Adapt changes to atomutils (#126)

* Adapt changes to atomutils * Update dep
nomad-coe · Sep 10, 2024 · eebca28 · eebca28
1 parent cedaf41
commit eebca28
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Showing 4 changed files with 5 additions and 4 deletions.
diff --git a/atomisticparsers/gromacs/parser.py b/atomisticparsers/gromacs/parser.py
@@ -54,7 +54,7 @@
     x_gromacs_section_input_output_files,
 )
 from atomisticparsers.utils import MDAnalysisParser, MDParser
-from nomad.atomutils import get_bond_list_from_model_contributions
+from simulationworkflowschema.molecular_dynamics import get_bond_list_from_model_contributions
 
 re_float = r'[-+]?\d+\.*\d*(?:[Ee][-+]\d+)?'
 re_n = r'[\n\r]'

diff --git a/atomisticparsers/lammps/parser.py b/atomisticparsers/lammps/parser.py
@@ -46,7 +46,7 @@
     x_lammps_section_control_parameters,
 )
 from atomisticparsers.utils import MDAnalysisParser, MDParser
-from nomad.atomutils import get_bond_list_from_model_contributions
+from simulationworkflowschema.molecular_dynamics import get_bond_list_from_model_contributions
 
 
 re_float = r'[-+]?\d+\.*\d*(?:[Ee][-+]\d+)?'

diff --git a/atomisticparsers/utils/mdanalysis.py b/atomisticparsers/utils/mdanalysis.py
@@ -35,7 +35,8 @@
 
 from nomad.units import ureg
 from nomad.parsing.file_parser import FileParser
-from nomad.atomutils import BeadGroup, shifted_correlation_average
+from simulationworkflowschema.molecular_dynamics import BeadGroup, shifted_correlation_average
+
 
 MOL = 6.022140857e23
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -15,7 +15,7 @@ dependencies = [
     "nomad-schema-plugin-run@git+https://github.com/nomad-coe/nomad-schema-plugin-run.git@develop",
     "simulationparsers@git+https://github.com/nomad-coe/simulation-parsers.git@develop",
     "lxml>=5.2",
-    "MDAnalysis",
+    "mdanalysis==2.7.0",
     "panedr>=0.2",
     "scipy>=1.7.1",
     "pydantic>=1.10.8,<2.0.0",