| Next changeset 1:e2f40a02f31a (2019-06-04) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959 |
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added:
mordred_descriptors.py mordred_descriptors.xml test-data/10mol.sdf test-data/10sdf.tab test-data/8mol.smi test-data/8smi.tab |
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| diff -r 000000000000 -r ea68b86303e2 mordred_descriptors.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mordred_descriptors.py Thu May 23 18:31:43 2019 -0400 |
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| @@ -0,0 +1,71 @@ +import argparse +import numpy as np +import pandas as pd +from mordred import Calculator, descriptors +from mordred.error import Missing, Error +from rdkit import Chem +from rdkit.Chem.rdmolfiles import SDMolSupplier, SmilesMolSupplier + + +def convert_errors_to_nan(el): + """ + Remove elements from the Mordred dataframe which are not + in float or int format + """ + if type(el) == bool: + return int(el) + if type(el) not in [float, int, np.float64]: + return None + return el + + +def mol_supplier(filename, ext): + """ + Based on the file extension, use the appropriate RDKit function to + load a chemical data file (SMILES or SDF) containing multiple molecules + and return a list of RDKit Mol objects + """ + if ext == 'sdf': + return [n for n in SDMolSupplier(filename)] + with open(filename) as f: + mols = f.read().split('\n') + if ext == 'smi': + return [Chem.MolFromSmiles(mol, sanitize=True) for mol in mols] + if ext == 'inchi': + return [Chem.inchi.MolFromInchi(mol, sanitize=True) for mol in mols] + + +def mordred_descriptors(mols, output, header, use_3d): + """ + Calculate Mordred descriptors and save as tabular + """ + calc = Calculator(descriptors, ignore_3D=(not use_3d)) + invalid_mols = np.where(np.array(mols) == None)[0] # indices of invalid SMILES/SDMols + mols = [Chem.MolFromSmiles('') if n is None else n for n in mols] # replace invalid mols with placeholder + df = calc.pandas(mols, quiet=True) # calculate descriptors + for mol in invalid_mols: # remove placeholders + df.iloc[mol] = np.nan + df = df.applymap(convert_errors_to_nan) # remove descriptors which errored + df = df.round(6) + df.to_csv(output, na_rep='', sep='\t', index=False, header=header) # write output + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument('-i', '--infile', required=True, help='Path to the input file.') + parser.add_argument("--iformat", help="Specify the input file format.") + + parser.add_argument('-o', '--outfile', type=argparse.FileType('w+'), + help="Path to the result file") + + parser.add_argument("--3d", dest="use_3d", action="store_true", + default=False, + help="Use 3d descriptors - only with SDF input.") + + parser.add_argument("--header", dest="header", action="store_true", + default=False, + help="Write header line.") + 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 |
