From baaa0027102240e46d7e158e286183b8bd875a80 Mon Sep 17 00:00:00 2001 From: haeussma <83341109+haeussma@users.noreply.github.com> Date: Fri, 27 Sep 2024 18:02:42 +0200 Subject: [PATCH 1/6] fixed casing --- docs/examples/data/enzymeml_TmSAHH_SAH.json | 7910 +++++++++---------- pyproject.toml | 2 +- 2 files changed, 3956 insertions(+), 3956 deletions(-) diff --git a/docs/examples/data/enzymeml_TmSAHH_SAH.json b/docs/examples/data/enzymeml_TmSAHH_SAH.json index 86e89e2..1c02334 100644 --- a/docs/examples/data/enzymeml_TmSAHH_SAH.json +++ b/docs/examples/data/enzymeml_TmSAHH_SAH.json @@ -18,7 +18,7 @@ "exponent": 1, "multiplier": null, "scale": 1.0, - "ld_id": "enzml:BaseUnit/e3a5826c-6a95-4a55-8d70-7de603caeeef", + "ld_id": "enzml:BaseUnit/81c05bc9-70c3-4f29-ad33-00f966715729", "ld_type": [ "enzml:BaseUnit" ], @@ -29,7 +29,7 @@ } } ], - "ld_id": "enzml:UnitDefinition/030e3102-7730-43e2-9ed9-098399412c85", + "ld_id": "enzml:UnitDefinition/361dc948-8bed-4388-961c-acb6fa45804a", "ld_type": [ "OBO:UO_0000000" ], @@ -40,7 +40,7 @@ } }, "constant": true, - "ld_id": "enzml:Vessel/76a8dec5-3654-4573-8098-9ea3331235ba", + "ld_id": "enzml:Vessel/c42db070-f545-4b32-9af7-2e28fe60f695", "ld_type": [ "enzml:Vessel", "OBO:OBI_0400081" @@ -69,7 +69,7 @@ "organism": null, "organism_tax_id": null, "references": [], - "ld_id": "enzml:Protein/dff2284a-054b-4e66-96ba-f92ee185a7bb", + "ld_id": "enzml:Protein/e37cd02b-5970-4148-9da7-ec235bf289d8", "ld_type": [ "enzml:Protein", "schema:Protein" @@ -107,7 +107,7 @@ "organism": null, "organism_tax_id": null, "references": [], - "ld_id": "enzml:Protein/4961f179-e073-41ca-bce4-0286377a06d8", + "ld_id": "enzml:Protein/30bed91a-58e6-474d-8353-182cf5f71bfb", "ld_type": [ "enzml:Protein", "schema:Protein" @@ -145,7 +145,7 @@ "organism": null, "organism_tax_id": null, "references": [], - "ld_id": "enzml:Protein/2179befa-30d1-4f17-884e-a057038b06c4", + "ld_id": "enzml:Protein/07beb141-f4e1-4f32-93f6-94b5667ef86a", "ld_type": [ "enzml:Protein", "schema:Protein" @@ -183,7 +183,7 @@ "organism": null, "organism_tax_id": null, "references": [], - "ld_id": "enzml:Protein/eb200fcd-3007-4fb7-a7cc-a5f06e77dd6f", + "ld_id": "enzml:Protein/42d4da0d-eed3-44a9-874d-d14ac9c03bf7", "ld_type": [ "enzml:Protein", "schema:Protein" @@ -223,7 +223,7 @@ "inchi": null, "inchikey": null, "references": [], - "ld_id": "enzml:SmallMolecule/f481edf4-a76a-48b1-84f8-640cb112c2b3", + "ld_id": "enzml:SmallMolecule/fba052b8-88dd-4416-9942-d2dc37c57d69", "ld_type": [ "enzml:SmallMolecule" ], @@ -425,7 +425,7 @@ "exponent": 1, "multiplier": null, "scale": -6.0, - "ld_id": "md:BaseUnit/b02ad738-ba90-4fad-be33-88df3b4d6217", + "ld_id": "md:BaseUnit/4c434b8c-d129-474b-82bc-e2780b03f8d0", "ld_type": [ "md:BaseUnit" ], @@ -438,7 +438,7 @@ "exponent": -1, "multiplier": null, "scale": 1.0, - "ld_id": "md:BaseUnit/5e3848e3-b8bf-4ef6-88d2-04775d342dd6", + "ld_id": "md:BaseUnit/ca6f41aa-5b10-4012-b989-5ab8cbf023b0", "ld_type": [ "md:BaseUnit" ], @@ -468,7 +468,7 @@ "exponent": 1, "multiplier": 60.0, "scale": 1.0, - "ld_id": "md:BaseUnit/0d62b5c2-bb61-4574-9653-0ac6dbc3b5c8", + "ld_id": "md:BaseUnit/49f7f5c0-1364-4e2d-b025-4944bbfdddac", "ld_type": [ "md:BaseUnit" ], @@ -486,7 +486,93 @@ } }, "is_simulated": false, - "ld_id": "enzml:MeasurementData/e89451cc-ed51-4555-9e95-009af83fab5a", + "ld_id": "enzml:MeasurementData/a1bbe0d1-102e-497d-a4be-cf3a1413b6b3", + "ld_type": [ + "enzml:MeasurementData" + ], + "ld_context": { + "enzml": "http://www.enzymeml.org/v2/", + "schema": "https://schema.org/", + "OBO": "http://purl.obolibrary.org/obo/", + "species_id": { + "@type": "@id" + } + } + }, + { + "species_id": "TmSAHH", + "initial": 5.0, + "data_unit": { + "id": null, + "name": "umol / l", + "base_units": [ + { + "kind": "mole", + "exponent": 1, + "multiplier": null, + "scale": -6.0, + "ld_id": "md:BaseUnit/4c434b8c-d129-474b-82bc-e2780b03f8d0", + "ld_type": [ + "md:BaseUnit" + ], + "ld_context": { + "md": "https://github.com/FAIRChemistry/MTPHandler" + } + }, + { + "kind": "litre", + "exponent": -1, + "multiplier": null, + "scale": 1.0, + "ld_id": "md:BaseUnit/ca6f41aa-5b10-4012-b989-5ab8cbf023b0", + "ld_type": [ + "md:BaseUnit" + ], + "ld_context": { + "md": "https://github.com/FAIRChemistry/MTPHandler" + } + } + ], + "ld_id": "OBO:UO_0000064", + "ld_type": [ + "OBO:UO_0000000" + ], + "ld_context": { + "md": "https://github.com/FAIRChemistry/MTPHandler" + } + }, + "data_type": "http://purl.obolibrary.org/obo/PATO_0000033", + "prepared": 5.0, + "data": [], + "time": [], + "time_unit": { + "id": null, + "name": "s", + "base_units": [ + { + "kind": "second", + "exponent": 1, + "multiplier": 60.0, + "scale": 1.0, + "ld_id": "md:BaseUnit/49f7f5c0-1364-4e2d-b025-4944bbfdddac", + "ld_type": [ + "md:BaseUnit" + ], + "ld_context": { + "md": "https://github.com/FAIRChemistry/MTPHandler" + } + } + ], + "ld_id": "OBO:UO_0000031", + "ld_type": [ + "OBO:UO_0000000" + ], + "ld_context": { + "md": "https://github.com/FAIRChemistry/MTPHandler" + } + }, + "is_simulated": false, + "ld_id": "enzml:MeasurementData/ef69eda3-bc49-4974-9ac3-e965e97ce289", "ld_type": [ "enzml:MeasurementData" ], @@ -501,7 +587,7 @@ }, { "species_id": "TNB", - "initial": -1.7261984578282223, + "initial": 0.0, "data_unit": { "id": null, "name": "umol / l", @@ -511,7 +597,7 @@ "exponent": 1, "multiplier": null, "scale": -6.0, - "ld_id": "md:BaseUnit/b02ad738-ba90-4fad-be33-88df3b4d6217", + "ld_id": "md:BaseUnit/4c434b8c-d129-474b-82bc-e2780b03f8d0", "ld_type": [ "md:BaseUnit" ], @@ -524,7 +610,7 @@ "exponent": -1, "multiplier": null, "scale": 1.0, - "ld_id": "md:BaseUnit/5e3848e3-b8bf-4ef6-88d2-04775d342dd6", + "ld_id": "md:BaseUnit/ca6f41aa-5b10-4012-b989-5ab8cbf023b0", "ld_type": [ "md:BaseUnit" ], @@ -544,162 +630,162 @@ "data_type": "http://purl.obolibrary.org/obo/PATO_0000033", "prepared": 0.0, "data": [ - -1.7261984578282223, - -1.6791165926000609, - -1.632057653315173, - -1.6085367683564555, - -1.5145103430328746, - -1.3736415008856648, - 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177.2433942011039, + 177.30787943766978, + 177.29498218449066, + 177.24339420110394, 177.2562910427068, 177.14022315892382, 177.14022315892382, 177.12732723881453, - 177.11443142070442, - 177.0628491667004, - 177.04995385741967, - 176.99837363484554, - 176.933900633533, - 176.9467950318184, - 176.92100633608072, + 177.11443142070445, + 177.06284916670037, + 177.0499538574197, + 176.99837363484556, + 176.93390063353297, + 176.94679503181837, + 176.92100633608075, 176.85653635859796, 176.85653635859796, - 176.79206889029354, - 176.75338960967915, - 176.7404967157366, - 176.6889261358754, - 176.6889261358754, - 176.66314144240383, - 176.5728981360755, - 176.61157324527596, + 176.79206889029356, + 176.75338960967912, + 176.74049671573664, + 176.68892613587542, + 176.68892613587542, + 176.66314144240386, + 176.57289813607548, + 176.611573245276, 176.54711522337186, 176.45687812775176, 176.48265966409616, 176.4439875065623, 176.40531622999532, - 176.36664583230393, - 176.31508666557463, - 176.2635290526187, + 176.3666458323039, + 176.3150866655746, + 176.26352905261874, 176.25063989157636, 176.18619553567498, 176.21197298848293, - 176.14753007879747, + 176.1475300787975, 176.0830895717375, 176.09597748140342, 176.0830895717375, @@ -11365,265 +11623,7 @@ "exponent": 1, "multiplier": 60.0, "scale": 1.0, - "ld_id": "md:BaseUnit/0d62b5c2-bb61-4574-9653-0ac6dbc3b5c8", - "ld_type": [ - "md:BaseUnit" - ], - "ld_context": { - "md": "https://github.com/FAIRChemistry/MTPHandler" - } - } - ], - "ld_id": "OBO:UO_0000031", - "ld_type": [ - "OBO:UO_0000000" - ], - "ld_context": { - "md": "https://github.com/FAIRChemistry/MTPHandler" - } - }, - "is_simulated": false, - "ld_id": "enzml:MeasurementData/57b6cc4c-f81b-44cc-bb90-5e5fc4450702", - "ld_type": [ - "enzml:MeasurementData" - ], - "ld_context": { - "enzml": "http://www.enzymeml.org/v2/", - "schema": "https://schema.org/", - "OBO": "http://purl.obolibrary.org/obo/", - "species_id": { - "@type": "@id" - } - } - }, - { - "species_id": "Hyc", - "initial": 0.0, - "data_unit": { - "id": null, - "name": "umol / l", - "base_units": [ - { - "kind": "mole", - "exponent": 1, - "multiplier": null, - "scale": -6.0, - "ld_id": "md:BaseUnit/b02ad738-ba90-4fad-be33-88df3b4d6217", - "ld_type": [ - "md:BaseUnit" - ], - "ld_context": { - "md": "https://github.com/FAIRChemistry/MTPHandler" - } - }, - { - "kind": "litre", - "exponent": -1, - "multiplier": null, - "scale": 1.0, - "ld_id": "md:BaseUnit/5e3848e3-b8bf-4ef6-88d2-04775d342dd6", - "ld_type": [ - "md:BaseUnit" - ], - "ld_context": { - "md": "https://github.com/FAIRChemistry/MTPHandler" - } - } - ], - "ld_id": "OBO:UO_0000064", - "ld_type": [ - "OBO:UO_0000000" - ], - "ld_context": { - "md": "https://github.com/FAIRChemistry/MTPHandler" - } - }, - "data_type": "http://purl.obolibrary.org/obo/PATO_0000033", - "prepared": 0.0, - "data": [], - "time": [], - "time_unit": { - "id": null, - "name": "s", - "base_units": [ - { - "kind": "second", - "exponent": 1, - "multiplier": 60.0, - "scale": 1.0, - "ld_id": "md:BaseUnit/0d62b5c2-bb61-4574-9653-0ac6dbc3b5c8", - "ld_type": [ - "md:BaseUnit" - ], - "ld_context": { - "md": "https://github.com/FAIRChemistry/MTPHandler" - } - } - ], - "ld_id": "OBO:UO_0000031", - "ld_type": [ - "OBO:UO_0000000" - ], - "ld_context": { - "md": "https://github.com/FAIRChemistry/MTPHandler" - } - }, - "is_simulated": false, - "ld_id": "enzml:MeasurementData/bb5d1657-5ae7-4a95-ac06-8b4ccc425e3d", - "ld_type": [ - "enzml:MeasurementData" - ], - "ld_context": { - "enzml": "http://www.enzymeml.org/v2/", - "schema": "https://schema.org/", - "OBO": "http://purl.obolibrary.org/obo/", - "species_id": { - "@type": "@id" - } - } - }, - { - "species_id": "TmSAHH", - "initial": 5.0, - "data_unit": { - "id": null, - "name": "umol / l", - "base_units": [ - { - "kind": "mole", - "exponent": 1, - "multiplier": null, - "scale": -6.0, - "ld_id": "md:BaseUnit/b02ad738-ba90-4fad-be33-88df3b4d6217", - "ld_type": [ - "md:BaseUnit" - ], - "ld_context": { - "md": "https://github.com/FAIRChemistry/MTPHandler" - } - }, - { - "kind": "litre", - "exponent": -1, - "multiplier": null, - "scale": 1.0, - "ld_id": "md:BaseUnit/5e3848e3-b8bf-4ef6-88d2-04775d342dd6", - "ld_type": [ - "md:BaseUnit" - ], - "ld_context": { - "md": "https://github.com/FAIRChemistry/MTPHandler" - } - } - ], - "ld_id": "OBO:UO_0000064", - "ld_type": [ - "OBO:UO_0000000" - ], - "ld_context": { - "md": "https://github.com/FAIRChemistry/MTPHandler" - } - }, - "data_type": "http://purl.obolibrary.org/obo/PATO_0000033", - "prepared": 5.0, - "data": [], - "time": [], - "time_unit": { - "id": null, - "name": "s", - "base_units": [ - { - "kind": "second", - "exponent": 1, - "multiplier": 60.0, - "scale": 1.0, - "ld_id": "md:BaseUnit/0d62b5c2-bb61-4574-9653-0ac6dbc3b5c8", - "ld_type": [ - "md:BaseUnit" - ], - "ld_context": { - "md": "https://github.com/FAIRChemistry/MTPHandler" - } - } - ], - "ld_id": "OBO:UO_0000031", - "ld_type": [ - "OBO:UO_0000000" - ], - "ld_context": { - "md": "https://github.com/FAIRChemistry/MTPHandler" - } - }, - "is_simulated": false, - "ld_id": "enzml:MeasurementData/b4aa2989-d17f-42cc-978e-2a2b9b108f69", - "ld_type": [ - "enzml:MeasurementData" - ], - "ld_context": { - "enzml": "http://www.enzymeml.org/v2/", - "schema": "https://schema.org/", - "OBO": "http://purl.obolibrary.org/obo/", - "species_id": { - "@type": "@id" - } - } - }, - { - "species_id": "SAH", - "initial": 200.0, - "data_unit": { - "id": null, - "name": "umol / l", - "base_units": [ - { - "kind": "mole", - "exponent": 1, - "multiplier": null, - "scale": -6.0, - "ld_id": "md:BaseUnit/b02ad738-ba90-4fad-be33-88df3b4d6217", - "ld_type": [ - "md:BaseUnit" - ], - "ld_context": { - "md": "https://github.com/FAIRChemistry/MTPHandler" - } - }, - { - "kind": "litre", - "exponent": -1, - "multiplier": null, - "scale": 1.0, - "ld_id": "md:BaseUnit/5e3848e3-b8bf-4ef6-88d2-04775d342dd6", - "ld_type": [ - "md:BaseUnit" - ], - "ld_context": { - "md": "https://github.com/FAIRChemistry/MTPHandler" - } - } - ], - "ld_id": "OBO:UO_0000064", - "ld_type": [ - "OBO:UO_0000000" - ], - "ld_context": { - "md": "https://github.com/FAIRChemistry/MTPHandler" - } - }, - "data_type": "http://purl.obolibrary.org/obo/PATO_0000033", - "prepared": 200.0, - "data": [], - "time": [], - "time_unit": { - "id": null, - "name": "s", - "base_units": [ - { - "kind": "second", - "exponent": 1, - "multiplier": 60.0, - "scale": 1.0, - "ld_id": "md:BaseUnit/0d62b5c2-bb61-4574-9653-0ac6dbc3b5c8", + "ld_id": "md:BaseUnit/49f7f5c0-1364-4e2d-b025-4944bbfdddac", "ld_type": [ "md:BaseUnit" ], @@ -11641,7 +11641,7 @@ } }, "is_simulated": false, - "ld_id": "enzml:MeasurementData/83887dfb-858a-4173-a81b-70f19b5dc597", + "ld_id": "enzml:MeasurementData/cea0876a-0211-4ef9-94f0-1a4b5869a86b", "ld_type": [ "enzml:MeasurementData" ], @@ -11667,7 +11667,7 @@ "exponent": 1, "multiplier": null, "scale": 1.0, - "ld_id": "md:BaseUnit/b85e7df2-91c7-4053-8f1e-7ca0084e8f3b", + "ld_id": "md:BaseUnit/20052bb1-27f2-4381-8471-04397c4d54bd", "ld_type": [ "md:BaseUnit" ], @@ -11676,7 +11676,7 @@ } } ], - "ld_id": "md:UnitDefinition/fe60fc54-3434-45e8-9f6c-209a362451b7", + "ld_id": "md:UnitDefinition/ce4c4f8f-2f77-4742-8019-a843971fafd8", "ld_type": [ "OBO:UO_0000000" ], @@ -11684,7 +11684,7 @@ "md": "https://github.com/FAIRChemistry/MTPHandler" } }, - "ld_id": "enzml:Measurement/c7afd438-d8db-4b0a-9d3a-a90f06961ebf", + "ld_id": "enzml:Measurement/641891db-8f42-4156-8961-3133f526fd32", "ld_type": [ "enzml:Measurement" ], @@ -11704,7 +11704,7 @@ ], "equations": [], "parameters": [], - "ld_id": "enzml:EnzymeMLDocument/fd4c9792-95e8-40e5-a4ef-cd0f2cdb3a93", + "ld_id": "enzml:EnzymeMLDocument/1003e96e-2fff-464d-814f-842a0a2bf0ab", "ld_type": [ "enzml:EnzymeMLDocument" ], diff --git a/pyproject.toml b/pyproject.toml index e822e1a..4567c7d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -5,7 +5,7 @@ description = "Tool to work with microtiter plate data." authors = ["haeussma <83341109+haeussma@users.noreply.github.com>"] license = "MIT License" readme = "README.md" -packages = [{ include = "mtphandler" }] +packages = [{ include = "MTPHandler" }] include = ["mtphandler/units/ontomaps.toml"] From b4aaaa627de960b21ebfe17c1a3d550a7695acb8 Mon Sep 17 00:00:00 2001 From: haeussma <83341109+haeussma@users.noreply.github.com> Date: Fri, 27 Sep 2024 18:08:02 +0200 Subject: [PATCH 2/6] Refactor package name in pyproject.toml --- docs/examples/data/enzymeml_TmSAHH_SAH.json | 6034 +++++++++---------- pyproject.toml | 2 +- 2 files changed, 3018 insertions(+), 3018 deletions(-) diff --git a/docs/examples/data/enzymeml_TmSAHH_SAH.json b/docs/examples/data/enzymeml_TmSAHH_SAH.json index 1c02334..7ddcb40 100644 --- a/docs/examples/data/enzymeml_TmSAHH_SAH.json +++ b/docs/examples/data/enzymeml_TmSAHH_SAH.json @@ -18,7 +18,7 @@ "exponent": 1, "multiplier": null, "scale": 1.0, - "ld_id": "enzml:BaseUnit/81c05bc9-70c3-4f29-ad33-00f966715729", + "ld_id": "enzml:BaseUnit/02b35b91-7bce-483b-9ceb-e014d76f0c1a", "ld_type": [ "enzml:BaseUnit" ], @@ -29,7 +29,7 @@ } } ], - "ld_id": "enzml:UnitDefinition/361dc948-8bed-4388-961c-acb6fa45804a", + "ld_id": "enzml:UnitDefinition/e5a4d4cc-b42d-4f49-8de2-762969247e91", "ld_type": [ "OBO:UO_0000000" ], @@ -40,7 +40,7 @@ } }, "constant": true, - "ld_id": "enzml:Vessel/c42db070-f545-4b32-9af7-2e28fe60f695", + "ld_id": "enzml:Vessel/04116260-8ead-4ffe-803f-e2ffe544462e", "ld_type": [ "enzml:Vessel", "OBO:OBI_0400081" @@ -69,7 +69,7 @@ "organism": null, "organism_tax_id": null, "references": [], - "ld_id": "enzml:Protein/e37cd02b-5970-4148-9da7-ec235bf289d8", + "ld_id": "enzml:Protein/71015437-943f-47a8-a984-19cb4c28c361", "ld_type": [ "enzml:Protein", "schema:Protein" @@ -107,7 +107,7 @@ "organism": null, "organism_tax_id": null, "references": [], - "ld_id": "enzml:Protein/30bed91a-58e6-474d-8353-182cf5f71bfb", + "ld_id": "enzml:Protein/e6d94d0c-9f4e-4512-877e-f3b513512676", "ld_type": [ "enzml:Protein", "schema:Protein" @@ -145,7 +145,7 @@ "organism": null, "organism_tax_id": null, "references": [], - "ld_id": "enzml:Protein/07beb141-f4e1-4f32-93f6-94b5667ef86a", + "ld_id": "enzml:Protein/8c065b9f-2ac7-452a-91c1-e1210cf3dfd4", "ld_type": [ "enzml:Protein", "schema:Protein" @@ -183,7 +183,7 @@ "organism": null, "organism_tax_id": null, "references": [], - "ld_id": "enzml:Protein/42d4da0d-eed3-44a9-874d-d14ac9c03bf7", + "ld_id": "enzml:Protein/58e92cdc-1d39-4ec0-801b-d6300407805b", "ld_type": [ "enzml:Protein", "schema:Protein" @@ -223,7 +223,7 @@ "inchi": null, "inchikey": null, "references": [], - "ld_id": "enzml:SmallMolecule/fba052b8-88dd-4416-9942-d2dc37c57d69", + "ld_id": "enzml:SmallMolecule/a18cec50-7806-45e8-a1c3-5f1437bf0c08", "ld_type": [ "enzml:SmallMolecule" ], @@ -425,7 +425,7 @@ "exponent": 1, "multiplier": null, "scale": -6.0, - "ld_id": "md:BaseUnit/4c434b8c-d129-474b-82bc-e2780b03f8d0", + "ld_id": "md:BaseUnit/7403b5e7-0ee0-473c-9189-530cccc435d3", "ld_type": [ "md:BaseUnit" ], @@ -438,7 +438,7 @@ "exponent": -1, "multiplier": null, "scale": 1.0, - "ld_id": "md:BaseUnit/ca6f41aa-5b10-4012-b989-5ab8cbf023b0", + "ld_id": "md:BaseUnit/c4b90fd7-47a4-4116-b5c5-fe5a34aabb29", "ld_type": [ "md:BaseUnit" ], @@ -468,7 +468,7 @@ "exponent": 1, "multiplier": 60.0, "scale": 1.0, - "ld_id": "md:BaseUnit/49f7f5c0-1364-4e2d-b025-4944bbfdddac", + "ld_id": "md:BaseUnit/dff722b4-d69f-4d21-b1d6-82bc7c5e05a6", "ld_type": [ "md:BaseUnit" ], @@ -486,7 +486,7 @@ } }, "is_simulated": false, - "ld_id": "enzml:MeasurementData/a1bbe0d1-102e-497d-a4be-cf3a1413b6b3", + "ld_id": "enzml:MeasurementData/e677ac8e-6d33-4179-9980-bb26ba91599c", "ld_type": [ "enzml:MeasurementData" ], @@ -511,7 +511,7 @@ "exponent": 1, "multiplier": null, "scale": -6.0, - "ld_id": "md:BaseUnit/4c434b8c-d129-474b-82bc-e2780b03f8d0", + "ld_id": "md:BaseUnit/7403b5e7-0ee0-473c-9189-530cccc435d3", "ld_type": [ "md:BaseUnit" ], @@ -524,7 +524,7 @@ "exponent": -1, "multiplier": null, "scale": 1.0, - "ld_id": "md:BaseUnit/ca6f41aa-5b10-4012-b989-5ab8cbf023b0", + "ld_id": "md:BaseUnit/c4b90fd7-47a4-4116-b5c5-fe5a34aabb29", "ld_type": [ "md:BaseUnit" ], @@ -554,7 +554,7 @@ "exponent": 1, "multiplier": 60.0, "scale": 1.0, - "ld_id": "md:BaseUnit/49f7f5c0-1364-4e2d-b025-4944bbfdddac", + "ld_id": "md:BaseUnit/dff722b4-d69f-4d21-b1d6-82bc7c5e05a6", "ld_type": [ "md:BaseUnit" ], @@ -572,7 +572,7 @@ } }, "is_simulated": false, - "ld_id": "enzml:MeasurementData/ef69eda3-bc49-4974-9ac3-e965e97ce289", + "ld_id": "enzml:MeasurementData/3f40c4a6-648b-4f38-a9d6-a37fa718ed5f", "ld_type": [ "enzml:MeasurementData" ], @@ -587,7 +587,7 @@ }, { "species_id": "TNB", - "initial": 0.0, + "initial": -1.7261984578282223, "data_unit": { "id": null, "name": "umol / l", @@ -597,7 +597,7 @@ "exponent": 1, "multiplier": null, "scale": -6.0, - "ld_id": "md:BaseUnit/4c434b8c-d129-474b-82bc-e2780b03f8d0", + "ld_id": "md:BaseUnit/7403b5e7-0ee0-473c-9189-530cccc435d3", "ld_type": [ "md:BaseUnit" ], 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177.11443142070442, + 177.0628491667004, + 177.04995385741967, + 176.99837363484554, + 176.933900633533, + 176.9467950318184, + 176.92100633608072, 176.85653635859796, 176.85653635859796, - 176.79206889029356, - 176.75338960967912, - 176.74049671573664, - 176.68892613587542, - 176.68892613587542, - 176.66314144240386, - 176.57289813607548, - 176.611573245276, + 176.79206889029354, + 176.75338960967915, + 176.7404967157366, + 176.6889261358754, + 176.6889261358754, + 176.66314144240383, + 176.5728981360755, + 176.61157324527596, 176.54711522337186, 176.45687812775176, 176.48265966409616, 176.4439875065623, 176.40531622999532, - 176.3666458323039, - 176.3150866655746, - 176.26352905261874, + 176.36664583230393, + 176.31508666557463, + 176.2635290526187, 176.25063989157636, 176.18619553567498, 176.21197298848293, - 176.1475300787975, + 176.14753007879747, 176.0830895717375, 176.09597748140342, 176.0830895717375, @@ -11623,7 +11623,7 @@ "exponent": 1, "multiplier": 60.0, "scale": 