Figlinq Python Library
This package contains utilities for interfacing with Plotly's Chart Studio and Figlinq services. The project has been cloned from chart-studio 1.1.0. The original package has been modified so that credentials and configuration can be set from environment variables (see figlinq.tools.get_credentials() and figlinq.tools.get_config()). Additional functions have been added to support the Figlinq service. The original package is licensed under the MIT license, and this package is also licensed under the MIT license.
Installation
pip install figlinq
Editing figures: figlinq.open_figure
figlinq.open_figure(fid) edits a Figlinq figure (a multi-panel page of plots, images and text) from Python. All its methods are coroutines, so use await (in a script, asyncio.run(main())).
import figlinq
fig = figlinq.open_figure("alice:12") # the figure's fid
state = await fig.state() # read first: page, layers, nodes, selection
await fig.add_content(["alice:12", "alice:15"], layout={"type": "grid", "cols": 2})
await fig.modify_plots(fids=["alice:12"], layout={"title": {"text": "Growth"}}, traceActions=["no_modify"])
async with fig.batch() as b: # several operations, all or none
t = b.add_text("A", 10, 10) # a Ref to the new text's id
b.align([t], "left")
img = await fig.image() # a PNG of the page
In a script or a plain Python session every call goes to the server and is stored at once as one revision of the figure. It is guarded by the figure's ETag, so a figure that changed in the meantime raises VersionConflict: read state() again. Inside the Figlinq web app (Flows, the assistant) with the figure open in the editor, the changes are live in the editor and are not saved until the user saves. modify_plots rewrites the plot files at once on both. Errors are subclasses of figlinq.FigureEditorError (figlinq.figure_editor.VersionConflict, ReadOnly, NotFound, PermissionDenied, ...) with a .code. See the docstring of figlinq.figure_editor for the full list of operations.
Reading and editing structures: figlinq.open_structure
figlinq.open_structure(fid) reads and edits a Figlinq chemistry file (a molecule or reaction drawn in the structure editor) from Python. A chemistry file is one canvas, so operations have no targets and results have no ids. All methods are coroutines. In a script, set the server and your API key first, for example in the environment (export FIGLINQ_USERNAME=alice FIGLINQ_API_KEY=... FIGLINQ_API_DOMAIN=https://figlinq.example.org), or in Python with figlinq.session.sign_in("alice", "<api key>", plotly_api_domain="https://figlinq.example.org").
import asyncio
import figlinq
async def main():
s = figlinq.open_structure("alice:7") # the structure file's fid
state = await s.state() # SMILES, InChI, InChIKey, formula, weights, atom and bond counts
print(state)
await s.set("c1ccccc1O") # SMILES, molfile, rxn or Ketcher JSON (the format is detected)
await s.add("CC(=O)O") # draw a second structure beside it
img = await s.image(format="png") # a picture on a white page
open("structure.png", "wb").write(img.png) # in the Figlinq app: img.display()
async with s.batch() as b: # several operations, all or none
b.set("CCO")
b.layout()
b.state(["smiles", "ket"])
print(b.results)
asyncio.run(main())
(In a notebook cell or the Figlinq assistant, top-level await works and figlinq.open_structure() without a fid edits the structure open in the editor.)
state(include=[...]) can add ket (Ketcher JSON, the lossless form), molfile (V2000) and rxn; a part the engine cannot produce for this structure is None and named in state.unavailable. In a script every call goes to the server and is stored at once as one revision of the file, guarded by its ETag (VersionConflict if it changed in the meantime: read state() again). Inside the Figlinq web app with the file open in the editor the changes are live in the editor and not saved until the user saves. A .mol, .rxn or .smi file is never rewritten in another format: a change raises LossyFormat unless you pass save_as="ket" (server only), which creates a new .ket file beside the original (result.created has its fid). Errors are subclasses of figlinq.StructureEditorError (figlinq.structure_editor.VersionConflict, InvalidStructure, NoEditor, Rejected with failed_index and results_so_far, ...) with a .code.
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Release files for figlinq 0.15.0
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