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dssp
Commit 05c339e9 by Maarten L. Hekkelman
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Merge branch 'trunk' of github.com:PDB-REDO/dssp into trunk

parents 9258a8c3 56561e18
Showing with 3139 additions and 72 deletions
.gitignore
...@@ -8,3 +8,7 @@ build ...@@ -8,3 +8,7 @@ build
**/*.dssp **/*.dssp
src/revision.hpp src/revision.hpp
out/ out/
node_modules
docroot/fonts
docroot/scripts
docroot/css
CMakeLists.txt
...@@ -25,7 +25,7 @@ ...@@ -25,7 +25,7 @@
cmake_minimum_required(VERSION 3.15) cmake_minimum_required(VERSION 3.15)
# set the project name # set the project name
project(mkdssp VERSION 4.2.2.1 LANGUAGES CXX) project(mkdssp VERSION 4.3 LANGUAGES CXX)
list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake") list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
...@@ -52,6 +52,7 @@ endif() ...@@ -52,6 +52,7 @@ endif()
# Optionally build a version to be installed inside CCP4 # Optionally build a version to be installed inside CCP4
option(BUILD_FOR_CCP4 "Build a version to be installed in CCP4" OFF) 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(BUILD_FOR_CCP4)
if("$ENV{CCP4}" STREQUAL "" OR NOT EXISTS $ENV{CCP4}) if("$ENV{CCP4}" STREQUAL "" OR NOT EXISTS $ENV{CCP4})
...@@ -105,6 +106,11 @@ find_package(Threads) ...@@ -105,6 +106,11 @@ find_package(Threads)
if(NOT PDB_REDO_META) if(NOT PDB_REDO_META)
find_package(libmcfp REQUIRED) find_package(libmcfp REQUIRED)
find_package(cifpp 5.0.8 REQUIRED) find_package(cifpp 5.0.8 REQUIRED)
if(BUILD_WEBSERVER)
find_package(zeep REQUIRED)
find_package(gxrio REQUIRED)
endif()
endif() endif()
# The DSSP code is in a separate library, optionally to be used by others # The DSSP code is in a separate library, optionally to be used by others
...@@ -124,12 +130,52 @@ add_executable(mkdssp ...@@ -124,12 +130,52 @@ add_executable(mkdssp
${PROJECT_SOURCE_DIR}/src/dssp-io.hpp ${PROJECT_SOURCE_DIR}/src/dssp-io.hpp
${PROJECT_SOURCE_DIR}/src/mkdssp.cpp) ${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) target_link_libraries(mkdssp PRIVATE dssp cifpp::cifpp libmcfp::libmcfp dssp::dssp)
if(USE_RSRC) if(USE_RSRC)
message("Using resources compiled with ${MRC}") mrc_target_resources(mkdssp
mrc_target_resources(mkdssp ${CIFPP_SHARE_DIR}/mmcif_pdbx.dic ${CIFPP_SHARE_DIR}/mmcif_ddl.dic) ${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 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
${PROJECT_SOURCE_DIR}/docroot/)
endif() endif()
# Install rules # Install rules
......
README.md
DSSP 4.0 DSSP 4.3
======== ========
This is a rewrite of DSSP, now offering full mmCIF support. The difference This is a rewrite of DSSP, now offering full mmCIF support. The difference
with previous releases of DSSP is that it now writes out an annotated mmCIF with previous releases of DSSP is that it now writes out an annotated mmCIF
file by default, storing the secondary structure information in the file by default, storing the secondary structure information in the
_struct_conf category. _struct_conf category.
Another new feature in this version of DSSP is that it now defines Another new feature in this version of DSSP is that it now defines
...@@ -33,20 +33,15 @@ Make sure you install [libcif++](https://github.com/PDB-REDO/libcifpp) and [libm ...@@ -33,20 +33,15 @@ Make sure you install [libcif++](https://github.com/PDB-REDO/libcifpp) and [libm
After that, building should be as easy as typing: After that, building should be as easy as typing:
``` ```bash
git clone https://github.com/PDB-REDO/dssp.git git clone https://github.com/PDB-REDO/dssp.git
cd dssp cd dssp
mkdir build mkdir build
cd build cmake -S . -B build -DCMAKE_BUILD_TYPE=Release
cmake .. cmake --build build
cmake --build . --config Release cmake --install build
ctest -C Release
cmake --install .
``` ```
This will install the `mkdssp` program in `$HOME/.local/bin`. If you want to
install elsewhere, specify the prefix with the [CMAKE_INSTALL_PREFIX](https://cmake.org/cmake/help/v3.21/variable/CMAKE_INSTALL_PREFIX.html) variable.
Usage Usage
----- -----
......
changelog
Version 4.3
- Write new output by default
- Fix some issues with this new output, typo e.g.
- Added web service implementation
- Added mmcif_pdbx dictionary extension
Version 4.2.2.1 Version 4.2.2.1
- Fixed dependency on libcifpp - Fixed dependency on libcifpp
......
doc/mkdssp.1
...@@ -33,6 +33,9 @@ choose to output format, but if it is unclear, mmcif is the default. Use ...@@ -33,6 +33,9 @@ choose to output format, but if it is unclear, mmcif is the default. Use
this option to force output in either the old fixed column DSSP format or this option to force output in either the old fixed column DSSP format or
the new annotated mmCIF format. the new annotated mmCIF format.
.TP .TP
\fB--no-dssp-categories\fR
When writing mmCIF files, suppress the output of all dssp_ categories.
.TP
\fB--min-pp-stretch\fR \fB--min-pp-stretch\fR
This option can be used to define the minimal number of residues with PHI/PSI This option can be used to define the minimal number of residues with PHI/PSI
angles within the range required to assing a PP helix. angles within the range required to assing a PP helix.
......
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">
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<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>
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docroot/index.html 0 → 100644
<!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">
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<title>DSSP</title>
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<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>
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include/dssp.hpp
...@@ -135,15 +135,15 @@ class dssp ...@@ -135,15 +135,15 @@ class dssp
int pdb_seq_num() const; int pdb_seq_num() const;
std::string pdb_ins_code() const; std::string pdb_ins_code() const;
float alpha() const; std::optional<float> alpha() const;
float kappa() const; std::optional<float> kappa() const;
float phi() const; std::optional<float> phi() const;
float psi() const; std::optional<float> psi() const;
float tco() const; std::optional<float> tco() const;
float omega() const; std::optional<float> omega() const;
bool is_pre_pro() const; bool is_pre_pro() const;
bool is_cis() const { return std::abs(omega()) < 30.0f; } bool is_cis() const { return std::abs(omega().value_or(360)) < 30.0f; }
float chiral_volume() const; float chiral_volume() const;
std::size_t nr_of_chis() const; std::size_t nr_of_chis() const;
......
mmcif_pdbx/dssp-extension.dic 0 → 100644
## File: dssp-extension.dic
## Date: 30-May-2023
##
# Items containing Secondary Structure information as written by e.g. DSSP
#
#
data_mmcif_pdbx-def-dssp.dic
########################################
## Category dssp_struct_bridge_pairs ##
########################################
save_dssp_struct_bridge_pairs
#
_category.description 'dssp_struct_bridge_pairs describes bridge pairs as assigned by DSSP.'
_category.id dssp_struct_bridge_pairs
_category.mandatory_code no
#
_category_key.name '_dssp_struct_bridge_pairs.id'
loop_
_category_group.id 'inclusive_group'
'struct_group'
#
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example taken from 1cbs, first bridge pair
;
;
_dssp_struct_bridge_pairs.id 2
_dssp_struct_bridge_pairs.label_comp_id ASN
_dssp_struct_bridge_pairs.label_seq_id 2
_dssp_struct_bridge_pairs.label_asym_id A
_dssp_struct_bridge_pairs.auth_seq_id 2
_dssp_struct_bridge_pairs.auth_asym_id A
_dssp_struct_bridge_pairs.pdbx_PDB_ins_code ?
_dssp_struct_bridge_pairs.acceptor_1_label_comp_id PHE
_dssp_struct_bridge_pairs.acceptor_1_label_seq_id 3
_dssp_struct_bridge_pairs.acceptor_1_label_asym_id A
_dssp_struct_bridge_pairs.acceptor_1_auth_seq_id 3
_dssp_struct_bridge_pairs.acceptor_1_auth_asym_id A
_dssp_struct_bridge_pairs.acceptor_1_pdbx_PDB_ins_code ?
_dssp_struct_bridge_pairs.acceptor_1_energy -0.1
_dssp_struct_bridge_pairs.acceptor_2_label_comp_id SER
_dssp_struct_bridge_pairs.acceptor_2_label_seq_id 4
_dssp_struct_bridge_pairs.acceptor_2_label_asym_id A
_dssp_struct_bridge_pairs.acceptor_2_auth_seq_id 4
_dssp_struct_bridge_pairs.acceptor_2_auth_asym_id A
_dssp_struct_bridge_pairs.acceptor_2_pdbx_PDB_ins_code ?
_dssp_struct_bridge_pairs.acceptor_2_energy -0.1
_dssp_struct_bridge_pairs.donor_1_label_comp_id ASN
_dssp_struct_bridge_pairs.donor_1_label_seq_id 91
_dssp_struct_bridge_pairs.donor_1_label_asym_id A
_dssp_struct_bridge_pairs.donor_1_auth_seq_id 91
_dssp_struct_bridge_pairs.donor_1_auth_asym_id A
_dssp_struct_bridge_pairs.donor_1_pdbx_PDB_ins_code ?
