Repository 'chembl'
hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/chembl

Changeset 5:1ade252ebe08 (2020-07-28)
Previous changeset 4:59eea7d0d720 (2020-05-19) Next changeset 6:a57de37f12c2 (2020-10-07)
Commit message:
"planemo upload for repository https://github.com/chembl/chembl_webresource_client commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
modified:
chembl.py
chembl.xml
test-data/out3.smi
b
diff -r 59eea7d0d720 -r 1ade252ebe08 chembl.py
--- a/chembl.py Tue May 19 05:34:34 2020 -0400
+++ b/chembl.py Tue Jul 28 08:20:47 2020 -0400
[
@@ -13,7 +13,10 @@
     """ 
     smiles = set()
     for smi in res: 
-        smiles.add('{}\t{}'.format(smi['molecule_structures']['canonical_smiles'], smi['molecule_chembl_id']))
+        try:
+            smiles.add('{}\t{}'.format(smi['molecule_structures']['canonical_smiles'], smi['molecule_chembl_id']))
+        except TypeError:
+            continue
     return smiles
 
 def sim_search(smiles, tanimoto):
b
diff -r 59eea7d0d720 -r 1ade252ebe08 chembl.xml
--- a/chembl.xml Tue May 19 05:34:34 2020 -0400
+++ b/chembl.xml Tue Jul 28 08:20:47 2020 -0400
b
@@ -1,7 +1,7 @@
 <tool id="chembl" name="Search ChEMBL database" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
     <macros>
         <token name="@TOOL_VERSION@">0.10.1</token>
-        <token name="@GALAXY_VERSION@">1</token>
+        <token name="@GALAXY_VERSION@">2</token>
     </macros>
     <description>for compounds which are similar to a SMILES string</description>
     <requirements>
b
diff -r 59eea7d0d720 -r 1ade252ebe08 test-data/out3.smi
--- a/test-data/out3.smi Tue May 19 05:34:34 2020 -0400
+++ b/test-data/out3.smi Tue Jul 28 08:20:47 2020 -0400
[
