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dssp
Commit 6efb4d31 by Maarten L. Hekkelman
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start webserver

parent 69c1a69c
Showing with 1194 additions and 4 deletions
.gitignore
......@@ -8,3 +8,7 @@ build
**/*.dssp
src/revision.hpp
out/
node_modules
docroot/fonts
docroot/scripts
docroot/css
CMakeLists.txt
......@@ -25,7 +25,7 @@
cmake_minimum_required(VERSION 3.15)
# set the project name
project(mkdssp VERSION 4.2.2.1 LANGUAGES CXX)
project(mkdssp VERSION 4.2.3 LANGUAGES CXX)
list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
......@@ -52,6 +52,7 @@ endif()
# Optionally build a version to be installed inside CCP4
option(BUILD_FOR_CCP4 "Build a version to be installed in CCP4" OFF)
option(BUILD_WEBSERVER "Add code to run dssp as a web service" OFF)
if(BUILD_FOR_CCP4)
if("$ENV{CCP4}" STREQUAL "" OR NOT EXISTS $ENV{CCP4})
......@@ -105,6 +106,10 @@ find_package(Threads)
if(NOT PDB_REDO_META)
find_package(libmcfp REQUIRED)
find_package(cifpp 5.0.8 REQUIRED)
if(BUILD_WEBSERVER)
find_package(zeep REQUIRED)
endif()
endif()
# The DSSP code is in a separate library, optionally to be used by others
......@@ -124,12 +129,52 @@ add_executable(mkdssp
${PROJECT_SOURCE_DIR}/src/dssp-io.hpp
${PROJECT_SOURCE_DIR}/src/mkdssp.cpp)
target_include_directories(mkdssp PRIVATE ${PROJECT_BINARY_DIR})
target_link_libraries(mkdssp PRIVATE dssp cifpp::cifpp libmcfp::libmcfp dssp::dssp)
if(USE_RSRC)
message("Using resources compiled with ${MRC}")
mrc_target_resources(mkdssp ${CIFPP_SHARE_DIR}/mmcif_pdbx.dic ${CIFPP_SHARE_DIR}/mmcif_ddl.dic)
mrc_target_resources(mkdssp
${CIFPP_SHARE_DIR}/mmcif_pdbx.dic
${CIFPP_SHARE_DIR}/mmcif_ddl.dic)
endif()
if(BUILD_WEBSERVER)
find_program(YARN yarn REQUIRED)
add_executable(dsspd
${PROJECT_SOURCE_DIR}/src/dssp-io.cpp
${PROJECT_SOURCE_DIR}/src/dssp-server.cpp)
target_link_libraries(dsspd PRIVATE dssp cifpp::cifpp libmcfp::libmcfp dssp::dssp zeep::zeep)
# yarn rules for javascripts
set(webpack_input
${CMAKE_CURRENT_SOURCE_DIR}/webapp/pdb-redo-style.scss
${CMAKE_CURRENT_SOURCE_DIR}/webapp/index.js
${CMAKE_CURRENT_SOURCE_DIR}/webpack.config.js
)
set(webpack_output ${CMAKE_CURRENT_SOURCE_DIR}/docroot/scripts/index.js)
add_custom_command(OUTPUT ${CMAKE_CURRENT_SOURCE_DIR}/node_modules
COMMAND ${YARN}
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
VERBATIM)
add_custom_command(OUTPUT ${webpack_output}
DEPENDS ${webpack_input} ${CMAKE_CURRENT_SOURCE_DIR}/node_modules
COMMAND ${YARN} run $<IF:$<CONFIG:Debug>,build,build-production>
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
VERBATIM)
add_custom_target(generate_webpack DEPENDS ${webpack_output})
add_dependencies(dsspd generate_webpack)
mrc_target_resources(dsspd
${CIFPP_SHARE_DIR}/mmcif_pdbx.dic
${CIFPP_SHARE_DIR}/mmcif_ddl.dic
${PROJECT_SOURCE_DIR}/docroot/)
endif()
# Install rules
......
docroot/about.html 0 → 100644
<!DOCTYPE html SYSTEM "about:legacy-compat" [
<!ENTITY nbsp "&#160;">
]>
<html xmlns="http://www.w3.org/1999/xhtml" xmlns:z2="http://www.hekkelman.com/libzeep/m2" lang="nl">
<head z2:replace="~{head::head(~{::title},~{::head/script})}">
<meta charset="UTF-8" />
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no" />
<title>DSSP</title>
</head>
<body class="site">
<nav z2:replace="~{menu :: navbar('about')}" />
<div class="container site-content">
<article>
<h2>General</h2>
<!-- <p>This is the DSSP web server. Before using it, please read the <a z2:href="@{/privacy-policy}">privacy policy</a>.</p> -->
</article>
<article>
<h2>References</h2>
<!-- TODO: fill in -->
<p>bla bla.</p>
<div class="programListTable">
<table style="margin-left: 0;">
<tr>
<td><a href="https://doi.org/10.1107/S2052252514009324" target="_BLANK">Web&nbsp;server</a></td>
<td>Joosten RP, Long F, Murshudov GN, Perrakis A. The PDB_REDO server for macromolecular
structure model optimization. IUCrJ. 2014; 1(4):213-220.