_dssp_struct_bridge_pairs.donor_1_energy -0.0
_dssp_struct_bridge_pairs.donor_2_label_comp_id GLU
_dssp_struct_bridge_pairs.donor_2_label_seq_id 46
_dssp_struct_bridge_pairs.donor_2_label_asym_id A
_dssp_struct_bridge_pairs.donor_2_auth_seq_id 46
_dssp_struct_bridge_pairs.donor_2_auth_asym_id A
_dssp_struct_bridge_pairs.donor_2_pdbx_PDB_ins_code ?
_dssp_struct_bridge_pairs.donor_2_energy -0.0
;
save_
#
save__dssp_struct_bridge_pairs.id
_item.description
; The value of _dssp_struct_bridge_pairs.id must uniquely identify a record in the
dssp_struct_bridge_pairs list.
;
_item.name '_dssp_struct_bridge_pairs.id'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code yes
_item_type.code code
save_
save__dssp_struct_bridge_pairs.label_comp_id
_item.description
; A component of the identifier for this monomer.
This data item is a pointer to _chem_comp.id in the CHEM_COMP
category.
;
_item.name '_dssp_struct_bridge_pairs.label_comp_id'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code yes
_item_type.code ucode
save_
save__dssp_struct_bridge_pairs.label_seq_id
_item.description
; A component of the identifier for this monomer.
;
_item.name '_dssp_struct_bridge_pairs.label_seq_id'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_struct_bridge_pairs.label_asym_id
_item.description
; A component of the identifier for this monomer
;
_item.name '_dssp_struct_bridge_pairs.label_asym_id'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code yes
_item_type.code code
save_
save__dssp_struct_bridge_pairs.auth_seq_id
_item.description
; A component of the identifier for this monomer
;
_item.name '_dssp_struct_bridge_pairs.auth_seq_id'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code no
_item_type.code int
save_
save__dssp_struct_bridge_pairs.auth_asym_id
_item.description
; A component of the identifier for this monomer
;
_item.name '_dssp_struct_bridge_pairs.auth_asym_id'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code no
_item_type.code code
save_
save__dssp_struct_bridge_pairs.pdbx_PDB_ins_code
_item.description
; A component of the identifier for this monomer
;
_item.name '_dssp_struct_bridge_pairs.pdbx_PDB_ins_code'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code no
_item_type.code code
save_
save__dssp_struct_bridge_pairs.acceptor_1_label_comp_id
_item.description
; A component of the identifier of the first residue that forms a bridge pair
with this monomer where this monomer is the donor.
;
_item.name '_dssp_struct_bridge_pairs.acceptor_1_label_comp_id'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code no
_item_type.code ucode
save_
save__dssp_struct_bridge_pairs.acceptor_1_label_seq_id
_item.description
; A component of the identifier of the first residue that forms a bridge pair
with this monomer where this monomer is the donor.
;
_item.name '_dssp_struct_bridge_pairs.acceptor_1_label_seq_id'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code no
_item_type.code int
save_
save__dssp_struct_bridge_pairs.acceptor_1_label_asym_id
_item.description
; A component of the identifier of the first residue that forms a bridge pair
with this monomer where this monomer is the donor.
;
_item.name '_dssp_struct_bridge_pairs.acceptor_1_label_asym_id'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code yes
_item_type.code code
save_
save__dssp_struct_bridge_pairs.acceptor_1_auth_seq_id
_item.description
; A component of the identifier of the first residue that forms a bridge pair
with this monomer where this monomer is the donor.
;
_item.name '_dssp_struct_bridge_pairs.acceptor_1_auth_seq_id'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code no
_item_type.code int
save_
save__dssp_struct_bridge_pairs.acceptor_1_auth_asym_id
_item.description
; A component of the identifier of the first residue that forms a bridge pair
with this monomer where this monomer is the donor.
;
_item.name '_dssp_struct_bridge_pairs.acceptor_1_auth_asym_id'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code no
_item_type.code code
save_
save__dssp_struct_bridge_pairs.acceptor_1_pdbx_PDB_ins_code
_item.description
; A component of the identifier of the first residue that forms a bridge pair
with this monomer where this monomer is the donor.
;
_item.name '_dssp_struct_bridge_pairs.acceptor_1_pdbx_PDB_ins_code'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code no
_item_type.code code
save_
save__dssp_struct_bridge_pairs.acceptor_1_energy
_item.description
; The calculated energy for the H-bond between this residue and the first
acceptor.
;
_item.name '_dssp_struct_bridge_pairs.acceptor_1_energy'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code no
_item_type.code float
save_
save__dssp_struct_bridge_pairs.acceptor_2_label_comp_id
_item.description
; A component of the identifier of the second residue that forms a bridge pair
with this monomer where this monomer is the donor.
;
_item.name '_dssp_struct_bridge_pairs.acceptor_2_label_comp_id'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code no
_item_type.code ucode
save_
save__dssp_struct_bridge_pairs.acceptor_2_label_seq_id
_item.description
; A component of the identifier of the second residue that forms a bridge pair
with this monomer where this monomer is the donor.
;
_item.name '_dssp_struct_bridge_pairs.acceptor_2_label_seq_id'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code no
_item_type.code int
save_
save__dssp_struct_bridge_pairs.acceptor_2_label_asym_id
_item.description
; A component of the identifier of the second residue that forms a bridge pair
with this monomer where this monomer is the donor.
;
_item.name '_dssp_struct_bridge_pairs.acceptor_2_label_asym_id'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code yes
_item_type.code code
save_
save__dssp_struct_bridge_pairs.acceptor_2_auth_seq_id
_item.description
; A component of the identifier of the second residue that forms a bridge pair
with this monomer where this monomer is the donor.
;
_item.name '_dssp_struct_bridge_pairs.acceptor_2_auth_seq_id'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code no
_item_type.code int
save_
save__dssp_struct_bridge_pairs.acceptor_2_auth_asym_id
_item.description
; A component of the identifier of the second residue that forms a bridge pair
with this monomer where this monomer is the donor.
;
_item.name '_dssp_struct_bridge_pairs.acceptor_2_auth_asym_id'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code no
_item_type.code code
save_
save__dssp_struct_bridge_pairs.acceptor_2_pdbx_PDB_ins_code
_item.description
; A component of the identifier of the second residue that forms a bridge pair
with this monomer where this monomer is the donor.
;
_item.name '_dssp_struct_bridge_pairs.acceptor_2_pdbx_PDB_ins_code'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code no
_item_type.code code
save_
save__dssp_struct_bridge_pairs.acceptor_2_energy
_item.description
; The calculated energy for the H-bond between this residue and the second
acceptor.
;
_item.name '_dssp_struct_bridge_pairs.acceptor_2_energy'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code no
_item_type.code float
save_
save__dssp_struct_bridge_pairs.donor_1_label_comp_id
_item.description
; A component of the identifier of the first residue that forms a bridge pair
with this monomer where this monomer is the acceptor.
;
_item.name '_dssp_struct_bridge_pairs.donor_1_label_comp_id'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code no
_item_type.code ucode
save_
save__dssp_struct_bridge_pairs.donor_1_label_seq_id
_item.description
; A component of the identifier of the first residue that forms a bridge pair
with this monomer where this monomer is the acceptor.
;
_item.name '_dssp_struct_bridge_pairs.donor_1_label_seq_id'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code no
_item_type.code int
save_
save__dssp_struct_bridge_pairs.donor_1_label_asym_id
_item.description
; A component of the identifier of the first residue that forms a bridge pair
with this monomer where this monomer is the acceptor.
;
_item.name '_dssp_struct_bridge_pairs.donor_1_label_asym_id'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code yes
_item_type.code code
save_
save__dssp_struct_bridge_pairs.donor_1_auth_seq_id
_item.description
; A component of the identifier of the first residue that forms a bridge pair
with this monomer where this monomer is the acceptor.
;
_item.name '_dssp_struct_bridge_pairs.donor_1_auth_seq_id'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code no
_item_type.code int
save_
save__dssp_struct_bridge_pairs.donor_1_auth_asym_id
_item.description
; A component of the identifier of the first residue that forms a bridge pair
with this monomer where this monomer is the acceptor.
;
_item.name '_dssp_struct_bridge_pairs.donor_1_auth_asym_id'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code no
_item_type.code code
save_
save__dssp_struct_bridge_pairs.donor_1_pdbx_PDB_ins_code
_item.description
; A component of the identifier of the first residue that forms a bridge pair
with this monomer where this monomer is the acceptor.
;
_item.name '_dssp_struct_bridge_pairs.donor_1_pdbx_PDB_ins_code'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code no
_item_type.code code
save_
save__dssp_struct_bridge_pairs.donor_1_energy
_item.description
; The calculated energy for the H-bond between this residue and the first
donor.
;
_item.name '_dssp_struct_bridge_pairs.donor_1_energy'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code no
_item_type.code float
save_
save__dssp_struct_bridge_pairs.donor_2_label_comp_id
_item.description
; A component of the identifier of the second residue that forms a bridge pair
with this monomer where this monomer is the acceptor.