1.0, - "ld_id": "md:BaseUnit/49f7f5c0-1364-4e2d-b025-4944bbfdddac", + "ld_id": "md:BaseUnit/dff722b4-d69f-4d21-b1d6-82bc7c5e05a6", "ld_type": [ "md:BaseUnit" ], @@ -11641,7 +11641,7 @@ } }, "is_simulated": false, - "ld_id": "enzml:MeasurementData/cea0876a-0211-4ef9-94f0-1a4b5869a86b", + "ld_id": "enzml:MeasurementData/00b49427-8d8b-4526-8845-39cb38fa3f71", "ld_type": [ "enzml:MeasurementData" ], @@ -11667,7 +11667,7 @@ "exponent": 1, "multiplier": null, "scale": 1.0, - "ld_id": "md:BaseUnit/20052bb1-27f2-4381-8471-04397c4d54bd", + "ld_id": "md:BaseUnit/44128ba3-fd53-4196-838c-eb98bd83057e", "ld_type": [ "md:BaseUnit" ], @@ -11676,7 +11676,7 @@ } } ], - "ld_id": "md:UnitDefinition/ce4c4f8f-2f77-4742-8019-a843971fafd8", + "ld_id": "md:UnitDefinition/73c1b9d4-e3a1-4ed7-8ac8-881a0523e981", "ld_type": [ "OBO:UO_0000000" ], @@ -11684,7 +11684,7 @@ "md": "https://github.com/FAIRChemistry/MTPHandler" } }, - "ld_id": "enzml:Measurement/641891db-8f42-4156-8961-3133f526fd32", + "ld_id": "enzml:Measurement/64082fcf-5925-4cad-97d7-773ef09416ed", "ld_type": [ "enzml:Measurement" ], @@ -11704,7 +11704,7 @@ ], "equations": [], "parameters": [], - "ld_id": "enzml:EnzymeMLDocument/1003e96e-2fff-464d-814f-842a0a2bf0ab", + "ld_id": "enzml:EnzymeMLDocument/8cd42716-9bfc-4a97-b62c-3ff72ff9f386", "ld_type": [ "enzml:EnzymeMLDocument" ], diff --git a/pyproject.toml b/pyproject.toml index 4567c7d..e822e1a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -5,7 +5,7 @@ description = "Tool to work with microtiter plate data." authors = ["haeussma <83341109+haeussma@users.noreply.github.com>"] license = "MIT License" readme = "README.md" -packages = [{ include = "MTPHandler" }] +packages = [{ include = "mtphandler" }] include = ["mtphandler/units/ontomaps.toml"] From f27d1aa52d5fb2c044fbbcc5f0e170107a9b6583 Mon Sep 17 00:00:00 2001 From: haeussma <83341109+haeussma@users.noreply.github.com> Date: Fri, 27 Sep 2024 18:12:55 +0200 Subject: [PATCH 3/6] Refactor pyenzyme.py and SAHH_kinetics.ipynb --- docs/examples/SAHH_kinetics.ipynb | 73 +- docs/examples/data/enzymeml_TmSAHH_SAH.json | 2152 +++++++++---------- mtphandler/ioutils/pyenzyme.py | 1 - 3 files changed, 1107 insertions(+), 1119 deletions(-) diff --git a/docs/examples/SAHH_kinetics.ipynb b/docs/examples/SAHH_kinetics.ipynb index 7f553a2..ac55366 100644 --- a/docs/examples/SAHH_kinetics.ipynb +++ b/docs/examples/SAHH_kinetics.ipynb @@ -92,6 +92,20 @@ "cell_type": "code", "execution_count": 2, "metadata": {}, + "outputs": [], + "source": [ + "from mtphandler.molecule import Protein\n", + "\n", + "my_variant = Protein(\n", + " id=\"L191G\",\n", + " name=\"L191G\",\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, "outputs": [ { "data": { @@ -144486,7 +144500,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 4, "metadata": {}, "outputs": [], "source": [ @@ -144528,7 +144542,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 5, "metadata": {}, "outputs": [], "source": [ @@ -144572,19 +144586,19 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 6, "metadata": {}, "outputs": [ { "data": { "text/html": [ - "
📍 Assigned 228 initial concentration coditions for ['TmSAHH', 'SIH', 'McSAHH', 'BUFFER', 'MhSAHH', 'SAH', 'Hyc', \n",
-       "'MtSAHH', 'DTNB', 'TNB'] from data/plate_map_SAHH_kinetics.xlsx to the plate.\n",
+       "
📍 Assigned 228 initial concentration coditions for ['SAH', 'MhSAHH', 'SIH', 'Hyc', 'MtSAHH', 'BUFFER', 'McSAHH', \n",
+       "'TmSAHH', 'DTNB', 'TNB'] from data/plate_map_SAHH_kinetics.xlsx to the plate.\n",
        "
\n"
       ],
       "text/plain": [
-       "📍 Assigned \u001b[1;36m228\u001b[0m initial concentration coditions for \u001b[1;35m[\u001b[0m\u001b[1;35m'TmSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'SIH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'McSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'BUFFER'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'MhSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'SAH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'Hyc'\u001b[0m\u001b[1;35m, \u001b[0m\n",
-       "\u001b[1;35m'MtSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'DTNB'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'TNB'\u001b[0m\u001b[1;35m]\u001b[0m from data/plate_map_SAHH_kinetics.xlsx to the plate.\n"
+       "📍 Assigned \u001b[1;36m228\u001b[0m initial concentration coditions for \u001b[1;35m[\u001b[0m\u001b[1;35m'SAH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'MhSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'SIH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'Hyc'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'MtSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'BUFFER'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'McSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\n",
+       "\u001b[1;35m'TmSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'DTNB'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'TNB'\u001b[0m\u001b[1;35m]\u001b[0m from data/plate_map_SAHH_kinetics.xlsx to the plate.\n"
       ]
      },
      "metadata": {},
@@ -144620,7 +144634,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {
@@ -144837,7 +144851,9 @@
     "plate.blank_species(BUFFER)\n",
     "\n",
     "# Then the all other species\n",
-    "plate.blank_species(SAH)\n",
+    "plate.blank_species(\n",
+    "    SAH,\n",
+    ")\n",
     "plate.blank_species(SIH)\n",
     "plate.blank_species(McSAHH)\n",
     "plate.blank_species(MtSAHH)\n",
@@ -144858,7 +144874,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [
     {
@@ -144898,7 +144914,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [
     {
@@ -147666,7 +147682,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -147701,40 +147717,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "added temp unit s\n",
-      "added temp unit s\n",
-      "added temp unit s\n",
-      "added temp unit s\n",
-      "added temp unit s\n",
-      "added temp unit s\n",
-      "added temp unit s\n",
-      "added temp unit s\n",
-      "added temp unit s\n",
-      "added temp unit s\n",
-      "added temp unit s\n",
-      "added temp unit s\n",
-      "added temp unit s\n",
-      "added temp unit s\n",
-      "added temp unit s\n",
-      "added temp unit s\n",
-      "added temp unit s\n",
-      "added temp unit s\n",
-      "added temp unit s\n",
-      "added temp unit s\n",
-      "added temp unit s\n",
-      "added temp unit s\n",
-      "added temp unit s\n",
-      "added temp unit s\n",
-      "added temp unit s\n",
-      "added temp unit s\n",
-      "added temp unit s\n",
       "✅ Added measurements from 6 wells with concentration values to EnzymeMLDocument\n"
      ]
     }
@@ -147759,7 +147748,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [
     {
@@ -147818,7 +147807,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 13,
    "metadata": {},
    "outputs": [],
    "source": [
diff --git a/docs/examples/data/enzymeml_TmSAHH_SAH.json b/docs/examples/data/enzymeml_TmSAHH_SAH.json
index 7ddcb40..6b48bbd 100644
--- a/docs/examples/data/enzymeml_TmSAHH_SAH.json
+++ b/docs/examples/data/enzymeml_TmSAHH_SAH.json
@@ -18,7 +18,7 @@
                         "exponent": 1,
                         "multiplier": null,
                         "scale": 1.0,
-                        "ld_id": "enzml:BaseUnit/02b35b91-7bce-483b-9ceb-e014d76f0c1a",
+                        "ld_id": "enzml:BaseUnit/7507fc3b-6f31-4ce7-99e4-3df87993a41c",
                         "ld_type": [
                             "enzml:BaseUnit"
                         ],
@@ -29,7 +29,7 @@
                         }
                     }
                 ],
-                "ld_id": "enzml:UnitDefinition/e5a4d4cc-b42d-4f49-8de2-762969247e91",
+                "ld_id": "enzml:UnitDefinition/2d99c27f-949b-40f8-acb9-02e22fd46fc5",
                 "ld_type": [
                     "OBO:UO_0000000"
                 ],
@@ -40,7 +40,7 @@
                 }
             },
             "constant": true,
-            "ld_id": "enzml:Vessel/04116260-8ead-4ffe-803f-e2ffe544462e",
+            "ld_id": "enzml:Vessel/2c2bacab-9361-4a5a-bfc9-25ef526dc2f0",
             "ld_type": [
                 "enzml:Vessel",
                 "OBO:OBI_0400081"
@@ -69,7 +69,7 @@
             "organism": null,
             "organism_tax_id": null,
             "references": [],
-            "ld_id": "enzml:Protein/71015437-943f-47a8-a984-19cb4c28c361",
+            "ld_id": "enzml:Protein/4e6f2068-6568-4dc8-8bad-5ca5b43ac58b",
             "ld_type": [
                 "enzml:Protein",
                 "schema:Protein"
@@ -107,7 +107,7 @@
             "organism": null,
             "organism_tax_id": null,
             "references": [],
-            "ld_id": "enzml:Protein/e6d94d0c-9f4e-4512-877e-f3b513512676",
+            "ld_id": "enzml:Protein/7acc8306-c72d-46ef-b880-ab42b59c4d76",
             "ld_type": [
                 "enzml:Protein",
                 "schema:Protein"
@@ -145,7 +145,7 @@
             "organism": null,
             "organism_tax_id": null,
             "references": [],
-            "ld_id": "enzml:Protein/8c065b9f-2ac7-452a-91c1-e1210cf3dfd4",
+            "ld_id": "enzml:Protein/fedc65c2-97f9-40e1-b78a-deef15e47ae8",
             "ld_type": [
                 "enzml:Protein",
                 "schema:Protein"
@@ -183,7 +183,7 @@
             "organism": null,
             "organism_tax_id": null,
             "references": [],
-            "ld_id": "enzml:Protein/58e92cdc-1d39-4ec0-801b-d6300407805b",
+            "ld_id": "enzml:Protein/a407c986-a00e-4921-921b-2fc5b25c8314",
             "ld_type": [
                 "enzml:Protein",
                 "schema:Protein"
@@ -223,7 +223,7 @@
             "inchi": null,
             "inchikey": null,
             "references": [],
-            "ld_id": "enzml:SmallMolecule/a18cec50-7806-45e8-a1c3-5f1437bf0c08",
+            "ld_id": "enzml:SmallMolecule/014feb9b-1b64-4208-9c73-9bf56f5d1c79",
