psdi-data-conversion 0.0.23__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- psdi_data_conversion/__init__.py +11 -0
- psdi_data_conversion/app.py +242 -0
- psdi_data_conversion/bin/linux/atomsk +0 -0
- psdi_data_conversion/bin/linux/c2x +0 -0
- psdi_data_conversion/bin/mac/atomsk +0 -0
- psdi_data_conversion/bin/mac/c2x +0 -0
- psdi_data_conversion/constants.py +185 -0
- psdi_data_conversion/converter.py +459 -0
- psdi_data_conversion/converters/__init__.py +6 -0
- psdi_data_conversion/converters/atomsk.py +32 -0
- psdi_data_conversion/converters/base.py +702 -0
- psdi_data_conversion/converters/c2x.py +32 -0
- psdi_data_conversion/converters/openbabel.py +239 -0
- psdi_data_conversion/database.py +1064 -0
- psdi_data_conversion/dist.py +87 -0
- psdi_data_conversion/file_io.py +216 -0
- psdi_data_conversion/log_utility.py +241 -0
- psdi_data_conversion/main.py +776 -0
- psdi_data_conversion/scripts/atomsk.sh +32 -0
- psdi_data_conversion/scripts/c2x.sh +26 -0
- psdi_data_conversion/security.py +38 -0
- psdi_data_conversion/static/content/accessibility.htm +254 -0
- psdi_data_conversion/static/content/convert.htm +121 -0
- psdi_data_conversion/static/content/convertato.htm +65 -0
- psdi_data_conversion/static/content/convertc2x.htm +65 -0
- psdi_data_conversion/static/content/documentation.htm +94 -0
- psdi_data_conversion/static/content/feedback.htm +53 -0
- psdi_data_conversion/static/content/header-links.html +8 -0
- psdi_data_conversion/static/content/index-versions/header-links.html +8 -0
- psdi_data_conversion/static/content/index-versions/psdi-common-footer.html +99 -0
- psdi_data_conversion/static/content/index-versions/psdi-common-header.html +28 -0
- psdi_data_conversion/static/content/psdi-common-footer.html +99 -0
- psdi_data_conversion/static/content/psdi-common-header.html +28 -0
- psdi_data_conversion/static/content/report.htm +103 -0
- psdi_data_conversion/static/data/data.json +143940 -0
- psdi_data_conversion/static/img/colormode-toggle-dm.svg +3 -0
- psdi_data_conversion/static/img/colormode-toggle-lm.svg +3 -0
- psdi_data_conversion/static/img/psdi-icon-dark.svg +136 -0
- psdi_data_conversion/static/img/psdi-icon-light.svg +208 -0
- psdi_data_conversion/static/img/psdi-logo-darktext.png +0 -0
- psdi_data_conversion/static/img/psdi-logo-lighttext.png +0 -0
- psdi_data_conversion/static/img/social-logo-bluesky-black.svg +4 -0
- psdi_data_conversion/static/img/social-logo-bluesky-white.svg +4 -0
- psdi_data_conversion/static/img/social-logo-instagram-black.svg +1 -0
- psdi_data_conversion/static/img/social-logo-instagram-white.svg +1 -0
- psdi_data_conversion/static/img/social-logo-linkedin-black.png +0 -0
- psdi_data_conversion/static/img/social-logo-linkedin-white.png +0 -0
- psdi_data_conversion/static/img/social-logo-mastodon-black.svg +4 -0
- psdi_data_conversion/static/img/social-logo-mastodon-white.svg +4 -0
- psdi_data_conversion/static/img/social-logo-x-black.svg +3 -0
- psdi_data_conversion/static/img/social-logo-x-white.svg +3 -0
- psdi_data_conversion/static/img/social-logo-youtube-black.png +0 -0
- psdi_data_conversion/static/img/social-logo-youtube-white.png +0 -0
- psdi_data_conversion/static/img/ukri-epsr-logo-darktext.png +0 -0
- psdi_data_conversion/static/img/ukri-epsr-logo-lighttext.png +0 -0
- psdi_data_conversion/static/img/ukri-logo-darktext.png +0 -0
- psdi_data_conversion/static/img/ukri-logo-lighttext.png +0 -0
- psdi_data_conversion/static/javascript/accessibility.js +196 -0
- psdi_data_conversion/static/javascript/common.js +42 -0
- psdi_data_conversion/static/javascript/convert.js +296 -0
- psdi_data_conversion/static/javascript/convert_common.js +252 -0
- psdi_data_conversion/static/javascript/convertato.js +107 -0
- psdi_data_conversion/static/javascript/convertc2x.js +107 -0
- psdi_data_conversion/static/javascript/data.js +176 -0
- psdi_data_conversion/static/javascript/format.js +611 -0
- psdi_data_conversion/static/javascript/load_accessibility.js +89 -0
- psdi_data_conversion/static/javascript/psdi-common.js +177 -0
- psdi_data_conversion/static/javascript/report.js +381 -0
- psdi_data_conversion/static/styles/format.css +147 -0
- psdi_data_conversion/static/styles/psdi-common.css +705 -0
- psdi_data_conversion/templates/index.htm +114 -0
