align.py

#!/usr/bin/env python3

import sys
import IMP.multifit
from IMP import ArgumentParser

__doc__ = "Align proteomics graph with the EM map."

# analyse the ensemble, first we will do the rmsd stuff


class progressBar:

    def __init__(self, minValue=0, maxValue=10, totalWidth=12):
        self.progBar = "[]"   # This holds the progress bar string
        self.min = minValue
        self.max = maxValue
        self.span = maxValue - minValue
        self.width = totalWidth
        self.amount = 0       # When amount == max, we are 100% done
        self.updateAmount(0)  # Build progress bar string

    def updateAmount(self, newAmount=0):
        if newAmount < self.min:
            newAmount = self.min
        if newAmount > self.max:
            newAmount = self.max
        self.amount = newAmount

        # Figure out the new percent done, round to an integer
        diffFromMin = float(self.amount - self.min)
        percentDone = (diffFromMin / float(self.span)) * 100.0
        percentDone = round(percentDone)
        percentDone = int(percentDone)

        # Figure out how many hash bars the percentage should be
        allFull = self.width - 2
        numHashes = (percentDone / 100.0) * allFull
        numHashes = int(round(numHashes))

        # build a progress bar with hashes and spaces
        self.progBar = "[" + '#' * numHashes + \
            ' ' * (allFull - numHashes) + "]"

        # figure out where to put the percentage, roughly centered
        percentPlace = (len(self.progBar) // 2) - len(str(percentDone))
        percentString = str(percentDone) + "%"

        # slice the percentage into the bar
        self.progBar = self.progBar[
            0:percentPlace] + percentString + self.progBar[
            percentPlace + len(
                percentString):]

    def __str__(self):
        return str(self.progBar)


def parse_args():
    desc = """Align proteomics graph with the EM map."""
    p = ArgumentParser(description=desc)
    p.add_argument("-m", "--max", type=int, dest="max", default=999999999,
                   help="maximum number of fits considered")
    p.add_argument("assembly_file", help="assembly file name")
    p.add_argument("proteomics_file", help="proteomics file name")
    p.add_argument("mapping_file", help="mapping file name")
    p.add_argument("param_file", help="parameter file name")
    p.add_argument("combinations_file", help="combinations file name (output)")
    p.add_argument("scores_file", help="fitting scores file name (output)")

    return p.parse_args()


def report_solutions(asmb, mdl, mhs, restraint_set, dmap, mapping_data, combs,
                     combs_fn_output_fn, scored_comb_output_fn, max_comb):
    ensmb = IMP.multifit.Ensemble(asmb, mapping_data)
    # report scores
    for i, mh in enumerate(mhs):
        fn = asmb.get_component_header(i).get_transformations_fn()
        ensmb.add_component_and_fits(mh,
                                     IMP.multifit.read_fitting_solutions(fn))
    all_leaves = []
    for mh in mhs:
        mh_res = IMP.atom.get_by_type(mh, IMP.atom.RESIDUE_TYPE)
        s1 = IMP.atom.Selection(mh_res)
        s1.set_atom_types([IMP.atom.AtomType("CA")])
        all_leaves = all_leaves + s1.get_selected_particles()
    print("number of leaves:", len(all_leaves))
    print("Get number of restraints:", len(restraint_set.get_restraints()))
    pb = progressBar(0, len(combs))
    fitr = IMP.em.FitRestraint(all_leaves, dmap)
    ranked_combs = []
    sorted_combs = []
    print("going to calculate fits for:", len(combs))
    for i, comb in enumerate(combs):
        if i % 100 == 0:
            print("i:", i)
        ensmb.load_combination(comb)
        ranked_combs.append([comb, fitr.evaluate(False)])
        ensmb.unload_combination(comb)
        pb.updateAmount(i)
        # print pb
    print("end fitting")
    # Sort by score
    ranked_combs.sort(key=lambda a: a[1])
    # Remove excess combinations
    print("ranked combs:", len(ranked_combs))
    ranked_combs[max_comb:] = []
    print("ranked combs:", len(ranked_combs))
    for comb in ranked_combs:
        sorted_combs.append(comb[0])
    IMP.multifit.write_paths(sorted_combs, combs_fn_output_fn)
    output = open(scored_comb_output_fn, "w")
    for comb, score in ranked_combs:
        output.write("|")
        for ind in comb:
            output.write(str(ind) + " ")
        output.write("|" + str(1. - score) + "|\n")
    output.close()


def run(asmb_fn, proteomics_fn, mapping_fn, params_fn,
        combs_fn_output_fn, scored_comb_output_fn, max_comb):
    asmb = IMP.multifit.read_settings(asmb_fn)
    asmb.set_was_used(True)
    dmap = IMP.em.read_map(asmb.get_assembly_header().get_dens_fn())
    dmap.get_header().set_resolution(
        asmb.get_assembly_header().get_resolution())
    threshold = asmb.get_assembly_header().get_threshold()
    dmap.update_voxel_size(asmb.get_assembly_header().get_spacing())
    dmap.set_origin(asmb.get_assembly_header().get_origin())
    # get rmsd for subunits
    print(params_fn)
    alignment_params = IMP.multifit.AlignmentParams(params_fn)
    alignment_params.show()
    IMP.set_log_level(IMP.WARNING)
    prot_data = IMP.multifit.read_proteomics_data(proteomics_fn)
    print("=========3")
    mapping_data = IMP.multifit.read_protein_anchors_mapping(prot_data,
                                                             mapping_fn)
    print("=========4")
    _ = mapping_data.get_anchors()
    print("=========5")
    # load all proteomics restraints
    align = IMP.multifit.ProteomicsEMAlignmentAtomic(mapping_data, asmb,
                                                     alignment_params)
    print("align")
    align.set_fast_scoring(False)
    align.set_density_map(dmap, threshold)
    align.add_states_and_filters()
    align.add_all_restraints()

    print("before align")
    align.align()
    print("after align")
    combs = align.get_combinations()
    # print "after get combinations"
    if len(combs) == 0:
        f = open(combs_fn_output_fn, "w")
        f.write("NO SOLUTIONS FOUND\n")
        f.close()
        sys.exit(0)

    report_solutions(asmb, align.get_model(), align.get_molecules(),
                     align.get_restraint_set(), dmap,
                     mapping_data, combs, combs_fn_output_fn,
                     scored_comb_output_fn, max_comb)


def main():
    args = parse_args()
    run(args.assembly_file, args.proteomics_file, args.mapping_file,
        args.param_file, args.combinations_file, args.scores_file, args.max)


if __name__ == "__main__":
    main()