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dssp
Commit fedc1c0e by Maarten L. Hekkelman
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remove web server from main dssp code 

add annotation and writing to dssp library
parent 1cc1e91e
Showing with 47 additions and 1317 deletions
CMakeLists.txt
......@@ -25,7 +25,7 @@
cmake_minimum_required(VERSION 3.15)
# set the project name
project(mkdssp VERSION 4.3.1.1 LANGUAGES CXX)
project(mkdssp VERSION 4.3.2 LANGUAGES CXX)
list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
......@@ -106,15 +106,16 @@ find_package(Threads)
if(NOT PDB_REDO_META)
find_package(libmcfp REQUIRED)
find_package(cifpp 5.1.0 REQUIRED)
if(BUILD_WEBSERVER)
find_package(zeep REQUIRED)
find_package(gxrio REQUIRED)
endif()
endif()
# The DSSP code is in a separate library, optionally to be used by others
add_library(dssp ${PROJECT_SOURCE_DIR}/src/dssp.cpp ${PROJECT_SOURCE_DIR}/include/dssp.hpp)
add_library(dssp
${PROJECT_SOURCE_DIR}/src/dssp.cpp
${PROJECT_SOURCE_DIR}/include/dssp.hpp
${PROJECT_SOURCE_DIR}/src/dssp-io.cpp
${PROJECT_SOURCE_DIR}/src/dssp-io.hpp
)
add_library(dssp::dssp ALIAS dssp)
target_link_libraries(dssp PRIVATE cifpp::cifpp)
......@@ -125,10 +126,7 @@ target_include_directories(dssp
"$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>"
)
add_executable(mkdssp
${PROJECT_SOURCE_DIR}/src/dssp-io.cpp
${PROJECT_SOURCE_DIR}/src/dssp-io.hpp
${PROJECT_SOURCE_DIR}/src/mkdssp.cpp)
add_executable(mkdssp ${PROJECT_SOURCE_DIR}/src/mkdssp.cpp)
target_link_libraries(mkdssp PRIVATE dssp cifpp::cifpp libmcfp::libmcfp dssp::dssp)
......@@ -139,46 +137,6 @@ if(USE_RSRC)
${PROJECT_SOURCE_DIR}/mmcif_pdbx/dssp-extension.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 gxrio::gxrio)
# 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
install(TARGETS dssp
EXPORT dsspTargets
......
docroot/about.html deleted 100644 → 0
<!DOCTYPE html SYSTEM "about:legacy-compat" [
<!ENTITY nbsp "&#160;">
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<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>References</h2>
<p>If you use the DSSP software or databank please cite the appropriate paper:</p>
<div class="programListTable">
<table style="margin-left: 0;">
<tr>
<td><a href="https://doi.org/10.1093/nar/gkq1105" target="_BLANK">Current version</a></td>
<td>Joosten RP, te Beek TAH, Krieger E, Hekkelman ML, Hooft RWW, Schneider R, Sander C, Vriend
A series of PDB related databases for everyday needs. Nuc. Acids Res. 2010; 39:D411-D419.
</td>
</tr>
<tr>
<td><a href="https://doi.org/10.1002/bip.360221211" target="_BLANK">Original algorithm</a></td>
<td>Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of
hydrogen-bonded and geometrical features.
Biopolymers 1983; 22:2577-2637.