- psdi_data_conversion/testing/__init__.py +5 -0
- psdi_data_conversion/testing/constants.py +12 -0
- psdi_data_conversion/testing/conversion_callbacks.py +394 -0
- psdi_data_conversion/testing/conversion_test_specs.py +208 -0
- psdi_data_conversion/testing/utils.py +522 -0
- psdi_data_conversion-0.0.23.dist-info/METADATA +663 -0
- psdi_data_conversion-0.0.23.dist-info/RECORD +81 -0
- psdi_data_conversion-0.0.23.dist-info/WHEEL +4 -0
- psdi_data_conversion-0.0.23.dist-info/entry_points.txt +2 -0
- psdi_data_conversion-0.0.23.dist-info/licenses/LICENSE +201 -0
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<form name="gui">
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<h3>Format and Converter Selection</h3>
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<p>Select 'from' and 'to' file formats in the 'Convert from/to' boxes, in either order. Typing where indicated
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filters the options (case insensitive); for example, typing 'can' or 'NON' reduces the number of options to one:
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'can: Canonical SMILES.' If you change your mind about a conversion, it is advisable to click on the 'Reset'
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button. When both formats have been selected, converters able to carry out this conversion appear in the
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'Conversion options' box along with an indication of conversion quality (many conversions have not yet been
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tested) and whether or not the converter is supported on this site.</p>
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<p>Selecting a converter displays information
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about it, along with a link to a relevant website. Irrespective of the selected converter, an Open Babel
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conversion is offered if it can be carried out. Clicking on the 'Yes' button takes us to the 'Conversion' page.
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If a file format has not been found, or if there are no converters supporting a required conversion, please
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click on 'Report Missing Format/Conversion' in the navigation bar.</p><br>
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<h3>Conversion</h3>
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<h4>Open Babel</h4>
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<p>Zero to two option flag select boxes and zero to two sets of option flag check boxes may be displayed,
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depending on the conversion and the degree of completion of the database. Further information may be displayed
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underneath the select boxes if available. One or more input or output flags may be selected if required (command
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click [Mac] or control click [Windows] for multiple select box selections). To undo all selections in a box,
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click just underneath the final option. Ticking a check box reveals a text box for entry of required
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information, along with further explanation if available.</p>
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<p>If 2- or 3-dimensional atomic coordinates need to be calculated (e.g., if they do not already exist in the
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input file), select '2D' or '3D' and a speed/accuracy option ('fastest' is least accurate).
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Note that this calculation is not appropriate for all file formats, so in these cases selections will be
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ignored. Click on 'Choose file' and then select an input file of the correct format (and extension). Clicking
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on 'Convert' uploads and converts the file. The output file is automatically downloaded, along with a log file.