</td>
</tr>
<tr>
<td><a href="https://doi.org/10.1002/pro.3353" target="_BLANK">Databank</a></td>
<td>van
Beusekom B, Touw WG, Tatineni M, Somani S, Rajagopal G, Luo J, Gilliland GL,
Perrakis A, Joosten RP Homology-based hydrogen bond information improves
crystallographic structures in the PDB. Protein Science. 2018; 27:798-808.
</td>
</tr>
</table>
</div>
</article>
<article>
<h2>The Science behind DSSP</h2>
<!-- TODO: fill in -->
<!-- <p>Below are other publications that describe different algorithms and concepts of PDB-REDO.</p>
<div class="programListTable">
<table style="margin-left: 0;">
<tr>
<td><a href="https://doi.org/10.1126/science.317.5835.195" target="_BLANK">No data, no
PDB&#8209;REDO</a></td>
<td>Joosten RP, Vriend G. PDB improvement starts with data deposition. Science 2007;
317:195-196.
</td>
</tr>
<tr>
<td><a href="https://dx.doi.org/10.1107/S0907444908037591" target="_BLANK">The value of
re&#8209;refinement </a>
</td>
<td>Joosten RP, Womack T, Vriend G, Bricogne G. Re-refinement from deposited X&#8209;ray
data can deliver improved models for most PDB entries. Acta Cryst. 2009;
D65:176-185.
</td>
</tr>
<tr>
<td><a href="https://doi.org/10.1107/S0021889809008784" target="_BLANK">The first PDB-REDO</a></td>
<td>Joosten RP, et al and Vriend G. PDB_REDO: automated re&#8209;refinement of
X&#8209;ray
structure models in the PDB. J. Appl. Cryst. 2009; 42:376-384.
</td>
</tr><tr>
<td><a href="https://doi.org/10.1107/S0907444911054515" target="_BLANK">Decision making</a></td>
<td>Joosten RP, Joosten K, Murshudov GN, Perrakis A. PDB_REDO: constructive validation,
more
than just looking for errors. Acta Cryst. 2012; D68:484-496.
</td>
</tr>
<tr>
<td><a href="https://doi.org/10.1093/bioinformatics/btr590" target="_BLANK">Model rebuilding
</a>
</td>
<td>Joosten RP, Joosten K, Cohen SX, Vriend G, Perrakis A. Automatic rebuilding and
optimization of crystallographic structures in the Protein Data Bank. Bioinformatics
2011; 27:3392-3398.
</td>
</tr>
<tr>
<td><a href="https://doi.org/10.1002/pro.3353" target="_blank">Homology restraints</a></td>
<td>van
Beusekom B, Touw WG, Tatineni M, Somani S, Rajagopal G, Luo J, Gilliland GL,
Perrakis A, Joosten RP. Homology-based hydrogen bond information improves
crystallographic structures in the PDB. Protein Science. 2018; 27:798-808.
</td>
</tr>
<tr>
<td><a href="https://doi.org/10.1107/S2052252518010552" target="_blank">Loop building</a></td>
<td>van
Beusekom B, Joosten K, Hekkelman ML, Joosten RP,
Perrakis A. Homology-based loop modeling yields more complete crystallographic protein structures.
IUCrJ 2018; 5:585-594.
</td>
</tr>
<tr>
<td><a href="https://doi.org/10.1107/S2059798319003875" target="_blank">N-glycan building</a></td>
<td>van
Beusekom B, Wezel N, Hekkelman ML, Perrakis A, Emsley E, Joosten RP.
Building and rebuilding N-glycans in protein structure models.
Acta Cryst. 2019; D75:416-425.
</td>
</tr>
<tr>
<td><a href="https://doi.org/10.1107/S2059798321007610" target="_blank">Nucleic acids</a></td>
<td>de Vries I, Kwakman T, Lu X-J, Hekkelman ML, Deshpande M, Velankar S, Perrakis A, Joosten RP.
New restraints and validation approaches for nucleic acid structures in PDB-REDO.
Acta Cryst. 2021; D77:1127-1141.
</td>
</tr>
<tr>
<td><a href="https://doi.org/10.1107/S2059798316013036" target="_blank">Zinc sites</a></td>
<td>Touw WG, van Beusekom B, Evers JMG, Vriend G, Joosten RP.
