From 36534dc54130a0890cc068e0c8c6cee01c37e59c Mon Sep 17 00:00:00 2001 From: Alvin Noe Ladines Date: Thu, 15 Aug 2024 18:05:33 +0200 Subject: [PATCH 1/9] Add entry point --- pyproject.toml | 4 +- simulationworkflowschema/__init__.py | 146 ++++++++++++++++++--------- simulationworkflowschema/general.py | 8 +- 3 files changed, 107 insertions(+), 51 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 08a9472..ab37067 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -70,5 +70,5 @@ line-ending = "auto" [tool.setuptools.packages.find] include = ["simulationworkflowschema*"] -[tool.setuptools.package-data] -simulationworkflowschema = ["*/nomad_plugin.yaml"] +[project.entry-points.'nomad.plugin'] +simulationworkflowschema = "simulationworkflowschema:simulationworkflow_schema_entry_point" diff --git a/simulationworkflowschema/__init__.py b/simulationworkflowschema/__init__.py index dd0b831..5e9f2b5 100644 --- a/simulationworkflowschema/__init__.py +++ b/simulationworkflowschema/__init__.py @@ -16,52 +16,102 @@ # See the License for the specific language governing permissions and # limitations under the License. # -from .general import ( - SimulationWorkflow, - SimulationWorkflowMethod, - SimulationWorkflowResults, - ParallelSimulation, - SerialSimulation, - BeyondDFT, - DFTMethod, - ElectronicStructureOutputs, - MagneticOutputs, +import importlib + +from nomad.config.models.plugins import SchemaPackageEntryPoint + + +__all__ = [ + "SimulationWorkflow", + "SimulationWorkflowMethod", + "SimulationWorkflowResults", + "ParallelSimulation", + "SerialSimulation", + "BeyondDFT", + "DFTMethod", + "ElectronicStructureOutputs", + "MagneticOutputs", + "SinglePoint", + "SinglePointMethod", + "SinglePointResults", + "GeometryOptimization", + "GeometryOptimizationMethod", + "GeometryOptimizationResults", + "MolecularDynamics", + "MolecularDynamicsMethod", + "MolecularDynamicsResults", + "Phonon", + "PhononMethod", + "PhononResults", + "EquationOfState", + "EquationOfStateMethod", + "EquationOfStateResults", + "ChemicalReaction", + "ChemicalReactionMethod", + "ChemicalReactionResults", + "Elastic", + "ElasticMethod", + "ElasticResults", + "FirstPrinciplesPlusTB", + "FirstPrinciplesPlusTBMethod", + "FirstPrinciplesPlusTBResults", + "DFTPlusGW", + "DFTPlusGWMethod", + "DFTPlusGWResults", + "XS", + "XSMethod", + "XSResults" "DFTPlusTBPlusDMFT", + "DFTPlusTBPlusDMFTMethod", + "DFTPlusTBPlusDMFTResults", + "DMFTPlusMaxEnt", + "DMFTPlusMaxEntMethod", + "DMFTPlusMaxEntResults", + "PhotonPolarization", + "PhotonPolarizationMethod", + "PhotonPolarizationResults", + "Thermodynamics", + "ThermodynamicsMethod", + "ThermodynamicsResults", +] + + +def load_modules(): + sub_modules = [ + "general", + "single_point", + "geometry_optimization", + "molecular_dynamics", + "phonon", + "equation_of_state", + "chemical_reaction", + "elastic", + "tb", + "gw", + "xs", + "dmft", + "max_ent", + "photon_polarization", + "thermodynamics", + ] + import simulationworkflowschema + + for name in sub_modules: + sub_module = importlib.import_module(f"simulationworkflowschema.{name}") + for method in sub_module.__dict__: + if method in __all__: + setattr(simulationworkflowschema, method, sub_module.__dict__[method]) + + +class SimulationWorkflowSchemaEntryPoint(SchemaPackageEntryPoint): + def load(self): + load_modules() + + from .general import m_package + + return m_package + + +simulationworkflow_schema_entry_point = SimulationWorkflowSchemaEntryPoint( + name="SimulationWorkflowSchema", + description="Schema for the nomad simulation workflows.", ) -from .single_point import SinglePoint, SinglePointMethod, SinglePointResults -from .geometry_optimization import ( - GeometryOptimization, - GeometryOptimizationMethod, - GeometryOptimizationResults, -) -from .molecular_dynamics import ( - MolecularDynamics, - MolecularDynamicsMethod, - MolecularDynamicsResults, -) -from .phonon import Phonon, PhononMethod, PhononResults -from .equation_of_state import ( - EquationOfState, - EquationOfStateMethod, - EquationOfStateResults, -) -from .chemical_reaction import ( - ChemicalReaction, - ChemicalReactionMethod, - ChemicalReactionResults, -) -from .elastic import Elastic, ElasticMethod, ElasticResults -from .tb import ( - FirstPrinciplesPlusTB, - FirstPrinciplesPlusTBMethod, - FirstPrinciplesPlusTBResults, -) -from .gw import DFTPlusGW, DFTPlusGWMethod, DFTPlusGWResults -from .xs import XS, XSMethod, XSResults -from .dmft import DFTPlusTBPlusDMFT, DFTPlusTBPlusDMFTMethod, DFTPlusTBPlusDMFTResults -from .max_ent import DMFTPlusMaxEnt, DMFTPlusMaxEntMethod, DMFTPlusMaxEntResults -from .photon_polarization import ( - PhotonPolarization, - PhotonPolarizationMethod, - PhotonPolarizationResults, -) -from .thermodynamics import Thermodynamics, ThermodynamicsMethod, ThermodynamicsResults diff --git a/simulationworkflowschema/general.py b/simulationworkflowschema/general.py index 243292f..563f40f 100644 --- a/simulationworkflowschema/general.py +++ b/simulationworkflowschema/general.py @@ -19,7 +19,7 @@ import numpy as np from nomad.datamodel.data import ArchiveSection -from nomad.metainfo import SubSection, Section, Quantity, Reference +from nomad.metainfo import SubSection, Section, Quantity, Reference, Package from nomad.datamodel.metainfo.common import FastAccess from nomad.datamodel.metainfo.workflow import Workflow, Link, Task, TaskReference from runschema.method import ( @@ -41,6 +41,9 @@ ) +m_package = Package() + + def resolve_difference(values): delta_values = None @@ -497,3 +500,6 @@ class MagneticOutputs(SimulationWorkflowResults): Reference to the magnetic susceptibility tensors. """, ) + + +m_package.