. We have to shorten them. We can do that with ...@@ -76,8 +76,9 @@ a3m and fasta files are too long. We have to shorten them. We can do that with
Congratulations! Now, you have all the input files required for PRESCOTT: Congratulations! Now, you have all the input files required for PRESCOTT:
I. An input MSA: AKE_nogaps_short_names.fasta
II. An input PDB: myprotein.pdb #. An input MSA: AKE_nogaps_short_names.fasta
#. An input PDB: myprotein.pdb
......
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