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api [2019/09/25 20:23]
flack [Quote - Missing structures]
api [2021/03/24 14:41]
sanmark
Line 1: Line 1:
 API base url: https://mcule.com/api/v1/ API base url: https://mcule.com/api/v1/
  
-Examples are demonstrated with [[https://github.com/jkbrzt/httpie|HTTPie]].+Examples are demonstrated with [[https://httpie.org|HTTPie]]
 + 
 +Only the most important request/response headers are shown in the examples below.
  
 ====== Response status codes ====== ====== Response status codes ======
Line 63: Line 65:
             ],              ], 
             "last_updated": "2017-09-18",              "last_updated": "2017-09-18", 
-            "name": "Mcule Purchasable (full)"+            "name": "Mcule Purchasable (full)"
 +            "public": true
         },          }, 
         {         {
Line 83: Line 86:
             ],              ], 
             "last_updated": "2017-09-18",              "last_updated": "2017-09-18", 
-            "name": "Mcule Purchasable (in stock)"+            "name": "Mcule Purchasable (in stock)"
 +            "public": true
         }         }
     ]     ]
 } }
 </code> </code>
 +
 +If you call this API endpoint as an authenticated user (=you provide a [[api#authentication|valid token]]) you might get additional private entries if you have permission to access them.
  
  
Line 229: Line 235:
  
 Authentication is currently a token based authentication. Authentication is currently a token based authentication.
-If you would like to access our protected API endpoints, please drop us an email at support@mcule.com and we can provide you with token.+If you would like to access our protected API endpoints, please drop us an email at support@mcule.com including a brief summary on why and how you would like to use the API. We'll review your request, and if accepted, we'll provide you with an access token which you can use to call the API as an authenticated user.
  
 Once you have a valid token you have to send it in the Authorization header: Once you have a valid token you have to send it in the Authorization header:
Line 381: Line 387:
     "results": [     "results": [
         {         {
-            "input_index": 1,  +            "input_index": 1
-            "mcule_id": "MCULE-9380369173",  +            "matching_level": 40, 
-            "smiles": "COC(C1SC(C=CC2SC(C3=NC=CC=C3)=NC=2)=NC=1)=O", +            "matching_level_display": "Atom graph"
 +            "mcule_id": "MCULE-9380369173", 
 +            "query": "COC(C1SC(C=CC2SC(C3=NC=CC=C3)=NC=2)=NC=1)=O", 
 +            "smiles": "COC(C1SC(C=CC2SC(C3=NC=CC=C3)=NC=2)=NC=1)=O",
             "url": "https://mcule.com/MCULE-9380369173/"             "url": "https://mcule.com/MCULE-9380369173/"
-        }, +        },
         {         {
-            "input_index": 2,  +            "input_index": 2
-            "mcule_id": "MCULE-4016901520",  +            "matching_level": 20, 
-            "smiles": "CC1=C(C(N2CC3C(CCC3N)C2)=O)SC(CC2=CC=CC=C2)=N1", +            "matching_level_display": "Sp3 configuration"
 +            "mcule_id": "MCULE-4016901520", 
 +            "query": "CC1=C(C(N2CC3C(CCC3N)C2)=O)SC(CC2=CC=CC=C2)=N1", 
 +            "smiles": "CC1=C(C(N2CC3C(CCC3N)C2)=O)SC(CC2=CC=CC=C2)=N1",
             "url": "https://mcule.com/MCULE-4016901520/"             "url": "https://mcule.com/MCULE-4016901520/"
-        }, +        },
         {         {
-            "input_index": 3,  +            "input_index": 3
-            "mcule_id": "MCULE-7428195288",  +            "matching_level": 40, 
-            "smiles": "C1([C@H](C(C)C)NC(CCCC[C@H]2CCSS2)=O)NC2=C(C=CC=C2)N=1",  +            "matching_level_display": "Atom graph"
-            "url": "https://mcule.com/MCULE-7428195288/" +            "mcule_id": "MCULE-1039596211", 
-        }, +            "query": "C1([C@H](C(C)C)NC(CCCCC2CCSS2)=O)NC2=C(C=CC=C2)N=1", 
 +            "smiles": "C1(C(C(C)C)NC(CCCCC2CCSS2)=O)NC2=C(C=CC=C2)N=1", 
 +            "url": "https://mcule.com/MCULE-1039596211/" 
 +        },
         {         {
-            "input_index": 5,  +            "input_index": 5
-            "mcule_id": "MCULE-1259420189",  +            "matching_level": 40, 
-            "smiles": "CCCCC1=CC=C(CC(N(CC2CCN(C)CC2)C)=O)C=C1", +            "matching_level_display": "Atom graph"
 +            "mcule_id": "MCULE-1259420189", 
 +            "query": "CCCCC1=CC=C(CC(N(CC2CCN(C)CC2)C)=O)C=C1", 
 +            "smiles": "CCCCC1=CC=C(CC(N(CC2CCN(C)CC2)C)=O)C=C1",
             "url": "https://mcule.com/MCULE-1259420189/"             "url": "https://mcule.com/MCULE-1259420189/"
         }         }
Line 407: Line 425:
 } }
 </code> </code>
 +
 +Please note that in case the queries are InChIKeys, **matching_level** and **matching_level_display** will always be **null** in the response. 
  