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| diff -r 000000000000 -r ea68b86303e2 mordred_descriptors.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mordred_descriptors.xml Thu May 23 18:31:43 2019 -0400 |
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| @@ -0,0 +1,67 @@ +<tool id="ctb_mordred_descriptors" name="Calculate molecular descriptors" version="0.1.0"> + <description>with Mordred</description> + <requirements> + <requirement type="package" version="1.1.2">mordred</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + python '$__tool_directory__/mordred_descriptors.py' + -i '${input}' + --iformat '${input.ext}' + -o '${output}' + $header + $use_3d + ]]></command> + <inputs> + <param name="input" format="smi,sdf,inchi" type="data" label="Molecule data" + help="SDF, SMILES or InChi format"/> + <param name='header' type='boolean' truevalue='--header' falsevalue='' + label='Include a header line' help='Include names of the descriptors as the first line in the output file'/> + <param name='use_3d' type='boolean' truevalue='--3d' falsevalue='' + label='Calculate 3D descriptors' help='Include 3D as well as 2D descriptors - only valid if an SD-file is selected'/> + </inputs> + <outputs> + <data name="output" format="tabular" /> + </outputs> + <tests> + <test> + <param name="input" ftype='sdf' value="10mol.sdf" /> + <param name="header" value="True" /> + <param name="use_3d" value="True" /> + <output name="output" ftype='tabular' file="10sdf.tab" /> + </test> + <test> + <param name="input" ftype='smi' value="8mol.smi" /> + <param name="header" value="True" /> + <param name="use_3d" value="False" /> + <output name="output" ftype='tabular' file="8smi.tab" /> + </test> + </tests> + + <help><![CDATA[ +Calculates up to 1825 molecular descriptors using the Mordred package. A list of all +descriptors is located here_. + +.. _here: https://github.com/simonbray/mordred-descriptors + +.. class:: infomark + +**Input** + +A file containing multiples chemical structures, either in SMILES, InChi or SDF format. + +----- + +.. class:: infomark + +**Output** + +A tabular file, in which each column represents a molecular descriptor (1613 in total, +or 1825 if 3D descriptors are included). Each row describes a single molecule. Empty +cells indicate that a descriptor could not be calculated for that molecule. Rows which +are entirely empty most likely indicate a wrongly encoded molecule. + + ]]></help> + <citations> + <citation type="doi">10.1186/s13321-018-0258-y</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r ea68b86303e2 test-data/10mol.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/10mol.sdf Thu May 23 18:31:43 2019 -0400 |
