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annotate CADDSuite/data/OpenBabel/plugindefines.txt @ 0:bac3c274238f

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Migrated tool version 0.93 from old tool shed archive to new tool shed repository
author marcel
date Tue, 07 Jun 2011 16:43:30 -0400
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 # Data file for OBDefinable class.
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2 # A # in the first column or a # followed by whitespace introduces a comment and
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3 # the rest of the characters on a line are ignored.
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4 # White space is trimmed from the front and back of the line.
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5 #
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6 # There can be any number of lines containing only whitespace and
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7 # comment between objects, but none within an object.
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8 # Lines which have "\n" at the end have this replaced by a new line
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9 # character and the next line is concatenated.
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10
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11 #SmartsDescriptor
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12 #nHal # name of descriptor. Use for example --filter "nHal<3"
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13 #[F,Cl,Br,I,At] # SMARTS defining the descriptor
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14 #Number of halogen atoms\n #This comment has two lines because of \n at the end.
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15 #count fluorine, chlorine, etc. #When listing plugins, use verbose option to see lines after the first
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17 #OpTransform # Description() for the class includes a line "OpTransform is definable"
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18 #tautomers # ID. Commandline option to invoke is --tautomers
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19 #tautomers.txt # Datafile containing transforms. If filename is * the data follows later in the entry.
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20 #Replace tautomers with their standard forms. Not reliable at present. # An explanatory description.
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21
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22 #OpTransform
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23 #nodative # ID. Commandline option to invoke is --nodative
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24 #* # There is no datafile; the transforms are at the end of the entry
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25 #Replace [N+]([O-])=O by N(=O)=O
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26 #TRANSFORM [N+:1](=O)[O-:2] >> [N:1](=O)=[O:2]
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27
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28 CompoundFilter
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29 L5 # ID
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30 HBD<5 HBA1<10 MW<500 logP<5 # definition in terms of other descriptors or properties
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31 Lipinski Rule of Five # description
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32
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33 PatternFP
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34 MACCS # ID of this fingerprint type
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35 MACCS.txt # File containing the SMARTS patterns
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36
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37 SmartsDescriptor
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38 sbonds
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39 *-*
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40 Number of single bonds
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41
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42 SmartsDescriptor
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43 dbonds
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44 *=*
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45 Number of double bonds
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46
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47 SmartsDescriptor
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48 tbonds
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49 *#*
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50 Number of triple bonds
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51
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52 SmartsDescriptor
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53 abonds
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54 *:*
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55 Number of aromatic bonds
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56
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57 SmartsDescriptor
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58 bonds
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59 *~*
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60 Number of bonds\n
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61 Add or remove hydrogens to count total or bonds between heavy atoms
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62
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63 SmartsDescriptor
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64 atoms
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65 *
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66 Number of atoms\n
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67 Add or remove hydrogens to count total or heavy atoms