             "ld_type": [
                 "enzml:SmallMolecule"
             ],
@@ -425,7 +425,7 @@
                                 "exponent": 1,
                                 "multiplier": null,
                                 "scale": -6.0,
-                                "ld_id": "md:BaseUnit/7403b5e7-0ee0-473c-9189-530cccc435d3",
+                                "ld_id": "md:BaseUnit/992794ac-a609-4aa3-b945-577985bf5b56",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -438,7 +438,7 @@
                                 "exponent": -1,
                                 "multiplier": null,
                                 "scale": 1.0,
-                                "ld_id": "md:BaseUnit/c4b90fd7-47a4-4116-b5c5-fe5a34aabb29",
+                                "ld_id": "md:BaseUnit/bcbe0316-c8f1-468f-9c77-2fc254ead666",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -468,7 +468,7 @@
                                 "exponent": 1,
                                 "multiplier": 60.0,
                                 "scale": 1.0,
-                                "ld_id": "md:BaseUnit/dff722b4-d69f-4d21-b1d6-82bc7c5e05a6",
+                                "ld_id": "md:BaseUnit/e03d4232-6697-4aef-aed7-f4a700a9f7f0",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -486,93 +486,7 @@
                         }
                     },
                     "is_simulated": false,
-                    "ld_id": "enzml:MeasurementData/e677ac8e-6d33-4179-9980-bb26ba91599c",
-                    "ld_type": [
-                        "enzml:MeasurementData"
-                    ],
-                    "ld_context": {
-                        "enzml": "http://www.enzymeml.org/v2/",
-                        "schema": "https://schema.org/",
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-                    "species_id": "DTNB",
-                    "initial": 500.0,
+                    "species_id": "Hyc",
+                    "initial": 0.0,
                     "data_unit": {
                         "id": null,
                         "name": "umol / l",
@@ -9964,7 +9706,7 @@
                                 "exponent": 1,
                                 "multiplier": null,
                                 "scale": -6.0,
-                                "ld_id": "md:BaseUnit/7403b5e7-0ee0-473c-9189-530cccc435d3",
+                                "ld_id": "md:BaseUnit/992794ac-a609-4aa3-b945-577985bf5b56",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -9977,7 +9719,7 @@
                                 "exponent": -1,
                                 "multiplier": null,
                                 "scale": 1.0,
-                                "ld_id": "md:BaseUnit/c4b90fd7-47a4-4116-b5c5-fe5a34aabb29",
+                                "ld_id": "md:BaseUnit/bcbe0316-c8f1-468f-9c77-2fc254ead666",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -9995,7 +9737,7 @@
                         }
                     },
                     "data_type": "http://purl.obolibrary.org/obo/PATO_0000033",
-                    "prepared": 500.0,
+                    "prepared": 0.0,
                     "data": [],
                     "time": [],
                     "time_unit": {
@@ -10007,7 +9749,7 @@
                                 "exponent": 1,
                                 "multiplier": 60.0,
                                 "scale": 1.0,
-                                "ld_id": "md:BaseUnit/dff722b4-d69f-4d21-b1d6-82bc7c5e05a6",
+                                "ld_id": "md:BaseUnit/e03d4232-6697-4aef-aed7-f4a700a9f7f0",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -10025,7 +9767,7 @@
                         }
                     },
                     "is_simulated": false,
-                    "ld_id": "enzml:MeasurementData/badd5f01-096a-46b3-a7b3-26d4602a9869",
+                    "ld_id": "enzml:MeasurementData/6aa3013c-1fef-4334-b15c-de878d3b2c03",
                     "ld_type": [
                         "enzml:MeasurementData"
                     ],
@@ -10039,8 +9781,8 @@
                     }
                 },
                 {
-                    "species_id": "Hyc",
-                    "initial": 0.0,
+                    "species_id": "BUFFER",
+                    "initial": 50.0,
                     "data_unit": {
                         "id": null,
                         "name": "umol / l",
@@ -10050,7 +9792,7 @@
                                 "exponent": 1,
                                 "multiplier": null,
                                 "scale": -6.0,
-                                "ld_id": "md:BaseUnit/7403b5e7-0ee0-473c-9189-530cccc435d3",
+                                "ld_id": "md:BaseUnit/992794ac-a609-4aa3-b945-577985bf5b56",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -10063,7 +9805,7 @@
                                 "exponent": -1,
                                 "multiplier": null,
                                 "scale": 1.0,
-                                "ld_id": "md:BaseUnit/c4b90fd7-47a4-4116-b5c5-fe5a34aabb29",
+                                "ld_id": "md:BaseUnit/bcbe0316-c8f1-468f-9c77-2fc254ead666",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -10081,7 +9823,7 @@
                         }
                     },
                     "data_type": "http://purl.obolibrary.org/obo/PATO_0000033",
-                    "prepared": 0.0,
+                    "prepared": 50.0,
                     "data": [],
                     "time": [],
                     "time_unit": {
@@ -10093,7 +9835,7 @@
                                 "exponent": 1,
                                 "multiplier": 60.0,
                                 "scale": 1.0,
-                                "ld_id": "md:BaseUnit/dff722b4-d69f-4d21-b1d6-82bc7c5e05a6",
+                                "ld_id": "md:BaseUnit/e03d4232-6697-4aef-aed7-f4a700a9f7f0",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -10111,7 +9853,7 @@
                         }
                     },
                     "is_simulated": false,
-                    "ld_id": "enzml:MeasurementData/c16000da-8e43-4f5d-a520-b696256e0063",
+                    "ld_id": "enzml:MeasurementData/b541ae2b-5c8c-4956-b6ae-ae59440643c6",
                     "ld_type": [
                         "enzml:MeasurementData"
                     ],
@@ -10136,7 +9878,7 @@
                                 "exponent": 1,
                                 "multiplier": null,
                                 "scale": -6.0,
-                                "ld_id": "md:BaseUnit/7403b5e7-0ee0-473c-9189-530cccc435d3",
+                                "ld_id": "md:BaseUnit/992794ac-a609-4aa3-b945-577985bf5b56",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -10149,7 +9891,7 @@
                                 "exponent": -1,
                                 "multiplier": null,
                                 "scale": 1.0,
-                                "ld_id": "md:BaseUnit/c4b90fd7-47a4-4116-b5c5-fe5a34aabb29",
+                                "ld_id": "md:BaseUnit/bcbe0316-c8f1-468f-9c77-2fc254ead666",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -11623,7 +11365,265 @@
                                 "exponent": 1,
                                 "multiplier": 60.0,
                                 "scale": 1.0,
-                                "ld_id": "md:BaseUnit/dff722b4-d69f-4d21-b1d6-82bc7c5e05a6",
+                                "ld_id": "md:BaseUnit/e03d4232-6697-4aef-aed7-f4a700a9f7f0",
+                                "ld_type": [
+                                    "md:BaseUnit"
+                                ],
+                                "ld_context": {
+                                    "md": "https://github.com/FAIRChemistry/MTPHandler"
+                                }
+                            }
+                        ],
+                        "ld_id": "OBO:UO_0000031",
+                        "ld_type": [
+                            "OBO:UO_0000000"
+                        ],
+                        "ld_context": {
+                            "md": "https://github.com/FAIRChemistry/MTPHandler"
+                        }
+                    },
+                    "is_simulated": false,
+                    "ld_id": "enzml:MeasurementData/529a830f-8622-4a93-a841-5cd85f9ee7f0",
+                    "ld_type": [
+                        "enzml:MeasurementData"
+                    ],
+                    "ld_context": {
+                        "enzml": "http://www.enzymeml.org/v2/",
+                        "schema": "https://schema.org/",
+                        "OBO": "http://purl.obolibrary.org/obo/",
+                        "species_id": {
+                            "@type": "@id"
+                        }
+                    }
+                },
+                {
+                    "species_id": "SAH",
+                    "initial": 200.0,
+                    "data_unit": {
+                        "id": null,
+                        "name": "umol / l",
+                        "base_units": [
+                            {
+                                "kind": "mole",
+                                "exponent": 1,
+                                "multiplier": null,
+                                "scale": -6.0,
+                                "ld_id": "md:BaseUnit/992794ac-a609-4aa3-b945-577985bf5b56",
+                                "ld_type": [
+                                    "md:BaseUnit"
+                                ],
+                                "ld_context": {
+                                    "md": "https://github.com/FAIRChemistry/MTPHandler"
+                                }
+                            },
+                            {
+                                "kind": "litre",
+                                "exponent": -1,
+                                "multiplier": null,