| [ |
| b'@@ -0,0 +1,759 @@\n+\r\n+ SciTegic01171120562D\r\n+\r\n+ 26 30 0 0 0 0 999 V2000\r\n+ -8.6396 0.9568 0.0000 O 0 0\r\n+ -7.6023 1.5602 0.0000 C 0 0\r\n+ -7.6071 3.0602 0.0000 C 0 0\r\n+ -6.3104 3.8143 0.0000 C 0 0\r\n+ -5.0090 3.0685 0.0000 C 0 0\r\n+ -5.0040 1.5682 0.0000 C 0 0\r\n+ -6.3008 0.8143 0.0000 C 0 0\r\n+ -3.7006 0.8244 0.0000 C 0 0\r\n+ -3.7006 -0.6045 0.0000 N 0 0\r\n+ -2.4915 -1.3190 0.0000 C 0 0\r\n+ -2.5059 -2.8197 0.0000 N 0 0\r\n+ -1.2156 -3.5847 0.0000 C 0 0\r\n+ -1.2329 -5.0846 0.0000 C 0 0\r\n+ -2.5404 -5.8196 0.0000 O 0 0\r\n+ -3.8308 -5.0547 0.0000 C 0 0\r\n+ -3.8135 -3.5548 0.0000 C 0 0\r\n+ -1.2274 -0.6045 0.0000 C 0 0\r\n+ 0.0000 -1.3190 0.0000 O 0 0\r\n+ 1.2274 -0.6045 0.0000 C 0 0\r\n+ 2.4732 -1.3190 0.0000 N 0 0\r\n+ 3.7372 -0.6045 0.0000 C 0 0\r\n+ 3.7372 0.8244 0.0000 C 0 0\r\n+ 2.4732 1.5389 0.0000 C 0 0\r\n+ 1.2274 0.8244 0.0000 C 0 0\r\n+ -1.2274 0.8244 0.0000 C 0 0\r\n+ -2.4915 1.5389 0.0000 N 0 0\r\n+ 1 2 1 0\r\n+ 2 3 1 0\r\n+ 3 4 2 0\r\n+ 4 5 1 0\r\n+ 5 6 2 0\r\n+ 6 7 1 0\r\n+ 2 7 2 0\r\n+ 6 8 1 0\r\n+ 8 9 1 0\r\n+ 9 10 2 0\r\n+ 10 11 1 0\r\n+ 11 12 1 0\r\n+ 12 13 1 0\r\n+ 13 14 1 0\r\n+ 14 15 1 0\r\n+ 15 16 1 0\r\n+ 11 16 1 0\r\n+ 10 17 1 0\r\n+ 17 18 1 0\r\n+ 18 19 1 0\r\n+ 19 20 2 0\r\n+ 20 21 1 0\r\n+ 21 22 2 0\r\n+ 22 23 1 0\r\n+ 23 24 2 0\r\n+ 19 24 1 0\r\n+ 24 25 1 0\r\n+ 17 25 2 0\r\n+ 25 26 1 0\r\n+ 8 26 2 0\r\n+M END\r\n+> <mr_id>\r\n+4358263\r\n+\r\n+> <SMI>\r\n+Oc1cccc(c1)c2nc(N3CCOCC3)c4oc5ncccc5c4n2\r\n+\r\n+$$$$\r\n+\r\n+ SciTegic01171120562D\r\n+\r\n+ 43 51 0 0 1 0 999 V2000\r\n+ -4.7204 3.3431 0.0000 C 0 0\r\n+ -4.1471 2.2890 0.0000 O 0 0\r\n+ -2.6500 2.2500 0.0000 C 0 0 2 0 0 0\r\n+ -1.8100 3.5000 0.0000 C 0 0 1 0 0 0\r\n+ -0.2400 3.5200 0.0000 C 0 0\r\n+ 0.5000 2.1800 0.0000 C 0 0 1 0 0 0\r\n+ -1.0600 2.1800 0.0000 O 0 0\r\n+ -1.8300 0.9300 0.0000 C 0 0 1 0 0 0\r\n+ -3.0300 0.9300 0.0000 C 0 0\r\n+ -0.9800 -0.7800 0.0000 N 0 0\r\n+ -2.1300 -1.4600 0.0000 C 0 0\r\n+ -3.3200 -0.7600 0.0000 C 0 0\r\n+ -4.5500 -1.4800 0.0000 C 0 0\r\n+ -4.5800 -2.7700 0.0000 C 0 0\r\n+ -3.3400 -3.4700 0.0000 C 0 0\r\n+ -2.1300 -2.7900 0.0000 C 0 0\r\n+ 0.2400 -2.7700 0.0000 C 0 0\r\n+ 1.4300 -3.4700 0.0000 C 0 0\r\n+ 1.7600 -4.9700 0.0000 C 0 0\r\n+ 3.2600 -5.0800 0.0000 N 0 0\r\n+ 3.8500 -3.6300 0.0000 C 0 0\r\n+ 4.9971 -3.2777 0.0000 O 0 0\r\n+ 2.6600 -2.7500 0.0000 C 0 0\r\n+ 2.6800 -1.4600 0.0000 C 0 0\r\n+ 3.7900 0.5600 0.0000 C 0 0\r\n+ 4.9600 1.2800 0.0000 C 0 0\r\n+ 4.9600 2.6300 0.0000 C 0 0\r\n+ 3.8100 3.2900 0.0000 C 0 0\r\n+ 2.6400 2.5900 0.0000 C 0 0\r\n+ 2.6400 1.2400 