precision_rmsd.py

from __future__ import print_function
import os,sys
import numpy
import string
import IMP
import IMP.em
import pyRMSD.RMSDCalculator

def parse_custom_ranges(ranges_file):
    with open(ranges_file) as fh:
        d = {}
        exec(fh.read(), d)
    return d['density_custom_ranges']


def get_particles_from_superposed(cluster_conform_i, cluster_conform_0, align, ps, trans):
    def _to_vector3ds(numpy_array):
        # No need to fit the whole array - we only need 4 non-coplanar points,
        # so 100 should be plenty
        return [IMP.algebra.Vector3D(c) for c in numpy_array[:100]]

    if align:
        calculator = pyRMSD.RMSDCalculator.RMSDCalculator("QCP_SERIAL_CALCULATOR", numpy.array([cluster_conform_0, cluster_conform_i]))
    else:
        calculator = pyRMSD.RMSDCalculator.RMSDCalculator("NOSUP_SERIAL_CALCULATOR", numpy.array([cluster_conform_0, cluster_conform_i]))

    rmsd, superposed_fit = calculator.pairwise(0, 1, get_superposed_coordinates = True)
    # Get transformation from pyRMSD reference on the first call.
    # This is somewhat inefficient (since we are essentially repeating
    # the pyRMSD calculation) but pyRMSD doesn't appear to make its
    # reference orientation available.
    if trans is None:
        trans = IMP.algebra.get_transformation_aligning_first_to_second(
            _to_vector3ds(superposed_fit[0]), _to_vector3ds(cluster_conform_0))

    for particle_index in range(len(superposed_fit[1])):
        # Transform from pyRMSD back to original reference
        IMP.core.XYZ(ps[particle_index]).set_coordinates(trans * IMP.algebra.Vector3D(superposed_fit[1][particle_index]))

    return rmsd, ps, trans

def get_particles_from_superposed_amb(cluster_conform_i, cluster_conform_0, align, ps, trans, symm_groups):

    '''Modified superposed function to work with symmetric copies'''

    def _to_vector3ds(numpy_array):
        # No need to fit the whole array - we only need 4 non-coplanar points,
        # so 100 should be plenty
        return [IMP.algebra.Vector3D(c) for c in numpy_array[:100]]

    min_rmsd = 10000.0

    superposed_final_coords=[]

    for perm in pyRMSD.symmTools.symm_permutations(symm_groups): # for each permutation

        new_cluster_conform_i = cluster_conform_i

        for sg in perm: # for each symmetric group in perm

            for [particle0, particle1] in sg: # swap the particles if they are in non-standard order in this permutation

                if particle0 > particle1:

                    pyRMSD.symmTools.swap_atoms(new_cluster_conform_i, particle0, particle1)

        if align:
            calculator = pyRMSD.RMSDCalculator.RMSDCalculator("QCP_SERIAL_CALCULATOR", numpy.array([cluster_conform_0, new_cluster_conform_i]))
        else:
            calculator = pyRMSD.RMSDCalculator.RMSDCalculator("NOSUP_SERIAL_CALCULATOR", numpy.array([cluster_conform_0, new_cluster_conform_i]))

        rmsd, superposed_fit = calculator.pairwise(0, 1, get_superposed_coordinates = True)

        if rmsd < min_rmsd:
            min_rmsd = rmsd
            superposed_final_coords = superposed_fit

    # Get transformation from pyRMSD reference on the first call.
    # This is somewhat inefficient (since we are essentially repeating
    # the pyRMSD calculation) but pyRMSD doesn't appear to make its
    # reference orientation available.
    if trans is None:
        trans = IMP.algebra.get_transformation_aligning_first_to_second(_to_vector3ds(superposed_final_coords[0]), _to_vector3ds(cluster_conform_0))

    for particle_index in range(len(superposed_final_coords[1])):

        # Transform from pyRMSD back to original reference
        IMP.core.XYZ(ps[particle_index]).set_coordinates(trans * IMP.algebra.Vector3D(superposed_final_coords[1][particle_index]))

    return min_rmsd, ps, trans

class GetModelDensity(object):
    """Compute mean density maps from structures.
    Keeps a dictionary of density maps,
    keys are in the custom ranges. When you call add_subunits_density, it adds
    particle coordinates to the existing density maps.
    """

    def __init__(self, custom_ranges=None, resolution=20.0, voxel=5.0, bead_names = None):
        """Constructor.
        @param list of particles decorated with mass, radius, and XYZ
           @param resolution The MRC resolution of the output map (in Angstrom unit)
           @param voxel The voxel size for the output map (lower is slower)
        """

        self.MRCresolution = resolution
        self.voxel = voxel
        self.count_models = 0.0
        self.densities={}
        self.bead_names = bead_names
        self.custom_ranges=custom_ranges

