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Python FPbase API\n\n[![License](https://img.shields.io/pypi/l/fpbase.svg?color=green)](https://github.com/tlambert03/fpbasepy/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/fpbase.svg?color=green)](https://pypi.org/project/fpbase)\n[![Python Version](https://img.shields.io/pypi/pyversions/fpbase.svg?color=green)](https://python.org)\n[![CI](https://github.com/tlambert03/fpbasepy/actions/workflows/ci.yml/badge.svg)](https://github.com/tlambert03/fpbasepy/actions/workflows/ci.yml)\n[![codecov](https://codecov.io/gh/tlambert03/fpbasepy/branch/main/graph/badge.svg)](https://codecov.io/gh/tlambert03/fpbasepy)\n\nPython wrapper for FPBase.org GraphQL API.\n\nSee \u003chttps://www.fpbase.org/graphql\u003e for an interactive playground and full documentation on the graphql schema\n(click the little book icon on the top left corner).\n\n## Installation\n\n```sh\npip install fpbase\n```\n\n## API\n\nSee all response model types in `fpbase.models`.\n\n### Functions that return a single object\n\n* `fpbase.get_fluorophore` (can return either protein or dye)\n* `fpbase.get_protein` (will only return proteins)\n* `fpbase.get_microscope`\n* `fpbase.get_filter`\n* `fpbase.get_light_source`\n* `fpbase.get_camera`\n\n### Functions that return a list of available object keys\n\n* `fpbase.list_fluorophores` (includes both proteins and dyes)\n* `fpbase.list_proteins`\n* `fpbase.list_dyes`\n* `fpbase.list_microscopes`\n* `fpbase.list_filters`\n* `fpbase.list_light_sources`\n* `fpbase.list_cameras`\n\n### Other\n\n* `fpbase.graphql_query` : Send generic GraphQL query to FPbase (see \u003chttps://www.fpbase.org/graphql\u003e for full documentation on the graphql schema and an interactive playground)\n\n## Example Usage\n\n```python\nimport fpbase\n\nfpbase.get_fluorophore(\"mCherry\")\n# NOTE: you can also use `get_protein()` if you want to ensure that the\n# fluorophore is a protein and the response is an `fpbase.models.Protein`\n```\n\n\u003cdetails\u003e\n\n\u003csummary\u003eoutput\u003c/summary\u003e\n\n```python\nProtein(\n name='mCherry',\n id='ZERB6',\n default_state=State(\n id=336,\n name='mCherry',\n exMax=587.0,\n emMax=610.0,\n emhex='#f70000',\n exhex='#ff4600',\n ext_coeff=72000.0,\n qy=0.22,\n spectra=[\n Spectrum(id=79, subtype='EX', owner_filter=None, owner_camera=None, owner_light=None),\n Spectrum(id=80, subtype='EM', owner_filter=None, owner_camera=None, owner_light=None),\n Spectrum(id=158, subtype='A_2P', owner_filter=None, owner_camera=None, owner_light=None)\n ],\n lifetime=1.4\n ),\n seq='MVSKGEEDNMAIIKEFMRFKVHMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEASSERMYPEDGALKGEIKQRLKLKDGGHYDAEVKTTYKAKKPVQLPGAYNVNIKLDITSHNEDYTIVEQYERAEGRHSTGGMDELYK',\n pdb=['2H5Q'],\n genbank='AAV52164',\n uniprot='X5DSL3',\n agg=\u003cOlig.MONOMER: 'M'\u003e,\n switch_type=\u003cSwitchType.BASIC: 'B'\u003e,\n primary_reference=Reference(doi='10.1038/nbt1037', url='https://doi.org/10.1038/nbt1037'),\n references=[\n Reference(doi='10.1038/nbt1037', url='https://doi.org/10.1038/nbt1037'),\n Reference(doi='10.1021/bi060773l', url='https://doi.org/10.1021/bi060773l'),\n Reference(doi='10.1038/nmeth1062', url='https://doi.org/10.1038/nmeth1062'),\n Reference(doi='10.1038/nmeth.1596', url='https://doi.org/10.1038/nmeth.1596'),\n Reference(doi='10.1038/nmeth.1955', url='https://doi.org/10.1038/nmeth.1955'),\n Reference(doi='10.1091/mbc.e16-01-0063', url='https://doi.org/10.1091/mbc.e16-01-0063'),\n Reference(doi='10.1038/s41598-017-12212-x', url='https://doi.org/10.1038/s41598-017-12212-x'),\n Reference(doi='10.1038/s41598-018-28858-0', url='https://doi.org/10.1038/s41598-018-28858-0'),\n Reference(doi='10.1002/pld3.112', url='https://doi.org/10.1002/pld3.112'),\n Reference(doi='10.1371/journal.pone.0219886', url='https://doi.org/10.1371/journal.pone.0219886'),\n Reference(doi='10.1073/pnas.2017379117', url='https://doi.org/10.1073/pnas.2017379117'),\n