CD

momapy.celldesigner.io.celldesigner

Classes for reading CellDesigner files (extended SBML)

Classes:

Name	Description
CellDesignerReader	Class for CellDesigner reader objects

CellDesignerReader

Bases: Reader

Class for CellDesigner reader objects

Methods:

Name	Description
check_file	Return true if the file is a CellDesigner file, false otherwise
read	Read a CellDesigner file and return a reader result object

check_file classmethod

check_file(file_path: str | PathLike)

Return true if the file is a CellDesigner file, false otherwise

Source code in src/momapy/celldesigner/io/celldesigner.py

@classmethod
def check_file(cls, file_path: str | os.PathLike):
    """Return `true` if the file is a CellDesigner file, `false` otherwise"""
    try:
        with open(file_path) as f:
            for line in f:
                if "http://www.sbml.org/2001/ns/celldesigner" in line:
                    return True
    except UnicodeDecodeError:
        return False
    else:
        return False

read classmethod

read(
    file_path: str | PathLike,
    return_type: Literal["map", "model", "layout"] = "map",
    with_model=True,
    with_layout=True,
    with_annotations=True,
    with_notes=True,
) -> ReaderResult

Read a CellDesigner file and return a reader result object

Source code in src/momapy/celldesigner/io/celldesigner.py

@classmethod
def read(
    cls,
    file_path: str | os.PathLike,
    return_type: typing.Literal["map", "model", "layout"] = "map",
    with_model=True,
    with_layout=True,
    with_annotations=True,
    with_notes=True,
) -> momapy.io.ReaderResult:
    """Read a CellDesigner file and return a reader result object"""
    cd_document = lxml.objectify.parse(file_path)
    cd_sbml = cd_document.getroot()
    obj, annotations, notes, ids = cls._make_main_obj_from_cd_model(
        cd_model=cd_sbml.model,
        return_type=return_type,
        with_model=with_model,
        with_layout=with_layout,
        with_annotations=with_annotations,
        with_notes=with_notes,
    )
    result = momapy.io.ReaderResult(
        obj=obj,
        notes=notes,
        annotations=annotations,
        file_path=file_path,
        ids=ids,
    )
    return result