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if any issues are encountered (e.g., the output file does not download), please click on 'Provide Feedback' in
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the navigation bar.</p>
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<h4>Atomsk and c2x</h4>
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<p>Click on 'Choose file' and then select an input file of the correct format (and extension). Clicking on
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'Convert'
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uploads and converts the file. The output file is automatically downloaded, along with a log file. If any issues
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are
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encountered (e.g., the output file does not download), please click on 'Provide Feedback' in the navigation bar.
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</p><br>
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<h3>Report Missing Format/Conversion</h3>
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<p>Select the type of report (missing file format or conversion) and then follow the instructions that appear.
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Finally, click on 'Report.'</p><br>
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<h3>Provide feedback</h3>
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<p>To report issues other than missing formats or conversions, please click on the 'Feedback form' link. The form
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will open in a new tab.</p><br>
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<h3>Accessibility</h3>
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<p>Select accessibility settings below as required, in any order. Each new setting immediately comes into effect
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on this page only, in the first instance. Once the appearance of the page is satisfactory, clicking on the
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'Apply' button applies the settings to the entire website. Leaving the page without clicking on 'Apply' results
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in the changes being lost. Note that page appearance may vary slightly according to the browser used.</p>
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<p>The colour options here are not compatible with the dark-mode toggle in the header bar. If a custom dark scheme
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is desired, the appropriate colours can be selected in light-mode.</p>
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<script src="https://code.jquery.com/jquery-3.7.1.js" integrity="sha256-eKhayi8LEQwp4NKxN+CfCh+3qOVUtJn3QNZ0TciWLP4="
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crossorigin="anonymous"></script>
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<title>PSDI Data Conversion Service</title>
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<link rel="icon" type="image/x-icon" href="../img/psdi-icon-dark.svg">
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<link href="https://fonts.googleapis.com/css?family=Lato:400" rel="stylesheet" type="text/css">
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<link href="https://fonts.googleapis.com/css?family=Open+Sans+Condensed:700" rel="stylesheet" type="text/css">
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<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.6.3/jquery.min.js"></script>
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<p>To report issues other than missing formats or conversions, please click on the 'Feedback
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form' link below. The form will open in a new tab.</p>
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<a href="https://forms.office.com/Pages/ResponsePage.aspx?id=-XhTSvQpPk2-iWadA62p2Fa27wFj_AtEgNrXLTdVtPVUQzhCODEyWTRXNlFEVDg5WklURlY2MExLWiQlQCN0PWcu"
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target="_blank">
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Feedback form
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</a>
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crossorigin="anonymous"></script>
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directory. -->
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<a href="../../" class="navbar__item navbar__link">Home</a>
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<a href="report.htm" class="navbar__item navbar__link">Report Missing Format/Conversion</a>
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<a href="documentation.htm" class="navbar__item navbar__link">Documentation</a>
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<a href="accessibility.htm" class="navbar__item navbar__link">Accessibility</a>
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<a href="./" class="navbar__item navbar__link">Home</a>
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<a href="static/content/report.htm" class="navbar__item navbar__link">Report Missing Format/Conversion</a>
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that loads it. -->
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<div id="footer__links__left">
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<div class="footer__title">
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<h6>Funding</h6>
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</div>
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<h6 class="footer__title"><br></h6>
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<ul class="footer__col footer__items clean-list">
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<li class="funding-text">PSDI acknowledges the funding support by the EPSRC grants EP/X032701/1, EP/X032663/1
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and EP/W032252/1</li>
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</ul>
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<li>
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alt="UKRI logo">
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alt="UKRI logo">
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</li>
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alt="UKRI EPSR logo">
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alt="UKRI EPSR logo">
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</li>
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<h6>Useful Links</h6>
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<!-- This file contains the links that will appear in the top-right of the header bar for .html files in the index.htm page. --> <a href="./" class="navbar__item navbar__link">Home</a> <a href="static/content/report.htm" class="navbar__item navbar__link">Report Missing Format/Conversion</a> <a href="static/content/feedback.htm" class="navbar__item navbar__link">Provide Feedback</a> <a href="static/content/documentation.htm" class="navbar__item navbar__link">Documentation</a> <a href="static/content/accessibility.htm" class="navbar__item navbar__link">Accessibility</a> <a href="mailto: psdi@soton.ac.uk" class="navbar__item navbar__link" id="mail">Contact</a>
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<!-- This file contains the links that will appear in the top-right of the header bar for .html files in this directory. --> <a href="../../" class="navbar__item navbar__link">Home</a> <a href="report.htm" class="navbar__item navbar__link">Report Missing Format/Conversion</a> <a href="feedback.htm" class="navbar__item navbar__link">Provide Feedback</a> <a href="documentation.htm" class="navbar__item navbar__link">Documentation</a> <a href="accessibility.htm" class="navbar__item navbar__link">Accessibility</a> <a href="mailto:support@psdi.ac.uk" class="navbar__item navbar__link" id="mail">Contact Us</a>
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Version 1.0, 19th June 2024
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|
+
<br>Select the required 'to' and 'from' formats below.
