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annotate qed.py @ 3:52a8d34dd08f draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
author bgruening
date Fri, 30 Jul 2021 12:51:45 +0000
parents ab73abead7fa
children
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5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
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1 #!/usr/bin/env python
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
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2 __all__ = ["weights_max", "weights_mean", "weights_none", "default"]
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5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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3
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
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4 import argparse
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
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5 import os
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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6 import re
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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7 import sys
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5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
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8 # General
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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9 from copy import deepcopy
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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10 from math import exp, log
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52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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11
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
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12 from rdkit import Chem
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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13 # RDKit
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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14 from rdkit.Chem import Descriptors
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5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
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17 class SilicosItError(Exception):
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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18 """Base class for exceptions in Silicos-it code"""
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52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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19
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
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21 class WrongArgument(SilicosItError):
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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22 """
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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23 Exception raised when argument to function is not of correct type.
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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24
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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25 Attributes:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
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26 function -- function in which error occurred
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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27 msg -- explanation of the error
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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28 """
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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29
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
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30 def __init__(self, function, msg):
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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31 self.function = function
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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32 self.msg = msg
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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33
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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34
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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35 def check_filetype(filepath):
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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36 mol = False
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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37 possible_inchi = True
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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38 for line_counter, line in enumerate(open(filepath)):
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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39 if line_counter > 10000:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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40 break
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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41 if line.find("$$$$") != -1:
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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42 return "sdf"
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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43 elif line.find("@<TRIPOS>MOLECULE") != -1:
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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44 return "mol2"
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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45 elif line.find("ligand id") != -1:
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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46 return "drf"
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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47 elif possible_inchi and re.findall("^InChI=", line):
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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48 return "inchi"
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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49 elif re.findall("^M\s+END", line): # noqa W605
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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50 mol = True
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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51 # first line is not an InChI, so it can't be an InChI file
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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52 possible_inchi = False
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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53
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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54 if mol:
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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55 # END can occures before $$$$, so and SDF file will
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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56 # be recognised as mol, if you not using this hack'
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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57 return "mol"
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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58 return "smi"
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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59
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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60
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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61 AliphaticRings = Chem.MolFromSmarts("[$([A;R][!a])]")
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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62
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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63 AcceptorSmarts = [
