Galaxy |

Changeset 1:e2f40a02f31a (2019-06-04)

Previous changeset 0:ea68b86303e2 (2019-05-23) Next changeset 2:d074b0c2b54f (2019-11-06)

Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 7c47e7409a8cb19e20b4424329f5d0d9470f3b00

modified:
mordred_descriptors.py
test-data/8smi.tab

diff -r ea68b86303e2 -r e2f40a02f31a mordred_descriptors.py
--- a/mordred_descriptors.py Thu May 23 18:31:43 2019 -0400
+++ b/mordred_descriptors.py Tue Jun 04 10:29:10 2019 -0400

[

@@ -30,9 +30,9 @@
     with open(filename) as f:
         mols = f.read().split('\n')
     if ext == 'smi':
-        return [Chem.MolFromSmiles(mol, sanitize=True) for mol in mols]
+        return [Chem.MolFromSmiles(mol, sanitize=True) for mol in mols if mol != '']
     if ext == 'inchi':
-        return [Chem.inchi.MolFromInchi(mol, sanitize=True) for mol in mols]
+        return [Chem.inchi.MolFromInchi(mol, sanitize=True) for mol in mols if mol != '']

def mordred_descriptors(mols, output, header, use_3d):
@@ -68,4 +68,4 @@
     args = parser.parse_args()

     mols = mol_supplier(args.infile, args.iformat)
-    mordred_descriptors(mols, args.outfile, args.header, args.use_3d)
\ No newline at end of file
+    mordred_descriptors(mols, args.outfile, args.header, args.use_3d)

diff -r ea68b86303e2 -r e2f40a02f31a test-data/8smi.tab
--- a/test-data/8smi.tab Thu May 23 18:31:43 2019 -0400
+++ b/test-data/8smi.tab Tue Jun 04 10:29:10 2019 -0400

