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Merged
orbeckst merged 3 commits into from
Jul 14, 2025
Merged

Update lammps class #426

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6c4eed7
update lammps class
lilyminium May 9, 2025
e25453b
updated syrupy snapshots
orbeckst Jul 14, 2025
6f86217
reformat to make pre-commit happy
orbeckst Jul 14, 2025
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7 changes: 5 additions & 2 deletions doc/source/scripts/gen_topologyparser_attrs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,10 @@
from MDAnalysisTests.topology.test_gro import TestGROParser
from MDAnalysisTests.topology.test_gsd import TestGSDParser
from MDAnalysisTests.topology.test_hoomdxml import TestHoomdXMLParser
from MDAnalysisTests.topology.test_lammpsdata import LammpsBase, TestDumpParser
from MDAnalysisTests.topology.test_lammpsdata import (
LammpsBase,
TestDumpParserFull,
)
from MDAnalysisTests.topology.test_mmtf import TestMMTFParser
from MDAnalysisTests.topology.test_mol2 import TestMOL2Base
from MDAnalysisTests.topology.test_pdb import TestPDBParser
Expand Down Expand Up @@ -61,7 +64,7 @@
TestTXYZParser,
TestXPDBParser,
XYZBase,
TestDumpParser,
TestDumpParserFull,
)


Expand Down
8 changes: 5 additions & 3 deletions doc/source/scripts/tests/snapshot/__snapshots__/test_gen_topologyparser_attrs.ambr
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Original file line number Diff line number Diff line change
Expand Up @@ -71,7 +71,7 @@
'charge',
'charges',
'partial atomic charge',
':ref:`DATA <DATA-format>`, :ref:`DMS <DMS-format>`, :ref:`GSD <GSD-format>`, :ref:`MMTF <MMTF-format>`, :ref:`MOL2 <MOL2-format>`, :ref:`PDBQT <PDBQT-format>`, :ref:`PQR <PQR-format>`, :ref:`PSF <PSF-format>`, :ref:`TOP, PRMTOP, PARM7 <TOP-format>`, :ref:`TPR <TPR-format>`, :ref:`XML <XML-format>`',
':ref:`DATA <DATA-format>`, :ref:`DMS <DMS-format>`, :ref:`GSD <GSD-format>`, :ref:`LAMMPSDUMP <LAMMPSDUMP-format>`, :ref:`MMTF <MMTF-format>`, :ref:`MOL2 <MOL2-format>`, :ref:`PDBQT <PDBQT-format>`, :ref:`PQR <PQR-format>`, :ref:`PSF <PSF-format>`, :ref:`TOP, PRMTOP, PARM7 <TOP-format>`, :ref:`TPR <TPR-format>`, :ref:`XML <XML-format>`',
]),
list([
'chargegroup',
Expand Down Expand Up @@ -101,7 +101,7 @@
'element',
'elements',
'atom element',
':ref:`IN, FHIAIMS <IN-format>`, :ref:`MOL2 <MOL2-format>`, :ref:`PDB, ENT <PDB-format>`, :ref:`TPR <TPR-format>`, :ref:`TXYZ, ARC <TXYZ-format>`, :ref:`XYZ <XYZ-format>`',
':ref:`IN, FHIAIMS <IN-format>`, :ref:`LAMMPSDUMP <LAMMPSDUMP-format>`, :ref:`MOL2 <MOL2-format>`, :ref:`PDB, ENT <PDB-format>`, :ref:`TPR <TPR-format>`, :ref:`TXYZ, ARC <TXYZ-format>`, :ref:`XYZ <XYZ-format>`',
]),
list([
'epsilon',
Expand Down Expand Up @@ -288,6 +288,7 @@
':ref:`DATA <DATA-format>`',
':ref:`DMS <DMS-format>`',
':ref:`GSD <GSD-format>`',
':ref:`LAMMPSDUMP <LAMMPSDUMP-format>`',
':ref:`MMTF <MMTF-format>`',
':ref:`MOL2 <MOL2-format>`',
':ref:`PDBQT <PDBQT-format>`',
Expand All @@ -307,6 +308,7 @@
}),
'elements': set({
':ref:`IN, FHIAIMS <IN-format>`',
':ref:`LAMMPSDUMP <LAMMPSDUMP-format>`',
':ref:`MOL2 <MOL2-format>`',
':ref:`PDB, ENT <PDB-format>`',
':ref:`TPR <TPR-format>`',
Expand Down Expand Up @@ -509,7 +511,7 @@
list([
':ref:`LAMMPSDUMP <LAMMPSDUMP-format>`',
'LAMMPS ascii dump file',
'masses, types',
'charges, elements, masses, types',
'',
]),
list([
Expand Down
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