b'@@ -1,579 +1,55 @@\n-CN1CCCC1c1cnccc1N      CHEMBL193763\n-CC(C)(CO)NC(=O)c1cnn2ccc(N3CCC[C@@H]3c3cncc(F)c3)nc12  CHEMBL3676006\n-CN1CCC[C@H]1c1ccc[n+](CCCC#Cc2cc(C#CCCC[n+]3cccc([C@@H]4CCCN4C)c3)c(C#CCCC[n+]3cccc([C@@H]4CCCN4C)c3)cc2C#CCCC[n+]2cccc([C@@H]3CCCN3C)c2)c1.[Br-].[Br-].[Br-].[Br-]    CHEMBL2368590\n-CN1CCCC1c1ccc(Br)nc1   CHEMBL58231\n-CN1CCC[C@H]1c1ccc[n+](CCCCCCNCC2CCc3ccc(O)cc3O2)c1     CHEMBL3614072\n-CN1[C@H](c2cccnc2)CC[C@@H]1c1ccccc1    CHEMBL443018\n-O=C(N[C@@H]1CCC[C@H]1O)c1cnn2ccc(N3CCC[C@@H]3c3cncc(F)c3)nc12  CHEMBL3676007\n-COCCOc1ncccc1[C@@H]1C(C(=O)C(C)C)C(=O)C(=O)N1c1ccc(-c2ccsc2)cc1        CHEMBL3674905\n-CC1(NC(=O)c2cnn3ccc(N4CCC[C@@H]4c4cncc(F)c4)nc23)CC1   CHEMBL3675966\n-CS(=O)(=O)N1CCC(NC(=O)c2cnn3ccc(N4CCCC4c4cncc(F)c4)nc23)CC1    CHEMBL3675945\n-CN1CCCC1c1cccnc1       CHEMBL440464\n-CN1CCC[C@H]1c1ccc[n+](CCCCCCCCCCCC[n+]2cccc([C@@H]3CCCN3C)c2)c1.[Br-].[Br-]    CHEMBL420649\n-O=C(N[C@@H]1C2CC[C@@H](C2)[C@@H]1CO)c1cnn2ccc(N3CCCC3c3cncc(F)c3)nc12  CHEMBL3676012\n-O=C(N[C@H]1CC[C@H](O)C1)c1cnn2ccc(N3CCCC3c3cncc(F)c3)nc12      CHEMBL3675979\n-CN1C(=O)[C@@H](C(N)=O)C[C@@H]1c1cccnc1 CHEMBL3126036\n-CCCCC/C=C/CCC[n+]1cccc([C@@H]2CCCN2C)c1.[Br-]  CHEMBL559110\n-C[N@@+]1(Cc2ccc(Cl)c(Cl)c2)CCC[C@@H]1c1ccc[n+](Cc2ccc(Cl)c(Cl)c2)c1    CHEMBL1318824\n-CC1=C[C@H]2Cc3[nH]c(=O)ccc3[C@@]3(C1)[C@@H]2[C@H](C)CN3C       CHEMBL2409141\n-CC1CN(C)[C@H](c2cccnc2)C1C     CHEMBL334222\n-CN1CCC[C@H]1c1ccc[n+](CCCC#Cc2cc(C#CCCC[n+]3cccc([C@@H]4CCCN4C)c3)cc(C#CCCC[n+]3cccc([C@@H]4CCCN4C)c3)c2)c1.[Br-].[Br-].[Br-]  CHEMBL437574\n-c1cc2c(cn1)[C@@H]1N3CCC1(CC3)C2        CHEMBL2111859\n-CC(C)C(=O)C1C(=O)C(=O)N(c2ccc(-c3ccsc3)cc2)C1c1cccnc1Cl        CHEMBL3674784\n-COCCOc1ncccc1C1C(C(=O)C(C)C)C(=O)C(=O)N1c1ccc(-c2csc(C)c2)cc1  CHEMBL3674792\n-COc1ncc(F)cc1C1CCCN1c1ccn2ncc(C(=O)Nc3cc(C)n[nH]3)c2n1 CHEMBL3676102\n-COc1ncccc1C1C(C(=O)C(C)C)C(=O)C(=O)N1c1ccc(-c2ccsc2)cc1        CHEMBL3669826\n-CC(C)C(=O)C1C(=O)C(=O)N(c2ccc(-c3ccon3)cc2)C1c1cccnc1OCCO      CHEMBL3669819\n-C=CC[n+]1cccc([C@@H]2CCCN2C)c1.[I-]    CHEMBL558518\n-CCCCCCCCCCC[n+]1cccc2c1CC[C@@H]1CCN(C)[C@H]21  CHEMBL1185915\n-COCCOc1ncccc1C1C(C(=O)C(C)(C)C)C(=O)C(=O)N1c1ccc(-c2cccs2)cc1  CHEMBL3669795\n-CN1CCCC1c1ccc(Nc2c(C(=O)C3CC3)cnc3ccc(-c4cc(F)c(O)c(Cl)c4)cc23)nc1     CHEMBL3674294\n-CN1CCC[C@H]1c1ccc[n+](CCCCCCCCCCCCNCC2CCc3ccc(O)cc3O2)c1.