feat: add rdkit functions + add pubchem spectra and GHS functions

src/chemenv/modal_app.py

@@ -1,25 +1,32 @@
-from modal import App, Image
+from modal import App
 from chemenv.tools.cheminformatics import (
+    rdkit_image,
+    mendeleev_image,
     get_tanimoto_similarity as _get_tanimoto_similarity,
     get_number_of_topologically_distinct_atoms as _get_topologically_distinct_atoms,
     get_element_info as _get_element_info,
+    _get_number_atoms,
+    _get_number_heavy_atoms,
+    _get_canonical_smiles,
+    _get_compound_charge,
+    _get_number_rings,
+    _get_number_aromatic_rings,
+    _get_aromatic_rings,
+    _get_ring_sizes,
+    _get_chiral_centers,
+    _get_number_chiral_centers,
+    _get_number_cis_bonds,
+    _get_number_trans_bonds,
+    _get_molecular_properties,
+    _has_substructure,
+    _get_substructure_count,
 )
 from chemenv.tools.pubchem import (
     PubChem,
     pubchem_image as _pubchem_image,
 )
-from chemenv.tools.pubchem import (
-    Smiles2Name as _Smiles2Name,
-    converters_image as _converters_image,
-)
 import os
 
-# Define the images
-rdkit_image = (
-    Image.debian_slim(python_version="3.12").pip_install("rdkit").pip_install("numpy")
-)
-mendeleev_image = Image.debian_slim().pip_install("mendeleev")
-
 chemenv_name = os.getenv("CHEMENV_NAME", "")
 if chemenv_name and not chemenv_name.startswith("-"):
     chemenv_name = f"-{chemenv_name}"
@@ -38,13 +45,88 @@ def get_number_of_topologically_distinct_atoms(*args, **kwargs):
     return _get_topologically_distinct_atoms(*args, **kwargs)
 
 
+@app.function(image=rdkit_image)
+def get_number_atoms(*args, **kwargs):
+    return _get_number_atoms(*args, **kwargs)
+
+
+@app.function(image=rdkit_image)
+def get_number_heavy_atoms(*args, **kwargs):
+    return _get_number_heavy_atoms(*args, **kwargs)
+
+
+@app.function(image=rdkit_image)
+def get_canonical_smiles(*args, **kwargs):
+    return _get_canonical_smiles(*args, **kwargs)
+
+
+@app.function(image=rdkit_image)
+def get_compound_charge(*args, **kwargs):
+    return _get_compound_charge(*args, **kwargs)
+
+
+@app.function(image=rdkit_image)
+def get_number_rings(*args, **kwargs):
+    return _get_number_rings(*args, **kwargs)
+
+
+@app.function(image=rdkit_image)
+def get_ring_sizes(*args, **kwargs):
+    return _get_ring_sizes(*args, **kwargs)
+
+
+@app.function(image=rdkit_image)
+def get_number_aromatic_rings(*args, **kwargs):
+    return _get_number_aromatic_rings(*args, **kwargs)
+
+
+@app.function(image=rdkit_image)
+def get_aromatic_rings(*args, **kwargs):
+    return _get_aromatic_rings(*args, **kwargs)
+
+
+@app.function(image=rdkit_image)
+def get_chiral_centers(*args, **kwargs):
+    return _get_chiral_centers(*args, **kwargs)
+
+
+@app.function(image=rdkit_image)
+def get_number_chiral_centers(*args, **kwargs):
+    return _get_number_chiral_centers(*args, **kwargs)
+
+
+@app.function(image=rdkit_image)
+def get_number_cis_bonds(*args, **kwargs):
+    return _get_number_cis_bonds(*args, **kwargs)
+
+
+@app.function(image=rdkit_image)
+def get_number_trans_bonds(*args, **kwargs):
+    return _get_number_trans_bonds(*args, **kwargs)
+
+
+@app.function(image=rdkit_image)
+def get_molecular_properties(*args, **kwargs):
+    return _get_molecular_properties(*args, **kwargs)
+
+
+@app.function(image=rdkit_image)
+def has_substructure(*args, **kwargs):
+    return _has_substructure(*args, **kwargs)
+
+
+@app.function(image=rdkit_image)
+def get_substructure_count(*args, **kwargs):
+    return _get_substructure_count(*args, **kwargs)
+
+
 @app.function(image=mendeleev_image)
 def get_element_info(*args, **kwargs):
     return _get_element_info(*args, **kwargs)
 
 
 @app.function(image=_pubchem_image)
-async def get_number_atoms(compound_id: str) -> int:
+async def get_number_atoms_pubchem(compound_id: str) -> int:
     pubchem = await PubChem.create(compound_id)
     number_atoms = await pubchem._get_number_atoms()
     if number_atoms is None:
@@ -53,7 +135,7 @@ async def get_number_atoms(compound_id: str) -> int:
 
 
 @app.function(image=_pubchem_image)
-async def get_isomeric_smiles(compound_id: str) -> str:
+async def get_isomeric_smiles_pubchem(compound_id: str) -> str:
     pubchem = await PubChem.create(compound_id)
     isomeric_smiles = await pubchem._get_isomeric_smiles()
     if isomeric_smiles is None:
@@ -62,7 +144,7 @@ async def get_isomeric_smiles(compound_id: str) -> str:
 