+                                "scale": 1.0,
+                                "ld_id": "md:BaseUnit/bcbe0316-c8f1-468f-9c77-2fc254ead666",
+                                "ld_type": [
+                                    "md:BaseUnit"
+                                ],
+                                "ld_context": {
+                                    "md": "https://github.com/FAIRChemistry/MTPHandler"
+                                }
+                            }
+                        ],
+                        "ld_id": "OBO:UO_0000064",
+                        "ld_type": [
+                            "OBO:UO_0000000"
+                        ],
+                        "ld_context": {
+                            "md": "https://github.com/FAIRChemistry/MTPHandler"
+                        }
+                    },
+                    "data_type": "http://purl.obolibrary.org/obo/PATO_0000033",
+                    "prepared": 200.0,
+                    "data": [],
+                    "time": [],
+                    "time_unit": {
+                        "id": null,
+                        "name": "s",
+                        "base_units": [
+                            {
+                                "kind": "second",
+                                "exponent": 1,
+                                "multiplier": 60.0,
+                                "scale": 1.0,
+                                "ld_id": "md:BaseUnit/e03d4232-6697-4aef-aed7-f4a700a9f7f0",
+                                "ld_type": [
+                                    "md:BaseUnit"
+                                ],
+                                "ld_context": {
+                                    "md": "https://github.com/FAIRChemistry/MTPHandler"
+                                }
+                            }
+                        ],
+                        "ld_id": "OBO:UO_0000031",
+                        "ld_type": [
+                            "OBO:UO_0000000"
+                        ],
+                        "ld_context": {
+                            "md": "https://github.com/FAIRChemistry/MTPHandler"
+                        }
+                    },
+                    "is_simulated": false,
+                    "ld_id": "enzml:MeasurementData/77bb27c6-8023-4f8b-843f-ded739c6dd73",
+                    "ld_type": [
+                        "enzml:MeasurementData"
+                    ],
+                    "ld_context": {
+                        "enzml": "http://www.enzymeml.org/v2/",
+                        "schema": "https://schema.org/",
+                        "OBO": "http://purl.obolibrary.org/obo/",
+                        "species_id": {
+                            "@type": "@id"
+                        }
+                    }
+                },
+                {
+                    "species_id": "TmSAHH",
+                    "initial": 5.0,
+                    "data_unit": {
+                        "id": null,
+                        "name": "umol / l",
+                        "base_units": [
+                            {
+                                "kind": "mole",
+                                "exponent": 1,
+                                "multiplier": null,
+                                "scale": -6.0,
+                                "ld_id": "md:BaseUnit/992794ac-a609-4aa3-b945-577985bf5b56",
+                                "ld_type": [
+                                    "md:BaseUnit"
+                                ],
+                                "ld_context": {
+                                    "md": "https://github.com/FAIRChemistry/MTPHandler"
+                                }
+                            },
+                            {
+                                "kind": "litre",
+                                "exponent": -1,
+                                "multiplier": null,
+                                "scale": 1.0,
+                                "ld_id": "md:BaseUnit/bcbe0316-c8f1-468f-9c77-2fc254ead666",
+                                "ld_type": [
+                                    "md:BaseUnit"
+                                ],
+                                "ld_context": {
+                                    "md": "https://github.com/FAIRChemistry/MTPHandler"
+                                }
+                            }
+                        ],
+                        "ld_id": "OBO:UO_0000064",
+                        "ld_type": [
+                            "OBO:UO_0000000"
+                        ],
+                        "ld_context": {
+                            "md": "https://github.com/FAIRChemistry/MTPHandler"
+                        }
+                    },
+                    "data_type": "http://purl.obolibrary.org/obo/PATO_0000033",
+                    "prepared": 5.0,
+                    "data": [],
+                    "time": [],
+                    "time_unit": {
+                        "id": null,
+                        "name": "s",
+                        "base_units": [
+                            {
+                                "kind": "second",
+                                "exponent": 1,
+                                "multiplier": 60.0,
+                                "scale": 1.0,
+                                "ld_id": "md:BaseUnit/e03d4232-6697-4aef-aed7-f4a700a9f7f0",
+                                "ld_type": [
+                                    "md:BaseUnit"
+                                ],
+                                "ld_context": {
+                                    "md": "https://github.com/FAIRChemistry/MTPHandler"
+                                }
+                            }
+                        ],
+                        "ld_id": "OBO:UO_0000031",
+                        "ld_type": [
+                            "OBO:UO_0000000"
+                        ],
+                        "ld_context": {
+                            "md": "https://github.com/FAIRChemistry/MTPHandler"
+                        }
+                    },
+                    "is_simulated": false,
+                    "ld_id": "enzml:MeasurementData/b8ade515-0564-4685-917b-ef79f09213c6",
+                    "ld_type": [
+                        "enzml:MeasurementData"
+                    ],
+                    "ld_context": {
+                        "enzml": "http://www.enzymeml.org/v2/",
+                        "schema": "https://schema.org/",
+                        "OBO": "http://purl.obolibrary.org/obo/",
+                        "species_id": {
+                            "@type": "@id"
+                        }
+                    }
+                },
+                {
+                    "species_id": "DTNB",
+                    "initial": 500.0,
+                    "data_unit": {
+                        "id": null,
+                        "name": "umol / l",
+                        "base_units": [
+                            {
+                                "kind": "mole",
+                                "exponent": 1,
+                                "multiplier": null,
+                                "scale": -6.0,
+                                "ld_id": "md:BaseUnit/992794ac-a609-4aa3-b945-577985bf5b56",
+                                "ld_type": [
+                                    "md:BaseUnit"
+                                ],
+                                "ld_context": {
+                                    "md": "https://github.com/FAIRChemistry/MTPHandler"
+                                }
+                            },
+                            {
+                                "kind": "litre",
+                                "exponent": -1,
+                                "multiplier": null,
+                                "scale": 1.0,
+                                "ld_id": "md:BaseUnit/bcbe0316-c8f1-468f-9c77-2fc254ead666",
+                                "ld_type": [
+                                    "md:BaseUnit"
+                                ],
+                                "ld_context": {
+                                    "md": "https://github.com/FAIRChemistry/MTPHandler"
+                                }
+                            }
+                        ],
+                        "ld_id": "OBO:UO_0000064",
+                        "ld_type": [
+                            "OBO:UO_0000000"
+                        ],
+                        "ld_context": {
+                            "md": "https://github.com/FAIRChemistry/MTPHandler"
+                        }
+                    },
+                    "data_type": "http://purl.obolibrary.org/obo/PATO_0000033",
+                    "prepared": 500.0,
+                    "data": [],
+                    "time": [],
+                    "time_unit": {
+                        "id": null,
+                        "name": "s",
+                        "base_units": [
+                            {
+                                "kind": "second",
+                                "exponent": 1,
+                                "multiplier": 60.0,
+                                "scale": 1.0,
+                                "ld_id": "md:BaseUnit/e03d4232-6697-4aef-aed7-f4a700a9f7f0",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -11641,7 +11641,7 @@
                         }
                     },
                     "is_simulated": false,
-                    "ld_id": "enzml:MeasurementData/00b49427-8d8b-4526-8845-39cb38fa3f71",
+                    "ld_id": "enzml:MeasurementData/7a3c944e-98a4-4081-8158-c568833e4c1c",
                     "ld_type": [
                         "enzml:MeasurementData"
                     ],
@@ -11667,7 +11667,7 @@
                         "exponent": 1,
                         "multiplier": null,
                         "scale": 1.0,
