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Monomers downloaded from monomer.org are not in the correct format #30
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Now nothing is downloaded at all! |
Apologies, it is downloaded, but still in the old format. |
You might want to look at the schema definition on GitHub https://github.com/PistoiaHELM/HELMMonomerSets/blob/master/HELMmonomerSchema.json and not listed like you have. |
Would highly recommend that this is addressed as the limitations of the current approach will be apparent should other polymer types be implemented in HELM. |
Here is an example of the agreed JSON format for monomers.
{ "monomerType": "Backbone", "symbol": "12ddR", "rgroups": [ { "alternateId": "R1-H", "id": 0, "label": "R1", "capGroupSMILES": "[*:1][H]", "capGroupName": "H" }, { "alternateId": "R2-H", "id": 0, "label": "R2", "capGroupSMILES": "[*:2][H]", "capGroupName": "H" } ], "molfile": "\n Marvin 09110915502D \n\n 10 10 0 0 0 0 999 V2000\n -1.4258 10.5012 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -2.1396 10.0877 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0\n -0.7107 10.0897 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.9250 9.2912 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0\n -0.9231 9.2926 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.9238 8.4662 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -2.2881 10.9422 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -2.7596 11.2958 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -3.5846 11.4503 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n -1.2225 7.9123 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0 0\n 1 3 1 0 0 0 0\n 2 4 1 0 0 0 0\n 2 7 1 1 0 0 0\n 3 5 1 0 0 0 0\n 4 5 1 0 0 0 0\n 4 6 1 6 0 0 0\n 6 10 1 0 0 0 0\n 7 8 1 0 0 0 0\n 8 9 1 0 0 0 0\nM RGP 2 9 1 10 2\nM END\n\n$$$$\n", "smiles": "[H:1]OC[C@H]1OCC[C@@H]1O[H:2]", "author": "Pistoia Alliance", "name": "1',2'-Di-Deoxy-Ribose", "naturalAnalog": "R", "polymerType": "RNA", "id": 131, "createDate": "Tue Sep 05 17:43:09 CEST 2017" }
The download from monomer.org does not include the agreed array for R groups but flattens it and misses some of the information such as the capgroup SMILEs etc...
{ "monomerversionid": 518, "libraryid": 4, "librarykey": "Nucleotides", "libraryname": "Core Nucleotides", "molfile": "/n ChemDraw11272016482D/n/n 9 9 0 0 0 0 0 0 0 0999 V2000/n -0.9959 0.0314 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0/n -0.9959 -0.7936 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0/n -0.4125 -1.3770 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0/n 0.4125 -1.3770 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0/n 0.9959 -0.7936 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0/n 0.9959 0.0314 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0/n 0.4125 0.6148 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0/n -0.4125 0.6148 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0/n 0.7282 1.3770 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0/n 1 2 1 0 /n 2 3 1 0 /n 3 4 1 0 /n 4 5 1 0 /n 5 6 1 0 /n 6 7 1 0 /n 7 8 1 0 /n 8 1 1 0 /n 7 9 1 0 /nM END/n", "smiles": null, "symbol": "ac4C", "naturalanalog": "C", "name": "4-Acetylcytosine", "polymertype": "RNA", "monomertype": "Branch", "status": "draft", "r1": "H", "r2": null, "r3": null, "r4": null, "r5": null, "author": "Bellamy, Claire", "userid": 4, "createddate": 1606251619480, "modifieddate": 1606251619480 }
Please correct the monomer JSON download.
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