__init_metainfo__() \ No newline at end of file From d5074d634c08d8b2aecf02fdedf25e770e9f6829 Mon Sep 17 00:00:00 2001 From: Alvin Noe Ladines Date: Fri, 16 Aug 2024 09:58:03 +0200 Subject: [PATCH 2/9] Update run ref --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index ab37067..ffc2c2f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -11,7 +11,7 @@ authors = [{ name = "The NOMAD Authors" }] license = { text = "Apache-2.0" } dependencies = [ "nomad-lab>=1.2.0", - "nomad-schema-plugin-run@git+https://github.com/nomad-coe/nomad-schema-plugin-run.git@develop", + "nomad-schema-plugin-run@git+https://github.com/nomad-coe/nomad-schema-plugin-run.git@2e883fac63f6e9d78d2ea2077c4a091810d0b3f9", ] [project.urls] From 486cc359365ebb448526668965901a75f2f60fa1 Mon Sep 17 00:00:00 2001 From: Alvin Noe Ladines Date: Fri, 16 Aug 2024 10:08:59 +0200 Subject: [PATCH 3/9] Update run plugin --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index ffc2c2f..45c42f4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -11,7 +11,7 @@ authors = [{ name = "The NOMAD Authors" }] license = { text = "Apache-2.0" } dependencies = [ "nomad-lab>=1.2.0", - "nomad-schema-plugin-run@git+https://github.com/nomad-coe/nomad-schema-plugin-run.git@2e883fac63f6e9d78d2ea2077c4a091810d0b3f9", + "nomad-schema-plugin-run@git+https://github.com/nomad-coe/nomad-schema-plugin-run.git@f5d348fec5cef89e76021b42e48ff49b1832034b", ] [project.urls] From 33f2c76b642ea54e62ff966cafaffc6486fceea9 Mon Sep 17 00:00:00 2001 From: Alvin Noe Ladines Date: Fri, 16 Aug 2024 10:21:30 +0200 Subject: [PATCH 4/9] Linting fix --- simulationworkflowschema/__init__.py | 3 ++- simulationworkflowschema/general.py | 2 +- tests/conftest.py | 2 ++ 3 files changed, 5 insertions(+), 2 deletions(-) diff --git a/simulationworkflowschema/__init__.py b/simulationworkflowschema/__init__.py index 5e9f2b5..7086f59 100644 --- a/simulationworkflowschema/__init__.py +++ b/simulationworkflowschema/__init__.py @@ -60,7 +60,8 @@ "DFTPlusGWResults", "XS", "XSMethod", - "XSResults" "DFTPlusTBPlusDMFT", + "XSResults", + "DFTPlusTBPlusDMFT", "DFTPlusTBPlusDMFTMethod", "DFTPlusTBPlusDMFTResults", "DMFTPlusMaxEnt", diff --git a/simulationworkflowschema/general.py b/simulationworkflowschema/general.py index 563f40f..3ed76d1 100644 --- a/simulationworkflowschema/general.py +++ b/simulationworkflowschema/general.py @@ -502,4 +502,4 @@ class MagneticOutputs(SimulationWorkflowResults): ) -m_package.__init_metainfo__() \ No newline at end of file +m_package.__init_metainfo__() diff --git a/tests/conftest.py b/tests/conftest.py index a6bcab1..1c3f67e 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -75,6 +75,8 @@ ) from runschema.system import AtomsGroup, System, Atoms from nomad.datamodel.metainfo.workflow import Link, TaskReference +import simulationworkflowschema +simulationworkflowschema.simulationworkflow_schema_entry_point.load() from simulationworkflowschema.molecular_dynamics import ( DiffusionConstantValues, MeanSquaredDisplacement, From 6bdb7d489f6aa7cdefb3677577f346d1c4c64d71 Mon Sep 17 00:00:00 2001 From: Alvin Noe Ladines Date: Fri, 16 Aug 2024 10:33:59 +0200 Subject: [PATCH 5/9] Linting fix --- tests/conftest.py | 32 ++++++++++---------------------- 1 file changed, 10 insertions(+), 22 deletions(-) diff --git a/tests/conftest.py b/tests/conftest.py index 1c3f67e..d04e66d 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -85,28 +85,16 @@ RadialDistributionFunctionValues, ) from simulationworkflowschema.equation_of_state import EOSFit -from simulationworkflowschema import ( - MolecularDynamicsMethod, - MolecularDynamicsResults, - SinglePoint, - GeometryOptimization, - GeometryOptimizationMethod, - Elastic, - ElasticResults, - MolecularDynamics, - EquationOfState, - EquationOfStateResults, - DFTPlusGWMethod, - DFTPlusGW as GWworkflow, - DFTPlusTBPlusDMFTMethod, - DFTPlusTBPlusDMFT as DMFTworkflow, - PhotonPolarization, - PhotonPolarizationMethod, - PhotonPolarizationResults, - XS as XSworkflow, - DMFTPlusMaxEntMethod, - DMFTPlusMaxEnt as MaxEntworkflow, -) +from simulationworkflowschema.molecular_dynamics import MolecularDynamics, MolecularDynamicsMethod, MolecularDynamicsResults +from simulationworkflowschema.single_point import SinglePoint +from simulationworkflowschema.geometry_optimization import GeometryOptimization, GeometryOptimizationMethod +from simulationworkflowschema.elastic import Elastic, ElasticResults +from simulationworkflowschema.equation_of_state import EquationOfState, EquationOfStateResults +from simulationworkflowschema.gw import DFTPlusGWMethod, DFTPlusGW as GWworkflow +from simulationworkflowschema.dmft import DFTPlusTBPlusDMFTMethod, DFTPlusTBPlusDMFT as DMFTworkflow +from simulationworkflowschema.photon_polarization import PhotonPolarization, PhotonPolarizationMethod, PhotonPolarizationResults +from simulationworkflowschema.xs import XS as XSworkflow +from simulationworkflowschema.max_ent import DMFTPlusMaxEntMethod, DMFTPlusMaxEnt as MaxEntworkflow LOGGER = get_logger(__name__) From 3871ececa80e8f0e4126534bda62bc2a89284fc4 Mon Sep 17 00:00:00 2001 From: Alvin Noe Ladines Date: Fri, 16 Aug 2024 10:41:38 +0200 Subject: [PATCH 6/9] Fix test --- tests/conftest.