Source code for schrodinger.protein.properties

import csv
import os

from schrodinger import structure
from schrodinger.models import json
from schrodinger.models import jsonable
from schrodinger.models import parameters
from schrodinger.utils import csv_unicode
from schrodinger.utils import qt_utils

#===============================================================================
# Properties/Descriptors
#===============================================================================

PropertySource = jsonable.JsonableEnum("PropertySource",
                                       ["Residue", "Sequence", "Structure"])
PropertyType = jsonable.JsonableEnum("PropertyType",
                                     ["Descriptor", "StructureProperty"])

ALL_SEQ_DESCRIPTORS_FPATH = os.path.join(os.path.dirname(__file__),
                                         'all_seq_descriptors.csv')


def get_prop_name_to_display_name_map():
    with csv_unicode.reader_open(ALL_SEQ_DESCRIPTORS_FPATH) as infile:
        reader = csv.DictReader(infile)
        prop_name_to_display_name_map = dict()
        for row in reader:
            try:
                property_name = row['DESCRIPTOR']
                display_name = row['DISPLAY_NAME']
                prop_name_to_display_name_map[property_name] = display_name
            except KeyError:
                pass
        return prop_name_to_display_name_map


prop_name_to_display_name_map = get_prop_name_to_display_name_map()


@qt_utils.add_enums_as_attributes(PropertySource)
@qt_utils.add_enums_as_attributes(PropertyType)
class SequenceProperty(parameters.CompoundParam):
    visible: bool
    property_name: str
    property_source: PropertySource  # Residue, Sequence, or Structure
    property_type: PropertyType  # Descriptor or StructureProperty
    description: str = None
    display_name: str = None

    def __init__(self, *args, **kwargs):
        super().__init__(*args, **kwargs)
        self._setDefaultDisplayName()

    def _setDefaultDisplayName(self):
        if not self.display_name:
            if self.property_type == self.StructureProperty:
                self.display_name = structure.PropertyName(
                    self.property_name).userName()
            else:
                self.display_name = prop_name_to_display_name_map.get(
                    self.property_name, self.property_name)

    @json.adapter(version=50002)
    def adapter_50002(self, json_dict):
        """
        In 50002 we split the property_source param into two separate
        property_type and property_source params
        """
        old_prop_source = json_dict.pop("property_source")

        if old_prop_source == 4:  # Old Structure Property
            prop_type = PropertyType.StructureProperty.toJsonImplementation()
            prop_source = PropertySource.Sequence.toJsonImplementation()
        else:
            prop_type = PropertyType.Descriptor.toJsonImplementation()
            prop_source = old_prop_source
        json_dict["property_source"] = prop_source
        json_dict["property_type"] = prop_type
        return json_dict


def get_CA_atom_props(aln):
    """
    Get the CA atom properties of each structured residues in the
    alignment.

    :param aln: The alignment to use.
    :type aln: schrodinger.protein.alignment.BaseAlignment

    :return: list of sequence property object.
    :rtype: List[properties.SequenceProperty]
    """
    atom_props = []
    structured_residues = aln.getResiduesWithStructure()
    for res in structured_residues:
        for prop_name in res.getStructureResProperties():
            if prop_name[0] not in (structure.PROP_FLOAT,
                                    structure.PROP_INTEGER):
                continue
            atom_prop = SequenceProperty(
                property_name=prop_name,
                property_type=PropertyType.StructureProperty,
                property_source=PropertySource.Structure)
            if atom_prop not in atom_props:
                atom_props.append(atom_prop)
    return atom_props