-                        "ld_id": "md:BaseUnit/44128ba3-fd53-4196-838c-eb98bd83057e",
+                        "ld_id": "md:BaseUnit/d6cfa323-be66-4591-84d9-570e831169f8",
                         "ld_type": [
                             "md:BaseUnit"
                         ],
@@ -11676,7 +11676,7 @@
                         }
                     }
                 ],
-                "ld_id": "md:UnitDefinition/73c1b9d4-e3a1-4ed7-8ac8-881a0523e981",
+                "ld_id": "md:UnitDefinition/31f16537-09de-4045-ae55-ad3197ffcb70",
                 "ld_type": [
                     "OBO:UO_0000000"
                 ],
@@ -11684,7 +11684,7 @@
                     "md": "https://github.com/FAIRChemistry/MTPHandler"
                 }
             },
-            "ld_id": "enzml:Measurement/64082fcf-5925-4cad-97d7-773ef09416ed",
+            "ld_id": "enzml:Measurement/a1394bfd-038b-413d-aafb-2c28f8a3f465",
             "ld_type": [
                 "enzml:Measurement"
             ],
@@ -11704,7 +11704,7 @@
     ],
     "equations": [],
     "parameters": [],
-    "ld_id": "enzml:EnzymeMLDocument/8cd42716-9bfc-4a97-b62c-3ff72ff9f386",
+    "ld_id": "enzml:EnzymeMLDocument/01d7bf76-39ee-42af-987b-2a1b46c13e6a",
     "ld_type": [
         "enzml:EnzymeMLDocument"
     ],
diff --git a/mtphandler/ioutils/pyenzyme.py b/mtphandler/ioutils/pyenzyme.py
index 3de83ca..6c37522 100644
--- a/mtphandler/ioutils/pyenzyme.py
+++ b/mtphandler/ioutils/pyenzyme.py
@@ -367,7 +367,6 @@ def add_to_species_data(
                 time_unit=EnzML_UnitDef(**time_unit.model_dump()),
                 data_type=DataTypes.CONCENTRATION,
             )
-            print(f"added temp unit {time_unit.name}")
 
     @staticmethod
     def map_protein(protein: Protein, vessel_id: str) -> pe.Protein:

From feefe826d7496b321ddb9506e0cf4164589fdfe0 Mon Sep 17 00:00:00 2001
From: haeussma <83341109+haeussma@users.noreply.github.com>
Date: Fri, 27 Sep 2024 18:28:28 +0200
Subject: [PATCH 4/6] updated pyproject.toml

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index e822e1a..49ba9eb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,7 +1,7 @@
 [tool.poetry]
 name = "mtphandler"
 version = "0.2.11"
-description = "Tool to work with microtiter plate data."
+description = "Python package for processing, enriching, and converting microtiter plate data into standardized EnzymeML time-course data, ready for data science."
 authors = ["haeussma <83341109+haeussma@users.noreply.github.com>"]
 license = "MIT License"
 readme = "README.md"

From abd4768e5805428f15c326f19f6311dda30f6719 Mon Sep 17 00:00:00 2001
From: haeussma <83341109+haeussma@users.noreply.github.com>
Date: Fri, 27 Sep 2024 18:40:10 +0200
Subject: [PATCH 5/6] Refactor pyproject.toml and fix casing

---
 docs/examples/data/enzymeml_TmSAHH_SAH.json | 930 ++++++++++----------
 1 file changed, 465 insertions(+), 465 deletions(-)

diff --git a/docs/examples/data/enzymeml_TmSAHH_SAH.json b/docs/examples/data/enzymeml_TmSAHH_SAH.json
index 6b48bbd..9847b80 100644
--- a/docs/examples/data/enzymeml_TmSAHH_SAH.json
+++ b/docs/examples/data/enzymeml_TmSAHH_SAH.json
@@ -18,7 +18,7 @@
                         "exponent": 1,
                         "multiplier": null,
                         "scale": 1.0,
-                        "ld_id": "enzml:BaseUnit/7507fc3b-6f31-4ce7-99e4-3df87993a41c",
+                        "ld_id": "enzml:BaseUnit/5e0b185b-48eb-4282-8b06-365f5daf0665",
                         "ld_type": [
                             "enzml:BaseUnit"
                         ],
@@ -29,7 +29,7 @@
                         }
                     }
                 ],
-                "ld_id": "enzml:UnitDefinition/2d99c27f-949b-40f8-acb9-02e22fd46fc5",
+                "ld_id": "enzml:UnitDefinition/8e86dd4e-c6dd-4def-a82a-0326aea97524",
                 "ld_type": [
                     "OBO:UO_0000000"
                 ],
@@ -40,7 +40,7 @@
                 }
             },
             "constant": true,
-            "ld_id": "enzml:Vessel/2c2bacab-9361-4a5a-bfc9-25ef526dc2f0",
+            "ld_id": "enzml:Vessel/dddda8f2-2c71-4b4e-9721-0727fba436f6",
             "ld_type": [
                 "enzml:Vessel",
                 "OBO:OBI_0400081"
@@ -69,7 +69,7 @@
             "organism": null,
             "organism_tax_id": null,
             "references": [],
-            "ld_id": "enzml:Protein/4e6f2068-6568-4dc8-8bad-5ca5b43ac58b",
+            "ld_id": "enzml:Protein/46f25b1c-6827-4996-bdc6-aa5a1c1013aa",
             "ld_type": [
                 "enzml:Protein",
                 "schema:Protein"
@@ -107,7 +107,7 @@
             "organism": null,
             "organism_tax_id": null,
             "references": [],
-            "ld_id": "enzml:Protein/7acc8306-c72d-46ef-b880-ab42b59c4d76",
+            "ld_id": "enzml:Protein/e7555c43-6761-4551-a3eb-3f2d091335dc",
             "ld_type": [
                 "enzml:Protein",
                 "schema:Protein"
@@ -145,7 +145,7 @@
             "organism": null,
             "organism_tax_id": null,
             "references": [],
-            "ld_id": "enzml:Protein/fedc65c2-97f9-40e1-b78a-deef15e47ae8",
+            "ld_id": "enzml:Protein/13580886-c6ec-404c-af88-b1dca28f9ced",
             "ld_type": [
                 "enzml:Protein",
                 "schema:Protein"
@@ -183,7 +183,7 @@
             "organism": null,
             "organism_tax_id": null,
             "references": [],
-            "ld_id": "enzml:Protein/a407c986-a00e-4921-921b-2fc5b25c8314",
+            "ld_id": "enzml:Protein/0d401d19-df8b-4695-96f9-9f68e54d5867",
             "ld_type": [
                 "enzml:Protein",
                 "schema:Protein"
@@ -223,7 +223,7 @@
             "inchi": null,
             "inchikey": null,
             "references": [],
-            "ld_id": "enzml:SmallMolecule/014feb9b-1b64-4208-9c73-9bf56f5d1c79",
+            "ld_id": "enzml:SmallMolecule/742602e5-b8f4-42a8-bfdb-150595b822ab",
             "ld_type": [
                 "enzml:SmallMolecule"
             ],
@@ -414,8 +414,8 @@
             "name": "photometric measurement",
             "species_data": [
                 {
-                    "species_id": "BUFFER",
-                    "initial": 50.0,
+                    "species_id": "TmSAHH",
+                    "initial": 5.0,
                     "data_unit": {
                         "id": null,
                         "name": "umol / l",
@@ -425,7 +425,7 @@
                                 "exponent": 1,
                                 "multiplier": null,
                                 "scale": -6.0,
-                                "ld_id": "md:BaseUnit/992794ac-a609-4aa3-b945-577985bf5b56",
+                                "ld_id": "md:BaseUnit/3892e867-fe94-4f8a-9c25-03199976d932",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -438,7 +438,7 @@
                                 "exponent": -1,
                                 "multiplier": null,
                                 "scale": 1.0,
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@@ -1998,7 +1998,7 @@
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@@ -2145,7 +2145,7 @@
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                         "enzml:MeasurementData"
                     ],
@@ -11397,94 +11483,8 @@
                     }
                 },
                 {
-                    "species_id": "SAH",
-                    "initial": 200.0,
-                    "data_unit": {
-                        "id": null,
-                        "name": "umol / l",
-                        "base_units": [
-                            {
-                                "kind": "mole",
-                                "exponent": 1,
-                                "multiplier": null,
-                                "scale": -6.0,
-                                "ld_id": "md:BaseUnit/992794ac-a609-4aa3-b945-577985bf5b56",
-                                "ld_type": [
-                                    "md:BaseUnit"
-                                ],
-                                "ld_context": {
-                                    "md": "https://github.com/FAIRChemistry/MTPHandler"
-                                }
-                            },
-                            {
-                                "kind": "litre",
-                                "exponent": -1,
-                                "multiplier": null,
-                                "scale": 1.0,
-                                "ld_id": "md:BaseUnit/bcbe0316-c8f1-468f-9c77-2fc254ead666",
-                                "ld_type": [
-                                    "md:BaseUnit"
-                                ],
-                                "ld_context": {
-                                    "md": "https://github.com/FAIRChemistry/MTPHandler"
-                                }
-                            }
-                        ],
-                        "ld_id": "OBO:UO_0000064",
-                        "ld_type": [
-                            "OBO:UO_0000000"
-                        ],
-                        "ld_context": {
-                            "md": "https://github.com/FAIRChemistry/MTPHandler"
-                        }
-                    },
-                    "data_type": "http://purl.obolibrary.org/obo/PATO_0000033",
-                    "prepared": 200.0,
-                    "data": [],
-                    "time": [],
-                    "time_unit": {
-                        "id": null,
-                        "name": "s",
-                        "base_units": [
-                            {
-                                "kind": "second",
-                                "exponent": 1,
-                                "multiplier": 60.0,
-                                "scale": 1.0,
-                                "ld_id": "md:BaseUnit/e03d4232-6697-4aef-aed7-f4a700a9f7f0",
