qed: qed.py annotate

annotate qed.py @ 0:5ccd3a432785 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6

author	bgruening
date	Tue, 23 May 2017 03:57:14 -0400
parents
children	ab73abead7fa

rev	line source
0 5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	1 #!/usr/bin/env python
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	2 __all__ = ['weights_max', 'weights_mean', 'weights_none', 'default']
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	3
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	4 # RDKit
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	5 from rdkit.Chem import Descriptors
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	6 from rdkit import Chem
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	7
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	8 # General
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	9 from copy import deepcopy
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	10 from math import exp, log
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	11 import sys, os, re
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	12 import argparse
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	13
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	14
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	15 class SilicosItError(Exception):
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	16 """Base class for exceptions in Silicos-it code"""
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	17 pass
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	18
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	19 class WrongArgument(SilicosItError):
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	20 """
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	21 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 bgruening parents: diff changeset	22
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	23 Attributes:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	24 function -- function in which error occurred
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	25 msg -- explanation of the error
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	26 """
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	27 def __init__(self, function, msg):
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	28 self.function = function
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	29 self.msg = msg
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	30
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	31 def check_filetype(filepath):
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	32 mol = False
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	33 possible_inchi = True
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	34 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 bgruening parents: diff changeset	35 if line_counter > 10000:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	36 break
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	37 if line.find('$$$$') != -1:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	38 return 'sdf'
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	39 elif line.find('@<TRIPOS>MOLECULE') != -1:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	40 return 'mol2'
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	41 elif line.find('ligand id') != -1:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	42 return 'drf'
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	43 elif possible_inchi and re.findall('^InChI=', line):
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	44 return 'inchi'
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	45 elif re.findall('^M\s+END', line):
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	46 mol = True
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	47 # 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 bgruening parents: diff changeset	48 possible_inchi = False
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	49
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	50 if mol:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	51 # END can occures before $$$$, so and SDF file will
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	52 # be recognised as mol, if you not using this hack'
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	53 return 'mol'
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	54 return 'smi'
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	55
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	56 AliphaticRings = Chem.MolFromSmarts('[$([A;R][!a])]')
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	57
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	58 AcceptorSmarts = [
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	59 '[oH0;X2]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	60 '[OH1;X2;v2]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	61 '[OH0;X2;v2]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	62 '[OH0;X1;v2]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	63 '[O-;X1]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	64 '[SH0;X2;v2]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	65 '[SH0;X1;v2]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	66 '[S-;X1]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	67 '[nH0;X2]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	68 '[NH0;X1;v3]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	69 '[$([N;+0;X3;v3]);!$(N[C,S]=O)]'
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	70 ]
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	71 Acceptors = []
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	72 for hba in AcceptorSmarts:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	73 Acceptors.append(Chem.MolFromSmarts(hba))
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	74
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	75 StructuralAlertSmarts = [
