basic guesser features #3753
basic guesser features #3753
Commits on Jul 23, 2022
Commits on Jul 25, 2022
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remove guessing types and masses from parsers
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Merge branch 'guesser-basics' of https://github.com/aya9aladdin/mdana…
…lysis into guesser-basics
Commits on Jul 27, 2022
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Merge branch 'guesser-basics' of https://github.com/aya9aladdin/mdana…
…lysis into guesser-basics
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Merge branch 'guesser-basics' of https://github.com/aya9aladdin/mdana…
…lysis into guesser-basics
Commits on Jul 28, 2022
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Update package/MDAnalysis/core/universe.py
Co-authored-by: Jonathan Barnoud <[email protected]>
Commits on Aug 1, 2022
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remove assigning atomtypes to names in PDBParser
it breaks the current behavior of guessing masses
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Merge branch 'guesser-basics' of https://github.com/aya9aladdin/mdana…
…lysis into guesser-basics
Commits on Aug 4, 2022
Commits on Aug 5, 2022
Commits on Aug 6, 2022
Commits on Aug 8, 2022
Commits on Aug 18, 2022
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1- I transferred parser checking to happen at the universe initiation level, cause it makes no sense to check parser (which is only necessary for mass and types automatic guessing) whenever the user call the guess_topolgy_atrr API 2- I reorganized bond guessing process to avoid some use cases errors
Commits on Aug 21, 2022
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1- adding unit test for guess_topology_attr and DefaultGuesser 2- added parameters for calling DefualtGuesser methods directly without being restirectly tied to the guess_topology_attribute API, which give flexibility for using the DefualtGuesser class 3- transferring all parser checkpoints outside the api, cause it makes no sense after the universe intitiation to check parsers whenever the user call the guess_topology_attributes
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Commits on Aug 22, 2022
Commits on Aug 23, 2022
Commits on Aug 26, 2022
Commits on Sep 10, 2022
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bond guessing + updating guessing API code + minor updates
1- updating bond guessing (and other topology object guessing),. it is now directly guessed through guesser method not through the AtomGroup guess_bond method 2- adding force guessing feature 3- improving parser checkpoint for types and masses automatic guessing (this automatic guessing behavior goal is to mimic old parser guessing behavior, so it is not wise to add masses and types to the 'to_guess' parameter unconditionally. instead I improved the parser checkpoints and removed redundant logic from it) 4- fixing some styling issues 5- adding element attribute to the TXYZParser to avoid its special condition in mass guessing 6- other minor code fixes according to reviewers suggestions
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Commits on Sep 12, 2022
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Update testsuite/MDAnalysisTests/converters/test_rdkit_parser.py
Co-authored-by: Jonathan Barnoud <[email protected]>
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Update testsuite/MDAnalysisTests/guesser/test_default_guesser.py
Co-authored-by: Jonathan Barnoud <[email protected]>
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Update testsuite/MDAnalysisTests/core/test_universe.py
Co-authored-by: Jonathan Barnoud <[email protected]>
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Merge branch 'guesser-basics' of https://github.com/aya9aladdin/mdana…
…lysis into guesser-basics
Commits on Sep 17, 2022
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Apply suggestions from code review
Co-authored-by: Irfan Alibay <[email protected]>
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Commits on Sep 21, 2022
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adding partial guessing + parser tests + noValue topologyattr
1- added a placeholder noValue attribute to topologyattrs 2- modified guessAttr() methods to guess attributes partially if they already exist in the universe 3- set the noVal attribute of masses to nan 4- added tests to ParserBases to check that guessed masses and types have the same values as the old default behavior of parsers
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Apply suggestions from code review
Co-authored-by: Jonathan Barnoud <[email protected]>
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Merge branch 'guesser-basics' of https://github.com/aya9aladdin/mdana…
…lysis into guesser-basics