 ===== Multiple queries exact search with availability ===== ===== Multiple queries exact search with availability =====
Line 447: Line 467:
         {         {
             "availability": {             "availability": {
-                "availability_type": "in stock",  +                "availability_type": "in stock", 
-                "confirmed_amount": 242+                "confirmed_amount": 100,
                 "confirmed_amount_unit": "mg"                 "confirmed_amount_unit": "mg"
-            },  +            }, 
-            "input_index": 1,  +            "input_index": 1
-            "mcule_id": "MCULE-9380369173",  +            "matching_level": 40, 
-            "smiles": "COC(C1SC(C=CC2SC(C3=NC=CC=C3)=NC=2)=NC=1)=O", +            "matching_level_display": "Atom graph"
 +            "mcule_id": "MCULE-9380369173", 
 +            "query": "COC(C1SC(C=CC2SC(C3=NC=CC=C3)=NC=2)=NC=1)=O", 
 +            "smiles": "COC(C1SC(C=CC2SC(C3=NC=CC=C3)=NC=2)=NC=1)=O",
             "url": "https://mcule.com/MCULE-9380369173/"             "url": "https://mcule.com/MCULE-9380369173/"
-        }, +        },
         {         {
             "availability": {             "availability": {
-                "availability_type": "in stock",  +                "availability_type": "potentially purchasable", 
-                "confirmed_amount": null, +                "confirmed_amount": null,
                 "confirmed_amount_unit": "mg"                 "confirmed_amount_unit": "mg"
-            },  +            }, 
-            "input_index": 2,  +            "input_index": 2
-            "mcule_id": "MCULE-4016901520",  +            "matching_level": 20, 
-            "smiles": "CC1=C(C(N2CC3C(CCC3N)C2)=O)SC(CC2=CC=CC=C2)=N1", +            "matching_level_display": "Sp3 configuration"
 +            "mcule_id": "MCULE-4016901520", 
 +            "query": "CC1=C(C(N2CC3C(CCC3N)C2)=O)SC(CC2=CC=CC=C2)=N1", 
 +            "smiles": "CC1=C(C(N2CC3C(CCC3N)C2)=O)SC(CC2=CC=CC=C2)=N1",
             "url": "https://mcule.com/MCULE-4016901520/"             "url": "https://mcule.com/MCULE-4016901520/"
-        }, +        },
         {         {
             "availability": {             "availability": {
-                "availability_type": "in stock",  +                "availability_type": "in stock", 
-                "confirmed_amount": null+                "confirmed_amount": 50,
                 "confirmed_amount_unit": "mg"                 "confirmed_amount_unit": "mg"
-            },  +            }, 
-            "input_index": 3,  +            "input_index": 3
-            "mcule_id": "MCULE-7428195288",  +            "matching_level": 40, 
-            "smiles": "C1([C@H](C(C)C)NC(CCCC[C@H]2CCSS2)=O)NC2=C(C=CC=C2)N=1",  +            "matching_level_display": "Atom graph"
-            "url": "https://mcule.com/MCULE-7428195288/" +            "mcule_id": "MCULE-1039596211", 
-        }, +            "query": "C1([C@H](C(C)C)NC(CCCCC2CCSS2)=O)NC2=C(C=CC=C2)N=1", 
 +            "smiles": "C1(C(C(C)C)NC(CCCCC2CCSS2)=O)NC2=C(C=CC=C2)N=1", 
 +            "url": "https://mcule.com/MCULE-1039596211/" 
 +        },
         {         {
             "availability": {             "availability": {
-                "availability_type": "potentially purchasable",  +                "availability_type": "potentially purchasable", 
-                "confirmed_amount": null, +                "confirmed_amount": null,
                 "confirmed_amount_unit": "mg"                 "confirmed_amount_unit": "mg"
-            },  +            }, 
-            "input_index": 5,  +            "input_index": 5
-            "mcule_id": "MCULE-1259420189",  +            "matching_level": 40, 
-            "smiles": "CCCCC1=CC=C(CC(N(CC2CCN(C)CC2)C)=O)C=C1", +            "matching_level_display": "Atom graph"
 +            "mcule_id": "MCULE-1259420189", 
 +            "query": "CCCCC1=CC=C(CC(N(CC2CCN(C)CC2)C)=O)C=C1", 
 +            "smiles": "CCCCC1=CC=C(CC(N(CC2CCN(C)CC2)C)=O)C=C1",
             "url": "https://mcule.com/MCULE-1259420189/"             "url": "https://mcule.com/MCULE-1259420189/"