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	76 '1[O,S,N]1',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	77 '[S,C](=[O,S])[F,Br,Cl,I]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	78 '[CX4][Cl,Br,I]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	79 '[C,c]S(=O)(=O)O[C,c]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	80 '[$([CH]),$(CC)]#CC(=O)[C,c]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	81 '[$([CH]),$(CC)]#CC(=O)O[C,c]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	82 'n[OH]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	83 '[$([CH]),$(CC)]#CS(=O)(=O)[C,c]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	84 'C=C(C=O)C=O',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	85 'n1c([F,Cl,Br,I])cccc1',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	86 '[CH1](=O)',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	87 '[O,o][O,o]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	88 '[C;!R]=[N;!R]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	89 '[N!R]=[N!R]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	90 '[#6](=O)[#6](=O)',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	91 '[S,s][S,s]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	92 '[N,n][NH2]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	93 'C(=O)N[NH2]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	94 '[C,c]=S',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	95 '[$([CH2]),$([CH][CX4]),$(C([CX4])[CX4])]=[$([CH2]),$([CH][CX4]),$(C([CX4])[CX4])]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	96 'C1(=[O,N])C=CC(=[O,N])C=C1',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	97 'C1(=[O,N])C(=[O,N])C=CC=C1',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	98 'a21aa3a(aa1aaaa2)aaaa3',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	99 'a31a(a2a(aa1)aaaa2)aaaa3',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	100 'a1aa2a3a(a1)A=AA=A3=AA=A2',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	101 'c1cc([NH2])ccc1',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	102 '[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]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	103 'I',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	104 'OS(=O)(=O)[O-]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	105 '[N+](=O)[O-]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	106 'C(=O)N[OH]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	107 'C1NC(=O)NC(=O)1',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	108 '[SH]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	109 '[S-]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	110 'c1ccc([Cl,Br,I,F])c([Cl,Br,I,F])c1[Cl,Br,I,F]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	111 'c1cc([Cl,Br,I,F])cc([Cl,Br,I,F])c1[Cl,Br,I,F]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	112 '[CR1]1[CR1][CR1][CR1][CR1][CR1][CR1]1',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	113 '[CR1]1[CR1][CR1]cc[CR1][CR1]1',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	114 '[CR2]1[CR2][CR2][CR2][CR2][CR2][CR2][CR2]1',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	115 '[CR2]1[CR2][CR2]cc[CR2][CR2][CR2]1',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	116 '[CH2R2]1N[CH2R2][CH2R2][CH2R2][CH2R2][CH2R2]1',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	117 '[CH2R2]1N[CH2R2][CH2R2][CH2R2][CH2R2][CH2R2][CH2R2]1',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	118 'C#C',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	119 '[OR2,NR2]@[CR2]@[CR2]@[OR2,NR2]@[CR2]@[CR2]@[OR2,NR2]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	120 '[$([N+R]),$([n+R]),$([N+]=C)][O-]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	121 '[C,c]=N[OH]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	122 '[C,c]=NOC=O',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	123 '[C,c](=O)[CX4,CR0X3,O][C,c](=O)',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	124 'c1ccc2c(c1)ccc(=O)o2',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	125 '[O+,o+,S+,s+]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	126 'N=C=O',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	127 '[NX3,NX4][F,Cl,Br,I]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	128 'c1ccccc1OC(=O)[#6]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	129 '[CR0]=[CR0][CR0]=[CR0]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	130 '[C+,c+,C-,c-]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	131 'N=[N+]=[N-]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	132 'C12C(NC(N1)=O)CSC2',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	133 'c1c([OH])c([OH,NH2,NH])ccc1',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	134 'P',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	135 '[N,O,S]C#N',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	136 'C=C=O',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	137 '[Si][F,Cl,Br,I]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	138 '[SX2]O',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	139 '[SiR0,CR0](c1ccccc1)(c2ccccc2)(c3ccccc3)',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	140 'O1CCCCC1OC2CCC3CCCCC3C2',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	141 'N=[CR0][N,n,O,S]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	142 '[cR2]1[cR2][cR2]([Nv3X3,Nv4X4])[cR2][cR2][cR2]1[cR2]2[cR2][cR2][cR2]([Nv3X3,Nv4X4])[cR2][cR2]2',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	143 'C=[C!r]C#N',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	144 '[cR2]1[cR2]c([N+0X3R0,nX3R0])c([N+0X3R0,nX3R0])[cR2][cR2]1',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	145 '[cR2]1[cR2]c([N+0X3R0,nX3R0])[cR2]c([N+0X3R0,nX3R0])[cR2]1',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	146 '[cR2]1[cR2]c([N+0X3R0,nX3R0])[cR2][cR2]c1([N+0X3R0,nX3R0])',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	147 '[OH]c1ccc([OH,NH2,NH])cc1',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	148 'c1ccccc1OC(=O)O',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	149 '[SX2H0][N]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	150 'c12ccccc1(SC(S)=N2)',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	151 'c12ccccc1(SC(=S)N2)',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	152 'c1nnnn1C=O',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	153 's1c(S)nnc1NC=O',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	154 'S1C=CSC1=S',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	155 'C(=O)Onnn',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	156 'OS(=O)(=O)C(F)(F)F',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	157 'N#CC[OH]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	158 'N#CC(=O)',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	159 'S(=O)(=O)C#N',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	