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When fetching a mol from PubChem, use 2d pos if 3d pos not found #115

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Oct 9, 2023
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When fetching a mol from PubChem, use 2d pos if 3d pos not found #115

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13 changes: 9 additions & 4 deletions pyscf_ipu/nanoDFT/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -57,12 +57,16 @@ def get_mol_str_pubchem(entry: str):
'entry' is interpreted as Compound ID if it is a string of digits or as
name of a compound otherwise"""

if entry.isdigit(): # If all digits, we assume it is a CID
if entry.isdigit(): # If all digits, we assume it is a CID
print(f"Searching in PubChem for CID '{entry}'")
compound = pubchempy.get_compounds(entry, "cid", record_type='3d')
else:
print(f"Searching in PubChem for compound with name '{entry}'") # if not, we assume it is a name
if len(compound) == 0:
compound = pubchempy.get_compounds(entry, 'cid', record_type='2d')
else: # if not, we assume it is a name
print(f"Searching in PubChem for compound with name '{entry}'")
compound = pubchempy.get_compounds(entry, 'name', record_type='3d')
if len(compound) == 0:
compound = pubchempy.get_compounds(entry, 'name', record_type='2d')
mol_str = []
if len(compound) > 1:
print("INFO: PubChem returned more than one compound; using the first...", file=sys.stderr)
Expand All @@ -71,7 +75,8 @@ def get_mol_str_pubchem(entry: str):
return None
print(f"Found compound: {compound[0].synonyms[0]}")
for a in compound[0].atoms:
mol_str.append((a.element,np.array([a.x, a.y, a.z])))
z = a.z or 0.0
mol_str.append((a.element,np.array([a.x, a.y, z])))
return mol_str


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