</td>
</tr>
</table>
</div>
</article>
<article>
<h2>Using DSSP data</h2>
<p>DSSP provides an elaborate description of the secondary structure elements in a protein structure,
including backbone hydrogen bonding
and the topology of &beta;-sheets. The most popular feature is the per-residue assignment of secondary
structure with a single character code:
</p>
<ul>
<li>H = &alpha;-helix</li>
<li>B = residue in isolated &beta;-bridge</li>
<li>E = extended strand, participates in &beta; ladder</li>
<li>G = 3<sub>10</sub>-helix</li>
<li>I = &pi;-helix</li>
<li>P = &kappa;-helix (poly-proline II helix)</li>
<li>T = hydrogen-bonded turn</li>
<li>S = bend</li>
</ul>
<p>The full DSSP output is provided in two formats. The legacy DSSP format was origianlly designed for
structures that were in
PDB-formatted models. Now, 40 years later, the PDB format has become obsolete as it cannot capture the
large structure models that
modern structural biology methods can provide. The mmCIF format is the data format of choice for
structural biology as it has no
size limitations for structure models and it can hold extensive annotations and metadata. DSSP now
writes its data straight to these
mmCIF files by default. The legacy DSSP format can still be written but only for structure models that
fit.</p>
</article>
<article>
<a id="DSSP"></a>
<h2>DSSP format</h2>
<p>The output from DSSP contains secondary structure assignments and other information. Extract from
3kew.dssp (header):</p>
<pre><![CDATA[
==== Secondary Structure Definition by the program DSSP, NKI version 4.3 ==== DATE=2023-06-08 .
REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637 .
HEADER TRANSFERASE 26-OCT-09 3KEW .
COMPND MOL_ID: 1; MOLECULE: DHHA1 domain protein; CHAIN: A, B; FRAGMENT: N-TERMINAL FRAGMENT, RESIDUES 1-231; SYNONYM: A... .
SOURCE MOL_ID: 1; GENE: ALAS, CPF_0714; STRAIN: ATCC 13124; ORGANISM_SCIENTIFIC: Clostridium perfringens; ORGANISM_TAXID... .
AUTHOR Y.Patskovsky; R.Toro; M.Gilmore; S.Miller; J.M.Sauder; S.C.Almo; S.K.Burley; New York SGX Research Center for Str... .
458 3 0 0 0 TOTAL NUMBER OF RESIDUES, NUMBER OF CHAINS, NUMBER OF SS-BRIDGES(TOTAL,INTRACHAIN,INTERCHAIN) .
24682.5 ACCESSIBLE SURFACE OF PROTEIN (ANGSTROM**2) .
319 69.7 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(J) , SAME NUMBER PER 100 RESIDUES .
6 1.3 TOTAL NUMBER OF HYDROGEN BONDS IN PARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES .
144 31.4 TOTAL NUMBER OF HYDROGEN BONDS IN ANTIPARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-5), SAME NUMBER PER 100 RESIDUES .
2 0.4 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-4), SAME NUMBER PER 100 RESIDUES .
12 2.6 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-3), SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-2), SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-1), SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+0), SAME NUMBER PER 100 RESIDUES .
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+1), SAME NUMBER PER 100 RESIDUES .
50 10.9 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+2), SAME NUMBER PER 100 RESIDUES .
34 7.4 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+3), SAME NUMBER PER 100 RESIDUES .
84 18.3 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+4), SAME NUMBER PER 100 RESIDUES .
2 0.4 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+5), SAME NUMBER PER 100 RESIDUES .
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 *** HISTOGRAMS OF *** .
0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 2 0 0 0 0 0 RESIDUES PER ALPHA HELIX .
0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 PARALLEL BRIDGES PER LADDER .
4 0 4 8 2 6 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ANTIPARALLEL BRIDGES PER LADDER .
2 2 2 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 LADDERS PER SHEET .]]>
</pre>
<p>The first few lines are taken from the input model file, then some general statistics about the model and
hydrogen bonding
are given. The histograms describe the distribution of sizes of secondary structure elements. For
instance, this structure has
three helices, one short one consisting of 4 residues and two longer ones of 16 and 17 residues. Note
that beta sheets are described
as a collection of ladders, rather than strands. Ladders can be seen as two strands together with the
hydrogen bonds as the rungs
of the ladder. More formal definitions are given in the Kabsch and Sander paper.</p>
<p>The model statistics are followed by a detailed per-residue description. Extract from 3kew.dssp
(continued):</p>
<pre><![CDATA[....;....1....;....2....;....3....;....4....;....5....;....6....;....7..
