Source code for schrodinger.test.stu.outcomes.correlate_workup

import numpy
import scipy.stats.stats

from schrodinger import structure


def correlate_workup(reference_name, calculated_name, min_correl, *filenames):
    """
 Usage
 $SCHRODINGER/run correlate_workup.py <ct-level property 1> <ct-level property 2> <minimum correlation (R)> <files(s)>
 <ct-level-property 1> First proeprty for correlation.  Does not have to be in every frame (skipped if not) So should be used for experimental data.
 <ct-level-property 2> Second property for correlations.  Does have to be in every frame so should be used for calculated data (it's an error if any frame is missing data)
 <Minimum correlation> Correlation (R, not R-squared) should be less than this value if this is a negative value (more negative correlation) and more than this value if this is a positive value (more positive correlation)
 <file(s)> One or more Maestro-format structure files"""
    exp_data = []
    calc_data = []
    missing_data = []
    for fn in filenames:
        for ict, ct in enumerate(structure.StructureReader(fn)):
            if reference_name in ct.property:
                exp_data.append(ct.property[reference_name])
                try:
                    calc_data.append(ct.property[calculated_name])
                except KeyError:
                    missing_data.append("%s:%d" % (fn, ict + 1))
    if len(missing_data) > 0:
        msg = "Missing property {} in the following outputs {}".format(
            calculated_name, " ".join(missing_data))
        raise AssertionError(msg)
    if len(exp_data) < 3:
        msg = "Not enough data to calculate correlation"
        raise AssertionError(msg)
    results = scipy.stats.stats.linregress(numpy.array(exp_data),
                                           numpy.array(calc_data))
    r = results[2]

    if (min_correl < 0 and r < min_correl) or (min_correl >= 0 and
                                               r > min_correl):
        return True
    else:
        msg = f"Correlation {r}"
        raise AssertionError(msg)