|
|
59
|
+
<p>
|
|
60
|
+
<label for="searchFrom" id="fromLabel">Convert from:</label><br>
|
|
61
|
+
<input type="text" placeholder="-- type here to filter options --" id="searchFrom" class="large-width"><br>
|
|
62
|
+
<select size="4" id="fromList" class="large-width"></select>
|
|
63
|
+
</p>
|
|
64
|
+
<div class="smallGap"></div>
|
|
65
|
+
<p>
|
|
66
|
+
<label for="searchTo" id="toLabel">Convert to:</label><br>
|
|
67
|
+
<input type="text" placeholder="-- type here to filter options --" id="searchTo" class="large-width"><br>
|
|
68
|
+
<select size="4" id="toList" class="large-width"></select>
|
|
69
|
+
</p>
|
|
70
|
+
<input type="button" class="button" value=" Reset " name="resetButton2" id="resetButton2">
|
|
71
|
+
</div>
|
|
72
|
+
<select id="success" class="large-width"></select> <!-- Not for display. For convenience only. -->
|
|
73
|
+
<p id="userInput" class="init-hidden">
|
|
74
|
+
<span id="message"></span>
|
|
75
|
+
<br><span id="message1"></span>
|
|
76
|
+
<br><input type="text" placeholder="-- type here --" id="in" class="large-width">
|
|
77
|
+
<br><input type="button" class="button" value=" Report " id="reportButton">
|
|
78
|
+
</p>
|
|
79
|
+
<div class="medGap"></div>
|
|
80
|
+
</div>
|
|
81
|
+
</form>
|
|
82
|
+
|
|
83
|
+
<form name="gui" class="local-only">
|
|
84
|
+
<div class="max-width-box">
|
|
85
|
+
<div class="smallGap"></div>
|
|
86
|
+
<p>
|
|
87
|
+
To report a missing format or conversion, please use
|
|
88
|
+
<a href="https://psdidev2.azurewebsites.net/static/content/report.htm?origin=local">the interface on the public
|
|
89
|
+
web app</a>.
|
|
90
|
+
</p>
|
|
91
|
+
<div class="medGap"></div>
|
|
92
|
+
</div>
|
|
93
|
+
</form>
|
|
94
|
+
|
|
95
|
+
<script src="https://code.jquery.com/jquery-3.7.1.js" integrity="sha256-eKhayi8LEQwp4NKxN+CfCh+3qOVUtJn3QNZ0TciWLP4="
|
|
96
|
+
crossorigin="anonymous"></script>
|
|
97
|
+
<script src="../javascript/report.js" type="module" language="JavaScript"></script>
|
|
98
|
+
|
|
99
|
+
<footer class="footer" id="psdi-footer"></footer>
|
|
100
|
+
|
|
101
|
+
</body>
|
|
102
|
+
|
|
103
|
+
</html>
|