         }         }
     ]     ]
-+
 +</code> 
 + 
 +Please note that in case the queries are InChIKeys, **matching_level** and **matching_level_display** will always be **null** in the response.  
 + 
 + 
 +===== Similarity search ===== 
 +Similarity search currently accepts the following input identifiers: mcule ID, SMILES. 
 + 
 +== Endpoint: == 
 +<code>/search/sim/</code> 
 + 
 +== Example API request: == 
 +<code> 
 +echo '{"query": "MCULE-3601132784", "limit": 3, "threshold": 0.8}' | http https://mcule.com/api/v1/search/sim/ "Authorization: Token <your_token>" --print HBhb 
 +</code> 
 + 
 +or 
 + 
 +<code> 
 +echo '{"query": "CC1=C(C(CC2NC(=O)C3=C(SC(C4=CC=CC=C4)=C3)N=2)=O)C=CO1", "limit": 3, "threshold": 0.8}' | http https://mcule.com/api/v1/search/sim/ "Authorization: Token <your_token>" --print HBhb 
 +</code> 
 + 
 +== Request: == 
 +<code> 
 +POST /api/v1/search/sim/ HTTP/1.1 
 +Accept: application/json 
 +Accept-Encoding: gzip, deflate 
 +Authorization: Token <your_token> 
 +Content-Type: application/json 
 + 
 +
 +    "limit": 3, 
 +    "query": "MCULE-3601132784", 
 +    "threshold": 0.8 
 +
 +</code> 
 + 
 +== Response: == 
 +<code> 
 +HTTP/1.1 200 OK 
 +Allow: POST, OPTIONS 
 +Content-Encoding: gzip 
 +Content-Type: application/json 
 + 
 +
 +    "results":
 +        { 
 +            "mcule_id": "MCULE-3601132784", 
 +            "sim": 1.0, 
 +            "smiles": "CC1=C(C(CC2NC(=O)C3=C(SC(C4=CC=CC=C4)=C3)N=2)=O)C=CO1", 
 +            "url": "https://mcule.com/MCULE-3601132784/" 
 +        }, 
 +        { 
 +            "mcule_id": "MCULE-1000774360", 
 +            "sim": 0.8540706605222734, 
 +            "smiles": "O=C(C1OC=CC=1)CC1NC(=O)C2=C(SC(C3=CC=CC=C3)=C2)N=1", 
 +            "url": "https://mcule.com/MCULE-1000774360/" 
 +        }, 
 +        { 
 +            "mcule_id": "MCULE-9463088657", 
 +            "sim": 0.8529886914378029, 
 +            "smiles": "CC1SC2=C(C(NC(=N2)CC(C2=C(C)OC=C2)=O)=O)C=1", 
 +            "url": "https://mcule.com/MCULE-9463088657/" 
 +        } 
 +    ] 
 +
 +</code> 
 + 
 +The **threshold** field accepts values between 0.7 and 1.0, the default is 0.9. 
 + 
 +The **limit** field accepts values between 1 and 1000, the default is 100. 
 + 
 + 
 +===== Substructure search ===== 
 +Substructure search currently accepts the following input identifiers: mcule ID, SMILES. 
 + 
 +== Endpoint: == 
 +<code>/search/sss/</code> 
 + 
 +== Example API request: == 
 +<code> 
 +echo '{"query": "CC1=CC2=C(S1)N=CNC2=O", "limit": 5}' | http https://mcule.com/api/v1/search/sss/ "Authorization: Token <your_token>" --print HBhb 
 +</code> 
 + 
 +== Request: == 
 +<code> 
 +POST /api/v1/search/sss/ HTTP/1.1 
 +Accept: application/json 
 +Accept-Encoding: gzip, deflate 
 +Authorization: Token <your_token> 
 +Content-Type: application/json 
 + 
 +
 +    "limit": 5, 
 +    "query": "CC1=CC2=C(S1)N=CNC2=O" 
 +
 +</code> 
 + 
 +== Response: == 
 +<code> 
 +HTTP/1.1 200 OK 
 +Allow: POST, OPTIONS 
 +Content-Encoding: gzip 
 +Content-Type: application/json 
 + 
 +
 +    "results":
 +        { 
 +            "mcule_id": "MCULE-8112694353", 
 +            "smiles": "C12C(C)=C(SC=1N=CN(CC(NCCCC(=O)NC1CCCCC1)=O)C2=O)C", 
 +            "url": "https://mcule.com/MCULE-8112694353/" 
 +        }, 
 +        { 
 +            "mcule_id": "MCULE-8986577308", 
 +            "smiles": "C12SC3=C(CCCC3)C=1C(NC(SCC#C)=N2)=O", 
 +            "url": "https://mcule.com/MCULE-8986577308/" 
 +        }, 
 +        { 
 +            "mcule_id": "MCULE-4695228882", 
 +            "smiles": "C12SC3=C(CCCC3)C=1C(NC(SCCCC)=N2)=O", 
 +            "url": "https://mcule.com/MCULE-4695228882/" 
 +        }, 
 +        { 
 +            "mcule_id": "MCULE-1137030903", 
 +            "smiles": "N1(CC2C=NN(C)C=2)C(=O)C2C=C(SC=2N=C1S)CC", 
 +            "url": "https://mcule.com/MCULE-1137030903/" 
 +        }, 
 +        { 
 +            "mcule_id": "MCULE-1308684767", 
 +            "smiles": "C12SC3=C(CCCC3)C=1C(NC(SCC=C)=N2)=O", 
 +            "url": "https://mcule.com/MCULE-1308684767/" 
 +        } 
 +    ] 
 +}
 </code> </code>
  
