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xyz2mol implementation bug: DetermineBonds #8006

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simonmb opened this issue Nov 14, 2024 · 1 comment
Open

xyz2mol implementation bug: DetermineBonds #8006

simonmb opened this issue Nov 14, 2024 · 1 comment
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@simonmb
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simonmb commented Nov 14, 2024 •
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Describe the bug
the xyz2mol implementation in C mostly works for me, but for some xyz files it fails. My goal is to get the molecule from the smiles with a conformer based on the xyz. The example xyz file is below.

To Reproduce

from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import rdDetermineBonds

mol_from_SMILES = Chem.MolFromSmiles('CCCCCCCOc1ccc([N+](=O)[O-])cc1')
xyz_file = 'C13H19NO3_002_pnitrophenylheptylether_CnfS1.xyz'
xyz_mol = Chem.MolFromXYZFile(xyz_file)
rdDetermineBonds.DetermineBonds(xyz_mol, charge=0)
mol = AllChem.AssignBondOrdersFromTemplate(mol_from_SMILES, xyz_mol)

I am however getting the following error when DetermineBonds is run.

Final molecular charge (0) does not match input (-1); could not find valid bond ordering

If I run it using xy2mol, it works:

from xyz2mol import read_xyz_file, xyz2AC
atoms, charge, xyz_coordinates = read_xyz_file(xyz_file)
AC, xyz_mol = xyz2AC(atoms, xyz_coordinates, charge, use_huckel=True)
xyz_mol = Chem.RWMol(xyz_mol)
num_atoms = len(atoms)
for i in range(num_atoms):
    for j in range(i + 1, num_atoms): 
        if AC[i, j] == 1: 
            xyz_mol.AddBond(i, j, Chem.BondType.SINGLE)

mol = AllChem.AssignBondOrdersFromTemplate(mol_from_SMILES, xyz_mol)

Expected behavior
To get a mol with the correct Bonds and one Conformer based on the xyz.

Configuration:

  • RDKit version: 2024.09.1
  • OS: Win 11
  • Python version: 3.11.10
  • Are you using conda Yes, conda-forge
36

C  6.7913196335158501  -0.0448658610313100  0.6657633907078100
C  5.5796381893814502  0.0286675414187900  -0.2684145174546900
C  4.2393604310803497  -0.0268361981844300  0.4740726099932200
C  3.0209198674193800  0.0461533883047300  -0.4526702721837300
C  1.6831508946885501  -0.0109972306435300  0.2938834443797200
C  0.4715355465812700  0.0619997665046200  -0.6440958470506800
C  -0.8373788426356100  -0.0025410445776800  0.1221825576599700
O  -1.9234903022157599  0.0744104271091800  -0.8443248910804400
C  -3.1967180889728302  0.0355514345059300  -0.4009512081350500
C  -3.5642017909650900  -0.0746528518264800  0.9568073026649900
C  -4.9093297646275298  -0.1027946723510800  1.3045262937822999
C  -5.8877832777109198  -0.0227785871984700  0.3067001376863000
N  -7.2898630556333899  -0.0523339321938400  0.6785328450866200
O  -7.5874020266485296  -0.1410161538239700  1.8841807259675400
O  -8.1465471065379607  0.0124377451498300  -0.2225949913409100
C  -5.5342118890905603  0.0851213115809600  -1.0486319366136800
C  -4.1962487433409299  0.1141128838685000  -1.3975903430146399
H  7.7367790466899500  -0.0012604384347300  0.1049228998036600
H  6.7886991932650700  0.7903828120833700  1.3835407433032700
H  6.7884765650123100  -0.9811060759438101  1.2456323017121600
H  5.6236830224402103  -0.7995824244997400  -0.9966377145403600
H  5.6265729985551696  0.9593458727186900  -0.8600155348830300
H  4.1941040444386299  0.8026443577320700  1.2025062103669799
H  4.1911904380928302  -0.9580669195484099  1.0666987824009400
H  3.0676705916069902  0.9779253848865400  -1.0437696879672000
H  3.0657025514730400  -0.7830874863276700  -1.1807365251127500
H  1.6342544344790799  -0.9429248137014300  0.8835755621494200
H  1.6354285103149500  0.8187497301540700  1.0203984671524600
H  0.5039238206117000  0.9985901513697600  -1.2244550736297299
H  0.5072105009306700  -0.7699767718181200  -1.3663598959181800
H  -0.9301330721560700  0.8384182958424300  0.8282839207205001
H  -0.9274431092730200  -0.9475154040530700  0.6817977895860700
H  -2.8097825732277699  -0.1389389581432300  1.7381943786121801
H  -5.2060178016409404  -0.1875148498490600  2.3484973240248301
H  -6.3095329210376896  0.1458565657286300  -1.8101174146670900
H  -3.8935359148631199  0.1984230051920100  -2.4417193492260001
@simonmb simonmb added the bug label Nov 14, 2024
@simonmb simonmb changed the title xyz2mol implementation bug xyz2mol implementation bug: DetermineBonds Nov 18, 2024
@simonmb
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simonmb commented Nov 18, 2024

