Fixed issues around reduced format #41
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
declared List<Entity> entities transient to avoid serializing temporary data structures, added setMmtfProducer method.
comprehensive test for the reduced data structure.
josemduarte
requested changes
Jun 13, 2017
| else if (chainType.equals("non-polymer")){ | ||
| for(int i=0; i<structureDataInterface.getNumAtomsInGroup(groupType); i++){ | ||
| outList.add(i); | ||
| } else if (! structure.getGroupName(groupIndex).equals("HOH")){ |
There was a problem hiding this comment.
How about deuterated water?
| public void test() throws IOException, ParseException { | ||
| StructureDataInterface full = getDefaultFullData(); | ||
| StructureDataInterface reduced = ReducedEncoder.getReduced(getDefaultFullData()); | ||
| compareFullVsReduced(full.getStructureId(), full, reduced); |
There was a problem hiding this comment.
How about including a few more cases here, not only 4cup. E.g. structure with nucleotides, structure with water marked as non-polymer, structure with alt conformations, etc...
DOD as a solvent. Now also checking for DOD in the ReducedEncoder.
|
Thanks for the changes @pwrose ! One issue now, could you check why the tests are not passing? By the way, I forgot to mention yesterday that a possible way to do the tests is by using https://github.com/rcsb/mmtf/tree/master/test-suite |
|
Btw, I have used the test-suite files. I've put a local copy of the files
in the resources folder so the tests can be run offline.
…On Tue, Jun 13, 2017 at 8:36 AM, Jose Manuel Duarte < ***@***.***> wrote:
Thanks for the changes @pwrose <https://github.com/pwrose> ! One issue
now, could you check why the tests are not passing?
By the way, I forgot to mention yesterday that a possible way to do the
tests is by using https://github.com/rcsb/mmtf/tree/master/test-suite
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#41 (comment)>, or mute
the thread
<https://github.com/notifications/unsubscribe-auth/ADuwEO5fm40T_6wDXm8UHcbwSL27a5mwks5sDqxqgaJpZM4N331R>
.
|
josemduarte
approved these changes
Jun 13, 2017
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.