Improvements to LoadSDF and WriteSDF #513
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samoturk
commented
Jun 1, 2015
samoturk
commented
- I used WriteSDF a bit and noticed that it saves floats with E notation which confused some programs. I fixed it so that now it formats the floats "correctly" with decimal notation.
- When I tried to fix the code I also noticed that if no properties are given it just pulls the properties from mol objects in "ROMol" and writes those. I modified the code so that embedded properties are removed before molecule is written.
- I added few lines to remove embedded properties when loading sdf with LoadSDF. embedProps=False is the default now. I think this reasonable default since all the data is already in columns and as a bonus it will save some memory..
- And finally I also renamed parameters to be consistent with LoadSDF. Will only break code where "titleColumn" was used.
…nd correctly formats floats (not to E notation). I also renamed some parameters to be consistent with LoadSDF
| @@ -241,6 +241,10 @@ def LoadSDF(filename, idName='ID',molColName = 'ROMol',includeFingerprints=False | |||
| for i, mol in enumerate(Chem.ForwardSDMolSupplier(f)): | |||
| if mol is None: continue | |||
| row = dict((k, mol.GetProp(k)) for k in mol.GetPropNames()) | |||
| if embedProps == False: | |||
There was a problem hiding this comment.
better style here would be: if not embedProps:
|
I made a few suggestions as part of the code review. Once those are addressed I will merge it in. It's safe to ignore the travis failure above: it doesn't look like anything real failed there (this happens occasionally). |
|
Fixed! Thanks for your suggestions and code review! |
greglandrum
added a commit
that referenced
this pull request
Jun 2, 2015
Improvements to LoadSDF and WriteSDF
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