        # for each custom range get the particle indices that will be added to the density for that custom range
        self.particle_indices_in_custom_ranges={}

        for density_name in self.custom_ranges:
            self.particle_indices_in_custom_ranges[density_name]=[]

        # go through each bead, put it in the appropriate custom range(s)
        for index,beadname in enumerate(self.bead_names):
            for density_name in self.custom_ranges:
                for domain in self.custom_ranges[density_name]: # each domain in the list custom_ranges[density_name]
                    if self._is_contained(beadname,domain):
                        self.particle_indices_in_custom_ranges[density_name].append(index)
                        #print(beadname,"is in",domain)
                        break # already added particle to this custom range

    def normalize_density(self):
        pass

    def _create_density_from_particles(self, ps, name,
                                      kernel_type='GAUSSIAN'):
        '''Internal function for adding to densities.
        pass XYZR particles with mass and create a density from them.
        kernel type options are GAUSSIAN, BINARIZED_SPHERE, and SPHERE.'''
        kd = {
            'GAUSSIAN': IMP.em.GAUSSIAN,
            'BINARIZED_SPHERE': IMP.em.BINARIZED_SPHERE,
            'SPHERE': IMP.em.SPHERE}
        dmap = IMP.em.SampledDensityMap(ps, self.MRCresolution, self.voxel)
        dmap.calcRMS()
        dmap.set_was_used(True)

        if name not in self.densities:
            self.densities[name] = dmap
        else:
            bbox1 = IMP.em.get_bounding_box(self.densities[name])
            bbox2 = IMP.em.get_bounding_box(dmap)
            bbox1 += bbox2
            dmap3 = IMP.em.create_density_map(bbox1,self.voxel)
            dmap3.set_was_used(True)
            dmap3.add(dmap)
            dmap3.add(self.densities[name])
            self.densities[name] = dmap3

    def _is_contained(self,bead_name,domain):
        """ domain can be the name of a single protein or a tuple (start_residue,end_residue,protein_name)
        bead is a string of type moleculeName_startResidue_endResidue
        """

        (bead_protein, bead_res_start,
         bead_res_end, bead_copy) = bead_name.split("_")

        # protein name and copy number check
        if isinstance(domain, tuple):
            domain_protein = domain[2]
        else:
            domain_protein = domain
        # A period indicates that we have a copy number
        if "." in domain_protein:
            spl = domain_protein.split(".")
            domain_protein = spl[0]
            domain_copy = int(spl[1])
        else:
            domain_copy = bead_copy = -1

        if bead_protein != domain_protein or int(bead_copy) != domain_copy:
            return False

        # residue range check
        if isinstance(domain, tuple):
            bead_residues = set(range(int(bead_res_start),int(bead_res_end)+1))
            domain_residues = set(range(int(domain[0]),int(domain[1])+1))
            return not domain_residues.isdisjoint(bead_residues)
        else:
            return True

    def add_subunits_density(self, ps):
        """Add a frame to the densities.
        @param ps List of particles decorated with XYZR and Mass.
        """
        self.count_models += 1.0
        # initialize custom list of particles
        particles_custom_ranges={}
        for density_name in self.custom_ranges:
            particles_custom_ranges[density_name]=[]

        # add each particle to the relevant custom list
        for density_name in self.custom_ranges:
            for particle_index in self.particle_indices_in_custom_ranges[density_name]:
                particles_custom_ranges[density_name].append(ps[particle_index])

        # finally, add each custom particle list to the density
        for density_name in self.custom_ranges:
            self._create_density_from_particles(particles_custom_ranges[density_name],density_name)

    def get_density_keys(self):
        return list(self.densities.keys())

    def get_density(self,name):
        """Get the current density for some component name"""
        if name not in self.densities:
            return None
        else:
            return self.densities[name]

    def write_mrc(self, path=".", file_prefix=""):
        for density_name in self.densities:
            mrc = os.path.join(path, file_prefix + "_" + density_name + ".mrc")
            self.densities[density_name].multiply(1. / self.count_models)
            IMP.em.write_map(
                self.densities[density_name], mrc,
                IMP.em.MRCReaderWriter())
        if len(self.densities) == 1:
            return mrc
        else:
            return os.path.join(path, file_prefix + "_*.mrc")