;
_item.name '_dssp_struct_bridge_pairs.donor_2_label_comp_id'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code no
_item_type.code ucode
save_
save__dssp_struct_bridge_pairs.donor_2_label_seq_id
_item.description
; A component of the identifier of the second residue that forms a bridge pair
with this monomer where this monomer is the acceptor.
;
_item.name '_dssp_struct_bridge_pairs.donor_2_label_seq_id'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code no
_item_type.code int
save_
save__dssp_struct_bridge_pairs.donor_2_label_asym_id
_item.description
; A component of the identifier of the second residue that forms a bridge pair
with this monomer where this monomer is the acceptor.
;
_item.name '_dssp_struct_bridge_pairs.donor_2_label_asym_id'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code yes
_item_type.code code
save_
save__dssp_struct_bridge_pairs.donor_2_auth_seq_id
_item.description
; A component of the identifier of the second residue that forms a bridge pair
with this monomer where this monomer is the acceptor.
;
_item.name '_dssp_struct_bridge_pairs.donor_2_auth_seq_id'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code no
_item_type.code int
save_
save__dssp_struct_bridge_pairs.donor_2_auth_asym_id
_item.description
; A component of the identifier of the second residue that forms a bridge pair
with this monomer where this monomer is the acceptor.
;
_item.name '_dssp_struct_bridge_pairs.donor_2_auth_asym_id'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code no
_item_type.code code
save_
save__dssp_struct_bridge_pairs.donor_2_pdbx_PDB_ins_code
_item.description
; A component of the identifier of the second residue that forms a bridge pair
with this monomer where this monomer is the acceptor.
;
_item.name '_dssp_struct_bridge_pairs.donor_2_pdbx_PDB_ins_code'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code no
_item_type.code code
save_
save__dssp_struct_bridge_pairs.donor_2_energy
_item.description
; The calculated energy for the H-bond between this residue and the second
donor.
;
_item.name '_dssp_struct_bridge_pairs.donor_2_energy'
_item.category_id dssp_struct_bridge_pairs
_item.mandatory_code no
_item_type.code float
save_
########################################
## Category dssp_struct_ladder ##
########################################
save_dssp_struct_ladder
#
_category.description 'dssp_struct_ladder describes ladders as assigned by DSSP.'
_category.id dssp_struct_ladder
_category.mandatory_code no
#
_category_key.name '_dssp_struct_ladder.id'
loop_
_category_group.id 'inclusive_group'
'struct_group'
#
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example taken from 1cbs, first ladder
;
;
_dssp_struct_ladder.id A
_dssp_struct_ladder.type anti-parallel
_dssp_struct_ladder.beg_1_label_comp_id GLY
_dssp_struct_ladder.beg_1_label_asym_id A
_dssp_struct_ladder.beg_1_label_seq_id 5
_dssp_struct_ladder.pdbx_beg_1_PDB_ins_code ?
_dssp_struct_ladder.end_1_label_comp_id TRP
_dssp_struct_ladder.end_1_label_asym_id A
_dssp_struct_ladder.end_1_label_seq_id 7
_dssp_struct_ladder.pdbx_end_1_PDB_ins_code ?
_dssp_struct_ladder.beg_1_auth_comp_id GLY
_dssp_struct_ladder.beg_1_auth_asym_id A
_dssp_struct_ladder.beg_1_auth_seq_id 5
_dssp_struct_ladder.end_1_auth_comp_id TRP
_dssp_struct_ladder.end_1_auth_asym_id A
_dssp_struct_ladder.end_1_auth_seq_id 7
_dssp_struct_ladder.beg_2_label_comp_id ILE
_dssp_struct_ladder.beg_2_label_asym_id A
_dssp_struct_ladder.beg_2_label_seq_id 43
_dssp_struct_ladder.pdbx_beg_2_PDB_ins_code ?
_dssp_struct_ladder.end_2_label_comp_id VAL
_dssp_struct_ladder.end_2_label_asym_id A
_dssp_struct_ladder.end_2_label_seq_id 41
_dssp_struct_ladder.pdbx_end_2_PDB_ins_code ?
_dssp_struct_ladder.beg_2_auth_comp_id ILE
_dssp_struct_ladder.beg_2_auth_asym_id A
_dssp_struct_ladder.beg_2_auth_seq_id 43
_dssp_struct_ladder.end_2_auth_comp_id VAL
_dssp_struct_ladder.end_2_auth_asym_id A
_dssp_struct_ladder.end_2_auth_seq_id 41
;
save_
save__dssp_struct_ladder.id
_item.description
; The value of _dssp_struct_ladder.id must uniquely identify a record in the
dssp_struct_ladder list.
;
_item.name '_dssp_struct_ladder.id'
_item.category_id dssp_struct_ladder
_item.mandatory_code yes
_item_type.code code
save_
save__dssp_struct_ladder.type
_item.description
; The type of the ladder, be it parallel or anti-parallel
;
_item.name '_dssp_struct_ladder.type'
_item.category_id dssp_struct_ladder
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
parallel 'The strands forming a ladder are oriented parallel'
anti-parallel 'The strands forming a ladder are oriented anti-parallel'
save_
save__dssp_struct_ladder.beg_1_label_comp_id
_item.description
; A component of the identifier for the residue at which the
first ladder segment begins.
;
_item.name '_dssp_struct_ladder.beg_1_label_comp_id'
_item.category_id dssp_struct_ladder
_item.mandatory_code yes
_item_type.code ucode
save_
save__dssp_struct_ladder.beg_1_label_asym_id
_item.description
; A component of the identifier for the residue at which the
first ladder segment begins.
;
_item.name '_dssp_struct_ladder.beg_1_label_asym_id'
_item.category_id dssp_struct_ladder
_item.mandatory_code yes
_item_type.code code
save_
save__dssp_struct_ladder.beg_1_label_seq_id
_item.description
; A component of the identifier for the residue at which the
first ladder segment begins.
;
_item.name '_dssp_struct_ladder.beg_1_label_seq_id'
_item.category_id dssp_struct_ladder
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_struct_ladder.pdbx_beg_1_PDB_ins_code
_item.description
; A component of the identifier for the residue at which the
first ladder segment begins.
;
_item.name '_dssp_struct_ladder.pdbx_beg_1_PDB_ins_code'
_item.category_id dssp_struct_ladder
_item.mandatory_code no
_item_type.code code
save_
save__dssp_struct_ladder.end_1_label_comp_id
_item.description
; A component of the identifier for the residue at which the
first ladder segment ends.
;
_item.name '_dssp_struct_ladder.end_1_label_comp_id'
_item.category_id dssp_struct_ladder
_item.mandatory_code yes
_item_type.code ucode
save_
save__dssp_struct_ladder.end_1_label_asym_id
_item.description
; A component of the identifier for the residue at which the
first ladder segment ends.
;
_item.name '_dssp_struct_ladder.end_1_label_asym_id'
_item.category_id dssp_struct_ladder
_item.mandatory_code yes
_item_type.code code
save_
save__dssp_struct_ladder.end_1_label_seq_id
_item.description
; A component of the identifier for the residue at which the
first ladder segment ends.
;
_item.name '_dssp_struct_ladder.end_1_label_seq_id'
_item.category_id dssp_struct_ladder
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_struct_ladder.pdbx_end_1_PDB_ins_code
_item.description
; A component of the identifier for the residue at which the
first ladder segment ends.
;
_item.name '_dssp_struct_ladder.pdbx_end_1_PDB_ins_code'
_item.category_id dssp_struct_ladder
_item.mandatory_code no
_item_type.code code
save_
save__dssp_struct_ladder.beg_1_auth_comp_id
_item.description
; A component of the identifier for the residue at which the
first ladder segment begins.
;
_item.name '_dssp_struct_ladder.beg_1_auth_comp_id'
_item.category_id dssp_struct_ladder
_item.mandatory_code no
_item_type.code ucode
save_
save__dssp_struct_ladder.beg_1_auth_asym_id
_item.description
; A component of the identifier for the residue at which the
first ladder segment begins.
;
_item.name '_dssp_struct_ladder.beg_1_auth_asym_id'
_item.category_id dssp_struct_ladder
_item.mandatory_code no
_item_type.code code
save_
save__dssp_struct_ladder.beg_1_auth_seq_id
_item.description
; A component of the identifier for the residue at which the
first ladder segment begins.
;
_item.name '_dssp_struct_ladder.beg_1_auth_seq_id'
_item.category_id dssp_struct_ladder
_item.mandatory_code no
_item_type.code int
save_
save__dssp_struct_ladder.end_1_auth_comp_id
_item.description
; A component of the identifier for the residue at which the
first ladder segment ends.
;
_item.name '_dssp_struct_ladder.end_1_auth_comp_id'
_item.category_id dssp_struct_ladder
_item.mandatory_code no
_item_type.code ucode
save_
save__dssp_struct_ladder.end_1_auth_asym_id
_item.description
; A component of the identifier for the residue at which the
first ladder segment ends.
;
_item.name '_dssp_struct_ladder.end_1_auth_asym_id'
_item.category_id dssp_struct_ladder
_item.mandatory_code no
_item_type.code code
save_
save__dssp_struct_ladder.end_1_auth_seq_id
_item.description
; A component of the identifier for the residue at which the
first ladder segment ends.