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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64 "[oH0;X2]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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65 "[OH1;X2;v2]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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66 "[OH0;X2;v2]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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67 "[OH0;X1;v2]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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68 "[O-;X1]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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69 "[SH0;X2;v2]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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70 "[SH0;X1;v2]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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71 "[S-;X1]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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72 "[nH0;X2]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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73 "[NH0;X1;v3]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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74 "[$([N;+0;X3;v3]);!$(N[C,S]=O)]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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75 ]
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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76 Acceptors = []
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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77 for hba in AcceptorSmarts:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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78 Acceptors.append(Chem.MolFromSmarts(hba))
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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79
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
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80 StructuralAlertSmarts = [
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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81 "*1[O,S,N]*1",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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82 "[S,C](=[O,S])[F,Br,Cl,I]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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83 "[CX4][Cl,Br,I]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
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diff changeset
84 "[C,c]S(=O)(=O)O[C,c]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
85 "[$([CH]),$(CC)]#CC(=O)[C,c]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
86 "[$([CH]),$(CC)]#CC(=O)O[C,c]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
87 "n[OH]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
88 "[$([CH]),$(CC)]#CS(=O)(=O)[C,c]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
89 "C=C(C=O)C=O",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
90 "n1c([F,Cl,Br,I])cccc1",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
91 "[CH1](=O)",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
92 "[O,o][O,o]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
93 "[C;!R]=[N;!R]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
94 "[N!R]=[N!R]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
95 "[#6](=O)[#6](=O)",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
96 "[S,s][S,s]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
97 "[N,n][NH2]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
98 "C(=O)N[NH2]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
99 "[C,c]=S",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
100 "[$([CH2]),$([CH][CX4]),$(C([CX4])[CX4])]=[$([CH2]),$([CH][CX4]),$(C([CX4])[CX4])]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
101 "C1(=[O,N])C=CC(=[O,N])C=C1",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
102 "C1(=[O,N])C(=[O,N])C=CC=C1",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
103 "a21aa3a(aa1aaaa2)aaaa3",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
104 "a31a(a2a(aa1)aaaa2)aaaa3",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
105 "a1aa2a3a(a1)A=AA=A3=AA=A2",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
106 "c1cc([NH2])ccc1",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
107 "[Hg,Fe,As,Sb,Zn,Se,se,Te,B,Si,Na,Ca,Ge,Ag,Mg,K,Ba,Sr,Be,Ti,Mo,Mn,Ru,Pd,Ni,Cu,Au,Cd,Al,Ga,Sn,Rh,Tl,Bi,Nb,Li,Pb,Hf,Ho]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
108 "I",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
109 "OS(=O)(=O)[O-]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
110 "[N+](=O)[O-]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
111 "C(=O)N[OH]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
112 "C1NC(=O)NC(=O)1",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
113 "[SH]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
114 "[S-]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
115 "c1ccc([Cl,Br,I,F])c([Cl,Br,I,F])c1[Cl,Br,I,F]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
116 "c1cc([Cl,Br,I,F])cc([Cl,Br,I,F])c1[Cl,Br,I,F]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
117 "[CR1]1[CR1][CR1][CR1][CR1][CR1][CR1]1",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
118 "[CR1]1[CR1][CR1]cc[CR1][CR1]1",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
119 "[CR2]1[CR2][CR2][CR2][CR2][CR2][CR2][CR2]1",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
120 "[CR2]1[CR2][CR2]cc[CR2][CR2][CR2]1",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
121 "[CH2R2]1N[CH2R2][CH2R2][CH2R2][CH2R2][CH2R2]1",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
122 "[CH2R2]1N[CH2R2][CH2R2][CH2R2][CH2R2][CH2R2][CH2R2]1",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
123 "C#C",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
124 "[OR2,NR2]@[CR2]@[CR2]@[OR2,NR2]@[CR2]@[CR2]@[OR2,NR2]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
125 "[$([N+R]),$([n+R]),$([N+]=C)][O-]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
126 "[C,c]=N[OH]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
127 "[C,c]=NOC=O",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
128 "[C,c](=O)[CX4,CR0X3,O][C,c](=O)",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
129 "c1ccc2c(c1)ccc(=O)o2",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
130 "[O+,o+,S+,s+]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
131 "N=C=O",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
132 "[NX3,NX4][F,Cl,Br,I]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
133 "c1ccccc1OC(=O)[#6]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
134 "[CR0]=[CR0][CR0]=[CR0]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
135 "[C+,c+,C-,c-]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
136 "N=[N+]=[N-]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
137 "C12C(NC(N1)=O)CSC2",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
138 "c1c([OH])c([OH,NH2,NH])ccc1",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
139 "P",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
140 "[N,O,S]C#N",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
141 "C=C=O",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
142 "[Si][F,Cl,Br,I]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
143 "[SX2]O",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
144 "[SiR0,CR0](c1ccccc1)(c2ccccc2)(c3ccccc3)",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
145 "O1CCCCC1OC2CCC3CCCCC3C2",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
146 "N=[CR0][N,n,O,S]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
147 "[cR2]1[cR2][cR2]([Nv3X3,Nv4X4])[cR2][cR2][cR2]1[cR2]2[cR2][cR2][cR2]([Nv3X3,Nv4X4])[cR2][cR2]2",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
148 "C=[C!r]C#N",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
149 "[cR2]1[cR2]c([N+0X3R0,nX3R0])c([N+0X3R0,nX3R0])[cR2][cR2]1",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
150 "[cR2]1[cR2]c([N+0X3R0,nX3R0])[cR2]c([N+0X3R0,nX3R0])[cR2]1",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
151 "[cR2]1[cR2]c([N+0X3R0,nX3R0])[cR2][cR2]c1([N+0X3R0,nX3R0])",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
152 "[OH]c1ccc([OH,NH2,NH])cc1",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
153 "c1ccccc1OC(=O)O",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
154 "[SX2H0][N]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
155 "c12ccccc1(SC(S)=N2)",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
156 "c12ccccc1(SC(=S)N2)",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
157 "c1nnnn1C=O",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
158 "s1c(S)nnc1NC=O",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
159 "S1C=CSC1=S",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
160 "C(=O)Onnn",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
161 "OS(=O)(=O)C(F)(F)F",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
162 "N#CC[OH]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
163 "N#CC(=O)",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
