Source code for schrodinger.ui.sequencealignment.utils

[docs]def colorGradientBlueWhiteRed(value):
    """
    Return an RGB color triple using blue - white - red gradient
    for a given value. The value is clamped to a [-1..1] range.

    :type value: float
    :param value: numerical value

    :rtype: (int int int)
    :return: RGB color triple
    """
    if value < 0.0:
        if value < -1.0:
            value = -1.0
        r = int(255 * (value + 1.0))
        g = int(255 * (value + 1.0))
        b = 255
    elif value > 0.0:
        if value > 1.0:
            value = 1.0
        r = 255
        g = int(255 * (1.0 - value))
        b = int(255 * (1.0 - value))
    else:
        r = g = b = 255
    return (r, g, b)




[docs]def colorGradientGreenRed(value):
    """
    Return an RGB color triple using green - red gradient
    for a given value. The value is clamped to a [-1..1] range.

    :type value: float
    :param value: numerical value

    :rtype: (int int int)
    :return: RGB color triple
    """
    if value < 0.0:
        if value < -1.0:
            value = -1.0
        r = int(255 * (value + 1.0))
        b = int(255 * (value + 1.0))
        g = 255
    elif value > 0.0:
        if value > 1.0:
            value = 1.0
        r = 255
        b = int(255 * (1.0 - value))
        g = int(255 * (1.0 - value))
    else:
        r = g = b = 255
    return (r, g, b)




[docs]def matrixValue(matrix, first, second):
    """
    Return a similarity matrix vaule for a specified pair of residues.
    """
    if (first, second) in matrix:
        return matrix[(first, second)]
    if (second, first) in matrix:
        return matrix[(second, first)]
    return 0.0