Reference(doi='10.1038/s41467-023-40647-6', url='https://doi.org/10.1038/s41467-023-40647-6')\n ]\n)\n```\n\n\u003c/details\u003e\n\n```python\nfpbase.get_fluorophore(\"DAPI\")\n```\n\n\u003cdetails\u003e\n\n\u003csummary\u003eoutput\u003c/summary\u003e\n\n```python\nFluorophore(\n name='DAPI',\n id='15',\n default_state=State(\n id=15,\n name='DAPI',\n exMax=359.0,\n emMax=461.0,\n emhex='',\n exhex='',\n ext_coeff=None,\n qy=None,\n spectra=[\n Spectrum(id=7754, subtype='AB', owner_filter=None, owner_camera=None, owner_light=None),\n Spectrum(id=222, subtype='EX', owner_filter=None, owner_camera=None, owner_light=None),\n Spectrum(id=223, subtype='EM', owner_filter=None, owner_camera=None, owner_light=None)\n ],\n lifetime=None\n )\n)\n```\n\n\u003c/details\u003e\n\n```python\n# fetch info for \u003chttps://www.fpbase.org/microscope/i6WL2W/\u003e\nfpbase.get_microscope(\"i6WL2W\")\n```\n\n\u003cdetails\u003e\n\n\u003csummary\u003eoutput\u003c/summary\u003e\n\n```python\nMicroscope(\n id='i6WL2WdgcDMgJYtPrpZcaJ',\n name='Example Widefield (Sedat)',\n opticalConfigs=[\n OpticalConfig(\n name='Widefield Blue',\n filters=[\n FilterPlacement(\n path='EX',\n filter=Filter(\n id=52,\n name='Chroma ET395/25x',\n spectrum=Spectrum(id=375, subtype='BX', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer='',\n bandcenter=None,\n bandwidth=None,\n edge=None\n ),\n reflects=False\n ),\n FilterPlacement(\n path='BS',\n filter=Filter(\n id=10,\n name='Chroma T425lpxr',\n spectrum=Spectrum(id=333, subtype='LP', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer='',\n bandcenter=None,\n bandwidth=None,\n edge=None\n ),\n reflects=False\n ),\n FilterPlacement(\n path='EM',\n filter=Filter(\n id=47,\n name='Chroma ET460/50m',\n spectrum=Spectrum(id=370, subtype='BM', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer='',\n bandcenter=None,\n bandwidth=None,\n edge=None\n ),\n reflects=False\n )\n ],\n camera=Camera(\n id=4,\n name='Andor Zyla 4.2 PLUS',\n spectrum=Spectrum(id=1328, subtype='QE', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer=''\n ),\n light=LightSource(\n id=9,\n name='SOLA 395',\n spectrum=Spectrum(id=394, subtype='PD', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer=''\n ),\n laser=None\n ),\n OpticalConfig(\n name='Widefield Dual FRET',\n filters=[\n FilterPlacement(\n path='EX',\n filter=Filter(\n id=63,\n name='Lumencor 470/24x',\n spectrum=Spectrum(id=399, subtype='BX', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer='',\n bandcenter=None,\n bandwidth=None,\n edge=None\n ),\n reflects=False\n ),\n FilterPlacement(\n path='BS',\n filter=Filter(\n id=62,\n name='Chroma 59022bs',\n spectrum=Spectrum(id=385, subtype='BS', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer='',\n bandcenter=None,\n bandwidth=None,\n edge=None\n ),\n reflects=False\n ),\n FilterPlacement(\n path='EM',\n filter=Filter(\n id=689,\n name='Semrock FF02-641/75',\n spectrum=Spectrum(id=1025, subtype='BP', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer='',\n bandcenter=None,\n bandwidth=None,\n edge=None\n ),\n reflects=False\n )\n ],\n camera=Camera(\n id=4,\n name='Andor Zyla 4.2 PLUS',\n spectrum=Spectrum(id=1328, subtype='QE', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer=''\n ),\n light=LightSource(\n id=9,\n name='SOLA 395',\n spectrum=Spectrum(id=394, subtype='PD', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer=''\n ),\n laser=None\n ),\n OpticalConfig(\n name='Widefield Dual Green',\n filters=[\n FilterPlacement(\n path='EX',\n filter=Filter(\n id=63,\n name='Lumencor 470/24x',\n spectrum=Spectrum(id=399, subtype='BX', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer='',\n bandcenter=None,\n bandwidth=None,\n edge=None\n ),\n reflects=False\n ),\n FilterPlacement(\n path='BS',\n filter=Filter(\n id=62,\n name='Chroma 59022bs',\n spectrum=Spectrum(id=385, subtype='BS', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer='',\n bandcenter=None,\n bandwidth=None,\n edge=None\n ),\n reflects=False\n ),\n FilterPlacement(\n path='EM',\n filter=Filter(\n id=569,\n name='Semrock FF03-525/50',\n spectrum=Spectrum(id=905, subtype='BP', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer='',\n bandcenter=None,\n bandwidth=None,\n edge=None\n ),\n reflects=False\n )\n ],\n camera=Camera(\n id=4,\n name='Andor Zyla 4.2 PLUS',\n spectrum=Spectrum(id=1328, subtype='QE', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer=''\n ),\n light=LightSource(\n id=9,\n name='SOLA 395',\n spectrum=Spectrum(id=394, subtype='PD', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer=''\n ),\n laser=None\n ),\n OpticalConfig(\n name='Widefield Dual Red',\n filters=[\n FilterPlacement(\n path='EX',\n filter=Filter(\n id=67,\n name='Lumencor 575/25x',\n spectrum=Spectrum(id=403, subtype='BX', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer='',\n bandcenter=None,\n bandwidth=None,\n edge=None\n ),\n reflects=False\n ),\n FilterPlacement(\n path='BS',\n filter=Filter(\n id=62,\n name='Chroma 59022bs',\n spectrum=Spectrum(id=385, subtype='BS', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer='',\n bandcenter=None,\n bandwidth=None,\n edge=None\n ),\n reflects=False\n ),\n FilterPlacement(\n path='EM',\n filter=Filter(\n id=689,\n name='Semrock FF02-641/75',\n spectrum=Spectrum(id=1025, subtype='BP', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer='',\n bandcenter=None,\n bandwidth=None,\n edge=None\n ),\n reflects=False\n )\n ],\n camera=Camera(\n id=4,\n name='Andor Zyla 4.2 PLUS',\n spectrum=Spectrum(id=1328, subtype='QE', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer=''\n ),\n light=LightSource(\n id=9,\n name='SOLA 395',\n spectrum=Spectrum(id=394, subtype='PD', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer=''\n ),\n laser=None\n ),\n OpticalConfig(\n name='Widefield Far-Red',\n filters=[\n FilterPlacement(\n path='EX',\n filter=Filter(\n id=445,\n name='Chroma ET640/30x',\n spectrum=Spectrum(id=781, subtype='BX', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer='',\n bandcenter=None,\n bandwidth=None,\n edge=None\n ),\n reflects=False\n ),\n FilterPlacement(\n path='BS',\n filter=Filter(\n id=6,\n name='Chroma T660lpxr',\n spectrum=Spectrum(id=329, subtype='LP', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer='',\n bandcenter=None,\n bandwidth=None,\n edge=None\n ),\n reflects=False\n ),\n FilterPlacement(\n path='EM',\n filter=Filter(\n id=719,\n name='Semrock FF01-698/70',\n spectrum=Spectrum(id=1055, subtype='BP', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer='',\n bandcenter=None,\n bandwidth=None,\n edge=None\n ),\n reflects=False\n )\n ],\n camera=Camera(\n id=4,\n name='Andor Zyla 4.2 PLUS',\n spectrum=Spectrum(id=1328, subtype='QE', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer=''\n ),\n light=LightSource(\n id=9,\n name='SOLA 395',\n spectrum=Spectrum(id=394, subtype='PD', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer=''\n ),\n laser=None\n ),\n OpticalConfig(\n name='Widefield Triple Cyan',\n filters=[\n FilterPlacement(\n path='EX',\n filter=Filter(\n id=79,\n name='Lumencor 440/20x',\n spectrum=Spectrum(id=415, subtype='BX', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer='',\n bandcenter=None,\n bandwidth=None,\n edge=None\n ),\n reflects=False\n ),\n FilterPlacement(\n path='BS',\n filter=Filter(\n id=60,\n name='Chroma 69008bs',\n spectrum=Spectrum(id=383, subtype='BS', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer='',\n bandcenter=None,\n bandwidth=None,\n edge=None\n ),\n reflects=False\n ),\n FilterPlacement(\n path='EM',\n filter=Filter(\n id=46,\n name='Chroma ET470/24m',\n spectrum=Spectrum(id=369, subtype='BM', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer='',\n bandcenter=None,\n bandwidth=None,\n edge=None\n ),\n reflects=False\n )\n ],\n camera=Camera(\n id=4,\n name='Andor Zyla 4.2 PLUS',\n spectrum=Spectrum(id=1328, subtype='QE', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer=''\n ),\n light=LightSource(\n