;
_item.name '_dssp_struct_ladder.end_1_auth_seq_id'
_item.category_id dssp_struct_ladder
_item.mandatory_code no
_item_type.code int
save_
save__dssp_struct_ladder.beg_2_label_comp_id
_item.description
; A component of the identifier for the residue at which the
second ladder segment begins.
;
_item.name '_dssp_struct_ladder.beg_2_label_comp_id'
_item.category_id dssp_struct_ladder
_item.mandatory_code yes
_item_type.code ucode
save_
save__dssp_struct_ladder.beg_2_label_asym_id
_item.description
; A component of the identifier for the residue at which the
second ladder segment begins.
;
_item.name '_dssp_struct_ladder.beg_2_label_asym_id'
_item.category_id dssp_struct_ladder
_item.mandatory_code yes
_item_type.code code
save_
save__dssp_struct_ladder.beg_2_label_seq_id
_item.description
; A component of the identifier for the residue at which the
second ladder segment begins.
;
_item.name '_dssp_struct_ladder.beg_2_label_seq_id'
_item.category_id dssp_struct_ladder
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_struct_ladder.pdbx_beg_2_PDB_ins_code
_item.description
; A component of the identifier for the residue at which the
second ladder segment begins.
;
_item.name '_dssp_struct_ladder.pdbx_beg_2_PDB_ins_code'
_item.category_id dssp_struct_ladder
_item.mandatory_code no
_item_type.code code
save_
save__dssp_struct_ladder.end_2_label_comp_id
_item.description
; A component of the identifier for the residue at which the
second ladder segment ends.
;
_item.name '_dssp_struct_ladder.end_2_label_comp_id'
_item.category_id dssp_struct_ladder
_item.mandatory_code yes
_item_type.code ucode
save_
save__dssp_struct_ladder.end_2_label_asym_id
_item.description
; A component of the identifier for the residue at which the
second ladder segment ends.
;
_item.name '_dssp_struct_ladder.end_2_label_asym_id'
_item.category_id dssp_struct_ladder
_item.mandatory_code yes
_item_type.code code
save_
save__dssp_struct_ladder.end_2_label_seq_id
_item.description
; A component of the identifier for the residue at which the
second ladder segment ends.
;
_item.name '_dssp_struct_ladder.end_2_label_seq_id'
_item.category_id dssp_struct_ladder
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_struct_ladder.pdbx_end_2_PDB_ins_code
_item.description
; A component of the identifier for the residue at which the
second ladder segment ends.
;
_item.name '_dssp_struct_ladder.pdbx_end_2_PDB_ins_code'
_item.category_id dssp_struct_ladder
_item.mandatory_code no
_item_type.code code
save_
save__dssp_struct_ladder.beg_2_auth_comp_id
_item.description
; A component of the identifier for the residue at which the
second ladder segment begins.
;
_item.name '_dssp_struct_ladder.beg_2_auth_comp_id'
_item.category_id dssp_struct_ladder
_item.mandatory_code no
_item_type.code ucode
save_
save__dssp_struct_ladder.beg_2_auth_asym_id
_item.description
; A component of the identifier for the residue at which the
second ladder segment begins.
;
_item.name '_dssp_struct_ladder.beg_2_auth_asym_id'
_item.category_id dssp_struct_ladder
_item.mandatory_code no
_item_type.code code
save_
save__dssp_struct_ladder.beg_2_auth_seq_id
_item.description
; A component of the identifier for the residue at which the
second ladder segment begins.
;
_item.name '_dssp_struct_ladder.beg_2_auth_seq_id'
_item.category_id dssp_struct_ladder
_item.mandatory_code no
_item_type.code int
save_
save__dssp_struct_ladder.end_2_auth_comp_id
_item.description
; A component of the identifier for the residue at which the
second ladder segment ends.
;
_item.name '_dssp_struct_ladder.end_2_auth_comp_id'
_item.category_id dssp_struct_ladder
_item.mandatory_code no
_item_type.code ucode
save_
save__dssp_struct_ladder.end_2_auth_asym_id
_item.description
; A component of the identifier for the residue at which the
second ladder segment ends.
;
_item.name '_dssp_struct_ladder.end_2_auth_asym_id'
_item.category_id dssp_struct_ladder
_item.mandatory_code no
_item_type.code code
save_
save__dssp_struct_ladder.end_2_auth_seq_id
_item.description
; A component of the identifier for the residue at which the
second ladder segment ends.
;
_item.name '_dssp_struct_ladder.end_2_auth_seq_id'
_item.category_id dssp_struct_ladder
_item.mandatory_code no
_item_type.code int
save_
########################################
## Category dssp_statistics ##
########################################
save_dssp_statistics
#
_category.description 'dssp_statistics contains secondary structure statistics as calculated by DSSP.'
_category.id dssp_statistics
_category.mandatory_code no
#
_category_key.name '_dssp_statistics.entry_id'
loop_
_category_group.id 'inclusive_group'
'struct_group'
#
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example taken from 1cbs
;
;
_dssp_statistics.entry_id 1CBS
_dssp_statistics.nr_of_residues 137
_dssp_statistics.nr_of_chains 1
_dssp_statistics.nr_of_ss_bridges_total 0
_dssp_statistics.nr_of_ss_bridges_intra_chain 0
_dssp_statistics.nr_of_ss_bridges_inter_chain 0
_dssp_statistics.accessible_surface_of_protein 7905.01
;
save_
save__dssp_statistics.entry_id
_item.description
; The entry ID for which these statistics are calculated.
;
_item.name '_dssp_statistics.entry_id'
_item.category_id dssp_statistics
_item.mandatory_code yes
_item_type.code code
save_
save__dssp_statistics.nr_of_residues
_item.description
; The total number of residues to which secondary structure information was assigned.
;
_item.name '_dssp_statistics.nr_of_residues'
_item.category_id dssp_statistics
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics.nr_of_chains
_item.description
; The number of chains used
;
_item.name '_dssp_statistics.nr_of_chains'
_item.category_id dssp_statistics
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics.nr_of_ss_bridges_total
_item.description
; The number of sulfur-sulfur bridges assigned.
;
_item.name '_dssp_statistics.nr_of_ss_bridges_total'
_item.category_id dssp_statistics
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics.nr_of_ss_bridges_intra_chain
_item.description
; The number of intra-chain sulfur-sulfur bridges assigned.
;
_item.name '_dssp_statistics.nr_of_ss_bridges_intra_chain'
_item.category_id dssp_statistics
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics.nr_of_ss_bridges_inter_chain
_item.description
; The number of inter-chain sulfur-sulfur bridges assigned.
;
_item.name '_dssp_statistics.nr_of_ss_bridges_inter_chain'
_item.category_id dssp_statistics
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics.accessible_surface_of_protein
_item.description
; The total accessible surface of the protein in square Angstroms.
;
_item.name '_dssp_statistics.accessible_surface_of_protein'
_item.category_id dssp_statistics
_item.mandatory_code yes
_item_type.code float
save_
########################################
## Category dssp_statistics_hbond ##
########################################
save_dssp_statistics_hbond
#
_category.description 'dssp_statistics_hbond contains statistics for the collection of h-bond variants calculated by DSSP.'
_category.id dssp_statistics_hbond
_category.mandatory_code no
#
loop_
_category_key.name '_dssp_statistics_hbond.entry_id'
'_dssp_statistics_hbond.type'
loop_
_category_group.id 'inclusive_group'
'struct_group'
#
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example taken from 1cbs
;
;
_dssp_statistics_hbond.entry_id 1CBS
_dssp_statistics_hbond.type O(I)-->H-N(J)
_dssp_statistics_hbond.count 94
_dssp_statistics_hbond.count_per_100 68.6
;
save_
save__dssp_statistics_hbond.entry_id
_item.description
; The entry ID for which these statistics are calculated.
;
_item.name '_dssp_statistics_hbond.entry_id'
_item.category dssp_statistics_hbond
_item.mandatory_code yes
_item_type.code code
save_
save__dssp_statistics_hbond.type
_item.description
; The type of the h-bond
;
_item.name '_dssp_statistics_hbond.type'
_item.category dssp_statistics_hbond
_item.mandatory_code yes
_item_type.code text
loop_
_item_enumeration.value
_item_enumeration.detail
O(I)-->H-N(J) 'non-bridge h-bond with residue further away than 5 residues'
'PARALLEL BRIDGES' 'h-bond forming a parallel bridge'
'ANTIPARALLEL BRIDGES' 'h-bond forming a anti-parallel bridge'
O(I)-->H-N(I-5) 'h-bond with residue five residues before the current one'
O(I)-->H-N(I-4) 'h-bond with residue four residues before the current one'
O(I)-->H-N(I-3) 'h-bond with residue three residues before the current one'
O(I)-->H-N(I-2) 'h-bond with residue two residues before the current one'
O(I)-->H-N(I-1) 'h-bond with residue one residue before the current one'
O(I)-->H-N(I+0) 'h-bond with current residue itself'
O(I)-->H-N(I+1) 'h-bond with residue one residues after the current one'
O(I)-->H-N(I+2) 'h-bond with residue two residues after the current one'
O(I)-->H-N(I+3) 'h-bond with residue three residues after the current one'
O(I)-->H-N(I+4) 'h-bond with residue four residues after the current one'
O(I)-->H-N(I+5) 'h-bond with residue five residues after the current one'
save_
save__dssp_statistics_hbond.count
_item.description
; Absolute number of h-bonds of this type
;
_item.name '_dssp_statistics_hbond.count'
_item.category dssp_statistics_hbond
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics_hbond.count_per_100
_item.description
; Number of h-bonds of this type per hundred residues in the entire structure
;
_item.name '_dssp_statistics_hbond.count_per_100'
_item.category dssp_statistics_hbond
_item.mandatory_code yes
_item_type.code float
save_
########################################
## Category dssp_statistics_histogram ##
########################################
save_dssp_statistics_histogram
#
_category.description 'dssp_statistics_histogram contains the statistics for the ladders and helices in the form of a histogram as calculated by DSSP.'
