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BasisSetSelector #30

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220ab1c
basis set selector works for H,He,Li,Be,B,C,N,O,F,Ne,Na,Mg,Al,Si,P,S,…
Sep 16, 2022
a62cb64
multi-atom systems setup using addition of hartree energies
Sep 16, 2022
3230f0a
added pdb input capability
Sep 16, 2022
a1bee48
added additive homo-lumo to help pick basis sets that find the lowest…
Sep 16, 2022
7c7a45e
made the basis set selector command line usable
Sep 16, 2022
3cdec87
made the basis set selector command line usable
Sep 16, 2022
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64 changes: 64 additions & 0 deletions BasisSetSelector/basissetselector.py
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import pandas as pd
from rdkit.Chem import AllChem as Chem
import sys
from ast import literal_eval

def find_precision(theoretical, experimental):
return abs((theoretical-experimental)/experimental)

def find_optimal_basis_sets(smile, precisionInPercent, homoLumoConvergance):
bestBasisSets = []
bestHomoLumo = []
precisionDecimal = precisionInPercent / 100
groundStateDF = pd.read_csv("groundstateenergies.csv",index_col=0)
if(".pdb" in smile):
mol = Chem.MolFromPDBFile(smile)
else:
mol = Chem.MolFromSmiles(smile)
arrayOfAtomsInSmile = [atom.GetSymbol() for atom in mol.GetAtoms()]
groundStateSum = 0
ccpVTZb3lypSum = 0
augccpDZb3lypSum = 0
sixthreeoneb3lypsum = 0
for atom in arrayOfAtomsInSmile:
groundStateSum += groundStateDF["Experimental Ground State Energy from AE17 UMN (Hartree)"][atom]
ccpVTZb3lypSum += groundStateDF["cc-pVTZ + B3LYP"][atom]
sixthreeoneb3lypsum += groundStateDF["6-31G + B3LYP"][atom]
augccpDZb3lypSum += groundStateDF["aug-cc-pVDZ + B3LYP"][atom]

if(find_precision(ccpVTZb3lypSum,groundStateSum) <= precisionDecimal):
bestBasisSets.append("cc-pVTZ + B3LYP")
if(find_precision(sixthreeoneb3lypsum,groundStateSum) <= precisionDecimal):
bestBasisSets.append("6-31G + B3LYP")
if(find_precision(augccpDZb3lypSum,groundStateSum) <= precisionDecimal):
bestBasisSets.append("aug-cc-pVDZ + B3LYP")
if((find_precision(ccpVTZb3lypSum,groundStateSum) > precisionDecimal) and (find_precision(sixthreeoneb3lypsum,groundStateSum) > precisionDecimal) and (find_precision(augccpDZb3lypSum,groundStateSum) > precisionDecimal)):
bestBasisSets.append("cc-pVTZ + B3LYP,6-31G + B3LYP, and aug-cc-pVDZ + B3LYP are too imprecise. Please try another basis set")

if homoLumoConvergance == "homoLumoConvergance":
g3HomoLumoSum= 0
ccpVTZb3lypHomoLumoSum = 0
augccpDZb3lypHomoLumoSum = 0
sixthreeoneb3lypHomoLumosum = 0
for atom in arrayOfAtomsInSmile:
g3HomoLumoSum += groundStateDF["Gaussian3 (G3) HOMO-LUMO gap"][atom]
ccpVTZb3lypHomoLumoSum += groundStateDF["cc-pVTZ + B3LYP HOMO-LUMO gap"][atom]
sixthreeoneb3lypHomoLumosum += groundStateDF["6-31G + B3LYP HOMO-LUMO gap"][atom]
augccpDZb3lypHomoLumoSum += groundStateDF["aug-cc-pVDZ + B3LYP HOMO-LUMO gap"][atom]
minConvergance = min([g3HomoLumoSum,ccpVTZb3lypHomoLumoSum,augccpDZb3lypHomoLumoSum,sixthreeoneb3lypHomoLumosum])
if g3HomoLumoSum == minConvergance:
bestHomoLumo.append("Gaussian3 (G3)")
if ccpVTZb3lypHomoLumoSum == minConvergance:
bestHomoLumo.append("cc-pVTZ + B3LYP")
if sixthreeoneb3lypHomoLumosum == minConvergance:
bestHomoLumo.append("6-31G + B3LYP")
if augccpDZb3lypHomoLumoSum == minConvergance:
bestHomoLumo.append("aug-cc-pVDZ + B3LYP")
outputJSON = {"Best Basis Sets Based on Ground State Precision": bestBasisSets, "Best Basis Sets Based on HOMO-LUMO Gap Convergance": bestHomoLumo}
return outputJSON

