[Rdkit-discuss] Molecule losing properties

[Joos Kiener]

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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