Clean up docs #425
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Clean up docs #425
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Luthaf
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Jul 21, 2025
| to perform this kind of analyses. | ||
| This manual presents an overview of how to use the Chemiscope viewer in its standard | ||
| implementations, including the web tool and the Jupyter widget. It does not discuss in | ||
| detail how to build a low-dimensional representation of a chemical dataset - Chemiscope |
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| detail how to build a low-dimensional representation of a chemical dataset - Chemiscope | |
| detail how to build a low-dimensional representation of a chemical dataset - chemiscope |
| inside a jupyter notebook. | ||
| This section starts introducing the concept of structural and physical properties, | ||
| before describing how to use the different panels in the standard visualization. It | ||
| continues by presenting how you can generate a Chemiscope input file to load on |
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| continues by presenting how you can generate a Chemiscope input file to load on | |
| continues by presenting how you can generate a chemiscope input file to load on |
| continues by presenting how you can generate a Chemiscope input file to load on | ||
| https://chemiscope.org, as well as within a standalone HTML viewer that works offline. | ||
| See the :ref:`Python module documentation <python-module>` for how to interact with | ||
| Chemiscope in a script, or to explore a dataset directly inside a Jupyter notebook. |
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| Chemiscope in a script, or to explore a dataset directly inside a Jupyter notebook. | |
| chemiscope in a script, or to explore a dataset directly inside a Jupyter notebook. |
| resulting JSON file can be quite large and thus harder to share with | ||
| collaborators, the default chemiscope interface also allows to load JSON files | ||
| compressed with gzip. | ||
| The default Chemiscope interface loads all structures and properties of a dataset from a |
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| The default Chemiscope interface loads all structures and properties of a dataset from a | |
| The default chemiscope interface loads all structures and properties of a dataset from a |
| The default Chemiscope interface loads all structures and properties of a dataset from a | ||
| single JSON file. This section describe how to create such a file using provided Python | ||
| tools or by manually writing the JSON. As JSON files can become large and hard to share | ||
| with collaborators Chemiscope also supports loading JSON files compressed with gzip. |
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| with collaborators Chemiscope also supports loading JSON files compressed with gzip. | |
| with collaborators chemiscope also supports loading JSON files compressed with gzip. |
| structural representations or reduced-dimensionality features, using its command-line | ||
| interface. To generate these quantities, external packages like `scikit-matter`_ or | ||
| `ASAP`_ can be used. The ASAP package, for instance, can produce directly output in | ||
| Chemiscope-compatible format. |
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| Chemiscope-compatible format. | |
| chemiscope-compatible format. |
| `ASAP`_ can be used. The ASAP package, for instance, can produce directly output in | ||
| Chemiscope-compatible format. | ||
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| Alternatively, Chemiscope's :ref:` :py:func:chemiscope.explore <_explore-example>` |
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| Alternatively, Chemiscope's :ref:` :py:func:chemiscope.explore <_explore-example>` | |
| Alternatively, chemiscope's :ref:` :py:func:chemiscope.explore <_explore-example>` |
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| Quick overview | ||
| ~~~~~~~~~~~~~~ | ||
| The Chemiscope JSON file consists of these top-level entries: |
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| The Chemiscope JSON file consists of these top-level entries: | |
| The chemiscope JSON file consists of these top-level entries: |
| @@ -11,22 +11,22 @@ Online visualizer at chemiscope.org | |||
| Uploading datasets | |||
| ^^^^^^^^^^^^^^^^^^ | |||
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| The simplest way to share chemiscope dataset is to send the corresponding file | |||
| The simplest way to share the chemiscope dataset is to send the corresponding file | |||
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| The simplest way to share the chemiscope dataset is to send the corresponding file | |
| The simplest way to share a chemiscope dataset is to send the corresponding file |
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| Below is the detailed description of the values types and examlpes for each entry. | ||
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| Metadata (``meta``) |
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I still need to go through this section with a local build of the docs!
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The idea is to check the examples in the documentation are actual & do a small clean up (work in progress)