Joos,
I'm glad you found the issue. Perhaps GetMolFrags should retain or have an
option to retain public properties such as sd data.
----
Brian Kelley
> On Jan 21, 2016, at 8:14 AM, Joos Kiener <joos.kie...@gmail.com> wrote:
>
> 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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