160 'N[CH2]C#N',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	161 'C1(=O)NCC1',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	162 'S(=O)(=O)[O-,OH]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	163 'NC[F,Cl,Br,I]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	164 'C=[C!r]O',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	165 '[NX2+0]=[O+0]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	166 '[OR0,NR0][OR0,NR0]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	167 'C(=O)O[C,H1].C(=O)O[C,H1].C(=O)O[C,H1]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	168 '[CX2R0][NX3R0]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	169 'c1ccccc1[C;!R]=[C;!R]c2ccccc2',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	170 '[NX3R0,NX4R0,OR0,SX2R0][CX4][NX3R0,NX4R0,OR0,SX2R0]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	171 '[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]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	172 '[s,S,c,C,n,N,o,O]~[nX3+,NX3+](~[s,S,c,C,n,N])~[s,S,c,C,n,N]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	173 '[]=[N+]=[]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	174 '[SX3](=O)[O-,OH]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	175 'N#N',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	176 'F.F.F.F',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	177 '[R0;D2][R0;D2][R0;D2][R0;D2]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	178 '[cR,CR]~C(=O)NC(=O)~[cR,CR]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	179 'C=!@CC=[O,S]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	180 '[#6,#8,#16][C,c](=O)O[C,c]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	181 'c[C;R0](=[O,S])[C,c]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	182 'c[SX2][C;!R]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	183 'C=C=C',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	184 'c1nc([F,Cl,Br,I,S])ncc1',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	185 'c1ncnc([F,Cl,Br,I,S])c1',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	186 'c1nc(c2c(n1)nc(n2)[F,Cl,Br,I])',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	187 '[C,c]S(=O)(=O)c1ccc(cc1)F',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	188 '[15N]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	189 '[13C]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	190 '[18O]',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	191 '[34S]'
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	192 ]
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	193
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	194 StructuralAlerts = []
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	195 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	196 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	197
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 # 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	200 # 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	201 # 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	202 # ALOGP parameters from Gregory Gerebtzoff (2012, Roche)
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	203 pads1 = [ [2.817065973, 392.5754953, 290.7489764, 2.419764353, 49.22325677, 65.37051707, 104.9805561],
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	204 [0.486849448, 186.2293718, 2.066177165, 3.902720615, 1.027025453, 0.913012565, 145.4314800],
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	205 [2.948620388, 160.4605972, 3.615294657, 4.435986202, 0.290141953, 1.300669958, 148.7763046],
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	206 [1.618662227, 1010.051101, 0.985094388, 0.000000001, 0.713820843, 0.920922555, 258.1632616],
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	207 [1.876861559, 125.2232657, 62.90773554, 87.83366614, 12.01999824, 28.51324732, 104.5686167],
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	208 [0.010000000, 272.4121427, 2.558379970, 1.565547684, 1.271567166, 2.758063707, 105.4420403],
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	209 [3.217788970, 957.7374108, 2.274627939, 0.000000001, 1.317690384, 0.375760881, 312.3372610],
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	210 [0.010000000, 1199.094025, -0.09002883, 0.000000001, 0.185904477, 0.875193782, 417.7253140] ]
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	211 # ALOGP parameters from the original publication
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	212 pads2 = [ [2.817065973, 392.5754953, 290.7489764, 2.419764353, 49.22325677, 65.37051707, 104.9805561],
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	213 [3.172690585, 137.8624751, 2.534937431, 4.581497897, 0.822739154, 0.576295591, 131.3186604],
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	214 [2.948620388, 160.4605972, 3.615294657, 4.435986202, 0.290141953, 1.300669958, 148.7763046],
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	215 [1.618662227, 1010.051101, 0.985094388, 0.000000001, 0.713820843, 0.920922555, 258.1632616],
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	216 [1.876861559, 125.2232657, 62.90773554, 87.83366614, 12.01999824, 28.51324732, 104.5686167],
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	217 [0.010000000, 272.4121427, 2.558379970, 1.565547684, 1.271567166, 2.758063707, 105.4420403],
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	218 [3.217788970, 957.7374108, 2.274627939, 0.000000001, 1.317690384, 0.375760881, 312.3372610],
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	219 [0.010000000, 1199.094025, -0.09002883, 0.000000001, 0.185904477, 0.875193782, 417.7253140] ]
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	220
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	221 def ads(x, 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	222 return ((a+(b/(1+exp(-1(x-c+d/2)/e))(1-1/(1+exp(-1*(x-c-d/2)/f))))) / dmax)
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	223
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	224 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	225 """
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	226 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	227 """
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	228 matches = []
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	229 if mol is None:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	230 raise WrongArgument("properties(mol)", "mol argument is \'None\'")