Validation and correction of Zn–CysxHisy complexes.
Acta Cryst. 2016; D72:1110-1118.
</td>
</tr>
</table>
</div> -->
</article>
</div>
<footer z2:replace="~{footer::content}"></footer>
</body>
</html>
docroot/download.html 0 → 100644
<!DOCTYPE html SYSTEM "about:legacy-compat" [ <!ENTITY nbsp "&#160;">
]>
<html xmlns="http://www.w3.org/1999/xhtml" xmlns:z2="http://www.hekkelman.com/libzeep/m2" lang="nl">
<head z2:replace="~{head::head(~{::title},~{::head/script})}">
<meta charset="UTF-8" />
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no" />
<title>PDB-REDO</title>
</head>
<body class="site">
<nav z2:replace="~{menu :: navbar('download')}" />
<div class="container site-content">
<!-- TODO: fill in -->
<!-- <article>
<h2>Downloading the PDB-REDO software</h2>
<p>If you are working with sensistive data you can install PDB-REDO locally on <a
href="https://pdb-redo.eu/others/pdb-redo.tar.bz2">Linux and WSL</a>.
You can also use it to run large sets of custom PDB-REDO jobs. Alternatively, you can use the
<a z2:href="@{/api-doc}">PDB-REDO API</a> to commit batches of custom calculations.
</p>
</article>
<article>
<h2>Downloading PDB-REDO entries</h2>
<p>You can download PDB-REDO entries using you favorite molecular graphics program or manually. You can also
download the entire databank at once. Below are some basic examples, more data from the PDB-REDO
databank is described underneath.</p>
<h2>Molecular graphics:</h2>
<ul>
<li><a href="http://www.yasara.org" target="_blank">YASARA</a> has a native PDB-REDO <a
href="http://www.yasara.org/pdbredo.htm" target="_blank">interface to show models</a>.
</li>
<li><a href="http://www.ccp4.ac.uk/MG/" target="_blank">CCP4mg</a> can download PDB-REDO models and
maps.</li>
<li><a href="http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/" target="_blank">(Win)COOT</a> also
has a native
PDB-REDO interface that shows models, maps, and a guided tour through the model changes.
</li>
</ul>
<h2>Manual download (single entries) via the website or using <code>wget</code>:</h2>
<ul>
<li><code>wget https://pdb-redo.eu/db/9xyz/9xyz_final.pdb</code> downloads the fully optimised
(re-refined and
rebuilt) PDB file.
</li>
<li><code>wget https://pdb-redo.eu/db/9xyz/9xyz_final.mtz</code> downloads the MTZ files to generate
electron
density maps.
</li>
<li><code>wget https://pdb-redo.eu/db/9xyz.zip</code> downloads all files of a PDB-REDO entry.</li>
</ul>
<h2>Download entire PDB-REDO databank using <code>rsync</code>:</h2>
<ul>
<li><code>rsync -av rsync://rsync.pdb-redo.eu/pdb-redo/ pdb-redo/</code> downloads the entire archive.
</li>
</ul>
<h2>License</h2>
<p><a href="license.txt" z2:href="@{/license}">Here</a> you can find the data usage license.</p>
</article>
<article>
<h2>PDB-REDO entry description</h2>
<p>Each PDB-REDO entry consists of a set of files that describe the structure model in different states
(original,
re-refined, and re-refined &amp; rebuilt). Some of the data is provided for easy data mining. The table
below shows
the typical URLs of the files for the fictitious entry <code>9xyz</code>.</p>
<br />
<table>
<thead>
<tr>
<th>Description</th>
<th>Typical URL (for fictitious entry 9xyz)</th>
</tr>
</thead>
<tbody>
<tr>
<td colspan="2" class="group">Atomic coordinates</td>
</tr>
<tr>
<td>Initial model</td>
<td><code>https://pdb-redo.eu/db/9xyz/9xyz_0cyc.pdb.gz</code></td>
</tr>
<tr>
<td>Re-refined (only) model</td>
<td><code>https://pdb-redo.eu/db/9xyz/9xyz_besttls.pdb.gz</code></td>
</tr>
<tr>
<td>Re-refined &amp; rebuilt structure model</td>
<td><code>https://pdb-redo.eu/db/9xyz/9xyz_final.pdb</code></td>
</tr>
<tr>
<td>Re-refined &amp; rebuilt structure model with total B-factors (PDB)</td>
<td><code>https://pdb-redo.eu/db/9xyz/9xyz_final_tot.pdb</code></td>
</tr>
<tr>
<td>Re-refined &amp; rebuilt structure model with total B-factors (mmCIF)</td>