 
 @app.function(image=_pubchem_image)
-async def get_canonical_smiles(compound_id: str) -> str:
+async def get_canonical_smiles_pubchem(compound_id: str) -> str:
     pubchem = await PubChem.create(compound_id)
     smiles = await pubchem._get_canonical_smiles()
     if smiles is None:
@@ -71,7 +153,7 @@ async def get_canonical_smiles(compound_id: str) -> str:
 
 
 @app.function(image=_pubchem_image)
-async def get_compound_mass(compound_id: str) -> float:
+async def get_compound_mass_pubchem(compound_id: str) -> float:
     pubchem = await PubChem.create(compound_id)
     molecular_weight = await pubchem._get_compound_mass()
     if molecular_weight is None:
@@ -80,7 +162,7 @@ async def get_compound_mass(compound_id: str) -> float:
 
 
 @app.function(image=_pubchem_image)
-async def get_compound_charge(compound_id: str) -> int:
+async def get_compound_charge_pubchem(compound_id: str) -> int:
     pubchem = await PubChem.create(compound_id)
     charge = await pubchem._get_compound_charge()
     if charge is None:
@@ -89,7 +171,7 @@ async def get_compound_charge(compound_id: str) -> int:
 
 
 @app.function(image=_pubchem_image)
-async def get_compound_formula(compound_id: str) -> str:
+async def get_compound_formula_pubchem(compound_id: str) -> str:
     pubchem = await PubChem.create(compound_id)
     formula = await pubchem._get_compound_formula()
     if formula is None:
@@ -98,7 +180,7 @@ async def get_compound_formula(compound_id: str) -> str:
 
 
 @app.function(image=_pubchem_image)
-async def get_number_isomers(compound_id: str) -> int:
+async def get_number_isomers_pubchem(compound_id: str) -> int:
     pubchem = await PubChem.create(compound_id)
     number_isomers = await pubchem._get_number_isomers()
     if number_isomers is None:
@@ -107,7 +189,7 @@ async def get_number_isomers(compound_id: str) -> int:
 
 
 @app.function(image=_pubchem_image, timeout=86399)
-async def get_compound_isomers(*args, **kwargs):
+async def get_compound_isomers_pubchem(*args, **kwargs):
     pubchem = await PubChem.create(*args, **kwargs)
     data = await pubchem._get_compound_isomers()
     if data is None:
@@ -116,7 +198,7 @@ async def get_compound_isomers(*args, **kwargs):
 
 
 @app.function(image=_pubchem_image)
-async def get_number_heavy_atoms(compound_id: str) -> int:
+async def get_number_heavy_atoms_pubchem(compound_id: str) -> int:
     pubchem = await PubChem.create(compound_id)
     number_heavy_atoms = await pubchem._get_number_heavy_atoms()
     if number_heavy_atoms is None:
@@ -125,18 +207,54 @@ async def get_number_heavy_atoms(compound_id: str) -> int:
 
 
 @app.function(image=_pubchem_image)
-async def _get_number_chiral_atoms(compound_id: str) -> int:
+async def get_number_chiral_atoms_pubchem(compound_id: str) -> int:
     pubchem = await PubChem.create(compound_id)
     number_chiral_atoms = await pubchem._get_number_chiral_atoms()
     if number_chiral_atoms is None:
         raise ValueError("No chiral atoms found")
     return number_chiral_atoms
 
 
-@app.function(image=_converters_image)
-async def get_iupac_name(smiles: str) -> str:
-    converter = _Smiles2Name(smiles)
-    name = await converter.get_name()
-    if name is None:
-        return ""
-    return name
+@app.function(image=_pubchem_image)
+async def get_c_nmr_spectra_pubchem(compound_id: str) -> dict:
+    pubchem = await PubChem.create(compound_id)
+    c_nmr_spectra = await pubchem._get_c_nmr_spectra()
+    if c_nmr_spectra is None:
+        raise ValueError("No C-NMR spectra found")
+    return c_nmr_spectra
+
+
+@app.function(image=_pubchem_image)
+async def get_h_nmr_spectra_pubchem(compound_id: str) -> dict:
+    pubchem = await PubChem.create(compound_id)
+    h_nmr_spectra = await pubchem._get_h_nmr_spectra()
+    if h_nmr_spectra is None:
+        raise ValueError("No H-NMR spectra found")
+    return h_nmr_spectra
+
+
+@app.function(image=_pubchem_image)
+async def get_uv_spectra_pubchem(compound_id: str) -> dict:
+    pubchem = await PubChem.create(compound_id)
+    uv_spectra = await pubchem._get_uv_spectra()
+    if uv_spectra is None:
+        raise ValueError("No UV spectra found")
+    return uv_spectra
+
+
+@app.function(image=_pubchem_image)
+async def get_ms_spectra_pubchem(compound_id: str) -> dict:
+    pubchem = await PubChem.create(compound_id)
+    ms_spectra = await pubchem._get_ms_spectra()
+    if ms_spectra is None:
+        raise ValueError("No MS spectra found")
+    return ms_spectra
+
+
+@app.function(image=_pubchem_image)
+async def get_ghs_classification_pubchem(compound_id: str) -> str:
+    pubchem = await PubChem.create(compound_id)
+    ghs_classification = await pubchem._get_ghs_classification()
+    if ghs_classification is None:
+        raise ValueError("No GHS classification found")
+    return ghs_classification