From 412962278b60302a27d8fbc60b34ceba61f539cf Mon Sep 17 00:00:00 2001
From: Alvin Noe Ladines <ladinesalvinnoe@gmail.com>
Date: Tue, 17 Sep 2024 12:02:47 +0200
Subject: [PATCH] Adapt binary header fix

---
 atomisticparsers/__init__.py         | 8 ++------
 atomisticparsers/gromacs/parser.py   | 4 +++-
 atomisticparsers/lammps/parser.py    | 4 +++-
 atomisticparsers/utils/mdanalysis.py | 5 ++++-
 4 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/atomisticparsers/__init__.py b/atomisticparsers/__init__.py
index f2858f3..27328e5 100644
--- a/atomisticparsers/__init__.py
+++ b/atomisticparsers/__init__.py
@@ -40,11 +40,7 @@ class EntryPoint(ParserEntryPoint):
     def load(self):
         from nomad.parsing import MatchingParserInterface
 
-        return MatchingParserInterface(
-            **self.dict(),
-            mainfile_binary_header=self.mainfile_binary_header,
-            mainfile_binary_header_re=self.mainfile_binary_header_re,
-        )
+        return MatchingParserInterface(**self.dict())
 
 
 amber_parser_entry_point = EntryPoint(
@@ -78,7 +74,7 @@ def load(self):
     python_package='atomisticparsers.asap',
     mainfile_binary_header_re=b'AFFormatASE\\-Trajectory',
     mainfile_mime_re='application/octet-stream',
-    mainfile_name_re=r'.*.traj$', # can this be specified here? to directly check for the emt calculator maybe? somehow we need to seperate the general ase/traj parser from the asap parser
+    mainfile_name_re=r'.*.traj$',  # can this be specified here? to directly check for the emt calculator maybe? somehow we need to seperate the general ase/traj parser from the asap parser
     parser_class_name='atomisticparsers.asap.AsapParser',
     code_name='ASAP',
     code_homepage='https://wiki.fysik.dtu.dk/asap',
diff --git a/atomisticparsers/gromacs/parser.py b/atomisticparsers/gromacs/parser.py
index 6fa84a7..832c5c0 100644
--- a/atomisticparsers/gromacs/parser.py
+++ b/atomisticparsers/gromacs/parser.py
@@ -53,7 +53,9 @@
     x_gromacs_section_input_output_files,
 )
 from atomisticparsers.utils import MDAnalysisParser, MDParser
-from simulationworkflowschema.molecular_dynamics 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
index a200800..3d9b7fc 100644
--- a/atomisticparsers/lammps/parser.py
+++ b/atomisticparsers/lammps/parser.py
@@ -44,7 +44,9 @@
     x_lammps_section_control_parameters,
 )
 from atomisticparsers.utils import MDAnalysisParser, MDParser
-from simulationworkflowschema.molecular_dynamics 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
index a85187a..278b9e6 100644
--- a/atomisticparsers/utils/mdanalysis.py
+++ b/atomisticparsers/utils/mdanalysis.py
@@ -35,7 +35,10 @@
 
 from nomad.units import ureg
 from nomad.parsing.file_parser import FileParser
-from simulationworkflowschema.molecular_dynamics import BeadGroup, shifted_correlation_average
+from simulationworkflowschema.molecular_dynamics import (
+    BeadGroup,
+    shifted_correlation_average,
+)
 
 
 MOL = 6.022140857e23