annotate CADDSuite-1.0.1/data/OpenBabel/plugindefines.txt @ 9:2cff9609f2c7

Uploaded
author marcel
date Tue, 15 Nov 2011 10:40:26 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
1 # Data file for OBDefinable class.
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
2 # A # in the first column or a # followed by whitespace introduces a comment and
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
3 # the rest of the characters on a line are ignored.
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
4 # White space is trimmed from the front and back of the line.
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
5 #
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
6 # There can be any number of lines containing only whitespace and
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
7 # comment between objects, but none within an object.
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
8 # Lines which have "\n" at the end have this replaced by a new line
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
9 # character and the next line is concatenated.
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
10
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
11 #SmartsDescriptor
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
12 #nHal # name of descriptor. Use for example --filter "nHal<3"
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
13 #[F,Cl,Br,I,At] # SMARTS defining the descriptor
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
14 #Number of halogen atoms\n #This comment has two lines because of \n at the end.
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
15 #count fluorine, chlorine, etc. #When listing plugins, use verbose option to see lines after the first
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
16
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
17 #OpTransform # Description() for the class includes a line "OpTransform is definable"
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
18 #tautomers # ID. Commandline option to invoke is --tautomers
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
19 #tautomers.txt # Datafile containing transforms. If filename is * the data follows later in the entry.
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
20 #Replace tautomers with their standard forms. Not reliable at present. # An explanatory description.
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
21
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
22 #OpTransform
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
23 #nodative # ID. Commandline option to invoke is --nodative
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
24 #* # There is no datafile; the transforms are at the end of the entry
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
25 #Replace [N+]([O-])=O by N(=O)=O
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
26 #TRANSFORM [N+:1](=O)[O-:2] >> [N:1](=O)=[O:2]
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
27
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
28 CompoundFilter
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
29 L5 # ID
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
30 HBD<5 HBA1<10 MW<500 logP<5 # definition in terms of other descriptors or properties
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
31 Lipinski Rule of Five # description
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
32
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
33 PatternFP
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
34 MACCS # ID of this fingerprint type
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
35 MACCS.txt # File containing the SMARTS patterns
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
36
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
37 SmartsDescriptor
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
38 sbonds
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
39 *-*
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
40 Number of single bonds
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
41
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
42 SmartsDescriptor
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
43 dbonds
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
44 *=*
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
45 Number of double bonds
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
46
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
47 SmartsDescriptor
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
48 tbonds
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
49 *#*
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
50 Number of triple bonds
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
51
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
52 SmartsDescriptor
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
53 abonds
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
54 *:*
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
55 Number of aromatic bonds
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
56
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
57 SmartsDescriptor
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
58 bonds
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
59 *~*
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
60 Number of bonds\n
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
61 Add or remove hydrogens to count total or bonds between heavy atoms
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
62
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
63 SmartsDescriptor
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
64 atoms
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
65 *
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
66 Number of atoms\n
2cff9609f2c7 Uploaded
marcel
parents:
diff changeset
67 Add or remove hydrogens to count total or heavy atoms