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App Domain Pathway Prediction (#47)

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Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#47
This commit is contained in:
jebus
2025-08-19 02:53:56 +12:00
parent 3308d47071
commit c3c1d4f5cf
9 changed files with 424 additions and 178 deletions
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78
epdb/models.py
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@ -912,7 +912,8 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
'reaction_probability': link['reaction_probability'],
'scenarios': link['scenarios'],
'source': node_url_to_idx[link['start_node_urls'][0]],
'target': pseudo_idx
'target': pseudo_idx,
'app_domain': link.get('app_domain', None)
}
adjusted_links.append(new_link)
@ -927,7 +928,8 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
'reaction_probability': link['reaction_probability'],
'scenarios': link['scenarios'],
'source': pseudo_idx,
'target': node_url_to_idx[target]
'target': node_url_to_idx[target],
'app_domain': link.get('app_domain', None)
}
adjusted_links.append(new_link)
@ -1044,6 +1046,8 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin):
return '{}/node/{}'.format(self.pathway.url, self.uuid)
def d3_json(self):
app_domain_data = self.get_app_domain_assessment_data()
return {
"depth": self.depth,
"url": self.url,
@ -1053,6 +1057,10 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin):
"name": self.default_node_label.name,
"smiles": self.default_node_label.smiles,
"scenarios": [{'name': s.name, 'url': s.url} for s in self.scenarios.all()],
"app_domain": {
'inside_app_domain': app_domain_data['assessment']['inside_app_domain'] if app_domain_data else None,
'uncovered_functional_groups': False,
}
}
@staticmethod
@ -1078,6 +1086,32 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin):
def as_svg(self):
return IndigoUtils.mol_to_svg(self.default_node_label.smiles)
def get_app_domain_assessment_data(self):
data = self.kv.get('app_domain_assessment', None)
if data:
rule_ids = dict()
for e in Edge.objects.filter(start_nodes__in=[self]):
for r in e.edge_label.rules.all():
rule_ids[str(r.uuid)] = e
for t in data['assessment']['transformations']:
if t['rule']['uuid'] in rule_ids:
t['is_predicted'] = True
t['edge'] = rule_ids[t['rule']['uuid']].simple_json()
return data
def simple_json(self, include_description=False):
res = super().simple_json()
name = res.get('name', None)
if name == 'no name':
res['name'] = self.default_node_label.name
return res
class Edge(EnviPathModel, AliasMixin, ScenarioMixin):
pathway = models.ForeignKey('epdb.Pathway', verbose_name='belongs to', on_delete=models.CASCADE, db_index=True)
@ -1090,19 +1124,44 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin):
return '{}/edge/{}'.format(self.pathway.url, self.uuid)
def d3_json(self):
return {
edge_json = {
'name': self.name,
'id': self.url,
'url': self.url,
'image': self.url + '?image=svg',
'reaction': {'name': self.edge_label.name, 'url': self.edge_label.url } if self.edge_label else None,
'reaction_probability': self.kv.get('probability'),
# TODO
'start_node_urls': [x.url for x in self.start_nodes.all()],
'end_node_urls': [x.url for x in self.end_nodes.all()],
"scenarios": [{'name': s.name, 'url': s.url} for s in self.scenarios.all()],
}
for n in self.start_nodes.all():
app_domain_data = n.get_app_domain_assessment_data()
if app_domain_data:
for t in app_domain_data['assessment']['transformations']:
if 'edge' in t and t['edge']['uuid'] == str(self.uuid):
passes_app_domain = (
t['local_compatibility'] >= app_domain_data['ad_params']['local_compatibility_threshold']
) and (
t['reliability'] >= app_domain_data['ad_params']['reliability_threshold']
)
edge_json['app_domain'] = {
'passes_app_domain': passes_app_domain,
'local_compatibility': t['local_compatibility'],
'local_compatibility_threshold': app_domain_data['ad_params']['local_compatibility_threshold'],
'reliability': t['reliability'],
'reliability_threshold': app_domain_data['ad_params']['reliability_threshold'],
'times_triggered': t['times_triggered'],
}
break
return edge_json
@staticmethod
def create(pathway, start_nodes: List[Node], end_nodes: List[Node], rule: Optional[Rule] = None, name: Optional[str] = None,
description: Optional[str] = None):
@ -1136,6 +1195,14 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin):
def as_svg(self):
return self.edge_label.as_svg if self.edge_label else None
def simple_json(self, include_description=False):
res = super().simple_json()
name = res.get('name', None)
if name == 'no name':
res['name'] = self.edge_label.name
return res
class EPModel(PolymorphicModel, EnviPathModel):
package = models.ForeignKey('epdb.Package', verbose_name='Package', on_delete=models.CASCADE, db_index=True)
@ -1463,6 +1530,7 @@ class MLRelativeReasoning(EPModel):
return res
class ApplicabilityDomain(EnviPathModel):
model = models.ForeignKey(MLRelativeReasoning, on_delete=models.CASCADE)
@ -1614,7 +1682,7 @@ class ApplicabilityDomain(EnviPathModel):
'model': self.model.simple_json(),
'num_neighbours': self.num_neighbours,
'reliability_threshold': self.reliability_threshold,
'local_compatibilty_threshold': self.local_compatibilty_threshold,
'local_compatibility_threshold': self.local_compatibilty_threshold,
},
'assessment': {
'smiles': smiles,