def test_svg_annotation(component: Component, tmpdir_factory):
if not component.atoms_ids:
return
json_obj = None
wd = tmpdir_factory.mktemp('svg_json_test')
out_file = os.path.join(wd, f'{component.id}.json')
component.compute_2d(depictions)
component.export_2d_annotation(out_file)
assert os.path.isfile(out_file)
assert os.path.getsize(out_file) > 0
with open(out_file, 'r') as fp:
json_obj = json.load(fp)
assert json_obj['ccd_id'] == component.id
assert json_obj['resolution']['x'] >= 0
assert json_obj['resolution']['y'] >= 0
atom_names = [atom['name'] for atom in json_obj['atoms']]
assert len(json_obj['atoms']) == component.mol_no_h.GetNumAtoms()
assert len(json_obj['bonds']) >= component.mol_no_h.GetNumBonds()
assert any(
atom['label'] for atom in
json_obj['atoms']) # do we have any labels (not all atoms has one)
assert all(atom['name']
for atom in json_obj['atoms']) # do we have atom names?
assert all(bond['bgn'] in atom_names and bond['end'] in atom_names
for bond in json_obj['bonds']) # are all the atoms defined?
assert all(bond['coords']
for bond in json_obj['bonds']) # do we have coordinates?
assert all(bond['style']
for bond in json_obj['bonds']) # and its stylling?
def test_svg_annotation(component: Component, tmpdir_factory):
if not component.atoms_ids:
return
json_obj = None
wd = tmpdir_factory.mktemp("svg_json_test")
out_file = os.path.join(wd, f"{component.id}.json")
component.compute_2d(depictions)
component.export_2d_annotation(out_file)
assert os.path.isfile(out_file)
assert os.path.getsize(out_file) > 0
with open(out_file, "r") as fp:
json_obj = json.load(fp)
assert json_obj["ccd_id"] == component.id
assert json_obj["resolution"]["x"] >= 0
assert json_obj["resolution"]["y"] >= 0
atom_names = [atom["name"] for atom in json_obj["atoms"]]
assert len(json_obj["atoms"]) == component.mol_no_h.GetNumAtoms()
assert len(json_obj["bonds"]) >= component.mol_no_h.GetNumBonds()
assert all(atom["name"] for atom in json_obj["atoms"]) # do we have atom names?
assert all(
bond["bgn"] in atom_names and bond["end"] in atom_names
for bond in json_obj["bonds"]
) # are all the atoms defined?
assert all(
bond["coords"] for bond in json_obj["bonds"]
) # do we have coordinates?
assert all(bond["style"] for bond in json_obj["bonds"]) # and its stylling?
def _generate_depictions(self, component: Component):
"""Generate nice 2D depictions for the component. Presently depictions
are generated in the following resolutions (100,200,300,400,500) with
and without atom names.
Args:
component (Component): Component to be depicted.
depictions (DepictionManager): Helper class
to carry out depiction process.
parent_dir (str): Where the depiction should be stored
"""
parent_dir = os.path.join(self.output_dir, component.id[0],
component.id)
depiction_result = component.compute_2d(self.depictions)
if depiction_result.source == DepictionSource.Failed:
self.logger.debug('failed to generate 2D image.')
else:
if depiction_result.score > 0.99:
self.logger.debug(
'collision free image could not be generated.')
self.logger.debug(
f'2D generated using {depiction_result.source.name} with score {depiction_result.score}.'
)
wedge_bonds = depiction_result.template_name != 'cube'
for i in range(100, 600, 100):
component.export_2d_svg(os.path.join(parent_dir,
f'{component.id}_{i}.svg'),
width=i,
wedge_bonds=wedge_bonds)
component.export_2d_svg(os.path.join(
parent_dir, f'{component.id}_{i}_names.svg'),
width=i,
names=True,
wedge_bonds=wedge_bonds)
component.export_2d_annotation(os.path.join(
parent_dir, f'{component.id}_annotation.json'),
wedge_bonds=wedge_bonds)
def _generate_depictions(self, component: Component, out_dir: str):
"""Generate nice 2D depictions for the component and
depiction annotations in JSON format. Presently depictions
are generated in the following resolutions (100,200,300,400,500)
with and without atom names.
Args:
component (Component): Component to be depicted.
out_dir (str): Where the depictions should be stored.
"""
depiction_result = component.compute_2d(self.depictions)
if depiction_result.source == DepictionSource.Failed:
logging.debug("failed to generate 2D image.")
else:
if depiction_result.score > 0.99:
logging.debug("collision free image could not be generated.")
logging.debug(
f"2D generated using {depiction_result.source.name} with score {depiction_result.score}."
)
wedge_bonds = depiction_result.template_name != "cube"
for i in range(100, 600, 100):
component.export_2d_svg(
os.path.join(out_dir, f"{component.id}_{i}.svg"),
width=i,
wedge_bonds=wedge_bonds,
)
component.export_2d_svg(
os.path.join(out_dir, f"{component.id}_{i}_names.svg"),
width=i,
names=True,
wedge_bonds=wedge_bonds,
)
component.export_2d_annotation(
os.path.join(out_dir, f"{component.id}_annotation.json"),
wedge_bonds=wedge_bonds,
)