I have additionally found, that DetermineBonds completely freezes on the xyz file below:

It happens on the setup as described above but also on AlmaLinux release 8.10, python 3.11.7 and conda-forge rdkit 2024.03.6, while the xyz2mol version still works.

38

O  -4.7025628202143599  -1.8507205184287800  0.3039858372286700
N  -4.2153994361056402  -1.7233996392624999  -0.7949405839041100
O  -4.2705114336889398  -2.4437065089795000  -1.7635635876261300
O  -3.4388382785216902  -0.5160076353212300  -1.0782374702523301
C  -3.2670951603727501  0.3826565430823800  0.0393097517761500
C  -1.8861245279294301  0.2454836801298700  0.6779924520457800
O  -1.6936413893826801  -1.0896876055197899  1.1984618937406999
N  -2.0815889242898900  -1.2685518179715900  2.6123051031258999
O  -2.4988413260261599  -0.3058478680877800  3.2083804426540699
O  -1.9111833255751900  -2.4074529281344601  2.9668979164650300
C  -0.6980247575755100  0.4598938470530900  -0.2963213978786200
O  -0.8625779206994700  1.7603843593598401  -0.8904761268975800
N  -1.0757162355768199  1.7777540130060601  -2.3727687394289401
O  -1.0836759820660000  0.7233920745442400  -2.9536839253428600
O  -1.2120248517968699  2.9065490938642800  -2.7632187880991199
C  0.6722069585550600  0.4102600580062600  0.4110077046657600
O  0.7676263269579300  1.5325050024767599  1.3070956849996500
N  1.0057197220771501  1.1972704757614900  2.7473707017446598
O  1.0831631997253000  2.2010699488347001  3.4042239843335800
O  1.0848549018215199  0.0346786066724300  3.0494187000883701
C  1.8646013520186300  0.5095404045527000  -0.5759999030759100
C  3.2407978503136499  0.5402685118992701  0.0868819404199700
O  3.4608912090774400  -0.6076222397961200  0.9351119277104600
N  4.2857701013328198  -1.6658786768496801  0.3512818922959800
O  4.7671201914592896  -1.4843162758468000  -0.7426263006702400
O  4.3810691004045799  -2.6084193361632102  1.1012764833341000
O  1.7311797749145501  -0.6514580160632500  -1.4275189818972800
N  2.1396965886197101  -0.4413420998424300  -2.8310778667225800
O  2.5299006726248501  0.6566446570080000  -3.1451641901386300
O  2.0136444149573798  -1.4518450695333101  -3.4750286300380999
H  -3.3979089133890601  1.3904685744525700  -0.3768141439565000
H  -4.0485980800122698  0.2080701423807700  0.7884849792367500
H  -1.8243469602732501  0.9781716273387500  1.4964262049281700
H  -0.7150446380922800  -0.3115474985322000  -1.0794910331259899
H  0.7368083270945101  -0.5269577525562700  0.9821287271571700
H  1.7644203380506500  1.4263289105529600  -1.1764466406673100
H  3.3274375122524100  1.4111121127296800  0.7505679591599800
H  4.0267964193309700  0.6022588431824700  -0.6752319773888000

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@simonmb