4075652401

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github

Committed by GitHub

Commit Message

Merge 45ea1393e into d73e8c34f

Pull Request Pull Request #330: fix: data generation threading locked

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1046 of 1331 branches covered (78.59%)

Branch coverage included in aggregate %.

36 of 36 new or added lines in 2 files covered. (100.0%)

2949 of 3482 relevant lines covered (84.69%)

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80.0

/deeprankcore/features/exposure.py

import logging
import numpy as np
import warnings
from Bio.PDB.Atom import PDBConstructionWarning
from Bio.PDB.PDBParser import PDBParser
from Bio.PDB.ResidueDepth import get_surface, residue_depth
from Bio.PDB.HSExposure import HSExposureCA
from deeprankcore.domain import nodestorage as Nfeat
from deeprankcore.molstruct.atom import Atom
from deeprankcore.molstruct.residue import Residue
from deeprankcore.utils.graph import Graph
import sys
import signal


_log = logging.getLogger(__name__)


def handle_sigint(sig, frame): # pylint: disable=unused-argument
    print('SIGINT received, terminating.')
    sys.exit()


def handle_timeout(sig, frame): # pylint: disable=unused-argument
    raise TimeoutError('Timed out!')


def space_if_none(value):
    if value is None:
        return " "

    return value


def add_features(pdb_path: str, graph: Graph, *args, **kwargs): # pylint: disable=unused-argument

    signal.signal(signal.SIGINT, handle_sigint)
    signal.signal(signal.SIGALRM, handle_timeout)

    with warnings.catch_warnings(record=PDBConstructionWarning):
        parser = PDBParser()
        structure = parser.get_structure('_tmp', pdb_path)
    
    bio_model = structure[0]

    try:
        signal.alarm(20)
        surface = get_surface(bio_model)
        signal.alarm(0)
    except TimeoutError as e:
        raise TimeoutError('Bio.PDB.ResidueDepth.get_surface timed out.') from e
    else:
        hse = HSExposureCA(bio_model)

        for node in graph.nodes:

            # These can only be calculated per residue, not per atom.
            # So for atomic graphs, every atom gets its residue's value.
            if isinstance(node.id, Atom):
                atom = node.id
                residue = atom.residue
            elif isinstance(node.id, Residue):
                residue = node.id
            else:
                raise TypeError(f"Unexpected node type: {type(node)}")

            bio_residue = bio_model[residue.chain.id][residue.number]
            node.features[Nfeat.RESDEPTH] = residue_depth(bio_residue, surface)

            hse_key = (residue.chain.id, (" ", residue.number, space_if_none(residue.insertion_code)))
            if hse_key in hse:
                node.features[Nfeat.HSE] = hse[hse_key]
            else:
                node.features[Nfeat.HSE] = np.array((0, 0, 0))

1	import logging	1✔
2	import numpy as np	1✔
3	import warnings	1✔
4	from Bio.PDB.Atom import PDBConstructionWarning	1✔
5	from Bio.PDB.PDBParser import PDBParser	1✔
6	from Bio.PDB.ResidueDepth import get_surface, residue_depth	1✔
7	from Bio.PDB.HSExposure import HSExposureCA	1✔
8	from deeprankcore.domain import nodestorage as Nfeat	1✔
9	from deeprankcore.molstruct.atom import Atom	1✔
10	from deeprankcore.molstruct.residue import Residue	1✔
11	from deeprankcore.utils.graph import Graph	1✔
12	import sys	1✔
13	import signal	1✔
14
15
16	_log = logging.getLogger(__name__)	1✔
17
18
19	def handle_sigint(sig, frame): # pylint: disable=unused-argument	1✔
20	print('SIGINT received, terminating.')	×
21	sys.exit()	×
22
23
24	def handle_timeout(sig, frame): # pylint: disable=unused-argument	1✔
25	raise TimeoutError('Timed out!')	×
26
27
28	def space_if_none(value):	1✔
29	if value is None:	1!
30	return " "	1✔
31
32	return value	×
33
34
35	def add_features(pdb_path: str, graph: Graph, args, *kwargs): # pylint: disable=unused-argument	1✔
36
37	signal.signal(signal.SIGINT, handle_sigint)	1✔
38	signal.signal(signal.SIGALRM, handle_timeout)	1✔
39
40	with warnings.catch_warnings(record=PDBConstructionWarning):	1✔
41	parser = PDBParser()	1✔
42	structure = parser.get_structure('_tmp', pdb_path)	1✔
43
44	bio_model = structure[0]	1✔
45
46	try:	1✔
47	signal.alarm(20)	1✔
48	surface = get_surface(bio_model)	1✔
49	signal.alarm(0)	1✔
50	except TimeoutError as e:	×
51	raise TimeoutError('Bio.PDB.ResidueDepth.get_surface timed out.') from e	×
52	else:
53	hse = HSExposureCA(bio_model)	1✔
54
55	for node in graph.nodes:	1✔
56
57	# These can only be calculated per residue, not per atom.
58	# So for atomic graphs, every atom gets its residue's value.
59	if isinstance(node.id, Atom):	1!
60	atom = node.id	×
61	residue = atom.residue	×
62	elif isinstance(node.id, Residue):	1!
63	residue = node.id	1✔
64	else:
65	raise TypeError(f"Unexpected node type: {type(node)}")	×
66
67	bio_residue = bio_model[residue.chain.id][residue.number]	1✔
68	node.features[Nfeat.RESDEPTH] = residue_depth(bio_residue, surface)	1✔
69
70	hse_key = (residue.chain.id, (" ", residue.number, space_if_none(residue.insertion_code)))	1✔
71	if hse_key in hse:	1✔
72	node.features[Nfeat.HSE] = hse[hse_key]	1✔
73	else:
74	node.features[Nfeat.HSE] = np.array((0, 0, 0))	1✔

DeepRank / deeprank-core / 4075652401

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