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Modules

libvcell

sbml_to_finite_volume_input(sbml_content, output_dir_path)

Convert SBML content to finite volume input files

Parameters:

Name Type Description Default
sbml_content str

SBML content

 required
output_dir_path Path

output directory path

 required

Returns:

Type Description
tuple[bool, str]

tuple[bool, str]: A tuple containing the success status and a message
Source code in libvcell/solver_utils.py 
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def sbml_to_finite_volume_input(sbml_content: str, output_dir_path: Path) -> tuple[bool, str]:
    """
    Convert SBML content to finite volume input files

    Args:
        sbml_content (str): SBML content
        output_dir_path (Path): output directory path

    Returns:
        tuple[bool, str]: A tuple containing the success status and a message
    """
    native = VCellNativeCalls()
    return_value: ReturnValue = native.sbml_to_finite_volume_input(sbml_content, output_dir_path)
    return return_value.success, return_value.message

sbml_to_vcml(sbml_content, vcml_file_path)

Convert SBML content to finite volume input files

Parameters:

Name Type Description Default
sbml_content str

SBML content

 required
vcml_file_path Path

path to resulting VCML file

 required

Returns:

Type Description
tuple[bool, str]

tuple[bool, str]: A tuple containing the success status and a message
Source code in libvcell/model_utils.py 
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def sbml_to_vcml(sbml_content: str, vcml_file_path: Path) -> tuple[bool, str]:
    """
    Convert SBML content to finite volume input files

    Args:
        sbml_content (str): SBML content
        vcml_file_path (Path): path to resulting VCML file

    Returns:
        tuple[bool, str]: A tuple containing the success status and a message
    """
    native = VCellNativeCalls()
    return_value: ReturnValue = native.sbml_to_vcml(sbml_content=sbml_content, vcml_file_path=vcml_file_path)
    return return_value.success, return_value.message

vcml_to_finite_volume_input(vcml_content, simulation_name, output_dir_path)

Convert VCML content to finite volume input files

Parameters:

Name Type Description Default
vcml_content str

VCML content

 required
simulation_name str

simulation name

 required
output_dir_path Path

output directory path

 required

Returns:

Type Description
tuple[bool, str]

tuple[bool, str]: A tuple containing the success status and a message
Source code in libvcell/solver_utils.py 
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def vcml_to_finite_volume_input(vcml_content: str, simulation_name: str, output_dir_path: Path) -> tuple[bool, str]:
    """
    Convert VCML content to finite volume input files

    Args:
        vcml_content (str): VCML content
        simulation_name (str): simulation name
        output_dir_path (Path): output directory path

    Returns:
        tuple[bool, str]: A tuple containing the success status and a message
    """
    native = VCellNativeCalls()
    return_value: ReturnValue = native.vcml_to_finite_volume_input(vcml_content, simulation_name, output_dir_path)
    return return_value.success, return_value.message

vcml_to_sbml(vcml_content, application_name, sbml_file_path, round_trip_validation)

Convert VCML content to SBML file

Parameters:

Name Type Description Default
vcml_content str

VCML content

 required
application_name str

VCell Biomodel application name

 required
sbml_file_path Path

path to resulting SBML file

 required

Returns:

Type Description
tuple[bool, str]

tuple[bool, str]: A tuple containing the success status and a message
Source code in libvcell/model_utils.py 
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def vcml_to_sbml(
    vcml_content: str, application_name: str, sbml_file_path: Path, round_trip_validation: bool
) -> tuple[bool, str]:
    """
    Convert VCML content to SBML file

    Args:
        vcml_content (str): VCML content
        application_name (str): VCell Biomodel application name
        sbml_file_path (Path): path to resulting SBML file

    Returns:
        tuple[bool, str]: A tuple containing the success status and a message
    """
    native = VCellNativeCalls()
    return_value: ReturnValue = native.vcml_to_sbml(
        vcml_content=vcml_content,
        application_name=application_name,
        sbml_file_path=sbml_file_path,
        round_trip_validation=round_trip_validation,
    )
    return return_value.success, return_value.message

vcml_to_vcml(vcml_content, vcml_file_path)

