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modified guess_atom_element for more accurate guess #4168

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merged 19 commits into from
Aug 16, 2023
Merged

modified guess_atom_element for more accurate guess #4168

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921616b
modified guess_atom_element for more accurate guess
pillose Jun 14, 2023
e358dcb
Merge branch 'MDAnalysis:develop' into develop
pillose Jul 29, 2023
da13425
add test for new behavior
Jul 29, 2023
80c8eb2
Merge branch 'develop' of github.com:pillose/mdanalysis into develop
Jul 29, 2023
1ce5387
updated AUTHORS and CHANGELOG
Jul 29, 2023
76d6bec
revised the order of CHANGELOG
Aug 1, 2023
aa7f457
add commnets and modified the code a little
Aug 1, 2023
878b496
Merge branch 'develop' of github.com:pillose/mdanalysis into develop
Aug 1, 2023
35abfaa
add my username
Aug 1, 2023
3454ceb
Update package/CHANGELOG
pillose Aug 15, 2023
7b5285a
Update package/AUTHORS
pillose Aug 15, 2023
ed4bbb4
Update package/MDAnalysis/topology/guessers.py
pillose Aug 15, 2023
d1d4f54
Merge branch 'develop' of github.com:pillose/mdanalysis into develop
Aug 15, 2023
075f2dc
Merge branch 'develop' into develop
pillose Aug 16, 2023
f77c6f5
Update AUTHORS
pillose Aug 16, 2023
5fe84ab
add guesser tests
pillose Aug 16, 2023
9d30a1e
Update test_guessers.py
pillose Aug 16, 2023
575e6eb
Update guessers.py
pillose Aug 16, 2023
19511fc
Merge branch 'develop' into develop
pillose Aug 16, 2023
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1 change: 1 addition & 0 deletions package/AUTHORS
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Expand Up @@ -220,6 +220,7 @@ Chronological list of authors
- Mohit Kumar
- Shubham Kumar
- Zaheer Timol
- GeongiMoon
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@hmacdope hmacdope Aug 16, 2023 •
edited
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Needs a space, I am assuming?

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If not let me know, other than that looks good.

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I missed a space... Thank you!


External code
-------------
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3 changes: 2 additions & 1 deletion package/CHANGELOG
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Expand Up @@ -13,11 +13,12 @@ The rules for this file:
* release numbers follow "Semantic Versioning" http://semver.org

------------------------------------------------------------------------------
??/??/?? IAlibay
??/??/?? IAlibay, pillose

* 2.7.0

Fixes
* Fix Atom type guessing error (PR #4168, Issue #4167)

Enhancements

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9 changes: 7 additions & 2 deletions package/MDAnalysis/topology/guessers.py
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Expand Up @@ -202,9 +202,14 @@ def guess_atom_element(atomname):
try:
return tables.atomelements[atomname.upper()]
except KeyError:
# strip symbols and numbers
# strip symbols
no_symbols = re.sub(SYMBOLS, '', atomname)
name = re.sub(NUMBERS, '', no_symbols).upper()

# split name by numbers
no_numbers = re.split(NUMBERS, no_symbols)
no_numbers = list(filter(None, no_numbers)) #remove ''
# if no_numbers is not empty, use the first element of no_numbers
name = list(filter(None, no_numbers))[0].upper() if no_numbers else ''
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Apologies if I'm missing something obvious, but do you need to apply filter again here? You've already removed the '' entries and you shouldn't have any None entries ?

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Sorry, I think I made a mistake while modifying the code...


# just in case
if name in tables.atomelements:
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3 changes: 3 additions & 0 deletions testsuite/MDAnalysisTests/topology/test_guessers.py
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Expand Up @@ -104,6 +104,9 @@ def test_guess_atom_element_1H(self):
('zn', 'ZN'),
('Ca2+', 'CA'),
('CA', 'C'),
('N0A', 'N'),
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One more nit sorry could you test Na+ -> Na?

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I just added two tests for Na+ and Cu2+

('C0U', 'C'),
('C0S', 'C')
))
def test_guess_element_from_name(self, name, element):
assert guessers.guess_atom_element(name) == element
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