8.1.1.4.1.7. skimpy.io.yaml

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Copyright 2017 Laboratory of Computational Systems Biotechnology (LCSB), Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland

Licensed under the Apache License, Version 2.0 (the “License”); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

8.1.1.4.1.7.1. Module Contents

8.1.1.4.1.7.1.1. Functions

get_mechanism_subclasses()

get_boundary_subclasses()

get_modifier_subclasses()

parameter_representer(dumper, data)

reactant_representer(dumper, data)

compartment_representer(dumper, data)

mechanism_representer(dumper, data)

reaction_representer(dumper, data)

boundary_condition_representer(dumper, data)

refresh_representers()

This function refreshes the representers of custom-made reaction mechanisms

export_to_yaml(model, path=None, **kwargs)

get_mechanism(classdict)

This function should construct mechanism for the generic types

get_generic_constructor(s)

get_stoich(s)

load_yaml_model(path)

rebuild_dependent_mets(new, the_dict)

8.1.1.4.1.7.1.2. Attributes

ALL_GENERIC_MECHANISM_SUBCLASSES

FIELDS_TO_SERIALIZE

skimpy.get_mechanism_subclasses()
skimpy.get_boundary_subclasses()
skimpy.get_modifier_subclasses()
skimpy.ALL_GENERIC_MECHANISM_SUBCLASSES
skimpy.FIELDS_TO_SERIALIZE = ['boundary_conditions', 'parameters', 'constraints', 'reactions', 'name', 'initial_conditions',...
skimpy.parameter_representer(dumper, data)
skimpy.reactant_representer(dumper, data)
skimpy.compartment_representer(dumper, data)
skimpy.mechanism_representer(dumper, data)
skimpy.reaction_representer(dumper, data)
skimpy.boundary_condition_representer(dumper, data)
skimpy.refresh_representers()

This function refreshes the representers of custom-made reaction mechanisms (n-to-m Convenience Kinetics for example)

skimpy.export_to_yaml(model, path=None, **kwargs)
skimpy.get_mechanism(classdict)

This function should construct mechanism for the generic types and get the mechanism for modifiers and the defined types

Parameters

classdict – Looks like {‘class’:’MichaelisMenten’, ‘substrate1’:’atp_c’, ‘product1’ :’gtp_c’, }

Returns

skimpy.get_generic_constructor(s)
skimpy.get_stoich(s)
skimpy.load_yaml_model(path)
skimpy.rebuild_dependent_mets(new, the_dict)