nerdd-module 0.3.29__tar.gz → 0.3.31__tar.gz

{nerdd_module-0.3.29 → nerdd_module-0.3.31}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: nerdd-module
-Version: 0.3.29
+Version: 0.3.31
 Summary: Base package to create NERDD modules
 Author-email: Steffen Hirte <steffen.hirte@univie.ac.at>
 Maintainer-email: Steffen Hirte <steffen.hirte@univie.ac.at>
@@ -87,6 +87,7 @@ Provides-Extra: docs
 Requires-Dist: mkdocs; extra == "docs"
 Requires-Dist: mkdocs-material; extra == "docs"
 Requires-Dist: mkdocstrings; extra == "docs"
+Dynamic: license-file
 
 # NERDD Module
 

{nerdd_module-0.3.29 → nerdd_module-0.3.31}/nerdd_module/config/models.py

@@ -38,6 +38,14 @@ class Publication(BaseModel):
     doi: Optional[str]
 
 
+class ColorPalette(BaseModel):
+    type: Optional[str] = None
+    name: Optional[str] = None
+    domain: List[str]
+    range: List[str]
+    unknown: Optional[str] = None
+
+
 class JobParameterChoice(BaseModel):
     value: str
     label: Optional[str] = None
@@ -82,6 +90,7 @@ class ResultProperty(BaseModel):
     from_property: Optional[str] = None
     image_width: Optional[int] = None
     image_height: Optional[int] = None
+    color_palette: Optional[ColorPalette] = None
 
     def is_visible(self, output_format: str) -> bool:
         formats = self.formats

nerdd_module-0.3.31/nerdd_module/tests/representations.py

@@ -0,0 +1,129 @@
+import numpy as np
+from hypothesis import given as hgiven
+from hypothesis import seed, settings
+from hypothesis import strategies as st
+from hypothesis_rdkit import mols
+from pytest_bdd import given, parsers
+from rdkit.Chem import MolToInchi, MolToMolBlock, MolToSmiles
+from ..polyfills import BlockLogs
+from rdkit.Chem.rdMolDescriptors import CalcExactMolWt
+import re
+from functools import reduce
+
+
+@given(parsers.parse("a random seed set to {seed:d}"), target_fixture="random_seed")
+def random_seed(seed):
+    return seed
+
+
+@given(
+    parsers.parse("an input molecule specified by '{input}'"),
+    target_fixture="representations",
+)
+def representations_from_input(input):
+    return [input]
+
+
+@given(
+    parsers.parse("the representations of the molecules in {input_type} format"),
+    target_fixture="representations",
+)
+def representations_from_molecules(molecules, input_type):
+    input_type = input_type.lower()
+
+    if input_type == "smiles":
+        converter = MolToSmiles
+    elif input_type == "mol_block":
+        converter = MolToMolBlock
+    elif input_type == "inchi":
+        converter = MolToInchi
+    elif input_type == "rdkit_mol":
+        converter = lambda mol: mol
+    else:
+        raise ValueError(f"Unknown input_type: {input_type}")
+
+    with BlockLogs():
+        result = [converter(mol) if mol is not None else None for mol in molecules]
+
+    return result
+
+
+@given(
+    parsers.re(
+        r"a list of (?P<num>\d+) random molecules(?:, where(?P<conditions>[\s\S]*))?"
+    ),
+    target_fixture="molecules",
+)
+def molecules(num, conditions, random_seed=0):
+    num = int(num)
+
+    filters = []
+    maps = []
+
+    if conditions is not None:
+        def filter_weight(min_weight, max_weight):
+            min_weight = float(min_weight)
+            max_weight = float(max_weight)
+            return lambda mol: (min_weight <= CalcExactMolWt(mol) <= max_weight)
+
+        def map_to_none(num_none):
+            num_none = int(num_none)
+
+            # draw indices of molecules that should be set to None
+            indices = np.random.choice(num, num_none, replace=False)
+
+            return lambda ms: [m if i not in indices else None for i, m in enumerate(ms)]
+
+        expressions = [
+            # filters are functions that return True if the molecule should be kept
+            ("filter", r"each mol has a weight between (?P<min_weight>\d+) and (?P<max_weight>\d+)", filter_weight),
+            # maps are functions that modify the molecule
+            ("map", r"(?P<num_none>\d+) entries are None", map_to_none)
+        ]
+
+        conditions_list = [c for c in conditions.split("\n") if c.strip() != ""]
+
+        for condition in conditions_list:
+            for kind, expression, f in expressions:
+                # conditions might be a markdown list (starting with a star character)
+                expression = r"\s*(\*\s*)?" + expression + r"\s*"
+
+                match = re.match(expression, condition)
+                if match:
+                    params = match.groupdict()
+                    break
+            
+            assert match is not None, f"Could not parse condition: {condition}"
+
+            if kind == "filter":
+                filters.append(f(**params))
+            elif kind == "map":
+                maps.append(f(**params))
+            else:
+                raise ValueError(f"Unknown kind: {kind}")
+
+    filter_func = lambda mol: all(f(mol) for f in filters)
+    map_func = lambda ms: reduce(lambda ms, f: f(ms), maps, ms)
+
+    result = None
+
+    # pytest-bdd and hypothesis don't play well together (yet)
+    # --> use this workaround to generate random molecules
+    @hgiven(st.lists(mols().filter(filter_func), min_size=num, max_size=num, unique_by=MolToSmiles))
+    @settings(max_examples=1, deadline=None)
+    @seed(random_seed)
+    def generate(ms):
+        nonlocal result
+        result = ms
+
+    generate()
+
+    # apply maps
+    result = map_func(result)
+
+    for m in result:
+        if m is None:
+            continue
+        m.SetProp("_Name", "mol")
+
+    return result