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	231 x = [0] * 9
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	232 x[0] = Descriptors.MolWt(mol) # MW
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	233 x[1] = Descriptors.MolLogP(mol) # ALOGP
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	234 for hba in Acceptors: # HBA
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	235 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	236 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	237 x[2] += len(matches)
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	238 x[3] = Descriptors.NumHDonors(mol) # HBD
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	239 x[4] = Descriptors.TPSA(mol) # PSA
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	240 x[5] = Descriptors.NumRotatableBonds(mol) # ROTB
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	241 x[6] = Chem.GetSSSR(Chem.DeleteSubstructs(deepcopy(mol), AliphaticRings)) # AROM
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	242 for alert in StructuralAlerts: # ALERTS
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	243 if (mol.HasSubstructMatch(alert)): x[7] += 1
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	244 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	245 if x[3] > 5:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	246 ro5_failed += 1 #HBD
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	247 if x[2] > 10:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	248 ro5_failed += 1 #HBA
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	249 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	250 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	251 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	252 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	253 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	254 return x
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	255
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	256
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	257 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	258 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	259 if gerebtzoff:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	260 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	261 d[i] = ads(p[i], pads1[i][0], pads1[i][1], pads1[i][2], pads1[i][3], pads1[i][4], pads1[i][5], pads1[i][6])
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	262 else:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	263 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	264 d[i] = ads(p[i], pads2[i][0], pads2[i][1], pads2[i][2], pads2[i][3], pads2[i][4], pads2[i][5], pads2[i][6])
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	265 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	266 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	267 t += w[i] * log(d[i])
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	268 return (exp(t / sum(w)))
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	269
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	270
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	271 def weights_max(mol, gerebtzoff = True, props = False):
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	272 """
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	273 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	274 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	275 """
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	276 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	277 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	278 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	279
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	280
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	281 def weights_mean(mol, gerebtzoff = True, props = False):
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	282 """
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	283 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	284 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	285 """
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	286 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	287 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	288 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	289
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	290
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	291 def weights_none(mol, gerebtzoff = True, props = False):
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	292 """
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	293 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	294 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	295 """
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	296 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	297 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	298 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	299
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	300
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	301 def default(mol, gerebtzoff = True):
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	302 """
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	303 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	304 """
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	305 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	306
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	307
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	308 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	309 parser = argparse.ArgumentParser()
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	310 parser.add_argument('-i', '--input',
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	311 required=True,
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	312 help='path to the input file name')
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	313 parser.add_argument("-m", "--method",
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	314 dest="method",
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	315 choices=['max', 'mean', 'unweighted'],
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	316 default="mean",
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	317 help="Specify the method you want to use.")
