{"openapi":"3.0.1","info":{"title":"AILCBioChem","description":"AI Learning Companion for Biology and Chemistry","version":"1.0.1"},"paths":{"/obj/tamas.simon/anatomyPlot":{"get":{"summary":"Draws a 3D image of a body part or organ.","operationId":"anatomyPlot","parameters":[{"name":"anatomicalStructure","in":"query","description":"The main anatomical structure to be plotted.","required":true,"schema":{"type":"string"}},{"name":"backgroundAnatomicalStructure","in":"query","description":"Background anatomical structure for context, displayed as transparent gray.","required":false,"schema":{"type":"string","default":""}},{"name":"rangeAnatomicalStructure","in":"query","description":"Plot range specified as an anatomical structure allowing you to zoom in and out.","required":false,"schema":{"type":"string","default":""}},{"name":"viewPoint3D","in":"query","required":false,"schema":{"type":"string","default":"Automatic","enum":["Automatic","Above","Below","Front","Back","Left","Right"]}}],"responses":{"200":{"description":"Successful response"},"400":{"description":"Bad request, parameters are not correct."},"500":{"description":"Server error."},"503":{"description":"Error processing. Try again without backgroundAnatomicalStructure."}}}},"/obj/tamas.simon/getListOfChemicals":{"get":{"summary":"Get list of up to 20 chemicals based on class.","operationId":"getListOfChemicals","parameters":[{"name":"class","in":"query","description":"Class of chemicals e.g. AliphaticKetones, Allotropes, Alloys, AntimonyAllotropes, ArsenicAllotropes, BerkeliumAllotropes, Biomolecules, Carbides, CalciumCarbonatePolymorphs, CarbonAllotropes etc. ","required":true,"schema":{"type":"string"}}],"responses":{"200":{"description":"Successful response"},"400":{"description":"Bad request, parameters are not correct."},"500":{"description":"Server error."}}}},"/obj/tamas.simon/getIsomers":{"get":{"summary":"Get list of molecules with the same chemical formula as the input molecule.","operationId":"getIsomers","parameters":[{"name":"type","in":"query","description":"How the molecule will be specified in the molecule parameter. One of ChemicalName, SMILES","required":true,"schema":{"type":"string","enum":["ChemicalName","SMILES"]}},{"name":"molecule","in":"query","required":true,"schema":{"type":"string"}}],"responses":{"200":{"description":"Successful response"},"400":{"description":"Bad request, parameters are not correct."},"500":{"description":"Server error."}}}},"/obj/tamas.simon/getEntityPropertyList":{"get":{"summary":"Get list of the properties available for a chemical or an element. Then use these properties with getEntityValue.","operationId":"getEntityPropertyList","parameters":[{"name":"type","in":"query","required":true,"schema":{"type":"string","enum":["Chemical","Element"]}},{"name":"name","in":"query","required":true,"schema":{"type":"string"}}],"responses":{"200":{"description":"Successful response"},"400":{"description":"Bad request, parameters are not correct."},"500":{"description":"Server error."}}}},"/obj/tamas.simon/getEntityValue":{"get":{"summary":"Get the value for up to three properties a chemical or an element. For the list of properties use getEntityPropertyList ","operationId":"getEntityValue","parameters":[{"name":"type","in":"query","required":true,"schema":{"type":"string","enum":["Chemical","Element"]}},{"name":"name","in":"query","required":true,"schema":{"type":"string"}},{"name":"properties","in":"query","description":"Comma separated list of properties, up to three.","required":true,"schema":{"type":"string"}}],"responses":{"200":{"description":"Successful response"},"400":{"description":"Bad request, parameters are not correct."},"500":{"description":"Server error."}}}},"/obj/tamas.simon/moleculePlot":{"get":{"operationId":"moleculePlot","description":"Draws a 2D or 3D diagram of the molecule. Returns it as image. 