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

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