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	318 parser.add_argument("--iformat",
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	319 help="Input format. It must be supported by openbabel.")
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	320 parser.add_argument('-o', '--outfile', type=argparse.FileType('w+'),
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	321 default=sys.stdout,
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	322 help="path to the result file, default it sdtout")
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	323 parser.add_argument("--header", dest="header", action="store_true",
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	324 default=False,
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	325 help="Write header line.")
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	326
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	327
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	328 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	329
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	330 # 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	331 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	332 if not os.path.isfile(ifile):
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	333 print "Error: ", ifile, " is not a file or cannot be found."
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	334 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	335 if not os.path.exists(ifile):
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	336 print "Error: ", ifile, " does not exist or cannot be found."
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	337 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	338 if not os.access(ifile, os.R_OK):
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	339 print "Error: ", ifile, " is not readable."
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	340 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	341
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	342 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	343 # try to guess the filetype
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	344 filetype = check_filetype( ifile )
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	345 else:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	346 filetype = args.iformat # sdf or smi
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	347
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	348
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	349 """
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	350 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	351 """
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	352 if filetype == 'sdf':
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	353 supplier = Chem.SDMolSupplier( ifile )
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	354 # Process file
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	355 if args.header:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	356 args.outfile.write("MW\tALOGP\tHBA\tHBD\tPSA\tROTB\tAROM\tALERTS\tLRo5\tQED\tNAME\n")
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	357 count = 0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	358 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	359 count += 1
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	360 if mol is None:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	361 print "Warning: skipping molecule ", count, " and continuing with next."
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	362 continue
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	363 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	364
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	365 if args.method == 'max':
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	366 calc_qed = weights_max(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	367 elif args.method == 'unweighted':
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	368 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	369 else:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	370 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	371
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	372 args.outfile.write( "%.2f\t%.3f\t%d\t%d\t%.2f\t%d\t%d\t%d\t%s\t%.3f\t%-s\n" % (
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	373 props[0],
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	374 props[1],
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	375 props[2],
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	376 props[3],
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	377 props[4],
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	378 props[5],
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	379 props[6],
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	380 props[7],
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	381 props[8],
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	382 calc_qed,
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	383 mol.GetProp("_Name"),
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	384 ))
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	385 elif filetype == 'smi':
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	386 supplier = Chem.SmilesMolSupplier( ifile, " \t", 0, 1, False, True )
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	387
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	388 # Process file
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	389 if args.header:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	390 args.outfile.write("MW\tALOGP\tHBA\tHBD\tPSA\tROTB\tAROM\tALERTS\tLRo5\tQED\tNAME\tSMILES\n")
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	391 count = 0
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	392 for line in open(ifile):
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	393 tokens = line.strip().split('\t')
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	394 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	395 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	396 else:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	397 smiles = tokens[0]
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	398 title = ''
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	399 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	400 count += 1
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	401 if mol is None:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	402 print "Warning: skipping molecule ", count, " and continuing with next."
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	403 continue
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	404 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	405
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	406 if args.method == 'max':
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	407 calc_qed = weights_max(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	408 elif args.method == 'unweighted':
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	409 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	410 else:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	411 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	412
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	413 args.outfile.write( "%.2f\t%.3f\t%d\t%d\t%.2f\t%d\t%d\t%d\t%s\t%.3f\t%-s\t%s\n" % (
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	414 props[0],
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	415 props[1],
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	416 props[2],
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	417 props[3],
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	418 props[4],
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	419 props[5],
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	420 props[6],
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	421 props[7],
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	422 props[8],
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	423 calc_qed,
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	424 title,
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	425 smiles
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	426 ))
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	427 else:
5ccd3a432785 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: diff changeset	428 sys.exit("Error: unknown file-type: %s" % filetype)

Mercurial > repos > bgruening > qed

annotate qed.py @ 0:5ccd3a432785 draft