<td><code>https://pdb-redo.eu/db/9xyz/9xyz_final.cif</code></td>
</tr>
<tr>
<td colspan="2" class="group">Electron density</td>
</tr>
<tr>
<td>Map coefficients for the original model</td>
<td><code>https://pdb-redo.eu/db/9xyz/9xyz_0cyc.mtz.gz</code></td>
</tr>
<tr>
<td>Map coefficients for re-refined (only) model</td>
<td><code>https://pdb-redo.eu/db/9xyz/9xyz_besttls.mtz.gz</code></td>
</tr>
<tr>
<td>Map coefficients for re-refined &amp; rebuilt structure model</td>
<td><code>https://pdb-redo.eu/db/9xyz/9xyz_final.mtz</code></td>
</tr>
<tr>
<td colspan="2" class="group">Validation data</td>
</tr>
<tr>
<td>WHAT_CHECK report for initial model</td>
<td><code>https://pdb-redo.eu/db/9xyz/wo/pdbout.txt</code></td>
</tr>
<tr>
<td>WHAT_CHECK report for re-refined (only) model</td>
<td><code>https://pdb-redo.eu/db/9xyz/wc/pdbout.txt</code></td>
</tr>
<tr>
<td>WHAT_CHECK report for re-refined &amp; rebuilt model</td>
<td><code>https://pdb-redo.eu/db/9xyz/wf/pdbout.txt</code></td>
</tr>
<tr>
<td>Ligand and ligand interaction data for the initial and re-refined &amp; rebuilt structure
model</td>
<td><code>https://pdb-redo.eu/db/9xyz/9xyz_ligval.json</code> (only for entries with ligands; <a
href="id_ligval.json.schema" z2:href="@{/schema/id_ligval.json.schema}">JSON Schema</a>)
</td>
</tr>
<tr>
<td>Map fitting scores for the initial model <br />(RSCC, RSR, EDIAm, OPIA)</td>
<td><code>https://pdb-redo.eu/db/9xyz/9xyz_0cyc.json.gz</code> (<a href="id_0cyc.json.schema"
z2:href="@{/schema/id_0cyc.json.schema}">JSON Schema</a>)</td>
</tr>
<tr>
<td>Map fitting scores for the re-refined &amp; rebuilt model</td>
<td><code>https://pdb-redo.eu/db/9xyz/9xyz_final.json</code> (<a href="id_final.json.schema"
z2:href="@{/schema/id_final.json.schema}">JSON Schema</a>)</td>
</tr>
<tr>
<td>Data for model improvement sliders</td>
<td><code>https://pdb-redo.eu/db/9xyz/pdbe.json</code> (<a href="pdbe.json.schema"
z2:href="@{/schema/pdbe.json.schema}">JSON Schema</a>)</td>
</tr>
<tr>
<td colspan="2" class="group">Visual tools</td>
</tr>
<tr>
<td>COOT script to show model changes</td>
<td><code>https://pdb-redo.eu/db/9xyz/9xyz_final.py</code> (Python) or
<code>https://pdb-redo.eu/db/9xyz/9xyz_final.scm</code>
(Scheme)
</td>
</tr>
<tr>
<td colspan="2" class="group">Descriptive data</td>
</tr>
<tr>
<td>PDB-REDO statistics for data mining (crystal parameters, R-factors, validation scores, etc.)
</td>
<td><code>https://pdb-redo.eu/db/9xyz/data.json</code> (<a href="data.json.schema"
z2:href="@{/schema/data.json.schema}">JSON Schema</a>)</td>
</tr>
<tr>
<td>List of homologous entries in PDB-REDO databank</td>
<td><code>https://pdb-redo.eu/db/9xyz/9xyz_available_homologs.json</code> (<a
href="id_available_homologs.json.schema"
z2:href="@{/schema/id_available_homologs.json.schema}">JSON Schema</a>)</td>
</tr>
<tr>
<td>DSSP analysis of the re-refined &amp; rebuilt model</td>
<td><code>https://pdb-redo.eu/db/9xyz/9xyz_final.dssp</code></td>
</tr>
<tr>
<td>Software versions of all programs used</td>
<td><code>https://pdb-redo.eu/db/9xyz/versions.json</code> (<a href="versions.json.schema"
z2:href="@{/schema/versions.json.schema}">JSON Schema</a>)</td>
</tr>
</tbody>
</table>
</article> -->
</div>
<footer z2:replace="~{footer::content}"></footer>
</body>
</html>
docroot/footer.html 0 → 100644
<!DOCTYPE html>
<html xmlns:z2="http://www.hekkelman.com/libzeep/m2">
<body>
<footer z2:fragment="content">Maarten L. Hekkelman, Anastassis Perrakis &amp; Robbie P. Joosten
Department of Biochemistry, B8
Plesmanlaan 121, 1066CX Amsterdam
Tel: +31 20 512 1951</footer>
</body>
</html>
docroot/head.html 0 → 100644
<!DOCTYPE html SYSTEM "about:legacy-compat">
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lang="nl" >
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<meta http-equiv="Content-Security-Policy" content="default-src 'self' 'unsafe-inline'; child-src 'none'; img-src 'self' data:;" />