_category.id dssp_statistics_histogram
_category.mandatory_code no
#
loop_
_category_key.name '_dssp_statistics_histogram.entry_id'
'_dssp_statistics_histogram.type'
loop_
_category_group.id 'inclusive_group'
'struct_group'
#
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example taken from 1cbs
;
;
_dssp_statistics_histogram.entry_id 1CBS
_dssp_statistics_histogram.type antiparallel_bridges_per_ladder
_dssp_statistics_histogram.1 0
_dssp_statistics_histogram.2 0
_dssp_statistics_histogram.3 1
_dssp_statistics_histogram.4 1
_dssp_statistics_histogram.5 1
_dssp_statistics_histogram.6 1
_dssp_statistics_histogram.7 4
_dssp_statistics_histogram.8 1
_dssp_statistics_histogram.9 0
_dssp_statistics_histogram.10 0
_dssp_statistics_histogram.11 0
_dssp_statistics_histogram.12 0
_dssp_statistics_histogram.13 0
_dssp_statistics_histogram.14 0
_dssp_statistics_histogram.15 0
_dssp_statistics_histogram.16 0
_dssp_statistics_histogram.17 0
_dssp_statistics_histogram.18 0
_dssp_statistics_histogram.19 0
_dssp_statistics_histogram.20 0
_dssp_statistics_histogram.21 0
_dssp_statistics_histogram.22 0
_dssp_statistics_histogram.23 0
_dssp_statistics_histogram.24 0
_dssp_statistics_histogram.25 0
_dssp_statistics_histogram.26 0
_dssp_statistics_histogram.27 0
_dssp_statistics_histogram.28 0
_dssp_statistics_histogram.29 0
_dssp_statistics_histogram.30 0
;
save_
save__dssp_statistics_histogram.entry_id
_item.description
; The entry ID for which these statistics are calculated.
;
_item.name '_dssp_statistics_histogram.entry_id'
_item.category dssp_statistics_histogram
_item.mandatory_code yes
_item_type.code code
save_
save__dssp_statistics_histogram.type
_item.description
; The type for which this histogram contains data
;
_item.name '_dssp_statistics_histogram.type'
_item.category dssp_statistics_histogram
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
residues_per_alpha_helix 'residues per alpha helix'
parallel_bridges_per_ladder 'parallel bridges per ladder'
antiparallel_bridges_per_ladder 'antiparallel bridges per ladder'
ladders_per_sheet 'ladders per sheet'
save_
save__dssp_statistics_histogram.1
_item.description
; The count of this type of ladder with a length of 1 residues
;
_item.name '_dssp_statistics_histogram.1'
_item.category dssp_statistics_histogram
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics_histogram.2
_item.description
; The count of this type of ladder with a length of 2 residues
;
_item.name '_dssp_statistics_histogram.2'
_item.category dssp_statistics_histogram
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics_histogram.3
_item.description
; The count of this type of ladder with a length of 3 residues
;
_item.name '_dssp_statistics_histogram.3'
_item.category dssp_statistics_histogram
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics_histogram.4
_item.description
; The count of this type of ladder with a length of 4 residues
;
_item.name '_dssp_statistics_histogram.4'
_item.category dssp_statistics_histogram
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics_histogram.5
_item.description
; The count of this type of ladder with a length of 5 residues
;
_item.name '_dssp_statistics_histogram.5'
_item.category dssp_statistics_histogram
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics_histogram.6
_item.description
; The count of this type of ladder with a length of 6 residues
;
_item.name '_dssp_statistics_histogram.6'
_item.category dssp_statistics_histogram
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics_histogram.7
_item.description
; The count of this type of ladder with a length of 7 residues
;
_item.name '_dssp_statistics_histogram.7'
_item.category dssp_statistics_histogram
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics_histogram.8
_item.description
; The count of this type of ladder with a length of 8 residues
;
_item.name '_dssp_statistics_histogram.8'
_item.category dssp_statistics_histogram
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics_histogram.9
_item.description
; The count of this type of ladder with a length of 9 residues
;
_item.name '_dssp_statistics_histogram.9'
_item.category dssp_statistics_histogram
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics_histogram.10
_item.description
; The count of this type of ladder with a length of 10 residues
;
_item.name '_dssp_statistics_histogram.10'
_item.category dssp_statistics_histogram
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics_histogram.11
_item.description
; The count of this type of ladder with a length of 11 residues
;
_item.name '_dssp_statistics_histogram.11'
_item.category dssp_statistics_histogram
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics_histogram.12
_item.description
; The count of this type of ladder with a length of 12 residues
;
_item.name '_dssp_statistics_histogram.12'
_item.category dssp_statistics_histogram
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics_histogram.13
_item.description
; The count of this type of ladder with a length of 13 residues
;
_item.name '_dssp_statistics_histogram.13'
_item.category dssp_statistics_histogram
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics_histogram.14
_item.description
; The count of this type of ladder with a length of 14 residues
;
_item.name '_dssp_statistics_histogram.14'
_item.category dssp_statistics_histogram
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics_histogram.15
_item.description
; The count of this type of ladder with a length of 15 residues
;
_item.name '_dssp_statistics_histogram.15'
_item.category dssp_statistics_histogram
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics_histogram.16
_item.description
; The count of this type of ladder with a length of 16 residues
;
_item.name '_dssp_statistics_histogram.16'
_item.category dssp_statistics_histogram
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics_histogram.17
_item.description
; The count of this type of ladder with a length of 17 residues
;
_item.name '_dssp_statistics_histogram.17'
_item.category dssp_statistics_histogram
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics_histogram.18
_item.description
; The count of this type of ladder with a length of 18 residues
;
_item.name '_dssp_statistics_histogram.18'
_item.category dssp_statistics_histogram
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics_histogram.19
_item.description
; The count of this type of ladder with a length of 19 residues
;
_item.name '_dssp_statistics_histogram.19'
_item.category dssp_statistics_histogram
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics_histogram.20
_item.description
; The count of this type of ladder with a length of 20 residues
;
_item.name '_dssp_statistics_histogram.20'
_item.category dssp_statistics_histogram
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics_histogram.21
_item.description
; The count of this type of ladder with a length of 21 residues
;
_item.name '_dssp_statistics_histogram.21'
_item.category dssp_statistics_histogram
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics_histogram.22
_item.description
; The count of this type of ladder with a length of 22 residues
;
_item.name '_dssp_statistics_histogram.22'
_item.category dssp_statistics_histogram
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics_histogram.23
_item.description
; The count of this type of ladder with a length of 23 residues
;
_item.name '_dssp_statistics_histogram.23'
_item.category dssp_statistics_histogram
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics_histogram.24
_item.description
; The count of this type of ladder with a length of 24 residues
;
_item.name '_dssp_statistics_histogram.24'
_item.category dssp_statistics_histogram
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics_histogram.25
_item.description
; The count of this type of ladder with a length of 25 residues
;
_item.name '_dssp_statistics_histogram.25'
_item.category dssp_statistics_histogram
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics_histogram.26
_item.description
; The count of this type of ladder with a length of 26 residues
;
_item.name '_dssp_statistics_histogram.26'
_item.category dssp_statistics_histogram
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics_histogram.27
_item.description
; The count of this type of ladder with a length of 27 residues
;
_item.name '_dssp_statistics_histogram.27'
_item.category dssp_statistics_histogram
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics_histogram.28
_item.description
; The count of this type of ladder with a length of 28 residues
;
_item.name '_dssp_statistics_histogram.28'
_item.category dssp_statistics_histogram
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics_histogram.29
_item.description
; The count of this type of ladder with a length of 29 residues
;
_item.name '_dssp_statistics_histogram.29'
_item.category dssp_statistics_histogram
_item.mandatory_code yes
_item_type.code int
save_
save__dssp_statistics_histogram.30
_item.description
; The count of this type of ladder with a length of 30 or more residues
;
_item.name '_dssp_statistics_histogram.30'
_item.category dssp_statistics_histogram
_item.mandatory_code yes
_item_type.code int
save_
########################################
## Category dssp_struct_summary ##
########################################
save_dssp_struct_summary
#
_category.description 'dssp_struct_summary contains the extra secondary structure information per residue as calculated by DSSP.'
_category.id dssp_struct_summary
_category.mandatory_code no
#
loop_
_category_key.name '_dssp_struct_summary.entry_id'
'_dssp_struct_summary.label_asym_id'
'_dssp_struct_summary.label_seq_id'
'_dssp_struct_summary.label_comp_id'
loop_
_category_group.id 'inclusive_group'
'struct_group'
#
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example taken from 1cbs
;
;
_dssp_struct_summary.entry_id 1CBS
_dssp_struct_summary.label_comp_id PHE
_dssp_struct_summary.label_asym_id A
_dssp_struct_summary.label_seq_id 15
_dssp_struct_summary.secondary_structure H
_dssp_struct_summary.ss_bridge .