id=9,\n name='SOLA 395',\n spectrum=Spectrum(id=394, subtype='PD', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer=''\n ),\n laser=None\n ),\n OpticalConfig(\n name='Widefield Triple FRET',\n filters=[\n FilterPlacement(\n path='EX',\n filter=Filter(\n id=79,\n name='Lumencor 440/20x',\n spectrum=Spectrum(id=415, subtype='BX', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer='',\n bandcenter=None,\n bandwidth=None,\n edge=None\n ),\n reflects=False\n ),\n FilterPlacement(\n path='BS',\n filter=Filter(\n id=60,\n name='Chroma 69008bs',\n spectrum=Spectrum(id=383, subtype='BS', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer='',\n bandcenter=None,\n bandwidth=None,\n edge=None\n ),\n reflects=False\n ),\n FilterPlacement(\n path='EM',\n filter=Filter(\n id=36,\n name='Chroma ET535/30m',\n spectrum=Spectrum(id=359, subtype='BM', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer='',\n bandcenter=None,\n bandwidth=None,\n edge=None\n ),\n reflects=False\n )\n ],\n camera=Camera(\n id=4,\n name='Andor Zyla 4.2 PLUS',\n spectrum=Spectrum(id=1328, subtype='QE', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer=''\n ),\n light=LightSource(\n id=9,\n name='SOLA 395',\n spectrum=Spectrum(id=394, subtype='PD', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer=''\n ),\n laser=None\n ),\n OpticalConfig(\n name='Widefield Triple Red',\n filters=[\n FilterPlacement(\n path='EX',\n filter=Filter(\n id=67,\n name='Lumencor 575/25x',\n spectrum=Spectrum(id=403, subtype='BX', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer='',\n bandcenter=None,\n bandwidth=None,\n edge=None\n ),\n reflects=False\n ),\n FilterPlacement(\n path='BS',\n filter=Filter(\n id=60,\n name='Chroma 69008bs',\n spectrum=Spectrum(id=383, subtype='BS', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer='',\n bandcenter=None,\n bandwidth=None,\n edge=None\n ),\n reflects=False\n ),\n FilterPlacement(\n path='EM',\n filter=Filter(\n id=689,\n name='Semrock FF02-641/75',\n spectrum=Spectrum(id=1025, subtype='BP', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer='',\n bandcenter=None,\n bandwidth=None,\n edge=None\n ),\n reflects=False\n )\n ],\n camera=Camera(\n id=4,\n name='Andor Zyla 4.2 PLUS',\n spectrum=Spectrum(id=1328, subtype='QE', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer=''\n ),\n light=LightSource(\n id=9,\n name='SOLA 395',\n spectrum=Spectrum(id=394, subtype='PD', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer=''\n ),\n laser=None\n ),\n OpticalConfig(\n name='Widefield Triple Yellow',\n filters=[\n FilterPlacement(\n path='EX',\n filter=Filter(\n id=41,\n name='Chroma ET500/20x',\n spectrum=Spectrum(id=364, subtype='BX', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer='',\n bandcenter=None,\n bandwidth=None,\n edge=None\n ),\n reflects=False\n ),\n FilterPlacement(\n path='BS',\n filter=Filter(\n id=60,\n name='Chroma 69008bs',\n spectrum=Spectrum(id=383, subtype='BS', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer='',\n bandcenter=None,\n bandwidth=None,\n edge=None\n ),\n reflects=False\n ),\n FilterPlacement(\n path='EM',\n filter=Filter(\n id=36,\n name='Chroma ET535/30m',\n spectrum=Spectrum(id=359, subtype='BM', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer='',\n bandcenter=None,\n bandwidth=None,\n edge=None\n ),\n reflects=False\n )\n ],\n camera=Camera(\n id=4,\n name='Andor Zyla 4.2 PLUS',\n spectrum=Spectrum(id=1328, subtype='QE', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer=''\n ),\n light=LightSource(\n id=9,\n name='SOLA 395',\n spectrum=Spectrum(id=394, subtype='PD', owner_filter=None, owner_camera=None, owner_light=None),\n manufacturer=''\n ),\n laser=None\n )\n ]\n)\n```\n\n\u003c/details\u003e\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftlambert03%2Ffpbasepy","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftlambert03%2Ffpbasepy","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftlambert03%2Ffpbasepy/lists"}