<title z2:replace="${title}">DSSP - PDB-REDO version</title>
<script z2:src="@{/scripts/index.js}"></script>
<script z2:replace="${script}"></script>
<link z2:href="@{/css/index.css}" rel="stylesheet" />
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c3.535,0,5.94-0.425,7.215-1.274c1.275-0.849,1.912-2.303,1.912-4.361c0-2.058-0.637-3.514-1.912-4.367
c-1.274-0.854-3.68-1.28-7.215-1.28h-5.244V89.625z"/>
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c5.197,0,9.141,0.776,11.828,2.327c2.688,1.552,4.031,4.013,4.031,7.384S142.555,89.817,139.867,91.373z M134.476,79.343
c-1.327-1.04-3.473-1.561-6.437-1.561s-5.112,0.521-6.446,1.561s-2.001,2.589-2.001,4.646c0,2.059,0.667,3.605,2.001,4.642
c1.334,1.035,3.482,1.553,6.446,1.553s5.109-0.518,6.437-1.553c1.327-1.036,1.991-2.583,1.991-4.642
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</g>
<g>
<path fill="#FF9933" d="M23.095,52.253v19.542H18.2V24.766h20.604c6.278,0,11.138,1.254,14.578,3.764
c3.441,2.507,5.161,5.83,5.161,9.964c0,4.178-1.72,7.515-5.161,10.014c-3.44,2.499-8.3,3.746-14.578,3.746H23.095z M23.095,48.959
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v6.041c0,6.029-2.384,10.95-7.154,14.762c-4.772,3.813-10.816,5.717-18.136,5.717H60.034z M64.928,28.06V68.5h12.503
c5.921,0,10.794-1.622,14.618-4.873c3.825-3.249,5.737-7.358,5.737-12.329v-6.132c0-4.906-1.919-8.983-5.757-12.232
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c2.274,2.172,3.413,4.681,3.413,7.521c0,4.198-1.733,7.426-5.201,9.687c-3.47,2.259-8.109,3.389-13.921,3.389H104.607z
M109.5,45.857h13.778c4.33,0,7.683-0.747,10.054-2.245c2.371-1.496,3.558-3.698,3.558-6.605c0-2.972-1.263-5.206-3.784-6.702
c-2.522-1.498-6.195-2.245-11.021-2.245H109.5V45.857z M109.5,49.151V68.5h15.793c4.414,0,7.882-0.852,10.403-2.56
c2.522-1.705,3.784-4.092,3.784-7.162c0-2.812-1.146-5.118-3.434-6.922c-2.29-1.803-5.614-2.705-9.973-2.705H109.5z"/>
</g>
<g>
</g>
<g>
</g>
<g>
</g>
<g>
</g>
<g>
</g>
</svg>
docroot/index.html 0 → 100644
<!DOCTYPE html SYSTEM "about:legacy-compat" [
<!ENTITY nbsp "&#160;">
]>
<html xmlns="http://www.w3.org/1999/xhtml" xmlns:z2="http://www.hekkelman.com/libzeep/m2" lang="nl">
<head z2:replace="~{head::head(~{::title},~{::head/script})}">
<meta charset="UTF-8" />
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no" />
<title>DSSP</title>
</head>
<body class="site">
<nav z2:replace="~{menu :: navbar('home')}"></nav>
<div class="container site-content">
<article>
<h2>DSSP: Assign secondary structure to proteins</h2>
<p>bla bla bla
</p>
</article>
<article>
<h2>Submit your structure</h2>
</article>
</div>
<footer z2:replace="~{footer::content}"></footer>
</body>
</html>
docroot/menu.html 0 → 100644
<!DOCTYPE html SYSTEM "about:legacy-compat">
<html xmlns="http://www.w3.org/1999/xhtml" xmlns:z2="http://www.hekkelman.com/libzeep/m2" lang="nl">
<body>
<header z2:fragment="navbar(page)" class="d-flex">
<a href="https://pdb-redo.eu/" z2:href="@{/}"><img z2:src="@{/images/PDB_logo_rect_medium.svg}" /></a>
<div>
<div class="my-overflow">
<nav class="first">
<a href="http://www.nki.nl" target="_BLANK">NKI Research</a> |
<!-- <a href="http://www.nki.nl/divisions/biochemistry/" title="BioChemistry Homepage"
target="_BLANK">Biochemistry</a>
|-->
<a href="https://www.nki.nl/research/research-groups/anastassis-tassos-perrakis/" target="_BLANK">Perrakis
group</a>
</nav>
</div>
<nav class="navbar navbar-expand-md bg-nav-secondary navbar-light second">
<button class="navbar-toggler" type="button" data-bs-toggle="collapse"
data-bs-target="#navbarSupportedContent" aria-controls="navbarSupportedContent"
aria-expanded="false" aria-label="Toggle navigation">
<span class="navbar-toggler-icon"></span>
</button>
<div class="collapse navbar-collapse" id="navbarSupportedContent">
<ul class="navbar-nav mr-auto">
<li class="nav-item">