.-- sequential resnumber, including chain breaks as extra residues
| .-- original resname, not necessarily sequential, may contain letters for insertion codes
| | .-- one-letter chain ID
| | | .-- amino acid sequence in one letter code
| | | | .-- secondary structure summary based on columns 19-38
| | | | |.-- PPII (kappa) helix
| | | | ||.-- 3-10 helix
| | | | |||.-- alpha helix
| | | | ||||.-- pi helix
| | | | |||||.-- geometrical bend
| | | | ||||||.-- chirality
| | | | |||||||.-- beta bridge label
| | | | ||||||||.-- beta bridge label
| | | | ||||||||| .-- beta bridge partner resnum
| | | | ||||||||| | .-- beta bridge partner resnum
| | | | ||||||||| | |.-- beta sheet label
| | | | ||||||||| | || .-- solvent accessibility
| | | | ||||||||| | || |
# RESIDUE AA STRUCTURE BP1 BP2 ACC N-H-->O O-->H-N N-H-->O O-->H-N TCO KAPPA ALPHA PHI PSI X-CA Y-CA Z-CA
1 1 A L 0 0 119 0, 0.0 2,-0.3 0, 0.0 33,-0.2 0.000 360.0 360.0 360.0 168.8 8.7 6.9 63.0
2 2 A T E -a 34 0A 66 31,-2.0 33,-2.1 1,-0.1 2,-0.7 -0.456 360.0-169.6 -87.8 130.5 7.7 8.8 59.8
3 3 A K E > -a 35 0A 66 -2,-0.3 3,-1.2 31,-0.2 4,-0.2 -0.850 8.5-179.0-111.3 94.7 7.6 7.5 56.2
4 4 A L G >> S+ 0 0 23 31,-2.5 4,-2.9 -2,-0.7 3,-2.0 0.786 71.6 72.4 -65.6 -32.5 7.1 10.6 54.1
5 5 A Y G 34 S+ 0 0 2 30,-0.8 -1,-0.3 1,-0.3 31,-0.1 0.709 101.0 46.1 -56.9 -26.7 7.0 8.7 50.7
6 6 A Y G <4 S+ 0 0 39 -3,-1.2 -1,-0.3 2,-0.1 -2,-0.2 0.439 115.4 47.1 -93.5 -4.1 3.5 7.4 51.7
7 7 A E T <4 S- 0 0 138 -3,-2.0 2,-0.3 1,-0.2 -2,-0.2 0.825 135.2 -0.3 -99.6 -48.8 2.4 10.9 52.8
8 8 A D >< - 0 0 57 -4,-2.9 3,-1.4 3,-0.1 -1,-0.2 -0.852 61.5-167.8-144.3 106.0 3.6 13.0 49.9]]>
</pre>
<p>Below is a brief description of the data columns. More details are described in the Kabsch and Sander
paper.</p>
<h3>RESIDUE</h3>
<p>Two columns of residue numbers. First column is DSSP's sequential residue number, starting at the first
residue actually in the model set
and including chain breaks; this number is used to refer to residues throughout. The second column gives
the numbering as is used in the
structure model 'residue number','insertion code' and 'chain identifier'; these are given for reference
only.</p>
<h3>AA</h3>
<p>One letter amino acid code, non standard residues are marked as <em>X</em>. CYS in an SS-bridge are
marked by a lower case letter. So when cysteines
are bridged, then the first bridged cysteine in the sequence and its partner elsewhere in the sequence
are marked <em>a</em>. The next bridged cysteine,
that is not yet marked, and its partner are both marked <em>b</em>, etcetera. Unbridged cysteines remain
marked as <em>C</em>.</p>
<h3>STRUCTURE</h3>
<p>The first column (under the <em>S</em>) gives aone-letter summary of secondary structure, intended to approximate
crystallographers' intuition. This summary is based on the next 8 columns, which are the principal
result of DSSP analysis of the atomic coordinates. More details in the Kabsch and Sander paper.</p>
<h3>BP1 and BP2</h3>
<p>Residue numbers of the first and (if available) second beta bridge partner. The letter marked the B-sheet
that contains the bridges.</p>
<h3>ACC</h3>
<p>Water exposed surface in &Aring;ngstr&ouml;m<sup>2</sup>. <em>Note:</em>The values for solvent exposure may not mean what you
think:
<ul>
<li>Effects leading to larger than expected values: solvent exposure calculation ignores unusual
residues, like ACE, or residues with incomplete backbone.
it also ignores HETATOMS, like a heme or metal ligands. Also, side chains may not have all atoms
explicitly modeled.</li>
<li>Effects leading to smaller than expected values: in complexes, e.g. a dimer, solvent exposure is for
the entire assembly, not for the monomer.