if __name__ == '__main__':
if len(sys.argv) < 2:
print("Syntax: python basissetselector.py [.pdb file name location or smiles string] [percetage of precision wihtout %] [homoLumoConverganceif you want check for the HOMO-LUMO convergance]")
else:
print(find_optimal_basis_sets(sys.argv[1], literal_eval(sys.argv[2]), sys.argv[3]))
18 changes: 18 additions & 0 deletions BasisSetSelector/groundstateenergies.csv
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Element/Compound,Experimental Ground State Energy from AE17 UMN (Hartree),cc-pVTZ + B3LYP,6-31G + B3LYP,aug-cc-pVDZ + B3LYP,Gaussian3 (G3) HOMO-LUMO gap,cc-pVTZ + B3LYP HOMO-LUMO gap,6-31G + B3LYP HOMO-LUMO gap,aug-cc-pVDZ + B3LYP HOMO-LUMO gap
H,-0.50000,-0.502156,-0.500273,-0.501657,1.414,0.567,1.027,0.356
He,-2.90372,-2.914507,-2.907049,-2.909096,1.100,1.023,1.631,0
Li,-7.47806,-7.492016,-7.490902,-7.491452,0.207,0,0.108,0
Be,-14.66736,-14.672445,-14.668063,-14.671272,0.331,0,0.188,0
B,-24.65391,-24.663753,-24.652810,-24.661583,0.335,0.092,0.092,0.091
C,-37.84500,-37.858574,-37.843662,-37.854195,0.446,0.113,0.111,0.111
N,-54.58920,-54.601781,-54.582875,-54.593843,0.705,0.778,0.977,0.416
O,-75.06730,-75.091863,-75.058330,-75.077162,1.482,0.899,1.163,0.469
F,-99.73390,-99.762866,-99.713650,-99.739495,0.941,1.121,1.525,0.591
Ne,-128.93760,-128.961856,-128.894298,-128.927993,0.664,1.419,1.950,0.724
Na,-162.25460,-162.296979,-162.279879,-162.290737,0,0,0.109,0
Mg,-200.05300,-200.097698,-200.077941,-200.091270,0.274,0,0.164,0
Al,-242.34600,-242.389511,-242.365764,-242.383457,0.238,0.056,0.054,0.056
Si,-289.35900,-289.396332,-289.368888,-289.389841,0.287,0.066,0.062,0.065
P,-341.25900,-341.285850,-341.255345,-341.278393,0.461,0.494,0.475,0.283
S,-398.11000,-398.138716,-398.100687,-398.127993,0.494,0.555,0.539,0.319
Cl,-460.14800,-460.174665,-460.131370,-460.161474,0.992,0.663,0.681,0.401
38 changes: 38 additions & 0 deletions BasisSetSelector/proline.pdb
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COMPND 145742
AUTHOR GENERATED BY OPEN BABEL 3.1.0
ATOM 1 O PRO A 1 2.162 -0.951 -0.112 1.00 0.00 O
ATOM 2 OXT PRO A 1 1.569 1.216 -0.495 1.00 0.00 O
ATOM 3 N PRO A 1 -0.781 0.931 0.777 1.00 0.00 N
ATOM 4 CA PRO A 1 0.083 -0.248 0.725 1.00 0.00 C
ATOM 5 CB PRO A 1 -0.724 -1.317 -0.003 1.00 0.00 C
ATOM 6 CG PRO A 1 -1.989 -0.611 -0.475 1.00 0.00 C
ATOM 7 CD PRO A 1 -1.650 0.864 -0.393 1.00 0.00 C
ATOM 8 C PRO A 1 1.329 0.115 -0.024 1.00 0.00 C
ATOM 9 HA PRO A 1 0.362 -0.552 1.739 1.00 0.00 H
ATOM 10 HB1 PRO A 1 -0.987 -2.143 0.667 1.00 0.00 H
ATOM 11 HB2 PRO A 1 -0.192 -1.741 -0.862 1.00 0.00 H
ATOM 12 HG1 PRO A 1 -2.280 -0.916 -1.485 1.00 0.00 H
ATOM 13 HG2 PRO A 1 -2.819 -0.849 0.202 1.00 0.00 H
ATOM 14 HD1 PRO A 1 -1.120 1.193 -1.294 1.00 0.00 H
ATOM 15 HD2 PRO A 1 -2.542 1.483 -0.269 1.00 0.00 H
ATOM 16 H PRO A 1 -0.251 1.800 0.802 1.00 0.00 H
ATOM 17 H PRO A 1 2.984 -0.734 -0.601 1.00 0.00 H
CONECT 1 8 17
CONECT 2 8 8
CONECT 3 4 7 16
CONECT 4 3 5 8 9
CONECT 5 4 6 10 11
CONECT 6 5 7 12 13
CONECT 7 3 6 14 15
CONECT 8 1 2 2 4
CONECT 9 4
CONECT 10 5
CONECT 11 5
CONECT 12 6
CONECT 13 6
CONECT 14 7
CONECT 15 7
CONECT 16 3
CONECT 17 1
MASTER 0 0 0 0 0 0 0 0 17 0 17 0
END