_dssp_struct_summary.helix_3_10 .
_dssp_struct_summary.helix_alpha >
_dssp_struct_summary.helix_pi .
_dssp_struct_summary.helix_pp .
_dssp_struct_summary.bend S
_dssp_struct_summary.chirality +
_dssp_struct_summary.ladder_1 .
_dssp_struct_summary.ladder_2 .
_dssp_struct_summary.sheet .
_dssp_struct_summary.accessibility 23.1
_dssp_struct_summary.TCO 0.940
_dssp_struct_summary.kappa 73.9
_dssp_struct_summary.alpha 44.8
_dssp_struct_summary.phi -66.9
_dssp_struct_summary.psi -48.6
_dssp_struct_summary.x_ca 22.4
_dssp_struct_summary.y_ca 17.2
_dssp_struct_summary.z_ca 17.7
;
save_
save__dssp_struct_summary.entry_id
_item.description
; The entry ID for which these statistics are calculated.
;
_item.name '_dssp_struct_summary.entry_id'
_item.category dssp_struct_summary
_item.mandatory_code yes
_item_type.code code
save_
save__dssp_struct_summary.label_comp_id
_item.description
; A component of the identifier for this monomer.
This data item is a pointer to _chem_comp.id in the CHEM_COMP
category.
;
_item.name '_dssp_struct_summary.label_comp_id'
_item.category dssp_struct_summary
_item.mandatory_code yes
_item_type.code ucode
save_
save__dssp_struct_summary.label_asym_id
_item.description
; A component of the identifier for this monomer
;
_item.name '_dssp_struct_summary.label_asym_id'
_item.category dssp_struct_summary
_item.mandatory_code yes
_item_type.code code
save_
save__dssp_struct_summary.label_seq_id
_item.description
; A component of the identifier for this monomer
;
_item.name '_dssp_struct_summary.label_seq_id'
_item.category dssp_struct_summary
_item.mandatory_code yes
_item_type.code code
save_
save__dssp_struct_summary.secondary_structure
_item.description
; The secondary structure assigned to this residue in a single letter code
The value for this field may be empty in which case the assigned
secondary structure is Loop.
;
_item.name '_dssp_struct_summary.secondary_structure'
_item.category dssp_struct_summary
_item.mandatory_code no
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
H Alphahelix
B Betabridge
E Strand
G Helix_3
I Helix_5
P Helix_PPII
T Turn
S Bend
save_
save__dssp_struct_summary.ss_bridge
_item.description
; Identifier for the SS-Bridge formed by this residue
;
_item.name '_dssp_struct_summary.ss_bridge'
_item.category dssp_struct_summary
_item.mandatory_code no
_item_type.code int
save_
save__dssp_struct_summary.helix_3_10
_item.description
; In case this residue is a candidate to form a 3_10 helix, this
field contains the position of the residue in the helix.
;
_item.name '_dssp_struct_summary.helix_3_10'
_item.category dssp_struct_summary
_item.mandatory_code no
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'>' 'The residue has h-bond(s) is a candidate to start a 3_10 helix'
'3' 'The residue has h-bond(s) is a candidate to be within a 3_10 helix'
'<' 'The residue has h-bond(s) is a candidate to end a 3_10 helix'
'X' 'The residue has h-bond(s) is a candidate for both a start and an end of a 3_10 helix'
save_
save__dssp_struct_summary.helix_alpha
_item.description
; In case this residue is a candidate to form a alpha helix, this
field contains the position of the residue in the helix.
;
_item.name '_dssp_struct_summary.helix_alpha'
_item.category dssp_struct_summary
_item.mandatory_code no
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'>' 'The residue has h-bond(s) is a candidate to start a alpha helix'
'4' 'The residue has h-bond(s) is a candidate to be within a alpha helix'
'<' 'The residue has h-bond(s) is a candidate to end a alpha helix'
'X' 'The residue has h-bond(s) is a candidate for both a start and an end of a alpha helix'
save_
save__dssp_struct_summary.helix_pi
_item.description
; In case this residue is a candidate to form a pi helix, this
field contains the position of the residue in the helix.
;
_item.name '_dssp_struct_summary.helix_pi'
_item.category dssp_struct_summary
_item.mandatory_code no
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'>' 'The residue has h-bond(s) is a candidate to start a pi helix'
'5' 'The residue has h-bond(s) is a candidate to be within a pi helix'
'<' 'The residue has h-bond(s) is a candidate to end a pi helix'
'X' 'The residue has h-bond(s) is a candidate for both a start and an end of a pi helix'
save_
save__dssp_struct_summary.helix_pp
_item.description
; In case this residue is a candidate to form a poly-proline helix, this
field contains the position of the residue in the helix.
;
_item.name '_dssp_struct_summary.helix_pp'
_item.category dssp_struct_summary
_item.mandatory_code no
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'>' 'The residue has h-bond(s) is a candidate to start a poly-proline helix'
'P' 'The residue has h-bond(s) is a candidate to be within a poly-proline helix'
'<' 'The residue has h-bond(s) is a candidate to end a poly-proline helix'
'X' 'The residue has h-bond(s) is a candidate for both a start and an end of a poly-proline helix'
save_
save__dssp_struct_summary.bend
_item.description
; If this field contains S this indicates that the assigned secondary structure Turn actually forms a Bend.
;
_item.name '_dssp_struct_summary.bend'
_item.category dssp_struct_summary
_item.mandatory_code no
_item_type.code code
_item_enumeration.value S
_item_enumeration.detail 'The residue forms a Bend'
save_
save__dssp_struct_summary.chirality
_item.description
; The chirality for the virtual torsion angle (dihedral angle) defined by the four C-alpha atoms of residues I-1, I, I+1 and I+2.
;
_item.name '_dssp_struct_summary.chirality'
_item.category dssp_struct_summary
_item.mandatory_code no
_item_type.code code
loop_
_item_enumeration.value '+'
'-'
save_
save__dssp_struct_summary.ladder_1
_item.description
; Label for the first beta bridge of which this residue is part.
;
_item.name '_dssp_struct_summary.ladder_1'
_item.category dssp_struct_summary
_item.mandatory_code no
_item_type.code code
save_
save__dssp_struct_summary.ladder_2
_item.description
; Label for the second beta bridge of which this residue is part.
;
_item.name '_dssp_struct_summary.ladder_2'
_item.category dssp_struct_summary
_item.mandatory_code no
_item_type.code code
save_
save__dssp_struct_summary.sheet
_item.description
; Label for the sheet of which this residue is part.
;
_item.name '_dssp_struct_summary.sheet'
_item.category dssp_struct_summary
_item.mandatory_code no
_item_type.code code
save_
save__dssp_struct_summary.accessibility
_item.description
; Solvent accessibility for this residue in square Angstroms
;
_item.name '_dssp_struct_summary.accessibility'
_item.category dssp_struct_summary
_item.mandatory_code no
_item_type.code float
save_
save__dssp_struct_summary.TCO
_item.description
; The cosine of the 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.
Not used for structure definition.
;
_item.name '_dssp_struct_summary.TCO'
_item.category dssp_struct_summary
_item.mandatory_code no
_item_type.code float
save_
save__dssp_struct_summary.kappa
_item.description
; The virtual bond angle (bend angle) defined by the three C-alpha atoms of residues I-2, I and I+2.
Used to define bend (structure code 'S').
;
_item.name '_dssp_struct_summary.kappa'
_item.category dssp_struct_summary
_item.mandatory_code no
_item_type.code float
save_
save__dssp_struct_summary.alpha
_item.description
; The 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 '+' or '-').
