Exemple #1
0
    def testGamma(self):
        """
        The posterior of a gaussian scale mixture with gamma prior
        is a Student's t distribution, with parameters alpha and beta.

        Give enough samples, we shoud be able to estimate these parameters
        """
        pdbfile = self.config.getTestFile('ake-xray-ensemble-ca.pdb')
        ensemble = LegacyStructureParser(pdbfile).parse_models()
        X = numpy.array(ensemble[0].get_coordinates(['CA'], True))
        Y = numpy.array(ensemble[13].get_coordinates(['CA'], True))

               
        mixture = ScaleMixture(scales=X.shape[0],
                               prior=GammaPrior(), d=3)

        from csb.bio.utils import fit

        R, t = fit(X, Y)
        #numpy.random.seed(100)
        # gibbs sampling cycle
        for i in range(200):
            # apply rotation
            data = numpy.sum((X - numpy.dot(Y, numpy.transpose(R)) - t) ** 2, axis= -1) ** (1. / 2)
            # sample scales
            mixture.estimate(data)
            # sample rotations
            R, t = probabilistic_fit(X, Y, mixture.scales)

        self.assertEqual(mixture.scales.shape, (211,))
        
        R_opt = numpy.eye(3)
        t_opt = numpy.zeros((3,))
        
        for i in range(3):
            self.assertAlmostEqual(t[i], t_opt[i], delta=2.)
            for j in range(3):
                self.assertAlmostEqual(R_opt[i, j], R[i, j], delta=1e-1)
Exemple #2
0
def xfit(mobile, target, mobile_state=-1, target_state=-1, load_b=0,
        cycles=10, match='align', guide=1, seed=0, quiet=1,
        bfit=0, distribution='student', _self=cmd):
    '''
DESCRIPTION

    Weighted superposition of the model in the first selection on to the model
    in the second selection. The weights are estimated with maximum likelihood.

    The result should be very similar to "theseus".

    Requires CSB, https://github.com/csb-toolbox/CSB

ARGUMENTS

    mobile = string: atom selection
 
    target = string: atom selection

    mobile_state = int: object state of mobile selection {default: current}

    target_state = int: object state of target selection {default: current}

    load_b = 0 or 1: save -log(weights) into B-factor column {default: 0}

SEE ALSO

    intra_xfit, align, super, fit, cealign, theseus
    '''
    from numpy import asarray, identity, log, dot, zeros
    from csb.bio.utils import distance_sq, wfit, fit
    from . import querying

    cycles, quiet = int(cycles), int(quiet)
    mobile_state, target_state = int(mobile_state), int(target_state)
    mobile_obj = querying.get_object_name(mobile, 1)

    if mobile_state < 1: mobile_state = querying.get_object_state(mobile_obj)
    if target_state < 1: target_state = querying.get_selection_state(target)

    if int(guide):
        mobile = '(%s) and guide' % (mobile)
        target = '(%s) and guide' % (target)

    mm = MatchMaker(mobile, target, match)

    Y = asarray(querying.get_coords(mm.mobile, mobile_state))
    X = asarray(querying.get_coords(mm.target, target_state))

    if int(seed):
        R, t = identity(3), zeros(3)
    else:
        R, t = fit(X, Y)

    if int(bfit):
        # adapted from csb.apps.bfit

        from csb.bio.utils import distance, probabilistic_fit
        from csb.statistics.scalemixture import ScaleMixture

        mixture = ScaleMixture(scales=X.shape[0],
                prior=_bfit_get_prior(distribution), d=3)

        for _ in range(cycles):
            data = distance(Y, dot(X - t, R))
            mixture.estimate(data)
            R, t = probabilistic_fit(X, Y, mixture.scales)

        scales = mixture.scales

    else:
        for _ in range(cycles):
            data = distance_sq(Y, dot(X - t, R))
            scales = 1.0 / data.clip(1e-3)
            R, t = wfit(X, Y, scales)

    m = identity(4)
    m[0:3,0:3] = R
    m[0:3,3] = t
    cmd.transform_object(mobile_obj, list(m.flat))

    if int(load_b):
        b_iter = iter(-log(scales))
        cmd.alter(mm.mobile, 'b = next(b_iter)', space={'b_iter': b_iter, 'next': next})

    if not quiet:
        print(' xfit: %d atoms aligned' % (len(X)))
Exemple #3
0
def xfit(mobile, target, mobile_state=-1, target_state=-1, load_b=0,
        cycles=10, match='align', guide=1, seed=0, quiet=1,
        bfit=0, distribution='student', _self=cmd):
    '''
DESCRIPTION

    Weighted superposition of the model in the first selection on to the model
    in the second selection. The weights are estimated with maximum likelihood.

    The result should be very similar to "theseus".

    Requires CSB, https://github.com/csb-toolbox/CSB

ARGUMENTS

    mobile = string: atom selection
 
    target = string: atom selection

    mobile_state = int: object state of mobile selection {default: current}

    target_state = int: object state of target selection {default: current}

    load_b = 0 or 1: save -log(weights) into B-factor column {default: 0}

SEE ALSO

    intra_xfit, align, super, fit, cealign, theseus
    '''
    from numpy import asarray, identity, log, dot, zeros
    from csb.bio.utils import distance_sq, wfit, fit
    from . import querying

    cycles, quiet = int(cycles), int(quiet)
    mobile_state, target_state = int(mobile_state), int(target_state)
    mobile_obj = querying.get_object_name(mobile, 1, _self=_self)

    if mobile_state < 1: mobile_state = querying.get_object_state(mobile_obj, _self=_self)
    if target_state < 1: target_state = querying.get_selection_state(target, _self=_self)

    if int(guide):
        mobile = '(%s) and guide' % (mobile)
        target = '(%s) and guide' % (target)

    mm = MatchMaker(mobile, target, match, _self=_self)

    Y = asarray(_self.get_coords(mm.mobile, mobile_state))
    X = asarray(_self.get_coords(mm.target, target_state))

    if int(seed):
        R, t = identity(3), zeros(3)
    else:
        R, t = fit(X, Y)

    if int(bfit):
        # adapted from csb.apps.bfit

        from csb.bio.utils import distance, probabilistic_fit
        from csb.statistics.scalemixture import ScaleMixture

        mixture = ScaleMixture(scales=X.shape[0],
                prior=_bfit_get_prior(distribution), d=3)

        for _ in range(cycles):
            data = distance(Y, dot(X - t, R))
            mixture.estimate(data)
            R, t = probabilistic_fit(X, Y, mixture.scales)

        scales = mixture.scales

    else:
        for _ in range(cycles):
            data = distance_sq(Y, dot(X - t, R))
            scales = 1.0 / data.clip(1e-3)
            R, t = wfit(X, Y, scales)

    m = identity(4)
    m[0:3,0:3] = R
    m[0:3,3] = t
    _self.transform_object(mobile_obj, list(m.flat))

    if int(load_b):
        b_iter = iter(-log(scales))
        _self.alter(mm.mobile, 'b = next(b_iter)', space={'b_iter': b_iter, 'next': next})

    if not quiet:
        print(' xfit: %d atoms aligned' % (len(X)))