<a class="nav-link" z2:classappend="${page == 'home' ? 'active' : ''}"
z2:href="@{/}">Home</a>
</li>
<li class="nav-item dropdown">
<a class="nav-link dropdown-toggle" href="#" id="navbarDropdown2" role="button"
data-bs-toggle="dropdown" aria-expanded="false">
Tools
</a>
<ul class="dropdown-menu m-0" aria-labelledby="navbarDropdown2">
<li><a class="dropdown-item" href="https://alphafill.eu">AlphaFill</a></li>
<li><a class="dropdown-item" href="https://pdb-redo.eu/dssp">DSSP</a></li>
<li><a class="dropdown-item" href="https://pdb-redo.eu/tortoize">Tortoize</a></li>
<li><a class="dropdown-item" href="https://ccd.rhpc.nki.nl/">CCD</a></li>
<li><a class="dropdown-item" href="https://pdb-redo.eu/archive">Archive</a></li>
<li><a class="dropdown-item" href="https://lahma.pdb-redo.eu/">Lahma</a></li>
</ul>
</li>
<li class="nav-item">
<a class="nav-link" z2:classappend="${page == 'about' ? 'active' : ''}"
z2:href="@{/about}">About</a>
</li>
<li class="nav-item">
<a class="nav-link" z2:classappend="${page == 'download' ? 'active' : ''}"
z2:href="@{/download}">Download</a>
</li>
</ul>
</div>
</nav>
</div>
</header>
</body>
</html>
package.json 0 → 100644
{
"name": "dsspd",
"version": "1.0.0",
"description": "A web service for DSSP",
"main": "index.js",
"author": "Maarten L. Hekkelman",
"license": "BSD-2-Clause",
"scripts": {
"build": "webpack --config webpack.config.js",
"build-production": "webpack --config webpack.config.js --env PRODUCTION"
},
"devDependencies": {
"@babel/core": "^7.16.0",
"@babel/preset-env": "^7.16.0",
"@babel/preset-typescript": "^7.16.0",
"@popperjs/core": "^2.10.2",
"@webcomponents/webcomponentsjs": "^2.7.0",
"babel-loader": "^9.1.2",
"bs-custom-file-input": "^1.3.4",
"clean-webpack-plugin": "^4.0.0",
"crypto-es": "^1.2.7",
"css-loader": "^6.5.0",
"file-loader": "^6.2.0",
"lit": "^2.6.1",
"mini-css-extract-plugin": "^2.4.3",
"postcss-loader": "^7.0.2",
"sass": "^1.58.1",
"sass-loader": "^13.2.0",
"style-loader": "^3.3.1",
"terser-webpack-plugin": "^5.2.5",
"ts-loader": "^9.2.6",
"uglifyjs-webpack-plugin": "^2.2.0",
"webpack": "^5.76.0",
"webpack-cli": "^5.0.1"
},
"dependencies": {
"@babel/runtime-corejs3": "^7.20.13",
"bootstrap": "^5.1.3",
"bootstrap-icons": "^1.10.3",
"core-js": "^3.28.0"
},
"babel": {
"presets": [
"@babel/typescript",
[
"@babel/env",
{
"modules": false
}
]
]
}
}
src/dssp-server.cpp 0 → 100644
/*-
* SPDX-License-Identifier: BSD-2-Clause
*
* Copyright (c) 2023 NKI/AVL, Netherlands Cancer Institute
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#include "dssp-io.hpp"
#include "revision.hpp"
#include <mcfp.hpp>
#include <zeep/http/html-controller.hpp>
#include <zeep/http/rest-controller.hpp>
#include <zeep/http/daemon.hpp>
// --------------------------------------------------------------------
class dssp_html_controller : public zeep::http::html_controller
{
public:
dssp_html_controller(const std::string &prefix)
: zeep::http::html_controller(prefix)
{
mount("{css,scripts,fonts,images,favicon}/", &dssp_html_controller::handle_file);
mount("{favicon.ico,browserconfig.xml,manifest.json}", &dssp_html_controller::handle_file);
mount("", &dssp_html_controller::index);
}
void index(const zeep::http::request& request, const zeep::http::scope& scope, zeep::http::reply& reply)
{
get_template_processor().create_reply_from_template("index", scope, reply);
}
};
// --------------------------------------------------------------------
class dssp_rest_controller : public zeep::http::rest_controller
{
public:
dssp_rest_controller()
: zeep::http::rest_controller("")
{
// map_post_request("dssp", &dssp_rest_controller::calculate, "data");
}
};
// --------------------------------------------------------------------
int main(int argc, char *argv[])
{
using namespace std::literals;
namespace zh = zeep::http;
cif::compound_factory::init(true);
int result = 0;
auto &config = mcfp::config::instance();
