[feat] added mmcif get_model method #144
Closed
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
a-r-j
reviewed
Jul 7, 2024
biopandas/mmcif/pandas_mmcif.py
Outdated
| """ | ||
|
|
||
| df = copy.deepcopy(self) | ||
| breakpoint() |
a-r-j
reviewed
Jul 7, 2024
biopandas/mmcif/pandas_mmcif.py
Outdated
| structure subsetted to the given model. | ||
| """ | ||
|
|
||
| df = copy.deepcopy(self) |
There was a problem hiding this comment.
Would rename from df since this is not a dataframe.
a-r-j
reviewed
Jul 7, 2024
biopandas/mmcif/pandas_mmcif.py
Outdated
|
|
||
| df = copy.deepcopy(self) | ||
|
|
||
| if "ATOM" in df.df.keys(): |
There was a problem hiding this comment.
Took that pattern from the pandas_pdb and pandas_mmtf file, but can change all three of them
There was a problem hiding this comment.
named it atomic_df for now to adhere with patterns in the source code
There was a problem hiding this comment.
I wouldn't use df, since it's a PandasMmcif object. Maybe: pmmcif
There was a problem hiding this comment.
fair, tried to keep it generic so the method can be the same in the three different file objects. Maybe pandas_object? Or pandas_structure?
There was a problem hiding this comment.
Either is fine but I'd opt for biopandas over pandas to make this distinction clear.
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Outdated suggestions cannot be applied.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.
Code of Conduct
Description
Added
get_modelandget_modelsmethods toPandasMmcifclass, similar toPandasMmtf.Related issues or pull requests
Pull Request Checklist
./docs/sources/CHANGELOG.mdfile (if applicable)./biopandas/*/testsdirectories (if applicable)biopandas/docs/sources/(if applicable)PYTHONPATH='.' pytest ./biopandas -svand make sure that all unit tests pass (for small modifications, it might be sufficient to only run the specific test file, e.g.,PYTHONPATH='.' pytest ./biopandas/classifier/tests/test_stacking_cv_classifier.py -sv)flake8 ./biopandas