;
_item.name '_dssp_struct_summary.alpha'
_item.category dssp_struct_summary
_item.mandatory_code no
_item_type.code float
save_
save__dssp_struct_summary.phi
_item.description
; IUPAC peptide backbone torsion phi angle
;
_item.name '_dssp_struct_summary.phi'
_item.category dssp_struct_summary
_item.mandatory_code no
_item_type.code float
save_
save__dssp_struct_summary.psi
_item.description
; IUPAC peptide backbone torsion psi angle
;
_item.name '_dssp_struct_summary.psi'
_item.category dssp_struct_summary
_item.mandatory_code no
_item_type.code float
save_
save__dssp_struct_summary.x_ca
_item.description
; The x coordinate of the C-alpha atom for this residue
;
_item.name '_dssp_struct_summary.x_ca'
_item.category dssp_struct_summary
_item.mandatory_code no
_item_type.code float
save_
save__dssp_struct_summary.y_ca
_item.description
; The y coordinate of the C-alpha atom for this residue
;
_item.name '_dssp_struct_summary.y_ca'
_item.category dssp_struct_summary
_item.mandatory_code no
_item_type.code float
save_
save__dssp_struct_summary.z_ca
_item.description
; The z coordinate of the C-alpha atom for this residue
;
_item.name '_dssp_struct_summary.z_ca'
_item.category dssp_struct_summary
_item.mandatory_code no
_item_type.code float
save_
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-io.cpp
...@@ -91,7 +91,7 @@ std::string ResidueToDSSPLine(const dssp::residue_info &info) ...@@ -91,7 +91,7 @@ std::string ResidueToDSSPLine(const dssp::residue_info &info)
if (info.bend()) if (info.bend())
bend = 'S'; bend = 'S';
double alpha = residue.alpha(); double alpha = residue.alpha().value_or(360);
char chirality = alpha == 360 ? ' ' : (alpha < 0 ? '-' : '+'); char chirality = alpha == 360 ? ' ' : (alpha < 0 ? '-' : '+');
uint32_t bp[2] = {}; uint32_t bp[2] = {};
...@@ -139,7 +139,11 @@ std::string ResidueToDSSPLine(const dssp::residue_info &info) ...@@ -139,7 +139,11 @@ std::string ResidueToDSSPLine(const dssp::residue_info &info)
ss, helix[3], helix[0], helix[1], helix[2], bend, chirality, bridgelabel[0], bridgelabel[1], ss, helix[3], helix[0], helix[1], helix[2], bend, chirality, bridgelabel[0], bridgelabel[1],
bp[0], bp[1], sheet, floor(info.accessibility() + 0.5), bp[0], bp[1], sheet, floor(info.accessibility() + 0.5),
NHO[0], ONH[0], NHO[1], ONH[1], NHO[0], ONH[0], NHO[1], ONH[1],
residue.tco(), residue.kappa(), alpha, residue.phi(), residue.psi(), residue.tco().value_or(0),
residue.kappa().value_or(360),
residue.alpha().value_or(360),
residue.phi().value_or(360),
residue.psi().value_or(360),
cax, cay, caz) cax, cay, caz)
.str(); .str();
} }
...@@ -153,7 +157,7 @@ void writeDSSP(const dssp &dssp, std::ostream &os) ...@@ -153,7 +157,7 @@ void writeDSSP(const dssp &dssp, std::ostream &os)
std::time_t today = system_clock::to_time_t(system_clock::now()); std::time_t today = system_clock::to_time_t(system_clock::now());
std::tm *tm = std::gmtime(&today); std::tm *tm = std::gmtime(&today);
os << "==== Secondary Structure Definition by the program DSSP, NKI version 4.0 ==== DATE=" << std::put_time(tm, "%F") << " ." << std::endl os << "==== Secondary Structure Definition by the program DSSP, NKI version 4.3 ==== DATE=" << std::put_time(tm, "%F") << " ." << std::endl
<< "REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637 ." << std::endl << "REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637 ." << std::endl
<< dssp.get_pdb_header_line(dssp::pdb_record_type::HEADER) << '.' << std::endl << dssp.get_pdb_header_line(dssp::pdb_record_type::HEADER) << '.' << std::endl
<< dssp.get_pdb_header_line(dssp::pdb_record_type::COMPND) << '.' << std::endl << dssp.get_pdb_header_line(dssp::pdb_record_type::COMPND) << '.' << std::endl
...@@ -882,7 +886,7 @@ void writeStatistics(cif::datablock &db, const dssp &dssp) ...@@ -882,7 +886,7 @@ void writeStatistics(cif::datablock &db, const dssp &dssp)
using histogram_data_type = std::tuple<const char *, const uint32_t *>; using histogram_data_type = std::tuple<const char *, const uint32_t *>;
for (const auto &[type, values] : std::vector<histogram_data_type>{ for (const auto &[type, values] : std::vector<histogram_data_type>{
{ "parallel_bridges_per_ladder", stats.histogram.residues_per_alpha_helix }, { "residues_per_alpha_helix", stats.histogram.residues_per_alpha_helix },
{ "parallel_bridges_per_ladder", stats.histogram.parallel_bridges_per_ladder }, { "parallel_bridges_per_ladder", stats.histogram.parallel_bridges_per_ladder },
{ "antiparallel_bridges_per_ladder", stats.histogram.antiparallel_bridges_per_ladder }, { "antiparallel_bridges_per_ladder", stats.histogram.antiparallel_bridges_per_ladder },
{ "ladders_per_sheet", stats.histogram.ladders_per_sheet } }) { "ladders_per_sheet", stats.histogram.ladders_per_sheet } })
...@@ -930,6 +934,11 @@ void writeSummary(cif::datablock &db, const dssp &dssp) ...@@ -930,6 +934,11 @@ void writeSummary(cif::datablock &db, const dssp &dssp)
auto &dssp_struct_summary = db["dssp_struct_summary"]; auto &dssp_struct_summary = db["dssp_struct_summary"];
// prime the category with the field labels we need, this is to ensure proper order in writing out the data.
for (auto label : { "entry_id", "label_comp_id", "label_asym_id", "label_seq_id", "secondary_structure", "ss_bridge", "helix_3_10", "helix_alpha", "helix_pi", "helix_pp", "bend", "chirality", "ladder_1", "ladder_2", "sheet", "accessibility", "TCO", "kappa", "alpha", "phi", "psi", "x_ca", "y_ca", "z_ca"})
dssp_struct_summary.add_column(label);
for (auto res : dssp) for (auto res : dssp)
{ {
...@@ -979,10 +988,9 @@ void writeSummary(cif::datablock &db, const dssp &dssp) ...@@ -979,10 +988,9 @@ void writeSummary(cif::datablock &db, const dssp &dssp)
if (res.bend()) if (res.bend())
bend = "S"; bend = "S";
double alpha = res.alpha();
std::string chirality = "."; std::string chirality = ".";
if (alpha != 360) if (res.alpha().has_value())
chirality = alpha < 0 ? "-" : "+"; chirality = *res.alpha() < 0 ? "-" : "+";
std::string ladders[2] = { ".", "." }; std::string ladders[2] = { ".", "." };
...@@ -997,7 +1005,7 @@ void writeSummary(cif::datablock &db, const dssp &dssp) ...@@ -997,7 +1005,7 @@ void writeSummary(cif::datablock &db, const dssp &dssp)
auto const &[cax, cay, caz] = res.ca_location(); auto const &[cax, cay, caz] = res.ca_location();
dssp_struct_summary.emplace({ cif::row_initializer data{
{ "entry_id", db.name() }, { "entry_id", db.name() },
{ "label_comp_id", res.compound_id() }, { "label_comp_id", res.compound_id() },
{ "label_asym_id", res.asym_id() }, { "label_asym_id", res.asym_id() },
...@@ -1020,18 +1028,39 @@ void writeSummary(cif::datablock &db, const dssp &dssp) ...@@ -1020,18 +1028,39 @@ void writeSummary(cif::datablock &db, const dssp &dssp)
{ "sheet", res.sheet() ? cif::cif_id_for_number(res.sheet() - 1) : "." }, { "sheet", res.sheet() ? cif::cif_id_for_number(res.sheet() - 1) : "." },
{ "accesssibility", res.accessibility(), 1 }, { "accessibility", res.accessibility(), 1 },
{ "TCO", res.tco(), 3 },
{ "kappa", res.kappa(), 1 },
{ "alpha", res.alpha(), 1 },
{ "phi", res.phi(), 1 },
{ "psi", res.psi(), 1 },
{ "x_ca", cax, 1 }, { "x_ca", cax, 1 },
{ "y_ca", cay, 1 }, { "y_ca", cay, 1 },
{ "z_ca", caz, 1 }, { "z_ca", caz, 1 },
}); };
if (res.tco().has_value())
data.emplace_back("TCO", *res.tco(), 3);
else
data.emplace_back("TCO", ".");
if (res.kappa().has_value())
data.emplace_back("kappa", *res.kappa(), 1);
else
data.emplace_back("kappa", ".");
if (res.alpha().has_value())
data.emplace_back("alpha", *res.alpha(), 1);
else
data.emplace_back("alpha", ".");
if (res.phi().has_value())
data.emplace_back("phi", *res.phi(), 1);
else
data.emplace_back("phi", ".");
if (res.psi().has_value())
data.emplace_back("psi", *res.psi(), 1);
else
data.emplace_back("psi", ".");
dssp_struct_summary.emplace(std::move(data));
} }
} }
......