config.init("dsspd [options] start|stop|status|reload",
mcfp::make_option("help,h", "Display help message"),
mcfp::make_option("version", "Print version"),
mcfp::make_option("verbose,v", "verbose output"),
mcfp::make_option<std::string>("address", "0.0.0.0", "External address"),
mcfp::make_option<uint16_t>("port", 10351, "Port to listen to"),
mcfp::make_option<std::string>("user,u", "www-data", "User to run the daemon"),
mcfp::make_option<std::string>("context", "", "Root context for web server"),
mcfp::make_option("no-daemon,F", "Do not fork into background"),
mcfp::make_option<std::string>("config", "Config file to use"));
std::error_code ec;
config.parse(argc, argv, ec);
if (ec != std::errc())
{
std::cerr << "Error parsing command line arguments: " << ec.message() << std::endl
<< std::endl
<< config << std::endl;
exit(1);
}
config.parse_config_file("config", "dsspd.conf", { ".", "/etc" }, ec);
if (ec != std::errc())
{
std::cerr << "Error parsing config file: " << ec.message() << std::endl;
exit(1);
}
// --------------------------------------------------------------------
if (config.has("version"))
{
write_version_string(std::cout, config.has("verbose"));
exit(0);
}
if (config.has("help"))
{
std::cout << config << std::endl;
exit(0);
}
if (config.operands().empty())
{
std::cerr << "Missing command, should be one of start, stop, status or reload" << std::endl;
exit(1);
}
cif::VERBOSE = config.count("verbose");
std::string user = config.get<std::string>("user");
std::string address = config.get<std::string>("address");
uint16_t port = config.get<uint16_t>("port");
zh::daemon server([&]()
{
auto s = new zeep::http::server();
#ifndef NDEBUG
s->set_template_processor(new zeep::http::file_based_html_template_processor("docroot"));
#else
s->set_template_processor(new zeep::http::rsrc_based_html_template_processor());
#endif
s->add_controller(new dssp_rest_controller());
s->add_controller(new dssp_html_controller(config.get("context")));
return s;
}, kProjectName );
std::string command = config.operands().front();
if (command == "start")
{
std::cout << "starting server at http://" << address << ':' << port << '/' << std::endl;
if (config.has("no-daemon"))
result = server.run_foreground(address, port);
else
result = server.start(address, port, 2, 2, user);
}
else if (command == "stop")
result = server.stop();
else if (command == "status")
result = server.status();
else if (command == "reload")
result = server.reload();
else
{
std::cerr << "Invalid command" << std::endl;
result = 1;
}
return result;
}
\ No newline at end of file
webapp/index.js 0 → 100644
import "core-js/stable";
import "regenerator-runtime/runtime";
import '@popperjs/core';
import 'bootstrap';
import './pdb-redo-style.scss';
webapp/pdb-redo-style.scss 0 → 100644
@use "sass:math";
// (Required) Import Bootstrap
@import "bootstrap/scss/_functions";
@import "bootstrap/scss/_variables";
@import "bootstrap/scss/_mixins";
@import "~bootstrap-icons/font/bootstrap-icons.css";
.alert {
border: 1px solid;
}
@import "bootstrap/scss/_alert";
$font-family-sans-serif: "Verdana", "Arial", "Helvetica", "sans-serif";
$primary: rgb(100, 100, 100);
$primary-rgb: 100, 100, 100;
$nav-primary: #FF9933;
$nav-secondary: #ffecbf;
$nav-link: #3366cc;
$nav-primary-hover: #d8c7a5;
$dropdown-bg: $nav-secondary;
$dropdown-link-color: $nav-link;
$dropdown-link-hover-color: $nav-link;
$dropdown-link-hover-bg: $nav-primary-hover;
$dropdown-border-radius: 0;
$pdb-redo-colors: (
"primary": $primary,
"nav-primary": $nav-primary,
"nav-secondary": $nav-secondary,
);
$navbar-padding-y: 0;
$nav-link-padding-y: math.div($spacer, 2);
// (Required) Import Bootstrap
@import "bootstrap/scss/bootstrap";
$theme-colors: map-merge($pdb-redo-colors, $theme-colors);
@mixin hover-focus() {
&:hover,
&:focus {
@content;
}
}
.site {
display: flex;
min-height: 100vh;
height: 100%;
