PDBxParser.py

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"""
PDBx topology parser
====================


See Also
--------
:class:`MDAnalysis.coordinates.PDBx`

"""
import gemmi
import numpy as np

from .base import TopologyReaderBase, change_squash
from ..core.topology import Topology
from ..core.topologyattrs import (
    Atomnames,
    Atomids,
    AltLocs,
    Elements,
    ICodes,
    RecordTypes,
    Resids,
    Resnames,
    Segids,
)


class PDBxParser(TopologyReaderBase):
    """Read a Topology from a PDBx file

    Creates the following attributes from these "_atom_site" PDBx loop entries
    - "group_PDB" RecordType
    - "id" AtomId
    - "label_alt_id" AltLoc
    - "label_type_symbol" Element
    - "label_atom_id" AtomName
    - "auth_seq_id" Resid
    - "auth_comp_id" Resname
    - "pdbx_PDB_ins_code" ICode
    - "auth_asym_id" ChainID
    """
    format = ['PDBx', 'cif']

    def parse(self, **kwargs) -> Topology:
        doc = gemmi.cif.read(self.filename)
        block = doc.sole_block()

        attrs = []

        def objarr(x):
            return np.array(x, dtype=object)

        # hierarchy correspondence:
        # seq_id -> residues
        # entity_id -> chains
        if recordtypes := block.find('_atom_site.', ['group_PDB']):
            attrs.append(RecordTypes(recordtypes))
        ids = block.find_loop('_atom_site.id')
        n_atoms = len(ids)
        attrs.append(Atomids(ids))
        if altlocs := block.find_loop('_atom_site.label_alt_id'):
            altlocs = np.array(altlocs, dtype=object)
            altlocs[altlocs == '.'] = ''
            attrs.append(AltLocs(altlocs))
        if elements_loop := block.find_loop('_atom_site.type_symbol'):
            attrs.append(Elements(objarr(elements_loop)))
        if names_loop := block.find_loop('_atom_site.label_atom_id'):
            attrs.append(Atomnames(objarr(names_loop)))

        # sort out residues/segments
        # label_seq_id seems to not cover entire model unlike author versions
        resids = np.array(block.find_loop('_entity_poly_seq.num'))
        resnames = np.array(block.find_loop('_entity_poly_seq.mon_id'))
        icodes = np.array(block.find_loop('_atom_site.pdbx_PDB_ins_code'))
        chainids = np.array(block.find_loop('_atom_site.auth_asym_id'))

        try:
            residx, (resids, icodes, resnames, chainids) = change_squash(
            (resids, icodes), (resids, icodes, resnames, chainids)
        )
            segidx, (chainids,) = change_squash((chainids,), (chainids,))
        except IndexError:
            ...
        attrs.extend((
            Resids(resids),
            Resnames(objarr(resnames)),
            ICodes(objarr(icodes)),
            Segids(chainids),
        ))

        n_residues = len(resids)
        n_segments = len(chainids)

        return Topology(
            n_atoms=n_atoms,
            n_res=n_residues,
            n_seg=n_segments,
            attrs=attrs,
            atom_resindex=residx,
            residue_segindex=segidx,
        )