58820b8cdc60dfd492430246b03abc0845b0e470,rdkit_fixer.py,,UFFConstrainedOptimize,#,127

Before Change

    ff = UFFGetMoleculeForceField(submol, vdwThresh=cutoff,
                                  ignoreInterfragInteractions=False)
    for i in fixed_atoms:
        if i in amap:
            ff.AddFixedPoint(amap.index(i))
    ff.Initialize()
    ff.Minimize(energyTol=1e-2, forceTol=1e-2, maxIts=200)

    // get the positions backbone

After Change

    Chem.GetSSSR(submol)
    ff = UFFGetMoleculeForceField(submol, vdwThresh=cutoff,
                                  ignoreInterfragInteractions=False)
    for i, atom_id in enumerate(amap):
        if atom_id not in moving_atoms:
            ff.AddFixedPoint(i)
    ff.Initialize()
    ff.Minimize(energyTol=1e-2, forceTol=1e-2, maxIts=200)

    // get the positions backbone

Instances