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Merge pull request #141 from latrocinia/master

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protonate.py: Rename Vanadium element from Va to V
This commit is contained in:
Nathan Baker
2022-03-02 20:16:20 -08:00
committed by GitHub
parent beddb0ac87 b920f5aeec
commit ab80128c45
2 changed files with 14 additions and 1 deletions
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2
propka/protonate.py
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@@ -31,7 +31,7 @@ class Protonate:
'H': 1, 'He': 2, 'Li': 1, 'Be': 2, 'B': 3, 'C': 4, 'N': 5, 'H': 1, 'He': 2, 'Li': 1, 'Be': 2, 'B': 3, 'C': 4, 'N': 5,
'O': 6, 'F': 7, 'Ne': 8, 'Na': 1, 'Mg': 2, 'Al': 3, 'Si': 4, 'O': 6, 'F': 7, 'Ne': 8, 'Na': 1, 'Mg': 2, 'Al': 3, 'Si': 4,
'P': 5, 'S': 6, 'Cl': 7, 'Ar': 8, 'K': 1, 'Ca': 2, 'Sc': 2, 'P': 5, 'S': 6, 'Cl': 7, 'Ar': 8, 'K': 1, 'Ca': 2, 'Sc': 2,
'Ti': 2, 'Va': 2, 'Cr': 1, 'Mn': 2, 'Fe': 2, 'Co': 2, 'Ni': 2, 'Ti': 2, 'V': 2, 'Cr': 1, 'Mn': 2, 'Fe': 2, 'Co': 2, 'Ni': 2,
'Cu': 1, 'Zn': 2, 'Ga': 3, 'Ge': 4, 'As': 5, 'Se': 6, 'Br': 7, 'Cu': 1, 'Zn': 2, 'Ga': 3, 'Ge': 4, 'As': 5, 'Se': 6, 'Br': 7,
'Kr': 8, 'I': 7} 'Kr': 8, 'I': 7}
# TODO - consider putting charges in a configuration file # TODO - consider putting charges in a configuration file

13
tests/test_protonate.py Normal file
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@@ -0,0 +1,13 @@
import propka.atom
import propka.protonate
def test_protonate_atom():
atom = propka.atom.Atom(
"HETATM 4479 V VO4 A1578 -19.097 16.967 0.500 1.00 17.21 V "
)
assert not atom.is_protonated
p = propka.protonate.Protonate()
p.protonate_atom(atom)
assert atom.is_protonated
assert atom.number_of_protons_to_add == 6