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use pooch for PLB files
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previous solution used io.StringIO which rdkit doesn't like (and wasn't documented as accepted)
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@richardjgowers
richardjgowers committed Dec 20, 2023
1 parent 8658083 commit 215dace
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Showing 2 changed files with 50 additions and 82 deletions.
82 changes: 33 additions & 49 deletions gufe/tests/conftest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@
import importlib.resources
import urllib.request
from urllib.error import URLError
import io
import functools
import pooch
import pytest
from rdkit import Chem
from rdkit.Chem import AllChem
Expand All @@ -20,58 +20,42 @@
else:
HAS_INTERNET = True

PLB_files = pooch.create(
path=pooch.os_cache('pdbinf'),
base_url='https://github.com/openforcefield/protein-ligand-benchmark/raw/d3387602bbeb0167abf00dfb81753d8936775dd2/data/',
version=None,
registry={
'p38/01_protein/crd/protein.pdb': '3f0bf718644e7c29f5200cd3def4240ac25ef5fb1948b2e64deb5015d8a45aa4',
'mcl1/01_protein/crd/protein.pdb': 'f80ff9dd93a5d9dd6e90091e9631a8ce7fe0dc931e16543e22c1f92009660306',
'cdk2/01_protein/crd/protein.pdb': '15d1e509d7951ca45ea266d51a627d5f452dcf0bb5bd48751ae57eb29e28ab69',
'shp2/01_protein/crd/protein.pdb': 'd6759cbd135aaddaa658446064df4095d978d3681c014a0528b542d60b2c8770',
'pde2/01_protein/crd/protein.pdb': '3b7967c1717789215452cdf919520625602d5438a9d2a18620726b8b1b3a8ef0',
'cmet/01_protein/crd/protein.pdb': '155ec32941a9082dbdbbfde460ff97c88d4fe7e100e9a9577edb5a9e7b6467ae',
'ptp1b/01_protein/crd/protein.pdb': 'bfa0f9204e96aa463b80946b788c4153cd24701291007eb77638a16fd156634e',
'thrombin/01_protein/crd/protein.pdb': 'eb4ea18bef9c4c71dcdc922616d6719ee918112be87a0bd6b274c856eff1dd59',
'cdk8/01_protein/crd/protein.pdb': 'b058774526a19775d8f438b14e9d6da331b6de74e0ef9e96db575f6c0bb067b2',
'pfkfb3/01_protein/crd/protein.pdb': '4367710db0dbf284cc715ae9a8dd82d06bd77dcc3fb0885678e16632a2732dcc',
'tyk2/01_protein/crd/protein.pdb': '9090684f4bdae90afbe5f2698a14c778396c024c19ceb6333de4808d9e29fae6',
'syk/01_protein/crd/protein.pdb': 'f6199d0c1818eb5bb24e164426789cf39cae7aa32c8ca2e98f5f44d299a6f82f',
'tnks2/01_protein/crd/protein.pdb': 'fc7681a05dbf07590aa8de133f981b6d8ae9cebcc23d54addc2c4fe80be80299',
'eg5/01_protein/crd/protein.pdb': 'f2964a785c922502dc86fb4e2e5295d32d41d5b68b8c3246e989de5234c3fd0f',
'hif2a/01_protein/crd/protein.pdb': '5bbf520e7c102a65cc7ba0253fd66f43562f77284c82b3b9613e997b7ac76c93',

},
)

class URLFileLike:
def __init__(self, url, encoding='utf-8'):
self.url = url
self.encoding = encoding
self.data = None

def __call__(self):
@pytest.fixture(params=['p38', 'mcl1', 'cdk2', 'shp2', 'pde2', 'cmet', 'ptp1b',
'thrombin', 'cdk8', 'pfkfb3', 'tyk2', 'syk', 'tnks2',
'eg5', 'hif2a', '181l'])
def PDB_files(request):
if request.param == '181l':
with importlib.resources.path('gufe.tests.data', '181l.pdb') as file:
return str(file)
else:
if not HAS_INTERNET: # pragma: no-cover
pytest.skip("Skipping because internet seems faulty")

if self.data is None:
req = urllib.request.urlopen(self.url)
self.data = req.read().decode(self.encoding)

return io.StringIO(self.data)


def get_test_filename(filename):
with importlib.resources.path('gufe.tests.data', filename) as file:
return str(file)


_benchmark_pdb_names = [
"cmet_protein",
"hif2a_protein",
"mcl1_protein",
"p38_protein",
"ptp1b_protein",
"syk_protein",
"thrombin_protein",
"tnsk2_protein",
"tyk2_protein",
]


_pl_benchmark_url_pattern = (
"https://github.com/OpenFreeEnergy/openfe-benchmarks/blob/main/openfe_benchmarks/data/{name}.pdb?raw=true"
)


PDB_BENCHMARK_LOADERS = {
name: URLFileLike(url=_pl_benchmark_url_pattern.format(name=name))
for name in _benchmark_pdb_names
}

PDB_FILE_LOADERS = {
name: lambda: get_test_filename(name)
for name in ["181l.pdb"]
}