-                                "ld_type": [
-                                    "md:BaseUnit"
-                                ],
-                                "ld_context": {
-                                    "md": "https://github.com/FAIRChemistry/MTPHandler"
-                                }
-                            }
-                        ],
-                        "ld_id": "OBO:UO_0000031",
-                        "ld_type": [
-                            "OBO:UO_0000000"
-                        ],
-                        "ld_context": {
-                            "md": "https://github.com/FAIRChemistry/MTPHandler"
-                        }
-                    },
-                    "is_simulated": false,
-                    "ld_id": "enzml:MeasurementData/77bb27c6-8023-4f8b-843f-ded739c6dd73",
-                    "ld_type": [
-                        "enzml:MeasurementData"
-                    ],
-                    "ld_context": {
-                        "enzml": "http://www.enzymeml.org/v2/",
-                        "schema": "https://schema.org/",
-                        "OBO": "http://purl.obolibrary.org/obo/",
-                        "species_id": {
-                            "@type": "@id"
-                        }
-                    }
-                },
-                {
-                    "species_id": "TmSAHH",
-                    "initial": 5.0,
+                    "species_id": "Hyc",
+                    "initial": 0.0,
                     "data_unit": {
                         "id": null,
                         "name": "umol / l",
@@ -11494,7 +11494,7 @@
                                 "exponent": 1,
                                 "multiplier": null,
                                 "scale": -6.0,
-                                "ld_id": "md:BaseUnit/992794ac-a609-4aa3-b945-577985bf5b56",
+                                "ld_id": "md:BaseUnit/3892e867-fe94-4f8a-9c25-03199976d932",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -11507,7 +11507,7 @@
                                 "exponent": -1,
                                 "multiplier": null,
                                 "scale": 1.0,
-                                "ld_id": "md:BaseUnit/bcbe0316-c8f1-468f-9c77-2fc254ead666",
+                                "ld_id": "md:BaseUnit/55582c11-57ea-4f12-b140-1b520d243ce2",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -11525,7 +11525,7 @@
                         }
                     },
                     "data_type": "http://purl.obolibrary.org/obo/PATO_0000033",
-                    "prepared": 5.0,
+                    "prepared": 0.0,
                     "data": [],
                     "time": [],
                     "time_unit": {
@@ -11537,7 +11537,7 @@
                                 "exponent": 1,
                                 "multiplier": 60.0,
                                 "scale": 1.0,
-                                "ld_id": "md:BaseUnit/e03d4232-6697-4aef-aed7-f4a700a9f7f0",
+                                "ld_id": "md:BaseUnit/20988505-e1dc-4fee-9baa-edf58a9b95c7",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -11555,7 +11555,7 @@
                         }
                     },
                     "is_simulated": false,
-                    "ld_id": "enzml:MeasurementData/b8ade515-0564-4685-917b-ef79f09213c6",
+                    "ld_id": "enzml:MeasurementData/bcb8dea4-17f5-43c9-8d68-1fa6449dd338",
                     "ld_type": [
                         "enzml:MeasurementData"
                     ],
@@ -11569,8 +11569,8 @@
                     }
                 },
                 {
-                    "species_id": "DTNB",
-                    "initial": 500.0,
+                    "species_id": "BUFFER",
+                    "initial": 50.0,
                     "data_unit": {
                         "id": null,
                         "name": "umol / l",
@@ -11580,7 +11580,7 @@
                                 "exponent": 1,
                                 "multiplier": null,
                                 "scale": -6.0,
-                                "ld_id": "md:BaseUnit/992794ac-a609-4aa3-b945-577985bf5b56",
+                                "ld_id": "md:BaseUnit/3892e867-fe94-4f8a-9c25-03199976d932",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -11593,7 +11593,7 @@
                                 "exponent": -1,
                                 "multiplier": null,
                                 "scale": 1.0,
-                                "ld_id": "md:BaseUnit/bcbe0316-c8f1-468f-9c77-2fc254ead666",
+                                "ld_id": "md:BaseUnit/55582c11-57ea-4f12-b140-1b520d243ce2",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -11611,7 +11611,7 @@
                         }
                     },
                     "data_type": "http://purl.obolibrary.org/obo/PATO_0000033",
-                    "prepared": 500.0,
+                    "prepared": 50.0,
                     "data": [],
                     "time": [],
                     "time_unit": {
@@ -11623,7 +11623,7 @@
                                 "exponent": 1,
                                 "multiplier": 60.0,
                                 "scale": 1.0,
-                                "ld_id": "md:BaseUnit/e03d4232-6697-4aef-aed7-f4a700a9f7f0",
+                                "ld_id": "md:BaseUnit/20988505-e1dc-4fee-9baa-edf58a9b95c7",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -11641,7 +11641,7 @@
                         }
                     },
                     "is_simulated": false,
-                    "ld_id": "enzml:MeasurementData/7a3c944e-98a4-4081-8158-c568833e4c1c",
+                    "ld_id": "enzml:MeasurementData/57c293f9-f333-4843-af13-1c7424f00d2a",
                     "ld_type": [
                         "enzml:MeasurementData"
                     ],
@@ -11667,7 +11667,7 @@
                         "exponent": 1,
                         "multiplier": null,
                         "scale": 1.0,
-                        "ld_id": "md:BaseUnit/d6cfa323-be66-4591-84d9-570e831169f8",
+                        "ld_id": "md:BaseUnit/27193648-9452-4aeb-89f9-5bcce2e3bca7",
                         "ld_type": [
                             "md:BaseUnit"
                         ],
@@ -11676,7 +11676,7 @@
                         }
                     }
                 ],
-                "ld_id": "md:UnitDefinition/31f16537-09de-4045-ae55-ad3197ffcb70",
+                "ld_id": "md:UnitDefinition/3774b997-8640-4f02-8a57-24fcd38f8ec8",
                 "ld_type": [
                     "OBO:UO_0000000"
                 ],
@@ -11684,7 +11684,7 @@
                     "md": "https://github.com/FAIRChemistry/MTPHandler"
                 }
             },
-            "ld_id": "enzml:Measurement/a1394bfd-038b-413d-aafb-2c28f8a3f465",
+            "ld_id": "enzml:Measurement/885c2afe-f990-4dd9-8e59-53e38fcf5ea6",
             "ld_type": [
                 "enzml:Measurement"
             ],
@@ -11704,7 +11704,7 @@
     ],
     "equations": [],
     "parameters": [],
-    "ld_id": "enzml:EnzymeMLDocument/01d7bf76-39ee-42af-987b-2a1b46c13e6a",
+    "ld_id": "enzml:EnzymeMLDocument/54290bd3-e930-473e-b2f3-f2e8005b73e7",
     "ld_type": [
         "enzml:EnzymeMLDocument"
     ],

From f07fe616cfdad95597690d039c26e9d9ba8b5b90 Mon Sep 17 00:00:00 2001
From: haeussma <83341109+haeussma@users.noreply.github.com>
Date: Fri, 27 Sep 2024 19:02:46 +0200
Subject: [PATCH 6/6] rerun tests

---
 docs/examples/SAHH_kinetics.ipynb           |   42 +-
 docs/examples/data/enzymeml_TmSAHH_SAH.json | 1676 +++++++++----------
 2 files changed, 852 insertions(+), 866 deletions(-)

diff --git a/docs/examples/SAHH_kinetics.ipynb b/docs/examples/SAHH_kinetics.ipynb
index ac55366..032f852 100644
--- a/docs/examples/SAHH_kinetics.ipynb
+++ b/docs/examples/SAHH_kinetics.ipynb
@@ -92,20 +92,6 @@
    "cell_type": "code",
    "execution_count": 2,
    "metadata": {},
-   "outputs": [],
-   "source": [
-    "from mtphandler.molecule import Protein\n",
-    "\n",
-    "my_variant = Protein(\n",
-    "    id=\"L191G\",\n",
-    "    name=\"L191G\",\n",
-    ")"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
-   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -144500,7 +144486,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -144542,7 +144528,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -144586,19 +144572,19 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/html": [
-       "
📍 Assigned 228 initial concentration coditions for ['SAH', 'MhSAHH', 'SIH', 'Hyc', 'MtSAHH', 'BUFFER', 'McSAHH', \n",
-       "'TmSAHH', 'DTNB', 'TNB'] from data/plate_map_SAHH_kinetics.xlsx to the plate.\n",
+       "
📍 Assigned 228 initial concentration coditions for ['MhSAHH', 'MtSAHH', 'McSAHH', 'SAH', 'DTNB', 'Hyc', 'BUFFER', \n",
+       "'SIH', 'TmSAHH', 'TNB'] from data/plate_map_SAHH_kinetics.xlsx to the plate.\n",
        "
\n"
       ],
       "text/plain": [
-       "📍 Assigned \u001b[1;36m228\u001b[0m initial concentration coditions for \u001b[1;35m[\u001b[0m\u001b[1;35m'SAH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'MhSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'SIH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'Hyc'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'MtSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'BUFFER'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'McSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\n",
-       "\u001b[1;35m'TmSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'DTNB'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'TNB'\u001b[0m\u001b[1;35m]\u001b[0m from data/plate_map_SAHH_kinetics.xlsx to the plate.\n"