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/tests/conftest.py b/tests/conftest.py index d04e66d..604716c 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -73,6 +73,8 @@ DFT, GW, ) +import runschema +runschema.run_schema_entry_point.load() from runschema.system import AtomsGroup, System, Atoms from nomad.datamodel.metainfo.workflow import Link, TaskReference import simulationworkflowschema From decd6bc6f7df21513c56f276dc663977c44a22b1 Mon Sep 17 00:00:00 2001 From: Alvin Noe Ladines Date: Fri, 16 Aug 2024 10:48:06 +0200 Subject: [PATCH 7/9] Fix test --- tests/conftest.py | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/tests/conftest.py b/tests/conftest.py index 604716c..8165455 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -22,6 +22,12 @@ import ase.build import re +# Load schemas first +import runschema +runschema.run_schema_entry_point.load() +import simulationworkflowschema +simulationworkflowschema.simulationworkflow_schema_entry_point.load() + from nomad.units import ureg from nomad.normalizing import normalizers from nomad.utils import get_logger @@ -73,12 +79,8 @@ DFT, GW, ) -import runschema -runschema.run_schema_entry_point.load() from runschema.system import AtomsGroup, System, Atoms from nomad.datamodel.metainfo.workflow import Link, TaskReference -import simulationworkflowschema -simulationworkflowschema.simulationworkflow_schema_entry_point.load() from simulationworkflowschema.molecular_dynamics import ( DiffusionConstantValues, MeanSquaredDisplacement, From 4c5bc008ac9b15f66363c28b7c8106c0e56823ba Mon Sep 17 00:00:00 2001 From: Alvin Noe Ladines Date: Mon, 19 Aug 2024 13:34:34 +0200 Subject: [PATCH 8/9] Fix tests --- simulationworkflowschema/__init__.py | 138 ++-- .../molecular_dynamics.py | 10 +- tests/conftest.py | 38 +- tests/data/molecular_dynamics.archive.json | 303 +++------ tests/data/radius_of_gyration.archive.json | 15 +- tests/data/rdf_2.archive.json | 3 +- tests/data/rdf_and_msd.archive.json | 600 ++++++------------ 7 files changed, 407 insertions(+), 700 deletions(-) diff --git a/simulationworkflowschema/__init__.py b/simulationworkflowschema/__init__.py index 7086f59..fe854e8 100644 --- a/simulationworkflowschema/__init__.py +++ b/simulationworkflowschema/__init__.py @@ -22,82 +22,82 @@ __all__ = [ - "SimulationWorkflow", - "SimulationWorkflowMethod", - "SimulationWorkflowResults", - "ParallelSimulation", - "SerialSimulation", - "BeyondDFT", - "DFTMethod", - "ElectronicStructureOutputs", - "MagneticOutputs", - "SinglePoint", - "SinglePointMethod", - "SinglePointResults", - "GeometryOptimization", - "GeometryOptimizationMethod", - "GeometryOptimizationResults", - "MolecularDynamics", - "MolecularDynamicsMethod", - "MolecularDynamicsResults", - "Phonon", - "PhononMethod", - "PhononResults", - "EquationOfState", - "EquationOfStateMethod", - "EquationOfStateResults", - "ChemicalReaction", - "ChemicalReactionMethod", - "ChemicalReactionResults", - "Elastic", - "ElasticMethod", - "ElasticResults", - "FirstPrinciplesPlusTB", - "FirstPrinciplesPlusTBMethod", - "FirstPrinciplesPlusTBResults", - "DFTPlusGW", - "DFTPlusGWMethod", - "DFTPlusGWResults", - "XS", - "XSMethod", - "XSResults", - "DFTPlusTBPlusDMFT", - "DFTPlusTBPlusDMFTMethod", - "DFTPlusTBPlusDMFTResults", - "DMFTPlusMaxEnt", - "DMFTPlusMaxEntMethod", - "DMFTPlusMaxEntResults", - "PhotonPolarization", - "PhotonPolarizationMethod", - "PhotonPolarizationResults", - "Thermodynamics", - "ThermodynamicsMethod", - "ThermodynamicsResults", + 'SimulationWorkflow', + 'SimulationWorkflowMethod', + 'SimulationWorkflowResults', + 'ParallelSimulation', + 'SerialSimulation', + 'BeyondDFT', + 'DFTMethod', + 'ElectronicStructureOutputs', + 'MagneticOutputs', + 'SinglePoint', + 'SinglePointMethod', + 'SinglePointResults', + 'GeometryOptimization', + 'GeometryOptimizationMethod', + 'GeometryOptimizationResults', + 'MolecularDynamics', + 'MolecularDynamicsMethod', + 'MolecularDynamicsResults', + 'Phonon', + 'PhononMethod', + 'PhononResults', + 'EquationOfState', + 'EquationOfStateMethod', + 'EquationOfStateResults', + 'ChemicalReaction', + 'ChemicalReactionMethod', + 'ChemicalReactionResults', + 'Elastic', + 'ElasticMethod', + 'ElasticResults', + 'FirstPrinciplesPlusTB', + 'FirstPrinciplesPlusTBMethod', + 'FirstPrinciplesPlusTBResults', + 'DFTPlusGW', + 'DFTPlusGWMethod', + 'DFTPlusGWResults', + 'XS', + 'XSMethod', + 'XSResults', + 'DFTPlusTBPlusDMFT', + 'DFTPlusTBPlusDMFTMethod', + 'DFTPlusTBPlusDMFTResults', + 'DMFTPlusMaxEnt', + 'DMFTPlusMaxEntMethod', + 'DMFTPlusMaxEntResults', + 'PhotonPolarization', + 'PhotonPolarizationMethod', + 'PhotonPolarizationResults', + 'Thermodynamics', + 'ThermodynamicsMethod', + 'ThermodynamicsResults', ] def load_modules(): sub_modules = [ - "general", - "single_point", - "geometry_optimization", - "molecular_dynamics", - "phonon", - "equation_of_state", - "chemical_reaction", - "elastic", - "tb", - "gw", - "xs", - "dmft", - "max_ent", - "photon_polarization", - "thermodynamics", + 'general', + 'single_point', + 'geometry_optimization', + 'molecular_dynamics', + 'phonon', + 'equation_of_state', + 'chemical_reaction', + 'elastic', + 'tb', + 'gw', + 'xs', + 'dmft', + 'max_ent', + 'photon_polarization', + 'thermodynamics', ] import simulationworkflowschema for name in sub_modules: - sub_module = importlib.import_module(f"simulationworkflowschema.{name}") + sub_module = importlib.import_module(f'simulationworkflowschema.{name}') for method in sub_module.__dict__: if method in __all__: setattr(simulationworkflowschema, method, sub_module.