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I removed skipping tests if atoms type and masses are not guessed. Instead I modified the values to make sure that no unexpected guessing happens at universe creation
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Commits on Sep 25, 2022
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variable names update + partial guessing updates
1- update variable names 2- transferred 'is_value_missing' from topologyattr classes to guesser base.py
Commits on Sep 26, 2022
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Apply suggestions from code review
Co-authored-by: Jonathan Barnoud <[email protected]>
Commits on Sep 27, 2022
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1- added docstring to the guesser part 2- updated parsers docsting (version updates about removing atom and type guessing)
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Merge branch 'guesser-basics' of https://github.com/aya9aladdin/mdana…
…lysis into guesser-basics
Commits on Sep 28, 2022
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fix typo in topology tests + add element to ITPParser
1- I added deprecation warning for assigning masses to zero when guessing fail 2- added element attribute to ITPParser to fix mass guessing 3- transferred is_missing_value() method to topologyattrs 4- fixed some errors and typos in topologies tests
Commits on Sep 30, 2022
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Added tests for BaseGuesser + updating guess_Attr()
added more tests for BaseGuesser guess_Attr() method + solving some bugs found in guess_attr
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Commits on Oct 12, 2022
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Apply suggestions from code review
Co-authored-by: Jonathan Barnoud <[email protected]>
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Merge branch 'guesser-basics' of https://github.com/aya9aladdin/mdana…
…lysis into guesser-basics
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Commits on Oct 13, 2022
Commits on Oct 14, 2022
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passing empty attribute indices for partial guessing
I changed how partial guessing takes place; so instead of passing the parent values corresponding to empty attributes (ex: atom types for empty masses), I changed this to just pass the indices of the empty value, then guesser get the parents by index. This helped me solving some issues while working on PDBGuesser, such as getting the residue name of atoms for elements guessing. Dealing with indices instead of values is more straightforward, cause even in complete guessing retrieving residues list is not helpful cause it only contains the total residues of the universe not each atom's residue
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Merge branch 'guesser-basics' of https://github.com/aya9aladdin/mdana…
…lysis into guesser-basics
Commits on Oct 18, 2022
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1- guess_topologyAttr pep8 update 2- guesser/bas.py pep8 update 3- default_guesser pep8 update
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remove unrelated analysis module tests
I once added those tests to increase the codecove percentage, but they are not related to the pr
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Commits on Oct 19, 2022
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Co-authored-by: Jonathan Barnoud <[email protected]>
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removing autopep8 effect from irrelevant parts + adding pep styles
I removed the autopep8 effect in irrelevant parts of code and updated the style of the changed code to follow pep8 styling
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Merge branch 'guesser-basics' of https://github.com/aya9aladdin/mdana…
…lysis into guesser-basics
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I scanned all the touched package modules to make sure it is properly styled
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Commits on Oct 20, 2022
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restore a useful autopep8 change
code improvement that I removed by accident
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add guessing elements from masses to DefaultGuesser
1- I added to the guess_types method of DefaultGuesser the ability of guessing elements from masses if names is not available to the universe 2- corrected Bohrium mass in tables.py
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Commits on Jan 28, 2023
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Revert "Revert "Merge branch 'develop' into guesser-basics""
This reverts commit a463561.
Commits on Jan 29, 2023
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Revert "Revert "Merge branch 'develop' into guesser-basics""
This reverts commit a463561.
