usability fixes for mol_str, min interatomic dist

pyscf_ipu/nanoDFT/nanoDFT.py

@@ -601,7 +601,10 @@ def nanoDFT_options(
     if mol_str is None:
         exit(1)
 
-    print(f"Minimum interatomic distance: {utils.min_interatomic_distance(mol_str)}") # TODO: dies for --mol_str methane
+    m_i_d = utils.min_interatomic_distance(mol_str)
+    print(f"Minimum interatomic distance: {m_i_d}") # TODO: dies for --mol_str methane
+    if m_i_d < 0.7 or m_i_d > 1.8:
+        print("WARNING: the coordinates may be expressed in units other than angstrom")
 
     args = locals()
     mol_str = args["mol_str"]

pyscf_ipu/nanoDFT/utils.py

@@ -3,6 +3,7 @@
 import sys
 import h5py
 import pubchempy
+import pyscf
 import numpy as np
 from itertools import combinations
 from operator import itemgetter
@@ -63,15 +64,15 @@ def get_mol_str_pubchem(entry: str):
         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}'")
+        print(f"Searching in PubChem by name")
         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)
     elif len(compound) == 0:
-        print(f"No compound found with the name '{entry}' in PubChem")
+        print(f"No compound found in PubChem by CID or by name")
         return None
     print(f"Found compound: {compound[0].synonyms[0]}") 
     for a in compound[0].atoms:
@@ -138,9 +139,11 @@ def process_mol_str(mol_str: str):
     elif mol_str in spice_amino_acids:
         mol_str = get_mol_str_spice_aa(mol_str)
     else:
-        mol_str = get_mol_str_pubchem(mol_str)
-
-    return mol_str
+        mol_str_pubchem = get_mol_str_pubchem(mol_str)
+        if mol_str_pubchem is not None:
+            return mol_str_pubchem
+
+    return pyscf.gto.mole.Mole().format_atom(mol_str)
 
 
 def min_interatomic_distance(mol_str):