3D diagrams are also returned as an interactive 3D object on the web. Do NOT show the link to the interactive version unless the user is asking to see the molecule from different viewing angle.","parameters":[{"name":"type","in":"query","description":"How the molecule will be specified in the molecule parameter. One of ChemicalName, SMILES, DNA, RNA, Peptide, PubChemCompoundID, PubChemSubstanceID, InChI, ChEMBLID","required":true,"schema":{"type":"string","enum":["ChemicalName","SMILES","DNA","RNA","Peptide","PubChemCompoundID","PubChemSubstanceID","InChI","ChEMBLID"]}},{"name":"molecule","in":"query","description":"Letters representing molecule for types DNA, RNA and Peptide are:\nDNA: A (adenine), C (cytosine), G guanine, T (thymine)  \nDNA: A (adenine), C (cytosine), G guanine, U (uracil)  \nPeptide: A (alanine), C (cysteine), D (aspartic acid), E\t(glutamic acid), F (phenylalanine), G (glycine), H (histidine), I (isoleucine), K\t(lysine), L (leucine), M (methionine), N (asparagine), O\t(pyrrolysine), P (proline), Q (glutamine), R (arginine), S (serine), T (threonine), U\t(selenocysteine), V (valine), W (tryptophan), Y (tyrosine)\nPubChemCompoundID, PubChemSubstanceID, InChI and ChEMBLID are external identifiers.\n","required":true,"schema":{"type":"string"}},{"name":"highlightMoleculePatterns","in":"query","description":"Comma separated list of patterns to highlight in the diagram.  These can be named or SMARTS. Function groups, bonds and amino acids will be recognized by name. Prefer using names! e.g. \n 'nitro', 'sulfonate', 'acetal' , 'pyridyl2'\n'carbonyl', 'aldehyde', 'ketal', 'carbothioicSacid', 'carbothioicOacid', 'peptide', 'A', 'C', 'D' SMARTS Patterns Quick Reference:  Use '*' for any atom,  '[Cl,F,I]' to specify atoms, represent hydrogen explicitly as '[H]' or with count like '[C;H3]',  and use brackets '[]' for atom restrictions.  e.g. for amino acid Alanine, '[NX3][CX4H]([CH3X4])[CX3](=[OX1])' for carboxyl group use the pattern '[*]C(=O)O[H]'\n","required":false,"schema":{"type":"string","default":""}},{"name":"highlightPlotLegends","in":"query","description":"Comma separated list of names for the molecule patterns to highlight. These will appear at plot legends in the diagram. Make sure it is in sync with highlightMoleculePatterns above.","required":false,"schema":{"type":"string","default":""}},{"name":"autoHiglightPatterns","in":"query","description":"Automatically highlight all function groups including the longest alkyl group. In peptides highlights the peptide bind and different amino acids.","required":false,"schema":{"type":"boolean","default":false}},{"name":"plotTheme","in":"query","description":"2DValuePlot has to be used together with valuePlotProperty, BioSequence is a 2D schematic diagram for RNA, DNA and Peptide types. The rest is as their name suggests.","required":false,"schema":{"type":"string","default":"2DAromatic","enum":["2D","2DAromatic","3DBallAndStick","3DSpacefilling","3DTubes","3DWireframe","2DValuePlot","BioSequence"]}},{"name":"includeHydrogen","in":"query","description":"Show all atoms including Hydrogen atoms.","required":false,"schema":{"type":"boolean","default":false}},{"name":"viewPoint3D","in":"query","description":"Point in space from which 3D diagrams are to be viewed. It's ignored for 2D.","required":false,"schema":{"type":"string","default":"Automatic","enum":["Automatic","Above","Below","Front","Back","Left","Right"]}},{"name":"valuePlotProperty","in":"query","description":"Used only when the plotTheme is 2DValuePlot: Atom, Bond or Element property to be plotted.","required":false,"schema":{"type":"string","default":"","enum":["AtomIndex","FormalCharge","GasteigerPartialCharge","HydrogenCount","ImplicitHydrogenCount","ImplicitValence","OrbitalHybridization","OuterShellElectronCount","UnpairedElectronCount","Valence","BondLength","BondType","Electronegativity","AtomicRadius","ValenceElectronCount","VanDerWaalsRadius"]}}],"responses":{"200":{"description":"Successful response"},"400":{"description":"Bad request, parameters are not correct."},"500":{"description":"Server error."}}}},"/obj/tamas.simon/aboutThisGPTAILCBioChem":{"get":{"operationId":"aboutThisGPTAILCBioChem","summary":"Meta information about subscription to this GPT: support email, portal URL for registered users and subscribers, number of free invocations per month, subscription price.","responses":{"200":{"description":"OK"}},"parameters":[]}}},"servers":[{"url":"https://ailcbiochem.warmersun.com"}]}