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Merge branch 'guesser-basics' of https://github.com/aya9aladdin/mdana…
…lysis into guesser-basics
Commits on Feb 20, 2023
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silencing guessing processes in some tests
this part was removed when I merged the develop branch
Commits on Feb 25, 2023
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silencing guessing process in irrelevant tests
silencing guessing at universe creation in a recently added coordinates tests (merged from develop branch
Commits on Mar 3, 2023
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add guesser context + removing styling errors in ITP
- added guessing context to the copy() and _unpickle_U() (for deserialisation) methods of the universe - removed styling errors from ITPParser file
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Commits on Mar 10, 2023
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update changelog and versionchanged
added the new updates to the changelog and versionchanged for affected files
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Merge branch 'guesser-basics' of https://github.com/aya9aladdin/mdana…
…lysis into guesser-basics
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Commits on Apr 27, 2023
Commits on Apr 28, 2023
Commits on Sep 12, 2023
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improving guess_attr + updating changelog
I improved the logic of partial guessing in guess_atrr() method to just use mask for partial guessing instead of indices + updated the changelog
Commits on Sep 17, 2023
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removed types from FHIAMSParser and XYZParser
* updated versionchanged in some files * removed the previously added `types`= ` `elements` for FHIAMSParser and XYZParser as they shows no importance
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Commits on Nov 6, 2023
Commits on Dec 27, 2023
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Co-authored-by: Lily Wang <[email protected]>
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Co-authored-by: Lily Wang <[email protected]>
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Apply suggestions from code review
Co-authored-by: Lily Wang <[email protected]>
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silencing auto guessing in coordinates tests
silencing auto guessing of atom masses and types in coordinated tests as it produce errors during universe initialization, which is irrelevant to testing coordinates
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applying @lilyminium suggestions
* removed changes of sorted() method in bat.py * changed the topologyattr's is_value_missing() method to are_values_missing() for better performance * improved some lines guessTopologyAttributes() * replaced the guesser method are_guessable() with is_guessable() for raising a more meaningful valueError message when the attribute is not guessable * adding a test for the topologyatrrs's are_values_missing() method
Commits on Jan 6, 2024
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applying @lilyminium code review suggesitions
* added the full path of guess_TopologyAttributes in documentations * modified guess_bonds, guess_angles and guess_dihedrals to not alter the universe * removed coord parameter from guess_bonds method (just use atoms.positions) * some parameters renaming * modified some tests * removed rtol=1e-3 from assert_allclose * added test for are_value_missing for topologyattrs
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removed guessed_types/masses tests
I added those test to compare the output of guess_topologyAttributes with the original guessing behavior that used to take place inside each parser. but after giving it a second eye it seems those tests have no added value as the guessing API is already tested and work as expected, so I removed them
Commits on Feb 1, 2024
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Apply suggestions from code review
Co-authored-by: Lily Wang <[email protected]>
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Merge branch 'guesser-basics' of https://github.com/aya9aladdin/mdana…
…lysis into guesser-basics
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I added some more tests based on @lilyminium suggestions: * test 'missing_value_labels' * test for get_guesser's is_subclass condition * checking that expected guessed attributes have is_guessed = true * test for comparing guessed masses/types against real values in PDB and Mol2 parsers
Commits on Mar 16, 2024
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1- added more tests for DefaultGuesser 2- updated bonds, angles, dihedrals guessing methods (avoiding adding other guessed attributes to the universe as a side effect of calling those methods) 3- removed validate_atom_types method from DefaultGuesser as it has no usage case
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Commits on Mar 25, 2024
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* added tests for checking guessed types and masses values against the actual old values for different topologies * changed guess_topologyAtrributes name to guess_topologyAtrrs * fixed some pep style issues * updated changelog and versionchanged
Commits on Mar 26, 2024
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Merge branch 'guesser-basics' of https://github.com/aya9aladdin/mdana…
…lysis into guesser-basics
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Commits on Mar 30, 2024
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* updating some docs and removing docs of removed modules *updating are_value_missing() method
Commits on Mar 31, 2024
Commits on Apr 17, 2024
Commits on Apr 21, 2024
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Apply suggestions from code review
Co-authored-by: Irfan Alibay <[email protected]>
Commits on Apr 26, 2024
Commits on May 19, 2024
Commits on Sep 17, 2024
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Apply LAST suggestions from code review
Co-authored-by: Irfan Alibay <[email protected]>
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- removed guessing types from masses
- updated guess_TopologyAttrs docs - fixed some tests - capitalize atomtypes from elements in RDKitParser
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Commits on Sep 29, 2024
Commits on Oct 17, 2024
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Co-authored-by: Lily Wang <[email protected]>