[Br-] CHEMBL3612361\n-CCCCc1ccc(C2CCCN2C)cn1 CHEMBL320023\n-CC(C)C(=O)C1C(=O)C(=O)N(c2ccc(-c3ccoc3)cc2)C1c1cccnc1OCCO      CHEMBL3674760\n-CN1CCC[C@H]1c1ccc[n+](CCCCCCCC[n+]2cccc([C@@H]3CCCN3C)c2)c1.[I-].[I-]  CHEMBL105440\n-Cc1ccc(-c2ccc(N3C(=O)C(=O)C(C(=O)CC(C)C)C3c3cccnc3C(=O)OC(C)C)cc2)s1   CHEMBL3679770\n-CCC[n+]1cccc([C@@H]2CCCN2C)c1  CHEMBL1197124\n-CCCCC[n+]1cccc([C@@H]2CCCN2C)c1        CHEMBL3614075\n-Cc1ccc(-c2cc(C(=O)N3CCCC3c3cccnc3)[nH]n2)o1    CHEMBL3485246\n-CN1CCC[C@H]1c1ccc[n+](CCCCCC[n+]2cccc([C@@H]3CCCN3C)c2)c1.[I-].[I-]    CHEMBL104461\n-CNC(=O)c1cnn2ccc(N3CCC[C@@H]3c3cc(F)cnc3OC)nc12        CHEMBL3676024\n-Cc1cncc(C2CCCN2C)c1    CHEMBL364003\n-CC1(O)CN(C(=O)c2cnn3ccc(N4CCC[C@@H]4c4cncc(F)c4)nc23)C1        CHEMBL3675967\n-CN1CCC[C@H]1c1ccc(Nc2ncc3cc(Br)c(=O)n(C4CCCC4)c3n2)nc1 CHEMBL3990288\n-CCCCCCCCCCCC[n+]1cccc([C@@H]2CCCN2C)c1.[I-]    CHEMBL55606\n-COc1ncccc1C1C(C(=O)CC(C)(C)C)C(=O)C(=O)N1c1ccc(-c2ccsc2)cc1    CHEMBL3674964\n-CC[C@H]1C[C@@H](c2cccnc2)N(C)C1        CHEMBL115793\n-CCNC(=O)c1cc2c(N3CCCC3c3cccnc3)ccnc2[nH]1      CHEMBL4064004\n-CN1CCC[C@H]1c1ccc[n+](CCCCCCCCC[n+]2cccc([C@@H]3CCCN3C)c2)c1   CHEMBL1183837\n-CCOc1ncccc1C1C(C(=O)CC(C)C)C(=O)C(=O)N1c1ccc(-c2ccsc2)cc1      CHEMBL3674943\n-CCCCC#CCCCCCC[n+]1cccc(C2CCCN2C)c1.[Br-]       CHEMBL599540\n-C#Cc1cncc([C@@H]2CCCN2C)c1     CHEMBL111659\n-CCCCCCCCCC[n+]1cccc2c1CC[C@]1(C)CCN(C)[C@]21C  CHEMBL1183842\n-COCCOc1ncccc1C1C(C(=O)C(C)C)C(=O)C(=O)N1c1ccc(-c2ccc(C)o2)cc1  CHEMBL3674872\n-COc1cc(-c2ccc3ncc(C(=O)C4CC4)c(Nc4ccc(C5CCCN5C)cn4)c3c2)cc(Cl)c1O      CHEMBL3674295\n-CC(C)NC(=O)c1cnn2ccc(N3[C@H](CO)CC[C@@H]3c3cncc(F)c3)nc12      CHEMBL3676080\n-O=C(c1cccs1)N1CCCC1c1ccc(-c2cccc(Cl)c2)nc1     CHEMBL1808866'..b'L3675996\n-COc1ncc(F)cc1[C@H]1CCCN1c1ccn2ncc(C(=O)NCCCCO)c2n1     CHEMBL3676022\n-O=C(Nc1ccc(F)cn1)c1cnn2ccc(N3CCC[C@@H]3c3cncc(F)c3)nc12        