Also, atom OXT of c-terminal residues is treated like a side chain atom if it is listed as part of
the last residue.</li>
<li>Unknown or non-standard residues are named X on output and are not checked for the expected number
of sidechain atoms.</li>
<li>All explicit water molecules, like other hetatoms, are ignored.</li>
</ul>
</p>
<h3>N-H--&gt;O etc.</h3>
<p>Hydrogen bonds; e.g. -3,-1.4 means that this residue (i) has its HN atom H-bonded to O of residue i-3
with an electrostatic H-bond energy of -1.4 kcal/mol.
There are two columns for each type of H-bond, to allow for bifurcated H-bonds. <em>Note:</em>The marked
H-bonds are the best and second best candidate. The second best
and even the best (in rare occasions) may be unrealistically por H-bonds.</p>
<h3>TCO</h3>
<p>The cosine of angle between C=O of residue i and C=O of residue i-1. For &alpha;-helices, TCO is near +1,
for &beta;-sheets TCO is near -1.
These values are descriptive and not used for structure definition.</p>
<h3>KAPPA</h3>
<p>Virtual bond angle (bend angle) defined by the three C&alpha; atoms of residues i-2, i, and i+2. Used to
define bends (structure code <em>S</em>).</p>
<h3>ALPHA</h3>
<p>Virtual torsion angle (dihedral angle) defined by the four C&alpha; atoms of residues i-1, i, i+1, and
i+2. Used to define chirality (structure code <em>+</em> or <em>-</em>).</p>
<h3>PHI and PSI</h3>
<p>The peptide backbone torsion angles as described in the IUPAC standard</p>
<h3>X-CA, Y-CA, and Z-CA</h3>
<p>Just a copy of the C&alpha; atom coordinates in the structure model</p>
</article>
<article>
<a id="mmCIF"></a>
<h2>DSSP data in mmCIF files</h2>
<p>The mmCIF-formatted DSSP output caries the same information as the DSSP format but in a more scalable way
and with a formal description caputered in
an mmCIF dictionary. It is designed to be machine readable. Developers who create software to read these
annotations can use our
<a href="https://github.com/PDB-REDO/dssp/blob/trunk/mmcif_pdbx/dssp-extension.dic"
target="_BLANK">extension to the mmCIF dictionary</a> on GitHub.
<em>Note:</em> For sake of speed the solvent accessibility is not calculated by default when using mmCIF
output. The command-line switch
<code>--calculate-accessibility</code> can be used to switch this feature on.
</p>
</article>
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<h2>Using the DSSP software locally</h2>
<p>If you want to run large sets of DSSP calculations you can install DSSP locally by:
<ul>
<li>Downloading the current <a href="https://pdb-redo.eu/dssp/others/mkdssp.gz">Linux and WSL binary</a></li>
<li>Building DSSP from <a href="https://github.com/PDB-REDO/dssp">source</a></li>
<li>Installing the <a href="https://launchpad.net/ubuntu/+source/dssp">Debian/Ubuntu package</a> (note that this version is a bit older)</li>
<li>Installing the <a href="https://www.ccp4.ac.uk/">CCP4 suite</a> that comes with (an older version of) DSSP</li>
</ul>
Use <code>mkdssp -h</code> to get a short help message on how to run DSSP. Alternatively, you can use the
<a z2:href="@{/api-doc}">DSSP API</a> to commit batches of calculations.