 +The **limit** field accepts values between 1 and 1000, the default is 100.
  
  
Line 642: Line 809:
   * **target_volume**: The target volume (in ml), in case of solution based amount.   * **target_volume**: The target volume (in ml), in case of solution based amount.
   * **target_cc**: Target concentration (mM), in case of solution based amount.   * **target_cc**: Target concentration (mM), in case of solution based amount.
 +  * **extra_amount**: In case of solution based amount calculation the preferred extra amount (in mg) can be specified here.
 +  * **min_extra_amount**: In case of solution based amount calculation the acceptable minimum extra amount (in mg) can be specified here.
   * **customer_email**: The customer's email address. By default it will be filled with the email address associated with the user making the API request.   * **customer_email**: The customer's email address. By default it will be filled with the email address associated with the user making the API request.
   * **delivery_time**: Delivery time limit (working days). Door-to-door delivery time. Only offer molecules that are available within the specified number of working days. You can specify null if delivery time is not critical. (default: 21)   * **delivery_time**: Delivery time limit (working days). Door-to-door delivery time. Only offer molecules that are available within the specified number of working days. You can specify null if delivery time is not critical. (default: 21)
Line 1105: Line 1274:
         }         }
     ],      ], 
-    "missing_mcule_ids": [],  
     "name": "",      "name": "", 
     "order_data": null,      "order_data": null, 
Line 1286: Line 1454:
     * **structure_origin_mcule_id**: The mcule ID of the query molecule.     * **structure_origin_mcule_id**: The mcule ID of the query molecule.
     * **quote**: The ID of the quote this product level quote data belongs to.     * **quote**: The ID of the quote this product level quote data belongs to.
-  * **missing_mcule_ids**: list of missing mcule IDs from the query 
   * **name**: The name of the quote. Quotes created via the API don't have names.   * **name**: The name of the quote. Quotes created via the API don't have names.
   * **order_data**: Order data. (Should be neglected).   * **order_data**: Order data. (Should be neglected).
api.txt · Last modified: 2021/06/18 13:55 by flack