src/dssp-io.hpp
...@@ -31,3 +31,6 @@ ...@@ -31,3 +31,6 @@
void writeDSSP(const dssp& dssp, std::ostream& os); void writeDSSP(const dssp& dssp, 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, 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);
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 <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");
}
};
// --------------------------------------------------------------------
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
...@@ -531,7 +531,8 @@ struct dssp::residue ...@@ -531,7 +531,8 @@ struct dssp::residue
float mAccessibility = 0; float mAccessibility = 0;
float mChiralVolume = 0; float mChiralVolume = 0;
float mAlpha = 360, mKappa = 360, mPhi = 360, mPsi = 360, mTCO = 0, mOmega = 360; // float mAlpha = 360, mKappa = 360, mPhi = 360, mPsi = 360, mTCO = 0, mOmega = 360;
std::optional<float> mAlpha, mKappa, mPhi, mPsi, mTCO, mOmega;
residue_type mType; residue_type mType;
uint8_t mSSBridgeNr = 0; uint8_t mSSBridgeNr = 0;
...@@ -1114,8 +1115,8 @@ void CalculateAlphaHelices(std::vector<residue> &inResidues, statistics &stats, ...@@ -1114,8 +1115,8 @@ void CalculateAlphaHelices(std::vector<residue> &inResidues, statistics &stats,
for (auto &r : inResidues) for (auto &r : inResidues)
{ {
double kappa = r.mKappa; if (r.mKappa.has_value())
r.SetBend(kappa != 360 and kappa > 70); r.SetBend(*r.mKappa > 70);
} }
for (uint32_t i = 1; i + 4 < inResidues.size(); ++i) for (uint32_t i = 1; i + 4 < inResidues.size(); ++i)
...@@ -1216,8 +1217,8 @@ void CalculatePPHelices(std::vector<residue> &inResidues, statistics &stats, int ...@@ -1216,8 +1217,8 @@ void CalculatePPHelices(std::vector<residue> &inResidues, statistics &stats, int
for (uint32_t i = 1; i + 1 < inResidues.size(); ++i) for (uint32_t i = 1; i + 1 < inResidues.size(); ++i)
{ {
phi[i] = static_cast<float>(inResidues[i].mPhi); phi[i] = static_cast<float>(inResidues[i].mPhi.value_or(360));
psi[i] = static_cast<float>(inResidues[i].mPsi); psi[i] = static_cast<float>(inResidues[i].mPsi.value_or(360));
} }
for (uint32_t i = 1; i + 3 < inResidues.size(); ++i) for (uint32_t i = 1; i + 3 < inResidues.size(); ++i)
...@@ -1888,32 +1889,32 @@ std::string dssp::residue_info::pdb_ins_code() const ...@@ -1888,32 +1889,32 @@ std::string dssp::residue_info::pdb_ins_code() const
return m_impl->mPDBInsCode; return m_impl->mPDBInsCode;
} }
float dssp::residue_info::alpha() const std::optional<float> dssp::residue_info::alpha() const
{ {
return m_impl->mAlpha; return m_impl->mAlpha;
} }
float dssp::residue_info::kappa() const std::optional<float> dssp::residue_info::kappa() const
{ {
return m_impl->mKappa; return m_impl->mKappa;
} }
float dssp::residue_info::omega() const std::optional<float> dssp::residue_info::omega() const
{ {
return m_impl->mOmega; return m_impl->mOmega;
} }
float dssp::residue_info::phi() const std::optional<float> dssp::residue_info::phi() const
{ {
return m_impl->mPhi; return m_impl->mPhi;
} }
float dssp::residue_info::psi() const std::optional<float> dssp::residue_info::psi() const
{ {
return m_impl->mPsi; return m_impl->mPsi;
} }
float dssp::residue_info::tco() const std::optional<float> dssp::residue_info::tco() const
{ {
return m_impl->mTCO; return m_impl->mTCO;
} }
......
src/mkdssp.cpp
...@@ -72,10 +72,8 @@ int d_main(int argc, const char *argv[]) ...@@ -72,10 +72,8 @@ int d_main(int argc, const char *argv[])
mcfp::make_option<std::string>("output-format", "Output format, can be either 'dssp' for classic DSSP or 'mmcif' for annotated mmCIF. The default is chosen based on the extension of the output file, if any."), mcfp::make_option<std::string>("output-format", "Output format, can be either 'dssp' for classic DSSP or 'mmcif' for annotated mmCIF. The default is chosen based on the extension of the output file, if any."),
mcfp::make_option<short>("min-pp-stretch", 3, "Minimal number of residues having PSI/PHI in range for a PP helix, default is 3"), mcfp::make_option<short>("min-pp-stretch", 3, "Minimal number of residues having PSI/PHI in range for a PP helix, default is 3"),
mcfp::make_option("write-other", "If set, write the type OTHER for loops, default is to leave this out"), mcfp::make_option("write-other", "If set, write the type OTHER for loops, default is to leave this out"),
mcfp::make_option("write-experimental", "If set, write the new, experimental DSSP output in mmCIF format, default is to leave this out"), mcfp::make_option("no-dssp-categories", "If set, will suppress output of new DSSP output in mmCIF format"),
// mcfp::make_option("components", po::value<std::string, "Location of the components.cif file from CCD")
// mcfp::make_option("extra-compounds", po::value<std::string, "File containing residue information for extra compounds in this specific target, should be either in CCD format or a CCP4 restraints file")
mcfp::make_option<std::string>("mmcif-dictionary", "Path to the mmcif_pdbx.dic file to use instead of default"), mcfp::make_option<std::string>("mmcif-dictionary", "Path to the mmcif_pdbx.dic file to use instead of default"),
mcfp::make_option("help,h", "Display help message"), mcfp::make_option("help,h", "Display help message"),
...@@ -120,17 +118,7 @@ int d_main(int argc, const char *argv[]) ...@@ -120,17 +118,7 @@ int d_main(int argc, const char *argv[])
// -------------------------------------------------------------------- // --------------------------------------------------------------------
// Load extra CCD definitions, if any // private mmcif_pdbx dictionary?
// if (config.has("compounds"))
// cif::add_file_resource("components.cif", config.get<std::string>("compounds"));
// else if (config.has("components"))
// cif::add_file_resource("components.cif", config.get<std::string>("components"));
// if (config.has("extra-compounds"))
// mmcif::CompoundFactory::instance().pushDictionary(config.get<std::string>("extra-compounds"));
// And perhaps a private mmcif_pdbx dictionary
if (config.has("mmcif-dictionary")) if (config.has("mmcif-dictionary"))
cif::add_file_resource("mmcif_pdbx.dic", config.get<std::string>("mmcif-dictionary")); cif::add_file_resource("mmcif_pdbx.dic", config.get<std::string>("mmcif-dictionary"));
...@@ -164,9 +152,13 @@ int d_main(int argc, const char *argv[]) ...@@ -164,9 +152,13 @@ int d_main(int argc, const char *argv[])
if (fmt.empty() and not output.empty()) if (fmt.empty() and not output.empty())
{ {
if (output.extension() == ".gz" or output.extension() == ".xz") if (output.extension() == ".gz" or output.extension() == ".xz")
output = output.stem(); {
if (output.stem().extension() == ".dssp")
if (output.extension() == ".dssp") fmt = "dssp";
else
fmt = "cif";
}
else if (output.extension() == ".dssp")
fmt = "dssp"; fmt = "dssp";
else else
fmt = "cif"; fmt = "cif";
...@@ -187,14 +179,14 @@ int d_main(int argc, const char *argv[]) ...@@ -187,14 +179,14 @@ int d_main(int argc, const char *argv[])
if (fmt == "dssp") if (fmt == "dssp")
writeDSSP(dssp, out); writeDSSP(dssp, out);
else else
annotateDSSP(f.front(), dssp, writeOther, config.has("write-experimental"), out); annotateDSSP(f.front(), dssp, writeOther, not config.has("no-dssp-categories"), out);
} }
else else
{ {
if (fmt == "dssp") if (fmt == "dssp")
writeDSSP(dssp, std::cout); writeDSSP(dssp, std::cout);
else else
annotateDSSP(f.front(), dssp, writeOther, config.has("write-experimental"), std::cout); annotateDSSP(f.front(), dssp, writeOther, not config.has("no-dssp-categories"), std::cout);
} }
return 0; return 0;
......
test/unit-test-dssp.cpp
...@@ -97,9 +97,9 @@ BOOST_AUTO_TEST_CASE(ut_dssp) ...@@ -97,9 +97,9 @@ BOOST_AUTO_TEST_CASE(ut_dssp)
std::string line_t, line_r; std::string line_t, line_r;
BOOST_CHECK(std::getline(test, line_t) and std::getline(reference, line_r)); BOOST_CHECK(std::getline(test, line_t) and std::getline(reference, line_r));
const char *kHeaderLineStart = "==== Secondary Structure Definition by the program DSSP, NKI version 4.0 ===="; const char *kHeaderLineStart = "==== Secondary Structure Definition by the program DSSP, NKI version 4.3 ====";
BOOST_CHECK(line_t.compare(0, std::strlen(kHeaderLineStart), kHeaderLineStart) == 0); BOOST_CHECK(line_t.compare(0, std::strlen(kHeaderLineStart), kHeaderLineStart) == 0);
BOOST_CHECK(line_r.compare(0, std::strlen(kHeaderLineStart), kHeaderLineStart) == 0); // BOOST_CHECK(line_r.compare(0, std::strlen(kHeaderLineStart), kHeaderLineStart) == 0);
for (int line_nr = 2;; ++line_nr) for (int line_nr = 2;; ++line_nr)
{ {
...@@ -115,7 +115,11 @@ BOOST_AUTO_TEST_CASE(ut_dssp) ...@@ -115,7 +115,11 @@ BOOST_AUTO_TEST_CASE(ut_dssp)
<< line_t << std::endl << line_t << std::endl
<< line_r << std::endl; << line_r << std::endl;
BOOST_CHECK(line_t == line_r); if (line_t != line_r)
{
BOOST_CHECK(line_t == line_r);
break;
}
} }
BOOST_CHECK(test.eof()); BOOST_CHECK(test.eof());
...@@ -164,7 +168,7 @@ BOOST_AUTO_TEST_CASE(dssp_1) ...@@ -164,7 +168,7 @@ BOOST_AUTO_TEST_CASE(dssp_1)
std::string line; std::string line;
getline(t, line); getline(t, line);
std::cout << line << std::endl; // std::cout << line << std::endl;
auto fld = cif::split(line, "\t"); auto fld = cif::split(line, "\t");
......
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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