Skip to content

05 Structure Checker

Jump to bottom
Levente Nagy edited this page Sep 22, 2026 · 1 revision

Structure Checker

For the concept of Structure Checker in general see Structure Checker User's Guide.

from chemaxon.io import import_mol
from chemaxon.structurechecker import StructureChecker

mol = import_mol('[NH3+]C1=CC(O)=CC=C1.O')
mol

svg

for r in StructureChecker('solvent..moleculecharge').check(mol).results:
    print('Checker name:', r.checker_name)
    print('Atoms:       ', r.atom_indices)
    print('Bonds:       ', r.bond_indices)
Checker name: Solvent Checker
Atoms:        [8]
Bonds:        []
Checker name: Molecule Charge Checker
Atoms:        [0]
Bonds:        []

StructureChecker('solvent..moleculecharge').check(mol).aggregated_colored_mol

svg

StructureChecker('solvent->removeatom..moleculecharge->neutralize').fix(mol).fixed_mol

svg

molecule_with_bond_errors = '''
  Mrv2401 07312513342D          

 10  9  0  0  0  0            999 V2000
   -7.5997    2.4004    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0588    1.4786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1708    1.5754    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4092    1.3850    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7418    1.5754    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0370    1.4496    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3129    1.5754    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5984    1.1629    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8832    2.1457    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5984    1.9879    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  3  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  7 10  1  0  0  0  0
M  END
'''

mol = import_mol(molecule_with_bond_errors)
StructureChecker('bondangle->clean').check(mol).aggregated_colored_mol

svg

StructureChecker('bondangle->clean').fix(mol).fixed_mol

svg

Home

Examples

Clone this wiki locally