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formats

DynamX_v3_cluster

Source code in hdxms_datasets/formats.py 
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class DynamX_v3_cluster:
    columns = [
        "Protein",
        "Start",
        "End",
        "Sequence",
        "Modification",
        "Fragment",
        "MaxUptake",
        "MHP",
        "State",
        "Exposure",
        "File",
        "z",
        "RT",
        "Inten",
        "Center",
    ]
    state_name = "State"
    exposure_name = "Exposure"
    aggregated = False

    def convert(self, df: nw.DataFrame) -> nw.DataFrame:
        """
        Convert the DataFrame to a standard format.
        """
        return from_dynamx_cluster(df)

convert(df)

Convert the DataFrame to a standard format.

Source code in hdxms_datasets/formats.py 
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def convert(self, df: nw.DataFrame) -> nw.DataFrame:
    """
    Convert the DataFrame to a standard format.
    """
    return from_dynamx_cluster(df)

DynamX_vx_state

There are also DynamX state data files which do not have 'Modification' and 'Fragment' columns. not sure which version this is.

Source code in hdxms_datasets/formats.py 
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class DynamX_vx_state:
    """There are also DynamX state data files which do not have 'Modification' and 'Fragment' columns.
    not sure which version this is.
    """

    columns = [
        "Protein",
        "Start",
        "End",
        "Sequence",
        "MaxUptake",
        "MHP",
        "State",
        "Exposure",
        "Center",
        "Center SD",
        "Uptake",
        "Uptake SD",
        "RT",
        "RT SD",
    ]

    state_name = "State"
    exposure_name = "Exposure"
    aggregated = True

    def convert(self, df: nw.DataFrame) -> nw.DataFrame:
        """
        Convert the DataFrame to a standard format.
        """
        return from_dynamx_state(df)

convert(df)

Convert the DataFrame to a standard format.

Source code in hdxms_datasets/formats.py 
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def convert(self, df: nw.DataFrame) -> nw.DataFrame:
    """
    Convert the DataFrame to a standard format.
    """
    return from_dynamx_state(df)

HDExaminer_v3

Source code in hdxms_datasets/formats.py 
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class HDExaminer_v3:
    columns = [
        "Protein State",
        "Deut Time",
        "Experiment",
        "Start",
        "End",
        "Sequence",
        "Charge",
        "Search RT",
        "Actual RT",
        "# Spectra",
        "Peak Width Da",
        "m/z Shift Da",
        "Max Inty",
        "Exp Cent",
        "Theor Cent",
        "Score",
        "Cent Diff",
        "# Deut",
        "Deut %",
        "Confidence",
    ]
    state_name = "Protein State"
    exposure_name = "Deut Time"
    aggregated = False

    def convert(self, df: nw.DataFrame) -> nw.DataFrame:
        """
        Convert the DataFrame to a standard format.
        """
        return from_hdexaminer(df)

convert(df)

Convert the DataFrame to a standard format.

Source code in hdxms_datasets/formats.py 
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def convert(self, df: nw.DataFrame) -> nw.DataFrame:
    """
    Convert the DataFrame to a standard format.
    """
    return from_hdexaminer(df)

HDXFormat

Bases: Protocol

Source code in hdxms_datasets/formats.py 
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class HDXFormat(Protocol):
    columns: list[str]
    state_name: str
    exposure_name: str
    aggregated: bool = False  # whether the data is aggregated or expanded as multiple replicates

    def convert(self, df: nw.DataFrame) -> nw.DataFrame:
        """
        Convert the DataFrame to a standard format.
        """
        ...

convert(df)

Convert the DataFrame to a standard format.

Source code in hdxms_datasets/formats.py 
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def convert(self, df: nw.DataFrame) -> nw.DataFrame:
    """
    Convert the DataFrame to a standard format.
    """
    ...

identify_format(cols, *, exact=True)

Identify which HDXFormat subclass the given column list matches.

Parameters:

Name Type Description Default
cols list[str]

The column names to check.

 required
exact bool

If True, order must match; otherwise, uses set equality.

 True

Returns:

Type Description
Optional[HDXFormat]

The matching HDXFormat subclass, or None if no match.
Source code in hdxms_datasets/formats.py 
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def identify_format(cols: list[str], *, exact: bool = True) -> Optional[HDXFormat]:
    """
    Identify which HDXFormat subclass the given column list matches.

    Args:
        cols: The column names to check.
        exact: If True, order must match; otherwise, uses set equality.

    Returns:
        The matching HDXFormat subclass, or None if no match.
    """
    for fmt_class in HDX_FORMATS:
        template = fmt_class.columns
        if exact and cols == template:
            return fmt_class
        elif not exact and set(cols) == set(template):
            return fmt_class
    return None