</p>
</article>
<article>
<h2>Downloading ready-made DSSP annotations</h2>
<p>For your convenience we have already run DSSP on the entire Protein Data Bank. All entries are available in <a z2:href="@{/about#mmCIF}">mmCIF format</a>
and, if they fit, in the <a z2:href="@{/about#DSSP}">legacy DSSP format.</a></p>
<h3>Manually download (single entries) via the website or using <code>wget</code>:</h3>
<ul>
<li><code>wget https://pdb-redo.eu/dssp/9xyz.cif.gz</code> downloads annotated mmCIF file</li>
<li><code>wget https://pdb-redo.eu/dssp/9xyz.dssp</code> downloads the legacy DSSP file (if available)</li>
</ul>
<h3>Download entire DSSP databank using <code>rsync</code>:</h3>
<ul>
<li><code>rsync -av rsync://rsync.pdb-redo.eu/dssp/ dssp/</code> downloads the entire archive.
</li>
</ul>
<h2>License</h2>
<p><a z2:href="@{/license}">Here</a> you can find the data usage license.</p>
</article>
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docroot/index.html deleted 100644 → 0
<!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>DSSP (Dictionary of Secondary Structure in Proteins) is an algorithm originally designed by Wolfgang Kabsch and Chris Sander to standardise secondary structure assigment based on atomic coordinates. DSSP does not predict secondary structure. You can run DSSP using the form below or you can <a z2:href="@{/download}">install</a> the program locally. Ready-made annotations of PDB entries are available below and you can also <a z2:href="@{/download}">download</a> the whole databank at once. More details about the DSSP output are <a z2:href="@{/about}">here</a>.
</p>
</article>
<article>
<h2>Submit your structure</h2>
<form z2:fragment="submit-form" name="job-form" method="post" enctype="multipart/form-data"
z2:action="@{/do}">
<div class="input-group mb-3">
<label class="input-group-text" for="input-group-pdb-file">Coordinates</label>
<input type="file" class="form-control" id="input-group-pdb-file" name="data" required="required" />
</div>
<div class="input-group mb-3">
<label class="input-group-text" for="format-select">Format</label>
<select class="form-select" id="format-select" name="format">
<option value="mmcif">Annotated mmCIF</option>
<option value="dssp">Historic DSSP format, may fail on larger structures</option>
</select>
</div>
<button type="submit" class="btn btn-sm btn-primary mt-3">Submit</button>
</form>
</article>
</div>
<footer z2:replace="~{footer::content}"></footer>
</body>
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docroot/license.html deleted 100644 → 0
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<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')}"></nav>
<div class="container site-content">
<article>
<h2>Usage Policy</h2>
<p>Data files contained in the DSSP databank (rsync://rsync.pdb-redo.eu/dssp; <a
z2:href="@{/db}">https://pdb-redo.eu/dssp</a>) are free of all copyright restrictions and made fully
and freely available for both non-commercial and commercial use. Users of the data should attribute
DSSP, the Protein Data Bank and the original authors of that structural data. By using the materials available in the
DSSP databank, the user agrees to abide by the conditions described below:</p>
<ul>
<li>The archival data files in the DSSP databank are made freely available to all users. Data files
within the archive may be redistributed in original form without restriction. Redistribution of
modified data files is allowed only if the parent data file is attributed.</li>
<li>Where applicable, the usage policy of the parent PDB archive entries applies.</li>
<li>The data in the DSSP databank are provided on an "as is" basis. Neither DSSP nor its parent
or comprising institutions can be held liable to any party for direct, indirect, special,
incidental, or consequential damages, including lost profits, arising from the use of DSSP
materials.</li>
<li>Resources on pdb-redo.eu/dssp are provided without warranty of any kind, either expressed or implied.
This includes but is not limited to merchantability or fitness for a particular purpose. The
institutions managing this site make no representation that these resources will not infringe any
patent or other proprietary right.</li>
</ul>
</article>
</div>
<footer z2:replace="~{footer::content}"></footer>
</body>
</html>
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<a href="https://pdb-redo.eu/"><img z2:src="@{/images/PDB_logo_rect_medium.svg}" /></a>
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<nav class="first">
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include/dssp.hpp
......@@ -246,6 +246,14 @@ class dssp
bool empty() const { return begin() == end(); }
// --------------------------------------------------------------------
// Writing out the data, either in legacy format...