Process VCML content to regenerated VCML file

Parameters:

Name Type Description Default
vcml_content str

VCML content

 required
vcml_file_path Path

path to resulting VCML file

 required

Returns:

Type Description
tuple[bool, str]

tuple[bool, str]: A tuple containing the success status and a message
Source code in libvcell/model_utils.py 
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def vcml_to_vcml(vcml_content: str, vcml_file_path: Path) -> tuple[bool, str]:
    """
    Process VCML content to regenerated VCML file

    Args:
        vcml_content (str): VCML content
        vcml_file_path (Path): path to resulting VCML file

    Returns:
        tuple[bool, str]: A tuple containing the success status and a message
    """
    native = VCellNativeCalls()
    return_value: ReturnValue = native.vcml_to_vcml(vcml_content=vcml_content, vcml_file_path=vcml_file_path)
    return return_value.success, return_value.message

Modules

libvcell

sbml_to_finite_volume_input(sbml_content, output_dir_path)

Convert SBML content to finite volume input files

Parameters:

Name Type Description Default
sbml_content str

SBML content

 required
output_dir_path Path

output directory path

 required

Returns:

Type Description
tuple[bool, str]

tuple[bool, str]: A tuple containing the success status and a message
Source code in libvcell/solver_utils.py 
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def sbml_to_finite_volume_input(sbml_content: str, output_dir_path: Path) -> tuple[bool, str]:
    """
    Convert SBML content to finite volume input files

    Args:
        sbml_content (str): SBML content
        output_dir_path (Path): output directory path

    Returns:
        tuple[bool, str]: A tuple containing the success status and a message
    """
    native = VCellNativeCalls()
    return_value: ReturnValue = native.sbml_to_finite_volume_input(sbml_content, output_dir_path)
    return return_value.success, return_value.message

sbml_to_vcml(sbml_content, vcml_file_path)

Convert SBML content to finite volume input files

Parameters:

Name Type Description Default
sbml_content str

SBML content

 required
vcml_file_path Path

path to resulting VCML file

 required

Returns:

Type Description
tuple[bool, str]

tuple[bool, str]: A tuple containing the success status and a message
Source code in libvcell/model_utils.py 
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def sbml_to_vcml(sbml_content: str, vcml_file_path: Path) -> tuple[bool, str]:
    """
    Convert SBML content to finite volume input files

    Args:
        sbml_content (str): SBML content
        vcml_file_path (Path): path to resulting VCML file

    Returns:
        tuple[bool, str]: A tuple containing the success status and a message
    """
    native = VCellNativeCalls()
    return_value: ReturnValue = native.sbml_to_vcml(sbml_content=sbml_content, vcml_file_path=vcml_file_path)
    return return_value.success, return_value.message

vcml_to_finite_volume_input(vcml_content, simulation_name, output_dir_path)

Convert VCML content to finite volume input files

Parameters:

Name Type Description Default
vcml_content str

VCML content

 required
simulation_name str

simulation name

 required
output_dir_path Path

output directory path

 required

Returns:

Type Description
tuple[bool, str]

tuple[bool, str]: A tuple containing the success status and a message
Source code in libvcell/solver_utils.py 
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def vcml_to_finite_volume_input(vcml_content: str, simulation_name: str, output_dir_path: Path) -> tuple[bool, str]:
    """
    Convert VCML content to finite volume input files

    Args:
        vcml_content (str): VCML content
        simulation_name (str): simulation name
        output_dir_path (Path): output directory path

    Returns:
        tuple[bool, str]: A tuple containing the success status and a message
    """
    native = VCellNativeCalls()
    return_value: ReturnValue = native.vcml_to_finite_volume_input(vcml_content, simulation_name, output_dir_path)
    return return_value.success, return_value.message

vcml_to_sbml(vcml_content, application_name, sbml_file_path, round_trip_validation)

