Mercurial > repos > marcel > caddsuite_linux_x86_64
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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| -1:000000000000 | 0:bac3c274238f |
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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 |