164 "S(=O)(=O)C#N",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
165 "N[CH2]C#N",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
166 "C1(=O)NCC1",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
167 "S(=O)(=O)[O-,OH]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
168 "NC[F,Cl,Br,I]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
169 "C=[C!r]O",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
170 "[NX2+0]=[O+0]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
171 "[OR0,NR0][OR0,NR0]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
172 "C(=O)O[C,H1].C(=O)O[C,H1].C(=O)O[C,H1]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
173 "[CX2R0][NX3R0]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
174 "c1ccccc1[C;!R]=[C;!R]c2ccccc2",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
175 "[NX3R0,NX4R0,OR0,SX2R0][CX4][NX3R0,NX4R0,OR0,SX2R0]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
176 "[s,S,c,C,n,N,o,O]~[n+,N+](~[s,S,c,C,n,N,o,O])(~[s,S,c,C,n,N,o,O])~[s,S,c,C,n,N,o,O]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
177 "[s,S,c,C,n,N,o,O]~[nX3+,NX3+](~[s,S,c,C,n,N])~[s,S,c,C,n,N]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
178 "[*]=[N+]=[*]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
179 "[SX3](=O)[O-,OH]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
180 "N#N",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
181 "F.F.F.F",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
182 "[R0;D2][R0;D2][R0;D2][R0;D2]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
183 "[cR,CR]~C(=O)NC(=O)~[cR,CR]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
184 "C=!@CC=[O,S]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
185 "[#6,#8,#16][C,c](=O)O[C,c]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
186 "c[C;R0](=[O,S])[C,c]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
187 "c[SX2][C;!R]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
188 "C=C=C",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
189 "c1nc([F,Cl,Br,I,S])ncc1",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
190 "c1ncnc([F,Cl,Br,I,S])c1",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
191 "c1nc(c2c(n1)nc(n2)[F,Cl,Br,I])",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
192 "[C,c]S(=O)(=O)c1ccc(cc1)F",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
193 "[15N]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
194 "[13C]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
195 "[18O]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
196 "[34S]",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
197 ]
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
198
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
199 StructuralAlerts = []
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
200 for smarts in StructuralAlertSmarts:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
201 StructuralAlerts.append(Chem.MolFromSmarts(smarts))
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
202
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
203
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
204 # ADS parameters for the 8 molecular properties: [row][column]
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
205 # rows[8]: MW, ALOGP, HBA, HBD, PSA, ROTB, AROM, ALERTS
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
206 # columns[7]: A, B, C, D, E, F, DMAX
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
207 # ALOGP parameters from Gregory Gerebtzoff (2012, Roche)
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
208 pads1 = [
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
209 [
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
210 2.817065973,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
211 392.5754953,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
212 290.7489764,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
213 2.419764353,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
214 49.22325677,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
215 65.37051707,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
216 104.9805561,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
217 ],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
218 [
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
219 0.486849448,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
220 186.2293718,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
221 2.066177165,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
222 3.902720615,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
223 1.027025453,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
224 0.913012565,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
225 145.4314800,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
226 ],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
227 [
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
228 2.948620388,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
229 160.4605972,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
230 3.615294657,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
231 4.435986202,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
232 0.290141953,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
233 1.300669958,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
234 148.7763046,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
235 ],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
236 [
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
237 1.618662227,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
238 1010.051101,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
239 0.985094388,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
240 0.000000001,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
241 0.713820843,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
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diff changeset
329 [
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
330 0.010000000,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
331 272.4121427,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
332 2.558379970,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
333 1.565547684,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
334 1.271567166,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
335 2.758063707,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
336 105.4420403,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
337 ],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
338 [
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
339 3.217788970,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
340 957.7374108,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
341 2.274627939,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
342 0.000000001,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
343 1.317690384,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
344 0.375760881,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
345 312.3372610,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
346 ],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
347 [
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
348 0.010000000,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
349 1199.094025,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
350 -0.09002883,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
351 0.000000001,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
352 0.185904477,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
353 0.875193782,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
354 417.7253140,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
355 ],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
356 ]
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
357
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
358
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
359 def ads(x, a, b, c, d, e, f, dmax):
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
360 return (
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
361 a
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
362 + (
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
363 b
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
364 / (1 + exp(-1 * (x - c + d / 2) / e))
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
365 * (1 - 1 / (1 + exp(-1 * (x - c - d / 2) / f)))
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
366 )
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
367 ) / dmax
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
368
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
369
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
370 def properties(mol):
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
371 """
