Source code for pestifer.objs.link

# Author: Cameron F. Abrams, <cfa22@drexel.edu>
"""
A Link is a covalent bond between two residues in a protein structure.
"""
from __future__ import annotations

import logging

import numpy as np

from mmcif.api.PdbxContainers import DataContainer
from pidibble.pdbrecord import PDBRecord, PDBRecordDict
from pydantic import Field
from typing import ClassVar, TYPE_CHECKING

from .mutation import MutationList
from .resid import ResID

from ..core.baseobj import BaseObj, BaseObjList
from ..util.coord import measure_dihedral

if TYPE_CHECKING:
    from ..molecule.atom import Atom
    from ..molecule.residue import Residue, ResidueList
    from ..molecule.segment import Segment, SegmentList

from ..psfutil.psfpatch import PSFLinkPatch

from ..util.cifutil import CIFdict

logger = logging.getLogger(__name__)






    


[docs]
def ic_reference_closest(res12: list["Residue"], ICmaps: list[dict]) -> str:
    """
    Given the two Residues in res12 and the maps in ICmaps, 
    return the mapping key to which the given IC values are
    closest in a Euclidean sense.

    This method will identify the four atoms of the IC and reference
    them directly when calling the measure_dihedral function. 
    
    The list of computed dihedral values from the set of atoms is a "point"
    in "IC-space", and each patch has its own "reference point" in this space.

    The reference point to which the point is closest is identified as the 
    desired result.

    Parameters
    ----------
    res12: list
       exactly two Residue objects which must have lists of atoms attributes
    ICMaps : list of dict
        A list of dictionaries, each with the following structure:

        +--------------+-----------------------------------------------------------+
        | Key          | Description                                               |
        +==============+===========================================================+
        | ICatomnames  | List of 4 atom names as they appear in the CHARMM FF IC.  |
        +--------------+-----------------------------------------------------------+
        | mapping      | Dictionary mapping patch names to IC values.              |
        +--------------+-----------------------------------------------------------+
    """
    for ic in ICmaps:
        # logger.debug(f'icmap {ic}')
        ic['atoms'] = []
        for n in ic['ICatomnames']:
            r = int(n[0])-1
            an = n[1:]
            at = res12[r].atoms.get(lambda x: x.name == an)
            ic['atoms'].append(at)
            # logger.debug(f'Assigned atom {at.name} of {at.resname}{at.resseqnum}')
    map_points = {}
    the_point = []
    for ic in ICmaps:
        value = measure_dihedral(*(ic['atoms'])) * 180.0 / np.pi
        # logger.debug(f'{ic["ICatomnames"]} value {value:.2f}')
        the_point.append(value)
        for m, v in ic['mapping'].items():
            if not m in map_points:
                map_points[m] = []
            map_points[m].append(v)
    for k, v in map_points.items():
        map_points[k] = np.array(v)
    the_point = np.array(the_point)
    # logger.debug(f'ic the point: {the_point}')
    # calculate Euclidean distance adhering to the periodicity
    # of dihedral-angle space
    displacements = {k: (the_point - v) for k, v in map_points.items()}
    for n, d in displacements.items():
        for i in range(len(d)):
            if d[i] < 180.0:
                d[i] += 180.0
            if d[i] > 180.0:
                d[i] -= 180.0
    norms = {k: np.linalg.norm(d) for k, d in displacements.items()}
    # logger.debug(f'norms {norms}')
    the_one = [k for (k, v) in sorted(norms.items(), key=lambda x: x[1])][0]
    # logger.debug(f'returning {the_one}')
    return the_one