Convert VCML content to SBML file

Parameters:

Name Type Description Default
vcml_content str

VCML content

 required
application_name str

VCell Biomodel application name

 required
sbml_file_path Path

path to resulting SBML file

 required

Returns:

Type Description
tuple[bool, str]

tuple[bool, str]: A tuple containing the success status and a message
Source code in libvcell/model_utils.py 
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def vcml_to_sbml(
    vcml_content: str, application_name: str, sbml_file_path: Path, round_trip_validation: bool
) -> tuple[bool, str]:
    """
    Convert VCML content to SBML file

    Args:
        vcml_content (str): VCML content
        application_name (str): VCell Biomodel application name
        sbml_file_path (Path): path to resulting SBML file

    Returns:
        tuple[bool, str]: A tuple containing the success status and a message
    """
    native = VCellNativeCalls()
    return_value: ReturnValue = native.vcml_to_sbml(
        vcml_content=vcml_content,
        application_name=application_name,
        sbml_file_path=sbml_file_path,
        round_trip_validation=round_trip_validation,
    )
    return return_value.success, return_value.message

vcml_to_vcml(vcml_content, vcml_file_path)

Process VCML content to regenerated VCML file

Parameters:

Name Type Description Default
vcml_content str

VCML content

 required
vcml_file_path Path

path to resulting VCML file

 required

Returns:

Type Description
tuple[bool, str]

tuple[bool, str]: A tuple containing the success status and a message
Source code in libvcell/model_utils.py 
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def vcml_to_vcml(vcml_content: str, vcml_file_path: Path) -> tuple[bool, str]:
    """
    Process VCML content to regenerated VCML file

    Args:
        vcml_content (str): VCML content
        vcml_file_path (Path): path to resulting VCML file

    Returns:
        tuple[bool, str]: A tuple containing the success status and a message
    """
    native = VCellNativeCalls()
    return_value: ReturnValue = native.vcml_to_vcml(vcml_content=vcml_content, vcml_file_path=vcml_file_path)
    return return_value.success, return_value.message

Functions

sbml_to_finite_volume_input

Convert SBML content to finite volume input files

Parameters:

Name Type Description Default
sbml_content str

SBML content

 required
output_dir_path Path

output directory path

 required

Returns:

Type Description
tuple[bool, str]

tuple[bool, str]: A tuple containing the success status and a message
Source code in libvcell/solver_utils.py 
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def sbml_to_finite_volume_input(sbml_content: str, output_dir_path: Path) -> tuple[bool, str]:
    """
    Convert SBML content to finite volume input files

    Args:
        sbml_content (str): SBML content
        output_dir_path (Path): output directory path

    Returns:
        tuple[bool, str]: A tuple containing the success status and a message
    """
    native = VCellNativeCalls()
    return_value: ReturnValue = native.sbml_to_finite_volume_input(sbml_content, output_dir_path)
    return return_value.success, return_value.message

vcml_to_finite_volume_input

Convert VCML content to finite volume input files

Parameters:

Name Type Description Default
vcml_content str

VCML content

 required
simulation_name str

simulation name

 required
output_dir_path Path

output directory path

 required

Returns:

Type Description
tuple[bool, str]

tuple[bool, str]: A tuple containing the success status and a message
Source code in libvcell/solver_utils.py 
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def vcml_to_finite_volume_input(vcml_content: str, simulation_name: str, output_dir_path: Path) -> tuple[bool, str]:
    """
    Convert VCML content to finite volume input files

    Args:
        vcml_content (str): VCML content
        simulation_name (str): simulation name
        output_dir_path (Path): output directory path

    Returns:
        tuple[bool, str]: A tuple containing the success status and a message
    """
    native = VCellNativeCalls()
    return_value: ReturnValue = native.vcml_to_finite_volume_input(vcml_content, simulation_name, output_dir_path)
    return return_value.success, return_value.message