__dict__[method]) @@ -113,6 +113,6 @@ def load(self): simulationworkflow_schema_entry_point = SimulationWorkflowSchemaEntryPoint( - name="SimulationWorkflowSchema", - description="Schema for the nomad simulation workflows.", + name='SimulationWorkflowSchema', + description='Schema for the nomad simulation workflows.', ) diff --git a/simulationworkflowschema/molecular_dynamics.py b/simulationworkflowschema/molecular_dynamics.py index fd008ca..d80e88c 100644 --- a/simulationworkflowschema/molecular_dynamics.py +++ b/simulationworkflowschema/molecular_dynamics.py @@ -1245,11 +1245,11 @@ def normalize(self, archive, logger): else [] ) sec_diffusion.error_type = 'Pearson correlation coefficient' - sec_diffusion.errors = ( - self._msd_results['error_diffusion_constant'][i_type] - if self._msd_results.get('error_diffusion_constant') is not None - else [] - ) + if self._msd_results.get('error_diffusion_constant') is not None: + errors = self._msd_results['error_diffusion_constant'][i_type] + sec_diffusion.errors = ( + list(errors) if isinstance(errors, (list, np.ndarray)) else [errors] + ) class MolecularDynamicsResults(ThermodynamicsResults): diff --git a/tests/conftest.py b/tests/conftest.py index 8165455..ab5126d 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -22,12 +22,6 @@ import ase.build import re -# Load schemas first -import runschema -runschema.run_schema_entry_point.load() -import simulationworkflowschema -simulationworkflowschema.simulationworkflow_schema_entry_point.load() - from nomad.units import ureg from nomad.normalizing import normalizers from nomad.utils import get_logger @@ -89,16 +83,36 @@ RadialDistributionFunctionValues, ) from simulationworkflowschema.equation_of_state import EOSFit -from simulationworkflowschema.molecular_dynamics import MolecularDynamics, MolecularDynamicsMethod, MolecularDynamicsResults +from simulationworkflowschema.molecular_dynamics import ( + MolecularDynamics, + MolecularDynamicsMethod, + MolecularDynamicsResults, +) from simulationworkflowschema.single_point import SinglePoint -from simulationworkflowschema.geometry_optimization import GeometryOptimization, GeometryOptimizationMethod +from simulationworkflowschema.geometry_optimization import ( + GeometryOptimization, + GeometryOptimizationMethod, +) from simulationworkflowschema.elastic import Elastic, ElasticResults -from simulationworkflowschema.equation_of_state import EquationOfState, EquationOfStateResults +from simulationworkflowschema.equation_of_state import ( + EquationOfState, + EquationOfStateResults, +) from simulationworkflowschema.gw import DFTPlusGWMethod, DFTPlusGW as GWworkflow -from simulationworkflowschema.dmft import DFTPlusTBPlusDMFTMethod, DFTPlusTBPlusDMFT as DMFTworkflow -from simulationworkflowschema.photon_polarization import PhotonPolarization, PhotonPolarizationMethod, PhotonPolarizationResults +from simulationworkflowschema.dmft import ( + DFTPlusTBPlusDMFTMethod, + DFTPlusTBPlusDMFT as DMFTworkflow, +) +from simulationworkflowschema.photon_polarization import ( + PhotonPolarization, + PhotonPolarizationMethod, + PhotonPolarizationResults, +) from simulationworkflowschema.xs import XS as XSworkflow -from simulationworkflowschema.max_ent import DMFTPlusMaxEntMethod, DMFTPlusMaxEnt as MaxEntworkflow +from simulationworkflowschema.max_ent import ( + DMFTPlusMaxEntMethod, + DMFTPlusMaxEnt as MaxEntworkflow, +) LOGGER = get_logger(__name__) diff --git a/tests/data/molecular_dynamics.archive.json b/tests/data/molecular_dynamics.archive.json index ea1aecf..399e121 100644 --- a/tests/data/molecular_dynamics.archive.json +++ b/tests/data/molecular_dynamics.archive.json @@ -1666,8 +1666,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -3296,8 +3295,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -4926,8 +4924,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -6556,8 +6553,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -8186,8 +8182,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -9816,8 +9811,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -11446,8 +11440,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -13076,8 +13069,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -14706,8 +14698,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -16336,8 +16327,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -17966,8 +17956,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -19596,8 +19585,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -21226,8 +21214,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -22856,8 +22843,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -24486,8 +24472,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -26116,8 +26101,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -27746,8 +27730,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -29376,8 +29359,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -31006,8 +30988,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -32636,8 +32617,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -34266,8 +34246,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -35896,8 +35875,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -37526,8 +37504,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -39156,8 +39133,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -40786,8 +40762,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -42416,8 +42391,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -44046,8 +44020,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -45676,8 +45649,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -47306,8 +47278,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -48936,8 +48907,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -50566,8 +50536,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -52196,8 +52165,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -53826,8 +53794,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -55456,8 +55423,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -57086,8 +57052,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -58716,8 +58681,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -60346,8 +60310,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -61976,8 +61939,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -63606,8 +63568,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -65236,8 +65197,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -66866,8 +66826,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -68496,8 +68455,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -70126,8 +70084,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -71756,8 +71713,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -73386,8 +73342,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -75016,8 +74971,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -76646,8 +76600,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -78276,8 +78229,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -79906,8 +79858,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -81536,8 +81487,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -83166,8 +83116,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -84796,8 +84745,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -86426,8 +86374,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -88056,8 +88003,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -89686,8 +89632,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -91316,8 +91261,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -92946,8 +92890,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -94576,8 +94519,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -96206,8 +96148,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -97836,8 +97777,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -99466,8 +99406,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -101096,8 +101035,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -102726,8 +102664,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -104356,8 +104293,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -105986,8 +105922,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -107616,8 +107551,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -109246,8 +109180,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -110876,8 +110809,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -112506,8 +112438,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -114136,8 +114067,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -115766,8 +115696,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -117396,8 +117325,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -119026,8 +118954,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -120656,8 +120583,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -122286,8 +122212,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -123916,8 +123841,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -125546,8 +125470,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -127176,8 +127099,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -128806,8 +128728,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -130436,8 +130357,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -132066,8 +131986,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -133696,8 +133615,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -135326,8 +135244,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -136956,8 +136873,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -138586,8 +138502,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -140216,8 +140131,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -141846,8 +141760,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -143476,8 +143389,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -145106,8 +145018,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -146736,8 +146647,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -148366,8 +148276,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -149996,8 +149905,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -151626,8 +151534,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -153256,8 +153163,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -154886,8 +154792,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -156516,8 +156421,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -158146,8 +158050,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -159776,8 +159679,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -161406,8 +161308,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -163036,8 +162937,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -164666,8 +164566,7 @@ true, true, true - ], - "bond_list": [] + ] } } ], diff --git a/tests/data/radius_of_gyration.archive.json b/tests/data/radius_of_gyration.archive.json index 9a0e828..e63622c 100644 --- a/tests/data/radius_of_gyration.archive.json +++ b/tests/data/radius_of_gyration.archive.json @@ -12136,8 +12136,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -13424,8 +13423,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -14712,8 +14710,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -16000,8 +15997,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -17288,8 +17284,7 @@ true, true, true - ], - "bond_list": [] + ] } } ], diff --git a/tests/data/rdf_2.archive.json b/tests/data/rdf_2.archive.json index 70f5fc0..189780b 100644 --- a/tests/data/rdf_2.archive.json +++ b/tests/data/rdf_2.archive.json @@ -69783,8 +69783,7 @@ true, true, true - ], - "bond_list": [] + ] } } ], diff --git a/tests/data/rdf_and_msd.archive.json b/tests/data/rdf_and_msd.archive.json index ebb8f66..33fe470 100644 --- a/tests/data/rdf_and_msd.archive.json +++ b/tests/data/rdf_and_msd.archive.json @@ -49681,8 +49681,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -53817,8 +53816,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -57953,8 +57951,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -62089,8 +62086,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -66225,8 +66221,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -70361,8 +70356,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -74497,8 +74491,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -78633,8 +78626,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -82769,8 +82761,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -86905,8 +86896,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -91041,8 +91031,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -95177,8 +95166,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -99313,8 +99301,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -103449,8 +103436,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -107585,8 +107571,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -111721,8 +111706,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -115857,8 +115841,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -119993,8 +119976,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -124129,8 +124111,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -128265,8 +128246,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -132401,8 +132381,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -136537,8 +136516,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -140673,8 +140651,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -144809,8 +144786,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -148945,8 +148921,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -153081,8 +153056,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -157217,8 +157191,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -161353,8 +161326,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -165489,8 +165461,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -169625,8 +169596,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -173761,8 +173731,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -177897,8 +177866,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -182033,8 +182001,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -186169,8 +186136,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -190305,8 +190271,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -194441,8 +194406,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -198577,8 +198541,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -202713,8 +202676,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -206849,8 +206811,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -210985,8 +210946,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -215121,8 +215081,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -219257,8 +219216,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -223393,8 +223351,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -227529,8 +227486,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -231665,8 +231621,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -235801,8 +235756,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -239937,8 +239891,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -244073,8 +244026,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -248209,8 +248161,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -252345,8 +252296,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -256481,8 +256431,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -260617,8 +260566,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -264753,8 +264701,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -268889,8 +268836,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -273025,8 +272971,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -277161,8 +277106,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -281297,8 +281241,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -285433,8 +285376,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -289569,8 +289511,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -293705,8 +293646,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -297841,8 +297781,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -301977,8 +301916,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -306113,8 +306051,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -310249,8 +310186,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -314385,8 +314321,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -318521,8 +318456,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -322657,8 +322591,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -326793,8 +326726,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -330929,8 +330861,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -335065,8 +334996,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -339201,8 +339131,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -343337,8 +343266,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -347473,8 +347401,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -351609,8 +351536,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -355745,8 +355671,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -359881,8 +359806,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -364017,8 +363941,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -368153,8 +368076,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -372289,8 +372211,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -376425,8 +376346,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -380561,8 +380481,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -384697,8 +384616,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -388833,8 +388751,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -392969,8 +392886,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -397105,8 +397021,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -401241,8 +401156,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -405377,8 +405291,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -409513,8 +409426,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -413649,8 +413561,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -417785,8 +417696,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -421921,8 +421831,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -426057,8 +425966,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -430193,8 +430101,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -434329,8 +434236,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -438465,8 +438371,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -442601,8 +442506,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -446737,8 +446641,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -450873,8 +450776,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -455009,8 +454911,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -459145,8 +459046,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -463281,8 +463181,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -467417,8 +467316,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -471553,8 +471451,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -475689,8 +475586,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -479825,8 +479721,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -483961,8 +483856,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -488097,8 +487991,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -492233,8 +492126,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -496369,8 +496261,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -500505,8 +500396,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -504641,8 +504531,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -508777,8 +508666,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -512913,8 +512801,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -517049,8 +516936,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -521185,8 +521071,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -525321,8 +525206,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -529457,8 +529341,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -533593,8 +533476,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -537729,8 +537611,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -541865,8 +541746,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -546001,8 +545881,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -550137,8 +550016,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -554273,8 +554151,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -558409,8 +558286,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -562545,8 +562421,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -566681,8 +566556,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -570817,8 +570691,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -574953,8 +574826,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -579089,8 +578961,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -583225,8 +583096,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -587361,8 +587231,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -591497,8 +591366,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -595633,8 +595501,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -599769,8 +599636,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -603905,8 +603771,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -608041,8 +607906,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -612177,8 +612041,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -616313,8 +616176,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -620449,8 +620311,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -624585,8 +624446,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -628721,8 +628581,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -632857,8 +632716,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -636993,8 +636851,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -641129,8 +640986,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -645265,8 +645121,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -649401,8 +649256,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -653537,8 +653391,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -657673,8 +657526,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -661809,8 +661661,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -665945,8 +665796,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -670081,8 +669931,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -674217,8 +674066,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -678353,8 +678201,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -682489,8 +682336,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -686625,8 +686471,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -690761,8 +690606,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -694897,8 +694741,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -699033,8 +698876,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -703169,8 +703011,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -707305,8 +707146,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -711441,8 +711281,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -715577,8 +715416,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -719713,8 +719551,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -723849,8 +723686,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -727985,8 +727821,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -732121,8 +731956,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -736257,8 +736091,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -740393,8 +740226,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -744529,8 +744361,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -748665,8 +748496,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -752801,8 +752631,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -756937,8 +756766,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -761073,8 +760901,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -765209,8 +765036,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -769345,8 +769171,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -773481,8 +773306,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -777617,8 +777441,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -781753,8 +781576,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -785889,8 +785711,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -790025,8 +789846,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -794161,8 +793981,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -798297,8 +798116,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -802433,8 +802251,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -806569,8 +806386,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -810705,8 +810521,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -814841,8 +814656,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -818977,8 +818791,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -823113,8 +822926,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -827249,8 +827061,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -831385,8 +831196,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -835521,8 +835331,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -839657,8 +839466,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -843793,8 +843601,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -847929,8 +847736,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -852065,8 +851871,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -856201,8 +856006,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -860337,8 +860141,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -864473,8 +864276,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -868609,8 +868411,7 @@ true, true, true - ], - "bond_list": [] + ] } }, { @@ -872745,8 +872546,7 @@ true, true, true - ], - "bond_list": [] + ] } } ], From a38ffc6aa9514d7d84099bcbd22804642e90d5f7 Mon Sep 17 00:00:00 2001 From: Alvin Noe Ladines Date: Mon, 19 Aug 2024 14:21:37 +0200 Subject: [PATCH 9/9] Temporary fix atoms group ref --- simulationworkflowschema/molecular_dynamics.py | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/simulationworkflowschema/molecular_dynamics.py b/simulationworkflowschema/molecular_dynamics.py index d80e88c..3274f0a 100644 --- a/simulationworkflowschema/molecular_dynamics.py +++ b/simulationworkflowschema/molecular_dynamics.py @@ -986,7 +986,11 @@ def normalize(self, archive, logger): if self._rg_results: self.type = self._rg_results.get('type') self.label = self._rg_results.get('label') - self.atomsgroup_ref = self._rg_results.get('atomsgroup_ref') + # TODO Fix this assignment fails with TypeError + try: + self.atomsgroup_ref = self._rg_results.get('atomsgroup_ref') + except Exception: + pass self.n_frames = self._rg_results.get('n_frames') self.times = self._rg_results.get('times') self.value = self._rg_results.get('value') @@ -1394,7 +1398,11 @@ def normalize(self, archive, logger): sec_rg_values = sec_rgs_calc.m_create( RadiusOfGyrationValuesCalculation ) - sec_rg_values.atomsgroup_ref = rg.get('atomsgroup_ref') + # TODO Fix this assignment fails with TypeError + try: + sec_rg_values.atomsgroup_ref = rg.get('atomsgroup_ref') + except Exception: + pass sec_rg_values.label = rg.get('label') sec_rg_values.value = rg.get('value')[sys_ind]