void write_legacy_output(std::ostream& os) const;
// ... or as annotation in the cif::datablock
void annotate(cif::datablock &db, bool writeOther, bool writeDSSPCategories) const;
// convenience method, when creating old style DSSP files
enum class pdb_record_type
......
package.json deleted 100644 → 0
{
"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-io.cpp
......@@ -1104,7 +1104,7 @@ void writeSummary(cif::datablock &db, const dssp &dssp)
}
}
void annotateDSSP(cif::datablock &db, const dssp &dssp, bool writeOther, bool writeExperimental, std::ostream &os)
void annotateDSSP(cif::datablock &db, const dssp &dssp, bool writeOther, bool writeExperimental)
{
using namespace std::literals;
......@@ -1244,6 +1244,4 @@ void annotateDSSP(cif::datablock &db, const dssp &dssp, bool writeOther, bool wr
{ "version", kVersionNumber },
{ "date", kBuildDate },
{ "classification", "model annotation" } });
db.write(os);
}
src/dssp-io.hpp
......@@ -29,8 +29,4 @@
#include "dssp.hpp"
void writeDSSP(const dssp& dssp, std::ostream& os);
void annotateDSSP(cif::datablock &db, const dssp& dssp, bool writeOther, bool writeExperimental, std::ostream& os);
void writeDSSP(std::istream &is, std::ostream& os);
void annotateDSSP(cif::datablock &db, const dssp& dssp, bool writeOther, bool writeExperimental, std::ostream& os);
void annotateDSSP(cif::datablock &db, const dssp& dssp, bool writeOther, bool writeExperimental);
src/dssp-server.cpp deleted 100644 → 0
/*-
* 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 <cif++.hpp>
#include <gxrio.hpp>
#include <mcfp.hpp>
#include <zeep/http/daemon.hpp>
#include <zeep/http/html-controller.hpp>
#include <zeep/http/rest-controller.hpp>
#include <zeep/streambuf.hpp>
// --------------------------------------------------------------------
class dssp_html_controller : public zeep::http::html_controller
{
public:
dssp_html_controller()
: zeep::http::html_controller()
{
mount("{css,scripts,fonts,images,favicon}/", &dssp_html_controller::handle_file);
mount("{favicon.ico,browserconfig.xml,manifest.json}", &dssp_html_controller::handle_file);
map_get("", "index");
map_get("about", "about");
map_get("download", "download");
map_get("license", "license");
}
};
// --------------------------------------------------------------------
class dssp_rest_controller : public zeep::http::rest_controller
{
public:
dssp_rest_controller()
: zeep::http::rest_controller("")
{
map_post_request("do", &dssp_rest_controller::work, "data", "format");
}
zeep::http::reply work(const zeep::http::file_param &coordinates, std::optional<std::string> format);
};
zeep::http::reply dssp_rest_controller::work(const zeep::http::file_param &coordinates, std::optional<std::string> format)
{
zeep::char_streambuf sb(coordinates.data, coordinates.length);
gxrio::istream in(&sb);
cif::file f = cif::pdb::read(in);
if (f.empty())
throw std::runtime_error("Invalid input file, is it empty?");
// --------------------------------------------------------------------
short pp_stretch = 3; //minPPStretch.value_or(3);
std::string fmt = format.value_or("mmcif");
dssp dssp(f.front(), 1, pp_stretch, true);
std::ostringstream os;
if (fmt == "dssp")
writeDSSP(dssp, os);
else
annotateDSSP(f.front(), dssp, true, true, os);
// --------------------------------------------------------------------
std::string name = f.front().name();
if (fmt == "dssp")
name += ".dssp";
else
name += ".cif";
zeep::http::reply rep{ zeep::http::ok };
rep.set_content(os.str(), "text/plain");
rep.set_header("content-disposition", "attachement; filename = \"" + name + '"');
return rep;
}
// --------------------------------------------------------------------
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::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::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");