b'@@ -1,10 +1,9 @@\n ABC\tABCGG\tnAcid\tnBase\tSpAbs_A\tSpMax_A\tSpDiam_A\tSpAD_A\tSpMAD_A\tLogEE_A\tVE1_A\tVE2_A\tVE3_A\tVR1_A\tVR2_A\tVR3_A\tnAromAtom\tnAromBond\tnAtom\tnHeavyAtom\tnSpiro\tnBridgehead\tnHetero\tnH\tnB\tnC\tnN\tnO\tnS\tnP\tnF\tnCl\tnBr\tnI\tnX\tATS0dv\tATS1dv\tATS2dv\tATS3dv\tATS4dv\tATS5dv\tATS6dv\tATS7dv\tATS8dv\tATS0d\tATS1d\tATS2d\tATS3d\tATS4d\tATS5d\tATS6d\tATS7d\tATS8d\tATS0s\tATS1s\tATS2s\tATS3s\tATS4s\tATS5s\tATS6s\tATS7s\tATS8s\tATS0Z\tATS1Z\tATS2Z\tATS3Z\tATS4Z\tATS5Z\tATS6Z\tATS7Z\tATS8Z\tATS0m\tATS1m\tATS2m\tATS3m\tATS4m\tATS5m\tATS6m\tATS7m\tATS8m\tATS0v\tATS1v\tATS2v\tATS3v\tATS4v\tATS5v\tATS6v\tATS7v\tATS8v\tATS0se\tATS1se\tATS2se\tATS3se\tATS4se\tATS5se\tATS6se\tATS7se\tATS8se\tATS0pe\tATS1pe\tATS2pe\tATS3pe\tATS4pe\tATS5pe\tATS6pe\tATS7pe\tATS8pe\tATS0are\tATS1are\tATS2are\tATS3are\tATS4are\tATS5are\tATS6are\tATS7are\tATS8are\tATS0p\tATS1p\tATS2p\tATS3p\tATS4p\tATS5p\tATS6p\tATS7p\tATS8p\tATS0i\tATS1i\tATS2i\tATS3i\tATS4i\tATS5i\tATS6i\tATS7i\tATS8i\tAATS0dv\tAATS1dv\tAATS2dv\tAATS3dv\tAATS4dv\tAATS5dv\tAATS6dv\tAATS7dv\tAATS8dv\tAATS0d\tAATS1d\tAATS2d\tAATS3d\tAATS4d\tAATS5d\tAATS6d\tAATS7d\tAATS8d\tAATS0s\tAATS1s\tAATS2s\tAATS3s\tAATS4s\tAATS5s\tAATS6s\tAATS7s\tAATS8s\tAATS0Z\tAATS1Z\tAATS2Z\tAATS3Z\tAATS4Z\tAATS5Z\tAATS6Z\tAATS7Z\tAATS8Z\tAATS0m\tAATS1m\tAATS2m\tAATS3m\tAATS4m\tAATS5m\tAATS6m\tAATS7m\tAATS8m\tAATS0v\tAATS1v\tAATS2v\tAATS3v\tAATS4v\tAATS5v\tAATS6v\tAATS7v\tAATS8v\tAATS0se\tAATS1se\tAATS2se\tAATS3se\tAATS4se\tAATS5se\tAATS6se\tAATS7se\tAATS8se\tAATS0pe\tAATS1pe\tAATS2pe\tAATS3pe\tAATS4pe\tAATS5pe\tAATS6pe\tAATS7pe\tAATS8pe\tAATS0are\tAATS1are\tAATS2are\tAATS3are\tAATS4are\tAATS5are\tAATS6are\tAATS7are\tAATS8are\tAATS0p\tAATS1p\tAATS2p\tAATS3p\tAATS4p\tAATS5p\tAATS6p\tAATS7p\tAATS8p\tAATS0i\tAATS1i\tAATS2i\tAATS3i\tAATS4i\tAATS5i\tAATS6i\tAATS7i\tAATS8i\tATSC0c\tATSC1c\tATSC2c\tATSC3c\tATSC4c\tATSC5c\tATSC6c\tATSC7c\tATSC8c\tATSC0dv\tATSC1dv\tATSC2dv\tATSC3dv\tATSC4dv\tATSC5dv\tATSC6dv\tATSC7dv\tATSC8dv\tATSC0d\tATSC1d\tATSC2d\tATSC3d\tATSC4d\tATSC5d\tATSC6d\tATSC7d\tATSC8d\tATSC0s\tATSC1s\tATSC2s\tATSC3s\tATSC4s\tATSC5s\tATSC6s\tATSC7s\tATSC8s\tATSC0Z\tATSC1Z\tATSC2Z\tATSC3Z\tATSC4Z\tATSC5Z\tATSC6Z\tATSC7Z\tATSC8Z\tATSC0m\tATSC1m\tATSC2m\tATSC3m\tATSC4m\tATSC5m\tATSC6m\tATSC7m\tATSC8m\tATSC0v\tATSC1v\tATSC2v\tATSC3v\tATSC4v\tATSC5v\tATSC6v\tATSC7v\tATSC8v\tATSC0se\tATSC1se\tATSC2se\tATSC3se\tATSC4se\tATSC5se\tATSC6se\tATSC7se\tATSC8se\tATSC0pe\tATSC1pe\tATSC2pe\tATSC3pe\tATSC4pe\tATSC5pe\tATSC6pe\tATSC7pe\tATSC8pe\tATSC0are\tATSC1are\tATSC2are\tATSC3are\tATSC4are\tATSC5are\tATSC6are\tATSC7are\tATSC8are\tATSC0p\tATSC1p\tATSC2p\tATSC3p\tATSC4p\tATSC5p\tATSC6p\tATSC7p\tATSC8p\tATSC0i\tATSC1i\tATSC2i\tATSC3i\tATSC4i\tATSC5i\tATSC6i\tATSC7i\tATSC8i\tAATSC0c\tAATSC1c\tAATSC2c\tAATSC3c\tAATSC4c\tAATSC5c\tAATSC6c\tAATSC7c\tAATSC8c\tAATSC0dv\tAATSC1dv\tAATSC2dv\tAATSC3dv\tAATSC4dv\tAATSC5dv\tAATSC6dv\tAATSC7dv\tAATSC8dv\tAATSC0d\tAATSC1d\tAATSC2d\tAATSC3d\tAATSC4d\tAATSC5d\tAATSC6d\tAATSC7d\tAATSC8d\tAATSC0s\tAATSC1s\tAATSC2s\tAATSC3s\tAATSC4s\tAATSC5s\tAATSC6s\tAATSC7s\tAATSC8s\tAATSC0Z\tAATSC1Z\tAATSC2Z\tAATSC3Z\tAATSC4Z\tAATSC5Z\tAATSC6Z\tAATSC7Z\tAATSC8Z\tAATSC0m\tAATSC1m\tAATSC2m\tAATSC3m\tAATSC4m\tAATSC5m\tAATSC6m\tAATSC7m\tAATSC8m\tAATSC0v\tAATSC1v\tAATSC2v\tAATSC3v\tAATSC4v\tAATSC5v\tAATSC6v\tAATSC7v\tAATSC8v\tAATSC0se\tAATSC1se\tAATSC2se\tAATSC3se\tAATSC4se\tAATSC5se\tAATSC6se\tAATSC7se\tAATSC8se\tAATSC0pe\tAATSC1pe\tAATSC2pe\tAATSC3pe\tAATSC4pe\tAATSC5pe\tAATSC6pe\tAATSC7pe\tAATSC8pe\tAATSC0are\tAATSC1are\tAATSC2are\tAATSC3are\tAATSC4are\tAATSC5are\tAATSC6are\tAATSC7are\tAATSC8are\tAATSC0p\tAATSC1p\tAATSC2p\tAATSC3p\tAATSC4p\tAATSC5p\tAATSC6p\tAATSC7p\tAATSC8p\tAATSC0i\tAATSC1i\tAATSC2i\tAATSC3i\tAATSC4i\tAATSC5i\tAATSC6i\tAATSC7i\tAATSC8i\tMATS1c\tMATS2c\tMATS3c\tMATS4c\tMATS5c\tMATS6c\tMATS7c\tMATS8c\tMATS1dv\tMATS2dv\tMATS3dv\tMATS4dv\tMATS5dv\tMATS6dv\tMATS7dv\tMATS8dv\tMATS1d\tMATS2d\tMATS3d\tMATS4d\tMATS5d\tMATS6d\tMATS7d\tMATS8d\tMATS1s\tMATS2s\tMATS3s\tMATS4s\tMATS5s\tMATS6s\tMATS7s\tMATS8s\tMATS1Z\tMATS2Z\tMATS3Z\tMATS4Z\tMATS5Z\tMATS6Z\tMATS7Z\tMATS8Z\tMATS1m\tMATS2m\tMATS3m\tMATS4m\tMATS5m\tMATS6m\tMATS7m\tMATS8m\tMATS1v\tMATS2v\tMATS3v\tMATS4v\tMATS5v\tMATS6v\tMATS7v\tMATS8v\tMATS1se\tMATS2se\tMATS3se\tMATS4se\tMATS5se\tMATS6se\tMATS7se\tMATS8se\tMATS1pe\tMATS2pe\tMATS3pe\tMATS4pe\tMATS5pe\tMATS6pe\tMATS7pe\tMATS8pe\tMATS1are\tMATS2are\tMATS3are\tMATS4are\tMATS5are\tMATS6are\tMATS7are\tMATS8are\tMATS1p\tMATS2p\tMATS3p\tMATS4p\tMATS5p\tMATS6p\tMATS7p\tMATS8p\tMATS1i\tMATS2i\tMATS3i\tMATS4i\tMA'..b'92\t47.928307\t73.099208\t97.854696\t7.527284\t47.928307\t-4.329177\t3.530593\t0.271584\t1.52383\t52.494386\t4.03803\t4.22307\t58.317014\t29.504775\t41.875882\t58.903006\t4.531\t29.504775\t0.692537\t3.546831\t0.272833\t1.528419\t51.806516\t3.985117\t4.20988\t343.222868\t20\t13\t12\t2\t0\t6\t8\t15\t5\t0.278567\t0.321952\t0\t0\t2\t5\t1\t1\t0\t0\t0\t0.111111\t0.111111\t0.0\t0.0\t0.0\t0.083333\t0.107038\t0.0\t0.0\t0.0\t0.027778\t0.025229\t1.044331\t0.0\t0.204124\t0.0\t0.25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