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

Migrated tool version 0.93 from old tool shed archive to new tool shed repository

# Data file for OBDefinable class.
# A # in the first column or a # followed by whitespace introduces a comment and
#   the rest of the characters on a line are ignored.
# White space is trimmed from the front and back of the line.
#   
# There can be any number of lines containing only whitespace and 
#   comment between objects, but none within an object.
# Lines which have "\n" at the end have this replaced by a new line
#   character and the next line is concatenated.

#SmartsDescriptor
#nHal             # name of descriptor. Use for example --filter "nHal<3" 
#[F,Cl,Br,I,At]   # SMARTS defining the descriptor
#Number of halogen atoms\n      #This comment has two lines because of \n at the end.
#count fluorine, chlorine, etc. #When listing plugins, use verbose option to see lines after the first

#OpTransform      # Description() for the class includes a line "OpTransform is definable"
#tautomers        # ID. Commandline option to invoke is --tautomers
#tautomers.txt    # Datafile containing transforms. If filename is * the data follows later in the entry.
#Replace tautomers with their standard forms. Not reliable at present. # An explanatory description.

#OpTransform
#nodative        # ID. Commandline option to invoke is --nodative
#*               # There is no datafile; the transforms are at the end of the entry
#Replace [N+]([O-])=O by N(=O)=O
#TRANSFORM [N+:1](=O)[O-:2] >> [N:1](=O)=[O:2]

CompoundFilter
L5                           # ID
HBD<5 HBA1<10 MW<500 logP<5  # definition in terms of other descriptors or properties
Lipinski Rule of Five        # description

PatternFP
MACCS          # ID of this fingerprint type
MACCS.txt      # File containing the SMARTS patterns

SmartsDescriptor
sbonds
*-*
Number of single bonds

SmartsDescriptor
dbonds
*=*
Number of double bonds

SmartsDescriptor
tbonds
*#*
Number of triple bonds

SmartsDescriptor
abonds
*:*
Number of aromatic bonds

SmartsDescriptor
bonds
*~*
Number of bonds\n
Add or remove hydrogens to count total or bonds between heavy atoms

SmartsDescriptor
atoms
*
Number of atoms\n
Add or remove hydrogens to count total or heavy atoms