emseqfinder/mldb/tools.py

import os


def get_sequence_from_pdb(pdb):
    '''
    from a standard pdb file, return all RESNAME entries
    from the Calpha atoms
    '''
    resnames = []
    f = open(pdb)
    for line in f.readlines():
        if line[13:15] == "CA":
            resnames.append(line[17:20])

    f.close()
    return resnames


def is_poly_ala(pdb):
    # Returns true if all residues are alanine
    resis = get_sequence_from_pdb(pdb)
    if all(r == 'ALA' for r in resis):
        return True
    else:
        return False


def is_length_correct(pdb):
    # returns
    # pdb :
    lenseq = int(os.path.basename(pdb).split("_")[-2])
    resis = get_sequence_from_pdb(pdb)
    if len(resis) == lenseq:
        return True
    else:
        return False


def is_length_correct_for_parts(pdb):
    # returns
    # pdb :
    resis = get_sequence_from_pdb(pdb)
    if len(resis) > 2:
        return True
    else:
        return False


def get_adjacent_values(em, voxel):
    # returns a list of the value of all voxels
    # plus one
    import IMP.algebra
    loc = em.get_location_by_voxel(voxel)
    values = []
    vecs = [(0, 0, 1), (0, 1, 0), (1, 0, 0),
            (0, 0, -1), (0, -1, 0), (-1, 0, 0)]

    disps = [IMP.algebra.Vector3D(v) for v in vecs]

    for d in disps:
        try:
            values.append(em.get_value(loc+d))
        except:  # noqa: E722
            pass

    return values


def get_voxel_position_string(dmap):
    vstring = ''
    for v in range(dmap.get_number_of_voxels()):
        vstring += str(dmap.get_location_by_voxel(v))+" "
    return vstring[0:-1]


def get_voxel_value_string(dmap, const=1):
    vstring = ""
    for v in range(dmap.get_number_of_voxels()):
        vstring += str(round(dmap.get_value(v), 4))+" "
    return vstring[0:-1]


def get_xml_line(xml, field):
    f = open(xml, "r")

    for line in f.readlines():
        if field in line:
            f.close()
            return line
    f.close()
    return None


def get_pdbid_from_xml(xml):
    line = get_xml_line(xml, "<fittedPDBEntryId>")
    if line is None:
        return line
    return line.strip().split("<fittedPDBEntryId>")[-1][0:4]


def get_threshold_from_xml(xml):
    line = get_xml_line(xml, "contourLevel")
    if line is None:
        return line
    return float(line.strip().split(">")[1].split("<")[0])


def get_resolution(emdb):
    # get resolution information from EMDB
    from config import get_xml
    return get_resolution_from_xml(get_xml(emdb))


def get_resolution_from_xml(xml):
    line = get_xml_line(xml, "<resolutionByAuthor>")
    if line is None:
        return line
    return float(line.strip().split("<resolutionByAuthor>")[-1].split("<")[0])


def get_spacing_from_xml(xml):
    line = get_xml_line(xml, "pixelX")
    return float(line.strip().split(">")[1].split("<")[0])


def get_statistics_from_xml(xml):
    # Returns voxel minimum, maximum, average and SD as a tuple
    line = get_xml_line(xml, "<minimum>")
    minimum = float(line.strip().split(">")[1].split("<")[0])
    line = get_xml_line(xml, "<maximum>")
    maximum = float(line.strip().split(">")[1].split("<")[0])
    line = get_xml_line(xml, "<average>")
    average = float(line.strip().split(">")[1].split("<")[0])
    line = get_xml_line(xml, "<std>")
    std = float(line.strip().split(">")[1].split("<")[0])
    return (minimum, maximum, average, std)


def catstring(stuff, delimiter=" "):
    outstring = ""
    for s in stuff:
        outstring += str(s)+delimiter

    return outstring[0:-1]


def tint(value, n=2):
    return int(value*10**n)/10**n