John May
What's happening?
-
Improved bondStereo conversion in CML
Small patch that fixes some trouble i was having with the CDK CML output/conversion. It seems that the CML tools I've been using (in Jumbo) don't use the property CDK sets and instead use the bondStereo XML Content. It was alos the case with importing a structure in ChemAxon's MarvinSketch. The bond is still marked with the "dictRef" but the XML content is now set as well.
2012-05-28 07:13:41 PDT in The Chemistry Dev...
-
Missing Atom Types
Whilst loading some mol files from MetaCyc i got a NoSuchAtomType exception. Investigating it seems that the CDKAtomTypeMatcher defines two types 'Se.2' and "Co.plus" that are present in the matcher but missing in the "cdk-atom-types.owl'. I've added the Co.plus type to the owl file (see. patch) but am not 100% sure on the Se.2 type. From looking at the naming convention...
2012-05-23 06:00:54 PDT in The Chemistry Dev...
-
Missing cdk module tag
org.openscience.cdk.structgen.RandomGenerator does not have a @cdk.module tag and thus is not packaged during 'dist-all' life cycle. I think it should go in cdk-structgen but wanted to check first. J.
2012-04-04 09:12:35 PDT in The Chemistry Dev...
-
Comment: Dynamic IO Settings
Okay have added two patch files. One is the core changes (as before) but this time patched against master. The other is the changes to the classes that use the IOSettings. * A made some minor changes to the core settings management where by if you add a setting which is already added then you get the original instance back. The manager is now also generic allowing it to store IOSetting's...
2012-03-23 03:06:11 PDT in The Chemistry Dev...
-
Comment: Dynamic IO Settings
Argh! Why does SF have no edit button! ...in the previous comment by change I meant: no usage so are in need removal.
2012-03-21 10:21:17 PDT in The Chemistry Dev...
-
Comment: Dynamic IO Settings
Quick question on 2. So I should still flag as deprecated in this patch, the bug report is to indicate the old methods need changing?.
2012-03-21 10:19:31 PDT in The Chemistry Dev...
-
Comment: Dynamic IO Settings
Okay sounds good, will try and get the changes done today. J.
2012-03-21 02:42:56 PDT in The Chemistry Dev...
-
Dynamic IO Settings
I was using IOSetting's class for the recent patch to IteratingMDLReader when I spotted lots of redundant code in the base reader/writer classes. The settings implementation was also quite constrained requiring access to a fixed size array via 'getIOSettings()'. I thought it would be nice to try and simplify the API by removing redundant code (mainly listener handling) and also added some...
2012-03-20 09:10:28 PDT in The Chemistry Dev...
-
Removing redundant code from test
Patch removes redundant code from the IteratingMDLTest. Code was left from when the test was being written.
2012-03-20 07:21:33 PDT in The Chemistry Dev...
-
Comment: IteratingMDLReader/IteratingSDFReader stalling
Sorry for long delay but I have been very busy. I've added a unit test for the skip feature using a chunk from the HMDB SDF i was having problems with. I tried 'synthesising' some broken mol files but the MDLV2000 reader was pretty robust and would return empty molecules instead of 'null' so I used some data I knew was breaking it. I would be easy to change it so it would skip molecules with 0...
2012-03-15 05:29:36 PDT in The Chemistry Dev...