flex-direction: column;
header,
footer {
flex: none;
}
footer {
clear: both;
border-top: 1px solid #888;
padding: 0.5em;
margin-top: 2em;
font-size: small;
color: #555;
white-space: pre;
}
.site-content {
flex: 1 0 auto;
padding: var(--space) var(--space) 0;
width: 100%;
&::after {
content: '\00a0';
/* &nbsp; */
display: block;
margin-top: var(--space);
height: 0px;
visibility: hidden;
}
}
}
// for the pdb-redo header
header {
min-height: 6em;
padding-bottom: 1em;
img {
min-height: calc(6em + 30px);
margin: -15px 0;
width: auto;
}
div {
flex: 1 0 0%;
}
div.my-overflow {
overflow: hidden;
white-space: nowrap;
}
nav.first {
padding: 0.8em !important;
}
.navbar {
.navbar-nav {
.nav-link {
color: $nav-link;
@include hover-focus() {
background-color: $nav-primary-hover;
}
&.active {
background-color: lighten($nav-link, 5%);
color: white;
}
&.disabled {
color: mix($nav-link, $nav-secondary, 50%);
}
}
}
.navbar-toggler {
border-color: rgba($black, .1);
}
.navbar-toggler-icon {
background: url("data:image/svg+xml,<svg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 30 30'><path stroke='#{$navbar-light-color}' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/></svg>");
}
}
.first {
background-color: $nav-primary;
color: white;
a {
color: white;
text-decoration: none;
}
}
.second {
background-color: $nav-secondary;
}
a {
text-decoration: none;
&:hover {
text-decoration: underline;
}
}
}
@media all and (max-width: 1024px) {
header {
min-height: 4em;
img {
min-height: calc(4em + 30px);
}
nav.first {
padding: 0.4em !important;
}
.second {
padding: 0.2em;
}
}
}
article {
margin-top: 1em;
margin-bottom: 2em;
}
article h2 {
margin-bottom: 0.5em;
font-size: x-large;
}
a {
color: #3366cc;
text-decoration: none;
&:hover {
text-decoration: underline;
}
}
.error-info {
list-style: none;
}
.nummer {
text-align: right;
}
.error-head-text {
font-size: large;
}
.logo img {
margin: -15px 0;
height: 2em;
background-color: white;
}
ul.error-info {
margin: 0;
list-style: none;
}
a.action {
color: #888;
}
a.action:hover {
color: #555;
}
.no-list {
list-style: none;
margin: 0;
padding: 1px;
}
webpack.config.js 0 → 100644
const MiniCssExtractPlugin = require('mini-css-extract-plugin');
const { CleanWebpackPlugin } = require('clean-webpack-plugin');
const webpack = require('webpack');
const TerserPlugin = require('terser-webpack-plugin');
const UglifyJsPlugin = require('uglifyjs-webpack-plugin');
const path = require('path');
const SCRIPTS = __dirname + "/webapp/";
const DEST = __dirname + "/docroot/scripts";
module.exports = (env) => {
const PRODUCTION = env != null && env.PRODUCTION;
const webpackConf = {
entry: {
index: SCRIPTS + "index.js"
},
output: {
path: DEST,
crossOriginLoading: 'anonymous'
},
module: {
rules: [
{
test: /\.js/,
exclude: /node_modules/,
use: {
loader: "babel-loader",
options: {
presets: ['@babel/preset-env']
}
}
},
{
test: /\.(sa|sc|c)ss$/i,
use: [
MiniCssExtractPlugin.loader,
"css-loader",
"postcss-loader",
"sass-loader"
]
},
{
test: /\.woff(2)?(\?v=[0-9]\.[0-9]\.[0-9])?$/,
include: path.resolve(__dirname, './node_modules/bootstrap-icons/font/fonts'),
type: 'asset/resource',
generator: {
filename: '../fonts/[name][ext]'
}
}
]
},
resolve: {
extensions: ['.js', '.scss'],
},
plugins: [
new MiniCssExtractPlugin({
filename: "../css/[name].css"
})
],
optimization: { minimizer: [] },
target: 'web'
};
if (PRODUCTION) {
webpackConf.mode = "production";
webpackConf.plugins.push(
new CleanWebpackPlugin({
verbose: true
}));
webpackConf.optimization.minimizer.push(
new TerserPlugin({ /* additional options here */ }),
new UglifyJsPlugin({ parallel: 4 })
);
} else {
webpackConf.mode = "development";
webpackConf.devtool = 'source-map';
webpackConf.plugins.push(new webpack.optimize.AggressiveMergingPlugin())
}
return webpackConf;
};
yarn.lock 0 → 100644
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