Hi Brian,
thanks for your reply. I now figured out the issue. The SDF I load has a
few multi-component entries and I wanted to just look at the first
component to avoid any issues with such molecules.
hence I had following step:
mols = [Chem.GetMolFrags(x, asMols=True)[0] for x in mols]
And this then breaks property for all molecules that where multi-component
but not for the other ones.
I fixed it by reassigning properties. If anyone know a nicer way to do this
would also be good:
for idx in range(0,len(mols)):
mol = mols[idx]
fragments = Chem.GetMolFrags(mol, asMols=True)
if len(fragments) > 1:
first_frag = fragments[0]
for prop in mol.GetPropNames():
first_frag.SetProp(prop, mol.GetProp(prop))
mols[idx]=first_frag
Best Regards,
Joos
2016-01-21 13:26 GMT+01:00 Brian Kelley <fustiga...@gmail.com>:
> Joos,
>
> In your second loop, could you "print repr(prop)"as opposed to "print
> prop" It could be that the name actually has a space in it which the sd
> format supports and can drive one to distraction.
>
> ----
> Brian Kelley
>
> On Jan 21, 2016, at 2:11 AM, Joos Kiener <joos.kie...@gmail.com> wrote:
>
> Hi all,
>
> I have a strange issue. I'm trying to display pairs of molecules (the pair
> has a certain similarity threshold) and show a property for both molecules.
> This is in IPyhton Notebook.
>
> The weird thing is the first molecule of the pair loses all properties:
>
> toShow=[]
>
> lbls=[]
>
> for idx in pairs:
>
> did=dindices[idx]
>
> mol1=und[did[0]] # und = list of molecules loaded from sd-file
>
> mol2=und[did[1]]
>
> toShow.append(mol1)
>
> toShow.append(mol2)
>
> lbls.append('Active: %.2f'%mol1.GetProp('Activ'))
>
> lbls.append('Active: %.2f'%mol2.GetProp('Activ'))
>
> Draw.MolsToGridImage(toShow,molsPerRow=2,legends=lbls)
>
> ---------------------------------------------------------------------------KeyError
> Traceback (most recent call
> last)<ipython-input-35-c0b7b4dd1606> in <module>() 7
> toShow.append(mol1) 8 toShow.append(mol2)----> 9
> lbls.append('Active: %.2f'%mol1.GetProp('Activ')) 10
> lbls.append('Active: %.2f'%mol2.GetProp('Activ')) 11
> Draw.MolsToGridImage(toShow,molsPerRow=2,legends=lbls)
> KeyError: 'Activ'
>
> If I change the code (remove the label) and print all properties of mol1, the
> are displayed correctly.
>
> toShow=[]
> lbls=[]
> for idx in pairs:
> did=dindices[idx]
> mol1=und[did[0]]
> mol2=und[did[1]]
> toShow.append(mol1)
> toShow.append(mol2)
> for prop in mol1.GetPropNames():
> print prop + ": " + mol1.GetProp(prop)
> #lbls.append('Active: %.2f'%mol1.GetProp('Activ'))
> #lbls.append('Active: %.2f'%mol2.GetProp('Activ'))
> Draw.MolsToGridImage(toShow,molsPerRow=2)
>
> This shows all the properties of mol1 plus draws the grid. No error.
>
> However directly accessing the property by name fails with key error:
>
> toShow=[]
>
> lbls=[]
>
> for idx in pairs:
>
> did=dindices[idx]
>
> mol1=und[did[0]]
>
> mol2=und[did[1]]
>
> toShow.append(mol1)
>
> toShow.append(mol2)
>
> print mol1.GetProp('Activ')
>
> #lbls.append('Active: %.2f'%mol1.GetProp('Activ'))
>
> #lbls.append('Active: %.2f'%mol2.GetProp('Activ'))
>
> Draw.MolsToGridImage(toShow,molsPerRow=2)
>
> ---------------------------------------------------------------------------KeyError
> Traceback (most recent call
> last)<ipython-input-46-b8538426dd74> in <module>() 7
> toShow.append(mol1) 8 toShow.append(mol2)----> 9 print
> mol1.GetProp('Activ') 10 #lbls.append('Active:
> %.2f'%mol1.GetProp('Activ')) 11 #lbls.append('Active:
> %.2f'%mol2.GetProp('Activ'))
> KeyError: 'Activ'
>
>
> This all works fine for mol2:
>
> toShow=[]
>
> lbls=[]
>
> for idx in pairs:
>
> did=dindices[idx]
>
> mol1=und[did[0]]
>
> mol2=und[did[1]]
>
> toShow.append(mol1)
>
> toShow.append(mol2)
>
> print mol2.GetProp('Activ')
>
> #lbls.append('Active: %.2f'%mol1.GetProp('Activ'))
>
> #lbls.append('Active: %.2f'%mol2.GetProp('Activ'))
>
> Draw.MolsToGridImage(toShow,molsPerRow=2)
>
> 2.5
> 7.7
> 10.93
> 2.0434
> 190.0
> 25.0
> ...
>
> What is going on here??? How can I resolve this?
>
> Best Regards,
>
> Joos
>
>
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