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Usability fixes for mol_str, min interatomic dist #130

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Usability fixes for mol_str, min interatomic dist #130

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5 changes: 4 additions & 1 deletion pyscf_ipu/nanoDFT/nanoDFT.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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"]
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13 changes: 8 additions & 5 deletions pyscf_ipu/nanoDFT/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
import sys
import h5py
import pubchempy
import pyscf
import numpy as np
from itertools import combinations
from operator import itemgetter
Expand Down Expand Up @@ -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:
Expand Down Expand Up @@ -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):
Expand Down