CHEMBL3675970\n-O=C(c1nccs1)N1CCCC1c1ccc(-c2cccc(Cl)c2)nc1     CHEMBL1808867\n-CC[C@H]1OC(=O)[C@H](C)[C@@H](OC(=O)N2CC(C)(C)C[C@@H]2c2cccnc2)[C@H](C)[C@@H](O[C@@H]2O[C@H](C)C[C@H](N(C)C)[C@H]2O)[C@](C)(OC)C[C@@H](C)C(=O)[C@H](C)[C@H]2NC(=O)O[C@]12C      CHEMBL2338710\n+CN1CCC[C@H]1c1cccnc1.O=C(O)C(O)C(O)C(=O)O\tCHEMBL1448280\n+Cn1cccc1-c1cc(C(=O)N2CCCC2c2cccnc2)[nH]n1\tCHEMBL3486928\n+O=C1[C@@H](NS(=O)(=O)c2ccc3cc(Cl)ccc3c2)CCCN1CC(=O)N1CCCC1c1cccnc1\tCHEMBL1923459\n+CN1CCCC1c1cccnc1.O=S(=O)(O)O\tCHEMBL2142095\n+CN1CCC[C@@H]1c1cccnc1.Cc1ccc(C(=O)OC(C(=O)O)C(OC(=O)c2ccc(C)cc2)C(=O)O)cc1\tCHEMBL2448607\n+NC(=O)c1ccc(Oc2ccc(CN3CCCC3c3cccnc3)cc2)c2ccccc12\tCHEMBL4095563\n+O=C(NC1CCN(Cc2ccn(-c3ccc(C(F)(F)F)cc3)c2)CC1)N1CCCC1c1cccnc1\tCHEMBL560283\n+O=C1NC(=O)/C(=C/c2cnn3c(NC4CC4)nc(N4CCCC4c4cccnc4)nc23)N1\tCHEMBL3984229\n+O=S(=O)(Nc1ncns1)c1ccc2c(N3CCC[C@H]3c3cccnc3)cccc2c1\tCHEMBL3692144\n+O=C(c1cc2c([nH]c1=O)CCC2)N1CCCC1c1cccnc1\tCHEMBL3458802\n+CC(C)C[C@H](N[C@H](CCN1C(=O)c2cc3ccccc3cc2C1=O)C(=O)O)C(=O)N1CCCC1c1cccnc1\tCHEMBL158622\n+c1ccc(CN2CCCC2c2cccnc2)cc1\tCHEMBL163552\n+Cc1ncsc1CCC(=O)N1CCCC1c1cccnc1\tCHEMBL3476252\n+O=C(c1cc(-c2ccc(O)cc2)n[nH]1)N1CCCC1c1cccnc1\tCHEMBL3474057\n+O=C(C(Nc1ccccc1F)c1cc2ccccc2s1)N1CCCC1c1cccnc1\tCHEMBL2348659\n+OC(COc1ccccc1-c1nc2ccccc2o1)CN1CCCC1c1cccnc1\tCHEMBL608832\n+O=C(Nc1ccccc1F)N1CCCC1c1cccnc1\tCHEMBL1870182\n+CN1CCC[C@H]1c1cccnc1.Cl\tCHEMBL225057\n+O=C(Nc1ccccc1C(F)(F)F)N1CCCC1c1cccnc1\tCHEMBL1353542\n+CN1CCC[C@H]1c1cccnc1.C[C@H](CCC(=O)O)[C@H]1CC[C@H]2[C@H]3[C@H](C[C@H](O)[C@@]21C)[C@@]1(C)CC[C@@H](O)C[C@H]1C[C@H]3O\tCHEMBL3114538\n+Cc1ccc2nc(CN3CCCC3c3cccnc3)cc(O)c2c1\tCHEMBL3485916\n+Cc1cc(N2CCCC2c2cccnc2)nc(C)n1\tCHEMBL3454373\n+O=S(=O)(Nc1ncns1)c1ccc2c(N3CCC[C@@H]3c3cccnc3)cccc2c1\tCHEMBL3682682\n+CN1CCCC1c1cccnc1\tCHEMBL440464\n+CN1CCC[C@@H]1c1cccnc1\tCHEMBL9732\n+Cc1cc(N(C)C)nc(N2CCCC2c2cccnc2)n1\tCHEMBL3454403\n+CN1CCC[C@H]1c1cccnc1.CN1CCC[C@H]1c1cccnc1.O=S(=O)(O)O\tCHEMBL3182465\n+CCCc1cc(C(=O)N2CCCC2c2cccnc2)