0.0000 C 0 0\r\n+ 1.4900 0.5400 0.0000 N 0 0\r\n+ 1.4500 -0.7600 0.0000 C 0 0\r\n+ 0.2400 -1.4400 0.0000 C 0 0\r\n+ -2.5511 4.8030 0.0000 N 0 0\r\n+ -1.9442 5.8382 0.0000 C 0 0\r\n+ -4.0519 4.8135 0.0000 C 0 0\r\n+ -4.6588 3.7783 0.0000 O 0 0\r\n+ -4.7941 6.1180 0.0000 C 0 0\r\n+ -6.2940 6.1306 0.0000 C 0 0\r\n+ -7.0331 7.4359 0.0000 C 0 0\r\n+ -6.2722 8.7286 0.0000 C 0 0\r\n+ -4.7723 8.7160 0.0000 C 0 0\r\n+ -4.0332 7.4108 0.0000 C 0 0\r\n+ 1 2 1 0\r\n+ 3 2 1 6\r\n+ 3 4 1 0\r\n+ 4 5 1 0\r\n+ 6 5 1 6\r\n+ 6 7 1 0\r\n+ 7 8 1 0\r\n+ 3 8 1 0\r\n+ 8 9 1 1\r\n+ 8 10 1 0\r\n+ 10 11 1 0\r\n+ 11 12 1 0\r\n+ 12 13 2 0\r\n+ 13 14 1 0\r\n+ 14 15 2 0\r\n+ 15 16 1 0\r\n+ 11 16 2 0\r\n+ 16 17 1 0\r\n+ 17 18 1 0\r\n+ 18 19 1 0\r\n+ 19 20 1 0\r\n+ 20 21 1 0\r\n+ 21 22 2 '..b' 0.0000 C 0 0\r\n+ -2.6500 2.2500 0.0000 C 0 0 2 0 0 0\r\n+ -4.1471 2.2892 0.0000 O 0 0\r\n+ -4.7748 1.2665 0.0000 C 0 0\r\n+ -0.9800 -0.7800 0.0000 N 0 0\r\n+ -2.1300 -1.4600 0.0000 C 0 0\r\n+ -3.3200 -0.7600 0.0000 C 0 0\r\n+ -4.5500 -1.4800 0.0000 C 0 0\r\n+ -4.5800 -2.7700 0.0000 C 0 0\r\n+ -3.3400 -3.4700 0.0000 C 0 0\r\n+ -2.1300 -2.7900 0.0000 C 0 0\r\n+ 0.2400 -2.7700 0.0000 C 0 0\r\n+ 1.4300 -3.4700 0.0000 C 0 0\r\n+ 1.7600 -4.9700 0.0000 C 0 0\r\n+ 3.2600 -5.0800 0.0000 N 0 0\r\n+ 3.8500 -3.6300 0.0000 C 0 0\r\n+ 4.9971 -3.2777 0.0000 O 0 0\r\n+ 2.6600 -2.7500 0.0000 C 0 0\r\n+ 2.6800 -1.4600 0.0000 C 0 0\r\n+ 3.7900 0.5600 0.0000 C 0 0\r\n+ 4.9600 1.2800 0.0000 C 0 0\r\n+ 4.9600 2.6300 0.0000 C 0 0\r\n+ 3.8100 3.2900 0.0000 C 0 0\r\n+ 2.6400 2.5900 0.0000 C 0 0\r\n+ 2.6400 1.2400 0.0000 C 0 0\r\n+ 1.4900 0.5400 0.0000 N 0 0\r\n+ 1.4500 -0.7600 0.0000 C 0 0\r\n+ 0.2400 -1.4400 0.0000 C 0 0\r\n+ 1 2 1 0\r\n+ 3 2 1 6\r\n+ 3 4 1 0\r\n+ 5 4 1 6\r\n+ 5 6 1 0\r\n+ 6 7 1 0\r\n+ 7 8 1 1\r\n+ 7 9 1 0\r\n+ 3 9 1 0\r\n+ 9 10 1 6\r\n+ 10 11 1 0\r\n+ 7 12 1 0\r\n+ 12 13 1 0\r\n+ 13 14 1 0\r\n+ 14 15 2 0\r\n+ 15 16 1 0\r\n+ 16 17 2 0\r\n+ 17 18 1 0\r\n+ 13 18 2 0\r\n+ 18 19 1 0\r\n+ 19 20 1 0\r\n+ 20 21 1 0\r\n+ 21 22 1 0\r\n+ 22 23 1 0\r\n+ 23 24 2 0\r\n+ 23 25 1 0\r\n+ 20 25 2 0\r\n+ 25 26 1 0\r\n+ 26 27 1 0\r\n+ 27 28 1 0\r\n+ 28 29 2 0\r\n+ 29 30 1 0\r\n+ 30 31 2 0\r\n+ 31 32 1 0\r\n+ 27 32 2 0\r\n+ 32 33 1 0\r\n+ 5 33 1 0\r\n+ 33 34 1 0\r\n+ 26 34 2 0\r\n+ 34 35 1 0\r\n+ 12 35 1 0\r\n+ 19 35 2 0\r\n+M END\r\n+> <mr_id>\r\n+66\r\n+\r\n+> <SMI>\r\n+CN[C@@H]1C[C@H]2O[C@@](C)([C@@H]1OC)n3c4ccccc4c5c6CNC(=O)c6c7c8ccccc8n2c7c35\r\n+\r\n+$$$$\r\n+\r\n+ SciTegic01171120562D\r\n+\r\n+ 32 35 0 0 1 0 999 V2000\r\n+ 7.1381 -2.1568 0.0000 C 0 0\r\n+ 6.0456 -2.6531 0.0000 C 0 0\r\n+ 4.7409 -1.9129 0.0000 N 0 0\r\n+ 3.6552 -2.9294 0.0000 C 0 0\r\n+ 2.1855 -2.6254 0.0000 C 0 0\r\n+ 1.7138 -1.2033 0.0000 C 0 0\r\n+ 2.5889 0.0182 0.0000 