Re: [Rdkit-discuss] Molecule losing properties

2016-01-21 Thread Brian Kelley 
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  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 :
>> 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  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)
>>>  in ()
>>>   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)
>>>  in ()
>>>   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
>>> --
>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>> APM + Mobile APM + RUM: Monitor

Re: [Rdkit-discuss] Molecule losing properties

2016-01-21 Thread Brian Kelley 
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  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)
>  in ()
>   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)
>  in ()
>   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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[Rdkit-discuss] Molecule losing properties

2016-01-20 Thread 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) in ()  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) in ()  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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APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
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