ALL_PDB_LOADERS = dict(**PDB_BENCHMARK_LOADERS, **PDB_FILE_LOADERS)
return PLB_files.fetch('{}/01_protein/crd/protein.pdb'.format(request.param))


@pytest.fixture
Expand Down
50 changes: 17 additions & 33 deletions gufe/tests/test_proteincomponent.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
from openmm import unit
from numpy.testing import assert_almost_equal

from .conftest import ALL_PDB_LOADERS
from .conftest import PLB_files


@pytest.fixture
Expand Down Expand Up @@ -94,11 +94,8 @@ class TestProteinComponent(GufeTokenizableTestsMixin):
def instance(self, PDB_181L_path):
return self.cls.from_pdb_file(PDB_181L_path, name="Steve")

# From
@pytest.mark.parametrize('in_pdb_path', ALL_PDB_LOADERS.keys())
def test_from_pdb_file(self, in_pdb_path):
in_pdb_io = ALL_PDB_LOADERS[in_pdb_path]()
p = self.cls.from_pdb_file(in_pdb_io, name="Steve")
def test_from_pdb_file(self, PDB_files):
p = self.cls.from_pdb_file(PDB_files, name="Steve")

assert isinstance(p, ProteinComponent)
assert p.name == "Steve"
Expand Down Expand Up @@ -177,21 +174,16 @@ def test_to_pdb_input_types(self, PDB_181L_OpenMMClean_path, tmp_path,
output_func=p.to_pdb_file
)

@pytest.mark.parametrize('in_pdb_path', ALL_PDB_LOADERS.keys())
def test_to_pdb_round_trip(self, in_pdb_path, tmp_path):
in_pdb_io = ALL_PDB_LOADERS[in_pdb_path]()

p = self.cls.from_pdb_file(in_pdb_io, name="Wuff")
out_file_name = "tmp_"+in_pdb_path+".pdb"
def test_to_pdb_round_trip(self, PDB_files, tmp_path):
p = self.cls.from_pdb_file(PDB_files, name="Wuff")
out_file_name = "tmp_foo.pdb"
out_file = tmp_path / out_file_name

p.to_pdb_file(str(out_file))

ref_in_pdb_io = ALL_PDB_LOADERS[in_pdb_path]()

# generate openMM reference file:
openmm_pdb = pdbfile.PDBFile(ref_in_pdb_io)
out_ref_file_name = "tmp_"+in_pdb_path+"_openmm_ref.pdb"
openmm_pdb = pdbfile.PDBFile(PDB_files)
out_ref_file_name = "tmp_foo_openmm_ref.pdb"
out_ref_file = tmp_path / out_ref_file_name

pdbfile.PDBFile.writeFile(openmm_pdb.topology, openmm_pdb.positions, file=open(str(out_ref_file), "w"))
Expand All @@ -213,33 +205,23 @@ def test_dummy_from_dict(self, PDB_181L_OpenMMClean_path):

assert p == p2

# parametrize
@pytest.mark.parametrize('in_pdb_path', ALL_PDB_LOADERS.keys())
def test_to_openmm_positions(self, in_pdb_path):
in_pdb_io = ALL_PDB_LOADERS[in_pdb_path]()
ref_in_pdb_io = ALL_PDB_LOADERS[in_pdb_path]()

openmm_pdb = pdbfile.PDBFile(ref_in_pdb_io)
def test_to_openmm_positions(self, PDB_files):
openmm_pdb = pdbfile.PDBFile(PDB_files)
openmm_pos = openmm_pdb.positions

p = self.cls.from_pdb_file(in_pdb_io, name="Bob")
p = self.cls.from_pdb_file(PDB_files, name="Bob")
gufe_openmm_pos = p.to_openmm_positions()

v1 = gufe_openmm_pos.value_in_unit(unit.nanometer)
v2 = openmm_pos.value_in_unit(unit.nanometer)

assert_almost_equal(actual=v1, desired=v2, decimal=6)

# parametrize
@pytest.mark.parametrize('in_pdb_path', ALL_PDB_LOADERS.keys())
def test_to_openmm_topology(self, in_pdb_path):
in_pdb_io = ALL_PDB_LOADERS[in_pdb_path]()
ref_in_pdb_io = ALL_PDB_LOADERS[in_pdb_path]()

openmm_pdb = pdbfile.PDBFile(ref_in_pdb_io)
def test_to_openmm_topology(self, PDB_files):
openmm_pdb = pdbfile.PDBFile(PDB_files)
openmm_top = openmm_pdb.topology

p = self.cls.from_pdb_file(in_pdb_io, name="Bob")
p = self.cls.from_pdb_file(PDB_files, name="Bob")
gufe_openmm_top = p.to_openmm_topology()
assert_topology_equal(openmm_top, gufe_openmm_top)

Expand Down Expand Up @@ -290,7 +272,9 @@ def test_protein_total_charge(self, PDB_181L_path):
assert m1.total_charge == 7

def test_protein_total_charge_thromb(self):
m1 = self.cls.from_pdb_file(ALL_PDB_LOADERS["thrombin_protein"]())
f = PLB_files.fetch('thrombin/01_protein/crd/protein.pdb')

m1 = self.cls.from_pdb_file(f)

assert m1.total_charge == 6

Expand Down

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