+       "📍 Assigned \u001b[1;36m228\u001b[0m initial concentration coditions for \u001b[1;35m[\u001b[0m\u001b[1;35m'MhSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'MtSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'McSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'SAH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'DTNB'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'Hyc'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'BUFFER'\u001b[0m\u001b[1;35m, \u001b[0m\n",
+       "\u001b[1;35m'SIH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'TmSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'TNB'\u001b[0m\u001b[1;35m]\u001b[0m from data/plate_map_SAHH_kinetics.xlsx to the plate.\n"
       ]
      },
      "metadata": {},
@@ -144634,7 +144620,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
@@ -144874,7 +144860,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {
@@ -144914,7 +144900,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [
     {
@@ -147682,7 +147668,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -147717,7 +147703,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [
     {
@@ -147748,7 +147734,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [
     {
@@ -147807,7 +147793,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [],
    "source": [
diff --git a/docs/examples/data/enzymeml_TmSAHH_SAH.json b/docs/examples/data/enzymeml_TmSAHH_SAH.json
index 9847b80..1c191ca 100644
--- a/docs/examples/data/enzymeml_TmSAHH_SAH.json
+++ b/docs/examples/data/enzymeml_TmSAHH_SAH.json
@@ -18,7 +18,7 @@
                         "exponent": 1,
                         "multiplier": null,
                         "scale": 1.0,
-                        "ld_id": "enzml:BaseUnit/5e0b185b-48eb-4282-8b06-365f5daf0665",
+                        "ld_id": "enzml:BaseUnit/085c0609-ab77-4c89-9686-e00e2628535c",
                         "ld_type": [
                             "enzml:BaseUnit"
                         ],
@@ -29,7 +29,7 @@
                         }
                     }
                 ],
-                "ld_id": "enzml:UnitDefinition/8e86dd4e-c6dd-4def-a82a-0326aea97524",
+                "ld_id": "enzml:UnitDefinition/380763e6-e15c-4f8e-b8a0-4a286d0da22d",
                 "ld_type": [
                     "OBO:UO_0000000"
                 ],
@@ -40,7 +40,7 @@
                 }
             },
             "constant": true,
-            "ld_id": "enzml:Vessel/dddda8f2-2c71-4b4e-9721-0727fba436f6",
+            "ld_id": "enzml:Vessel/42805267-b5a9-4bfe-b348-061d4f044a46",
             "ld_type": [
                 "enzml:Vessel",
                 "OBO:OBI_0400081"
@@ -69,7 +69,7 @@
             "organism": null,
             "organism_tax_id": null,
             "references": [],
-            "ld_id": "enzml:Protein/46f25b1c-6827-4996-bdc6-aa5a1c1013aa",
+            "ld_id": "enzml:Protein/efc8d1cb-4880-4115-9980-f0ae647afa2b",
             "ld_type": [
                 "enzml:Protein",
                 "schema:Protein"
@@ -107,7 +107,7 @@
             "organism": null,
             "organism_tax_id": null,
             "references": [],
-            "ld_id": "enzml:Protein/e7555c43-6761-4551-a3eb-3f2d091335dc",
+            "ld_id": "enzml:Protein/84b031d1-b665-4d92-b783-c50f39095dd7",
             "ld_type": [
                 "enzml:Protein",
                 "schema:Protein"
@@ -145,7 +145,7 @@
             "organism": null,
             "organism_tax_id": null,
             "references": [],
-            "ld_id": "enzml:Protein/13580886-c6ec-404c-af88-b1dca28f9ced",
+            "ld_id": "enzml:Protein/2d55f1d7-2376-4fc1-b65e-0261440fc0c4",
             "ld_type": [
                 "enzml:Protein",
                 "schema:Protein"
@@ -183,7 +183,7 @@
             "organism": null,
             "organism_tax_id": null,
             "references": [],
-            "ld_id": "enzml:Protein/0d401d19-df8b-4695-96f9-9f68e54d5867",
+            "ld_id": "enzml:Protein/abbc1199-549a-4ebb-8040-1873c6ea95f0",
             "ld_type": [
                 "enzml:Protein",
                 "schema:Protein"
@@ -223,7 +223,7 @@
             "inchi": null,
             "inchikey": null,
             "references": [],
-            "ld_id": "enzml:SmallMolecule/742602e5-b8f4-42a8-bfdb-150595b822ab",
+            "ld_id": "enzml:SmallMolecule/f5ddc0d9-cfb3-44ec-876e-17a4eeec3def",
             "ld_type": [
                 "enzml:SmallMolecule"
             ],
@@ -425,7 +425,7 @@
                                 "exponent": 1,
                                 "multiplier": null,
                                 "scale": -6.0,
-                                "ld_id": "md:BaseUnit/3892e867-fe94-4f8a-9c25-03199976d932",
+                                "ld_id": "md:BaseUnit/a7924577-c3ed-42b9-9574-0ac6a0b90357",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -438,7 +438,7 @@
                                 "exponent": -1,
                                 "multiplier": null,
                                 "scale": 1.0,
-                                "ld_id": "md:BaseUnit/55582c11-57ea-4f12-b140-1b520d243ce2",
+                                "ld_id": "md:BaseUnit/94a08161-ec0e-4dd7-a259-a1922ac4150e",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -468,7 +468,7 @@
                                 "exponent": 1,
                                 "multiplier": 60.0,
                                 "scale": 1.0,
-                                "ld_id": "md:BaseUnit/20988505-e1dc-4fee-9baa-edf58a9b95c7",
+                                "ld_id": "md:BaseUnit/703240e5-176d-43c5-bb5b-2caa43f67160",
                                 "ld_type": [
                                     "md:BaseUnit"
                                 ],
@@ -486,7 +486,93 @@
                         }
                     },
                     "is_simulated": false,
-                    "ld_id": "enzml:MeasurementData/5ff53c97-5633-4515-9781-05bce920409b",
+                    "ld_id": "enzml:MeasurementData/2d97c741-c14f-49cd-a02f-84a032d483e0",
+                    "ld_type": [
+                        "enzml:MeasurementData"
+                    ],
+                    "ld_context": {
+                        "enzml": "http://www.enzymeml.org/v2/",
+                        "schema": "https://schema.org/",
+                        "OBO": "http://purl.obolibrary.org/obo/",
+                        "species_id": {
+                            "@type": "@id"
+                        }
+                    }
+                },
+                {
+                    "species_id": "BUFFER",
+                    "initial": 50.0,
+                    "data_unit": {
+                        "id": null,
+                        "name": "umol / l",
+                        "base_units": [
+                            {
+                                "kind": "mole",
+                                "exponent": 1,
+                                "multiplier": null,
+                                "scale": -6.0,
+                                "ld_id": "md:BaseUnit/a7924577-c3ed-42b9-9574-0ac6a0b90357",
+                                "ld_type": [
+                                    "md:BaseUnit"
+                                ],
+                                "ld_context": {
+                                    "md": "https://github.com/FAIRChemistry/MTPHandler"
+                                }
+                            },
+                            {
+                                "kind": "litre",
+                                "exponent": -1,
+                                "multiplier": null,
+                                "scale": 1.0,
+                                "ld_id": "md:BaseUnit/94a08161-ec0e-4dd7-a259-a1922ac4150e",
+                                "ld_type": [
+                                    "md:BaseUnit"
+                                ],
+                                "ld_context": {
+                                    "md": "https://github.com/FAIRChemistry/MTPHandler"
+                                }
+                            }
+                        ],
+                        "ld_id": "OBO:UO_0000064",
+                        "ld_type": [
+                            "OBO:UO_0000000"
+                        ],
+                        "ld_context": {
+                            "md": "https://github.com/FAIRChemistry/MTPHandler"
+                        }
+                    },
+                    "data_type": "http://purl.obolibrary.org/obo/PATO_0000033",
+                    "prepared": 50.0,
+                    "data": [],
+                    "time": [],
+                    "time_unit": {
+                        "id": null,
+                        "name": "s",
+                        "base_units": [
+                            {
+                                "kind": "second",
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@@ -7803,10 +7889,61 @@
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                         "ld_type": [
                             "md:BaseUnit"
                         ],
@@ -11676,7 +11676,7 @@
                         }
                     }
                 ],
-                "ld_id": "md:UnitDefinition/3774b997-8640-4f02-8a57-24fcd38f8ec8",
+                "ld_id": "md:UnitDefinition/6ac5c79a-36fd-4f2c-acba-6ac83b58fdba",
                 "ld_type": [
                     "OBO:UO_0000000"
                 ],
@@ -11684,7 +11684,7 @@
                     "md": "https://github.com/FAIRChemistry/MTPHandler"
                 }
             },
-            "ld_id": "enzml:Measurement/885c2afe-f990-4dd9-8e59-53e38fcf5ea6",
+            "ld_id": "enzml:Measurement/3125d780-d5c9-40c7-9a7f-b4e5ade74f94",
             "ld_type": [
                 "enzml:Measurement"
             ],
@@ -11704,7 +11704,7 @@
     ],
     "equations": [],
     "parameters": [],
-    "ld_id": "enzml:EnzymeMLDocument/54290bd3-e930-473e-b2f3-f2e8005b73e7",
+    "ld_id": "enzml:EnzymeMLDocument/b8f2c4ae-16f4-4816-8450-3d543c6d7af2",
     "ld_type": [
         "enzml:EnzymeMLDocument"
     ],