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
372 Calculates the properties that are required to calculate the QED descriptor.
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
373 """
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
374 matches = []
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
375 if mol is None:
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
376 raise WrongArgument("properties(mol)", "mol argument is 'None'")
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
377 x = [0] * 9
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
378 x[0] = Descriptors.MolWt(mol) # MW
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
379 x[1] = Descriptors.MolLogP(mol) # ALOGP
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
380 for hba in Acceptors: # HBA
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
381 if mol.HasSubstructMatch(hba):
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
382 matches = mol.GetSubstructMatches(hba)
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
383 x[2] += len(matches)
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
384 x[3] = Descriptors.NumHDonors(mol) # HBD
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
385 x[4] = Descriptors.TPSA(mol) # PSA
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
386 x[5] = Descriptors.NumRotatableBonds(mol) # ROTB
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
387 x[6] = Chem.GetSSSR(Chem.DeleteSubstructs(deepcopy(mol), AliphaticRings)) # AROM
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
388 for alert in StructuralAlerts: # ALERTS
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
389 if mol.HasSubstructMatch(alert):
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
390 x[7] += 1
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
391 ro5_failed = 0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
392 if x[3] > 5:
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
393 ro5_failed += 1 # HBD
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
394 if x[2] > 10:
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
395 ro5_failed += 1 # HBA
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
396 if x[0] >= 500:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
397 ro5_failed += 1
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
398 if x[1] > 5:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
399 ro5_failed += 1
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
400 x[8] = ro5_failed
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
401 return x
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
402
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
403
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
404 def qed(w, p, gerebtzoff):
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
405 d = [0.00] * 8
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
406 if gerebtzoff:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
407 for i in range(0, 8):
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
408 d[i] = ads(
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
409 p[i],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
410 pads1[i][0],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
411 pads1[i][1],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
412 pads1[i][2],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
413 pads1[i][3],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
414 pads1[i][4],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
415 pads1[i][5],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
416 pads1[i][6],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
417 )
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
418 else:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
419 for i in range(0, 8):
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
420 d[i] = ads(
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
421 p[i],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
422 pads2[i][0],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
423 pads2[i][1],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
424 pads2[i][2],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
425 pads2[i][3],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
426 pads2[i][4],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
427 pads2[i][5],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
428 pads2[i][6],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
429 )
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
430 t = 0.0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
431 for i in range(0, 8):
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
432 t += w[i] * log(d[i])
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
433 return exp(t / sum(w))
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
434
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
435
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
436 def weights_max(mol, gerebtzoff=True, props=False):
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
437 """
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
438 Calculates the QED descriptor using maximal descriptor weights.
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
439 If props is specified we skip the calculation step and use the props-list of properties.
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
440 """
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
441 if not props:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
442 props = properties(mol)
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
443 return qed([0.50, 0.25, 0.00, 0.50, 0.00, 0.50, 0.25, 1.00], props, gerebtzoff)
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
444
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
445
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
446 def weights_mean(mol, gerebtzoff=True, props=False):
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
447 """
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
448 Calculates the QED descriptor using average descriptor weights.
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
449 If props is specified we skip the calculation step and use the props-list of properties.
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
450 """
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
451 if not props:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
452 props = properties(mol)
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
453 return qed([0.66, 0.46, 0.05, 0.61, 0.06, 0.65, 0.48, 0.95], props, gerebtzoff)
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
454
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
455
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
456 def weights_none(mol, gerebtzoff=True, props=False):
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
457 """
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
458 Calculates the QED descriptor using unit weights.
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
459 If props is specified we skip the calculation step and use the props-list of properties.
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
460 """
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
461 if not props:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
462 props = properties(mol)
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
463 return qed([1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00], props, gerebtzoff)
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
464
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
465
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
466 def default(mol, gerebtzoff=True):
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
467 """
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
468 Calculates the QED descriptor using average descriptor weights and Gregory Gerebtzoff parameters.
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
469 """
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
470 return weights_mean(mol, gerebtzoff)
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
471
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
472
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
473 if __name__ == "__main__":
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
474 parser = argparse.ArgumentParser()
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
475 parser.add_argument(
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
476 "-i", "--input", required=True, help="path to the input file name"
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
477 )
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
478 parser.add_argument(
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
479 "-m",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
480 "--method",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
481 dest="method",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
482 choices=["max", "mean", "unweighted"],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
483 default="mean",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
484 help="Specify the method you want to use.",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
485 )
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
486 parser.add_argument(
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
487 "--iformat", help="Input format. It must be supported by openbabel."