{nerdd_module-0.3.29 → nerdd_module-0.3.31}/nerdd_module.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: nerdd-module
-Version: 0.3.29
+Version: 0.3.31
 Summary: Base package to create NERDD modules
 Author-email: Steffen Hirte <steffen.hirte@univie.ac.at>
 Maintainer-email: Steffen Hirte <steffen.hirte@univie.ac.at>
@@ -87,6 +87,7 @@ Provides-Extra: docs
 Requires-Dist: mkdocs; extra == "docs"
 Requires-Dist: mkdocs-material; extra == "docs"
 Requires-Dist: mkdocstrings; extra == "docs"
+Dynamic: license-file
 
 # NERDD Module
 

{nerdd_module-0.3.29 → nerdd_module-0.3.31}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "nerdd-module"
-version = "0.3.29"
+version = "0.3.31"
 description = "Base package to create NERDD modules"
 readme = "README.md"
 license = { file = "LICENSE" }

nerdd_module-0.3.29/nerdd_module/tests/representations.py

@@ -1,81 +0,0 @@
-import numpy as np
-from hypothesis import given as hgiven
-from hypothesis import seed, settings
-from hypothesis import strategies as st
-# TODO: remove "type: ignore" later
-from hypothesis_rdkit import mols  # type: ignore
-from pytest_bdd import given, parsers
-from rdkit.Chem import MolToInchi, MolToMolBlock, MolToSmiles
-from ..polyfills import BlockLogs
-
-
-@given(parsers.parse("a random seed set to {seed:d}"), target_fixture="random_seed")
-def random_seed(seed):
-    return seed
-
-
-@given(
-    parsers.parse("an input molecule specified by '{input}'"),
-    target_fixture="representations",
-)
-def representations_from_input(input):
-    return [input]
-
-
-@given(
-    parsers.parse("the representations of the molecules in {input_type} format"),
-    target_fixture="representations",
-)
-def representations_from_molecules(molecules, input_type):
-    input_type = input_type.lower()
-
-    if input_type == "smiles":
-        converter = MolToSmiles
-    elif input_type == "mol_block":
-        converter = MolToMolBlock
-    elif input_type == "inchi":
-        converter = MolToInchi
-    elif input_type == "rdkit_mol":
-        converter = lambda mol: mol
-    else:
-        raise ValueError(f"Unknown input_type: {input_type}")
-
-    with BlockLogs():
-        result = [converter(mol) if mol is not None else None for mol in molecules]
-
-    return result
-
-
-@given(
-    parsers.re(
-        r"a list of (?P<num>\d+) random molecules(?:, where (?P<num_none>\d+) entries are None)?"
-    ),
-    target_fixture="molecules",
-)
-def molecules_with_none(num, num_none=None, random_seed=0):
-    num = int(num)
-    num_none = int(num_none) if num_none is not None else 0
-    result = None
-
-    # pytest-bdd and hypothesis don't play well together (yet)
-    # --> use this workaround to generate random molecules
-    @hgiven(st.lists(mols(), min_size=num, max_size=num, unique_by=MolToSmiles))
-    @settings(max_examples=1, deadline=None)
-    @seed(random_seed)
-    def generate(ms):
-        nonlocal result
-        result = ms
-
-    generate()
-
-    for m in result:
-        if m is None:
-            continue
-        m.SetProp("_Name", "mol")
-
-    # replace random entries with None
-    indices = np.random.choice(num, num_none, replace=False)
-    for i in indices:
-        result[i] = None
-
-    return result