[nH]n1\tCHEMBL3486295\n+O=C(c1ccc(F)c(F)c1)N1CCN2C(=O)c3ccccc3[C@@]12c1ccc(N2CCC[C@H]2c2cccnc2)cc1\tCHEMBL4100810\n+CN1CCC[C@H]1c1cccnc1.C[C@H](CCC(=O)O)[C@H]1CC[C@H]2[C@@H]3CC[C@@H]4C[C@H](O)CC[C@]4(C)[C@H]3C[C@H](O)[C@@]21C\tCHEMBL3114539\n+CCNC(=O)c1cc2c(N3CCCC3c3cccnc3)ccnc2[nH]1\tCHEMBL4064004\n+Cc1nn(C)c(Oc2cccc(Cl)c2Cl)c1C(=O)N1CCCC1c1cccnc1\tCHEMBL2336227\n+CN1CCC[C@H]1c1cccnc1.C[C@H](CCC(=O)O)[C@H]1CC[C@H]2[C@@H]3CC[C@@H]4C[C@H](O)CC[C@]4(C)[C@H]3CC[C@@]21C\tCHEMBL3114541\n+CC1=C(C(=O)N2CCCC2c2cccnc2)C(c2ccc(Cl)c(Cl)c2)n2nccc2N1\tCHEMBL601248\n+NC(=O)c1ccc(Oc2ccc(CN3CCCC3c3cccnc3)cc2)nc1\tCHEMBL1921840\n+c1cncc(C2CCCN2c2ccnc3[nH]ncc23)c1\tCHEMBL4066892\n+CN1CCC[C@H]1c1cccnc1\tCHEMBL3\n+CCO.CN1CCC[C@H]1c1cccnc1\tCHEMBL3137669\n+Cc1cc(C)nc(N2CCCC2c2cccnc2)n1\tCHEMBL3436596\n+Cc1ccc(-c2cc(C(=O)N3CCCC3c3cccnc3)[nH]n2)o1\tCHEMBL3485246\n+NC(=O)c1ccc(Oc2ccc(CN3CCCC3c3cccnc3)cc2)c(Cl)c1\tCHEMBL1921841\n+NC(=O)c1ccc(Oc2ccc(CN3CCC[C@@H]3c3cccnc3)cc2)c(Cl)c1\tCHEMBL1921843\n+NC(=O)c1ccc(Oc2ccc(CN3CCC[C@H]3c3cccnc3)cc2)c(Cl)c1\tCHEMBL1921842\n+CN1CCC[C@H]1c1cccnc1.O=C(O)C(O)C(O)C(=O)O.O=C(O)C(O)C(O)C(=O)O\tCHEMBL151515\n+O=C(C(Nc1ccccc1F)c1ccc(C(F)(F)F)cc1)N1CCCC1c1cccnc1\tCHEMBL2348671\n+CN1CCC[C@H]1c1cccnc1.O.O.O=C(O)C(O)C(O)C(=O)O.O=C(O)C(O)C(O)C(=O)O\tCHEMBL3989563\n+c1cncc(C2CCCN2C2c3ccccc3Oc3ccccc32)c1\tCHEMBL278775\n+CN1CCC[C@@H]1c1cccnc1.O=C(O)C(O)C(O)C(=O)O.O=C(O)C(O)C(O)C(=O)O\tCHEMBL2062338\n+Cn1cc(NC(=O)N2CCCC2c2cccnc2)ccc1=O\tCHEMBL3453894\n+CCN1CCCC1c1cccnc1\tCHEMBL163042\n+O=S(=O)(Nc1ncns1)c1ccc2c(N3CCCC3c3cccnc3)cccc2c1\tCHEMBL3682681\n+O=C(NC1COC1)c1cc2c(N3CCCC3c3cccnc3)ccnc2[nH]1\tCHEMBL4083992\n+O=CN1CCC[C@H]1c1cccnc1\tCHEMBL3126024\n+Cc1nc2ccccc2n1Cc1ccc(CNC(=O)[C@H](O)[C@@H](O)C(=O)N2CCCC2c2cccnc2)s1\tCHEMBL1779603\n+CC[C@H]1OC(=O)[C@H](C)[C@@H](OC(=O)N2CCC[C@@H]2c2cccnc2)[C@H](C)[C@@H](O[C@@H]2O[C@H](C)C[C@H](N(C)C)[C@H]2O)[C@](C)(OC)C[C@@H](C)C(=O)[C@H](C)[C@H]2NC(=O)O[C@]12C\tCHEMBL2338711\n\\ No newline at end of file\n'