Mol2, SDF and XYZ File Parsers #418
Open
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
to model in get_structure function needed. MOL2File and SDFFile prepared now ...
files with multiple models gained from conversion via openbabel
sybly atom types heuristic doesn't yet work though ...
now seems to work. Also covering all elements in sybyl_atom_type now, although heuristic not fully working.
changed tests ^^
for pdbx residue consistency
xyz and sdf files. For mol2 files it works as long as the atom_name represents the element and not an atom_name like "CA"
that are actual atom_names and not elements. Specifically this works with amino acids where the atom_names are written to the atom_name column. See TYR.mol2 for example in test cases.
|
Thanks for the PR. Prior to review, could you resolve the conflicts with the upstream branch? |
Before the logic for only doing that test when an amino acid in file name did create an empty list.
public functions. Internal functions and members have been made private.
as well as meta_information dictionaries working.
Reading of datetime from header working. But besides that
problems with read/write of header. These seem to stem from
the fact that programs such as openbabel to not adher to the
Chemical table file standard ..
Omitting this for now as one can in principle get the header
by acessing lines[1]
warning causes test suite to interpret this as failure..
save_structure. Cleaned up tests, also precision in XYZFiles did not match between loaded and stored.
|
Only took like a week more then expected -.- .... |
padix-key
requested changes
Sep 3, 2022
There was a problem hiding this comment.
Hi, here is the first part of my review. Some general remarks:
- I think for consistency reasons the
get_structure()methods should take themodelparameter analogous to for examplePDBFileand select the return type based on it. - There are some commented out lines of code that remain.
- Sometimes, there are (multiple) empty lines, without obvious structuring reason.
- You can add yourself to
CONTRIB.rstvia this PR, if you like.
Co-authored-by: Patrick Kunzmann <[email protected]>
Co-authored-by: Patrick Kunzmann <[email protected]>
Co-authored-by: Patrick Kunzmann <[email protected]>
Co-authored-by: Patrick Kunzmann <[email protected]>
Co-authored-by: Patrick Kunzmann <[email protected]>
Co-authored-by: Patrick Kunzmann <[email protected]>
adding get_model_count function.
to contributors list
some missing functionality with this (was not working properly before). Also made test_xyz.py conforming with PEP8 codestyle.
Made some changes also in conver to expose header get/set Also added tests for this.
that it should also work with windows paths.
with windows paths also...
in get_structure for multi model files). Some cleanup...
datetime is not matching. Tried to negelect this warning in the test but somehow mark.filterwarnings has no effect.
Closed
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.
The file parsers for those 3 files now essentially work.
There is some fine work missing, especially with the hybridization heuristics in mol2.
But reading small molecules, also with multiple models, should work and I have added some more files in all 3 formats for testing this.