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
488 )
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
489 parser.add_argument(
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
490 "-o",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
491 "--outfile",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
492 type=argparse.FileType("w+"),
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
493 default=sys.stdout,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
494 help="path to the result file, default it sdtout",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
495 )
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
496 parser.add_argument(
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
497 "--header",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
498 dest="header",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
499 action="store_true",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
500 default=False,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
501 help="Write header line.",
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
502 )
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
503
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
504 args = parser.parse_args()
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
505
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
506 # Elucidate filetype and open supplier
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
507 ifile = os.path.abspath(args.input)
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
508 if not os.path.isfile(ifile):
1
ab73abead7fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 0
diff changeset
509 print("Error: ", ifile, " is not a file or cannot be found.")
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
510 sys.exit(1)
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
511 if not os.path.exists(ifile):
1
ab73abead7fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 0
diff changeset
512 print("Error: ", ifile, " does not exist or cannot be found.")
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
513 sys.exit(1)
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
514 if not os.access(ifile, os.R_OK):
1
ab73abead7fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 0
diff changeset
515 print("Error: ", ifile, " is not readable.")
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
516 sys.exit(1)
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
517
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
518 if not args.iformat:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
519 # try to guess the filetype
1
ab73abead7fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 0
diff changeset
520 filetype = check_filetype(ifile)
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
521 else:
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
522 filetype = args.iformat # sdf or smi
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
523
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
524 """
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
525 We want to store the original SMILES in the output. So in case of a SMILES file iterate over the file and convert each line separate.
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
526 """
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
527 if filetype == "sdf":
1
ab73abead7fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 0
diff changeset
528 supplier = Chem.SDMolSupplier(ifile)
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
529 # Process file
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
530 if args.header:
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
531 args.outfile.write(
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
532 "MW\tALOGP\tHBA\tHBD\tPSA\tROTB\tAROM\tALERTS\tLRo5\tQED\tNAME\n"
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
533 )
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
534 count = 0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
535 for mol in supplier:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
536 count += 1
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
537 if mol is None:
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
538 print(
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
539 "Warning: skipping molecule ", count, " and continuing with next."
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
540 )
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
541 continue
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
542 props = properties(mol)
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
543
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
544 if args.method == "max":
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
545 calc_qed = weights_max(mol, True, props)
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
546 elif args.method == "unweighted":
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
547 calc_qed = weights_none(mol, True, props)
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
548 else:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
549 calc_qed = weights_mean(mol, True, props)
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
550
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
551 args.outfile.write(
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
552 "%.2f\t%.3f\t%d\t%d\t%.2f\t%d\t%d\t%d\t%s\t%.3f\t%-s\n"
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
553 % (
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
554 props[0],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
555 props[1],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
556 props[2],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
557 props[3],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
558 props[4],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
559 props[5],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
560 props[6],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
561 props[7],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
562 props[8],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
563 calc_qed,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
564 mol.GetProp("_Name"),
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
565 )
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
566 )
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
567 elif filetype == "smi":
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
568 supplier = Chem.SmilesMolSupplier(ifile, " \t", 0, 1, False, True)
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
569
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
570 # Process file
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
571 if args.header:
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
572 args.outfile.write(
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
573 "MW\tALOGP\tHBA\tHBD\tPSA\tROTB\tAROM\tALERTS\tLRo5\tQED\tNAME\tSMILES\n"
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
574 )
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
575 count = 0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
576 for line in open(ifile):
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
577 tokens = line.strip().split("\t")
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
578 if len(tokens) > 1:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
579 smiles, title = tokens
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
580 else:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
581 smiles = tokens[0]
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
582 title = ""
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
583 mol = Chem.MolFromSmiles(smiles)
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
584 count += 1
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
585 if mol is None:
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
586 print(
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
587 "Warning: skipping molecule ", count, " and continuing with next."
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
588 )
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
589 continue
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
590 props = properties(mol)
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
591
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
592 if args.method == "max":
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
593 calc_qed = weights_max(mol, True, props)
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
594 elif args.method == "unweighted":
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
595 calc_qed = weights_none(mol, True, props)
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
596 else:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
597 calc_qed = weights_mean(mol, True, props)
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
598
3
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
599 args.outfile.write(
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
600 "%.2f\t%.3f\t%d\t%d\t%.2f\t%d\t%d\t%d\t%s\t%.3f\t%-s\t%s\n"
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
601 % (
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
602 props[0],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
603 props[1],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
604 props[2],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
605 props[3],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
606 props[4],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
607 props[5],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
608 props[6],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
609 props[7],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
610 props[8],
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
611 calc_qed,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
612 title,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
613 smiles,
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
614 )
52a8d34dd08f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
bgruening
parents: 1
diff changeset
615 )
0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
616 else:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
parents:
diff changeset
617 sys.exit("Error: unknown file-type: %s" % filetype)