zeep::http::daemon server([&, context = config.get("context")]()
{
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());
s->set_context_name(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
src/dssp.cpp
......@@ -29,6 +29,8 @@
#include "dssp.hpp"
#include "queue.hpp"
#include "dssp-io.hpp"
#include <deque>
#include <iomanip>
#include <numeric>
......@@ -2242,3 +2244,17 @@ std::string dssp::get_pdb_header_line(pdb_record_type pdb_record) const
return {};
}
}
// --------------------------------------------------------------------
void dssp::write_legacy_output(std::ostream& os) const
{
writeDSSP(*this, os);
}
void dssp::annotate(cif::datablock &db, bool writeOther, bool writeDSSPCategories) const
{
annotateDSSP(db, *this, writeOther, writeDSSPCategories);
}
src/mkdssp.cpp
......@@ -37,8 +37,6 @@
#include <cif++.hpp>
#include "dssp.hpp"
#include "dssp-io.hpp"
#include "revision.hpp"
namespace fs = std::filesystem;
......@@ -185,16 +183,22 @@ int d_main(int argc, const char *argv[])
}
if (fmt == "dssp")
writeDSSP(dssp, out);
dssp.write_legacy_output(out);
else
annotateDSSP(f.front(), dssp, writeOther, not config.has("no-dssp-categories"), out);
{
dssp.annotate(f.front(), writeOther, not config.has("no-dssp-categories"));
out << f.front();
}
}
else
{
if (fmt == "dssp")
writeDSSP(dssp, std::cout);
dssp.write_legacy_output(std::cout);
else
annotateDSSP(f.front(), dssp, writeOther, not config.has("no-dssp-categories"), std::cout);
{
dssp.annotate(f.front(), writeOther, not config.has("no-dssp-categories"));
std::cout << f.front();
}
}
return 0;
......
test/unit-test-dssp.cpp
......@@ -138,7 +138,8 @@ BOOST_AUTO_TEST_CASE(ut_mmcif_2)
std::stringstream test;
annotateDSSP(f.front(), dssp, true, false, test);
dssp.annotate(f.front(), true, false);
test << f.front();
cif::file rf(gTestDir / "1cbs-dssp.cif");
......
webapp/index.js deleted 100644 → 0
import "core-js/stable";
import "regenerator-runtime/runtime";
import '@popperjs/core';
import 'bootstrap';
import './pdb-redo-style.scss';
webapp/pdb-redo-style.scss deleted 100644 → 0
@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: $nav-secondary;
}
a {
text-decoration: none;
&:hover {
text-decoration: underline;
}
}
}
@media all and (max-width: 1024px) {
header {
min-height: 4em;
img {
min-height: calc(4em + 30px);
}
nav.first {
padding: 0.4em !important;
}
.second {
padding: 0.2em;
}
}
}
article {
margin-top: 1em;
margin-bottom: 2em;
}
article h2 {
margin-bottom: 0.5em;
}
a {
color: #3366cc;
text-decoration: none;
&:hover {
text-decoration: underline;
}
}
.error-info {
list-style: none;
}
.nummer {
text-align: right;
}
.error-head-text {
font-size: large;
}
.logo img {
margin: -15px 0;
height: 2em;
background-color: white;
}
ul.error-info {
margin: 0;
list-style: none;
}
a.action {
color: #888;
}
a.action:hover {
color: #555;
}
.no-list {
list-style: none;
margin: 0;
padding: 1px;
}
webpack.config.js deleted 100644 → 0
const MiniCssExtractPlugin = require('mini-css-extract-plugin');
const { CleanWebpackPlugin } = require('clean-webpack-plugin');
const webpack = require('webpack');
const TerserPlugin = require('terser-webpack-plugin');
const UglifyJsPlugin = require('uglifyjs-webpack-plugin');
const path = require('path');
const SCRIPTS = __dirname + "/webapp/";
const DEST = __dirname + "/docroot/scripts";
module.exports = (env) => {
const PRODUCTION = env != null && env.PRODUCTION;
const webpackConf = {
entry: {
index: SCRIPTS + "index.js"
},
output: {
path: DEST,
crossOriginLoading: 'anonymous'
},
module: {
rules: [
{
test: /\.js/,
exclude: /node_modules/,
use: {
loader: "babel-loader",
options: {
presets: ['@babel/preset-env']
}
}
},
{
test: /\.(sa|sc|c)ss$/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 deleted 100644 → 0
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