C 0 0\r\n+ 3.7889 0.0269 0.0000 O 0 0\r\n+ 1.7138 1.2033 0.0000 N 0 0\r\n+ 0.2917 0.7475 0.0000 C 0 0\r\n+ -1.0028 1.5132 0.0000 C 0 0\r\n+ -2.3155 0.7475 0.0000 C 0 0\r\n+ -2.3155 -0.7475 0.0000 C 0 0\r\n+ -3.3560 -1.3452 0.0000 F 0 0\r\n+ -1.0028 -1.5132 0.0000 C 0 0\r\n+ 0.2917 -0.7475 0.0000 C 0 0\r\n+ 4.2542 -4.2907 0.0000 C 0 0\r\n+ 3.6559 -5.3308 0.0000 C 0 0\r\n+ 5.7448 -4.1226 0.0000 C 0 0\r\n+ 6.7580 -5.2264 0.0000 C 0 0\r\n+ 6.3978 -6.3710 0.0000 O 0 0\r\n+ 8.2231 -4.9012 0.0000 N 0 0\r\n+ 9.2380 -6.0068 0.0000 C 0 0\r\n+ 10.7032 -5.6816 0.0000 C 0 0 2 0 0 0\r\n+ 11.0634 -4.5369 0.0000 O 0 0\r\n+ 11.7181 -6.7872 0.0000 C 0 0\r\n+ 13.1833 -6.4620 0.0000 N 0 0\r\n+ 14.1993 -7.5656 0.0000 C 0 0\r\n+ 15.6630 -7.2376 0.0000 C 0 0\r\n+ 16.1108 -5.8060 0.0000 O 0 0\r\n+ 15.0949 -4.7024 0.0000 C 0 0\r\n+ 13.6312 -5.0304 0.0000 C 0 0\r\n+ 1 2 1 0\r\n+ 2 3 1 0\r\n+ 3 4 1 0\r\n+ 4 5 1 0\r\n+ 5 6 2 0\r\n+ 6 7 1 0\r\n+ 7 8 2 0\r\n+ 7 9 1 0\r\n+ 9 10 1 0\r\n+ 10 11 1 0\r\n+ 11 12 2 0\r\n+ 12 13 1 0\r\n+ 13 14 1 0\r\n+ 13 15 2 0\r\n+ 15 16 1 0\r\n+ 6 16 1 0\r\n+ 10 16 2 0\r\n+ 4 17 2 0\r\n+ 17 18 1 0\r\n+ 17 19 1 0\r\n+ 2 19 2 0\r\n+ 19 20 1 0\r\n+ 20 21 2 0\r\n+ 20 22 1 0\r\n+ 22 23 1 0\r\n+ 23 24 1 0\r\n+ 24 25 1 6\r\n+ 24 26 1 0\r\n+ 26 27 1 0\r\n+ 27 28 1 0\r\n+ 28 29 1 0\r\n+ 29 30 1 0\r\n+ 30 31 1 0\r\n+ 31 32 1 0\r\n+ 27 32 1 0\r\n+M END\r\n+> <mr_id>\r\n+4362206\r\n+\r\n+> <SMI>\r\n+Cc1[nH]c(/C=C/2\\C(=O)Nc3ccc(F)cc23)c(C)c1C(=O)NC[C@H](O)CN4CCOCC4\r\n+\r\n+$$$$\r\n' |
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| diff -r 000000000000 -r ea68b86303e2 test-data/10sdf.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/10sdf.tab Thu May 23 18:31:43 2019 -0400 |
| b |
| b'@@ -0,0 +1,11 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|
| b |
| diff -r 000000000000 -r ea68b86303e2 test-data/8mol.smi --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/8mol.smi Thu May 23 18:31:43 2019 -0400 |
| [ |
| @@ -0,0 +1,8 @@ +C1NC2=CC(=C(C=C2S(=O)(=O)N1)S(=O)(=O)N)Cl +C1=COC(=C1)CNC2=CC(=C(C=C2C(=O)O)S(=O)(=O)N)Cl +CO[C@H]1[C@@H](C[C@@H]2CN3CCC4=C([C@H]3C[C@@H]2[C@@H]1C(=O)OC)NC5=C4C=CC(=C5)OC)OC(=O)C6=CC(=C(C(=C6)OC)OC)OC +CO[C@H]1[C@@H](C[C@@H]2CN3CCC4=C([C@H]3C[C@@H]2[C@@H]1C(=O)OC)NC5=C4C=CC(=C5)OC)OC(=O)C6=CC(=C(C(=C6)OC)OC)OC.C1NC2=CC(=C(C=C2S(=O)(=O)N1)S(=O)(=O)N)Cl +CCC1(N=C2C=C3C(=NC4=CC=CC=C4N3C5=CC=CC=C5)C=C2N1C6=CC=CC=C6)CC +CCC1(N=C2C=C3C(=NC4=CC=CC=C4N3C5=CC=CC=C5)C=C2N1C6=CC=CC=C6)C +CC(=O)OC1=CC=CC=C1C(=O)[O-] +CC(=O)OC1=CC=CC=C1C(=O)[O-] |
| b |
| diff -r 000000000000 -r ea68b86303e2 test-data/8smi.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/8smi.tab Thu May 23 18:31:43 2019 -0400 |
| b |
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