segmentation fault

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segmentation fault

david.lagorce
Dear all

I am in trouble with some molecules which are ending my script. When I run in a python interpreter with a sample molecule I get that message:

Python 2.6.6 (r266:84292, Feb 11 2011, 09:52:37)
[GCC 4.3.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import pybel
>>> mol = pybel.readstring("smi","[C@]123[C@@]4([C@H]([N](CC5CC5)CC3)C)Cc3c1c(O[C@H]2C(=O)CC4)c(cc3)O)O")
Segmentation Fault

Is someone can help me...?

thanks for all
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Re: segmentation fault

Noel O'Boyle
Administrator
Somethings wrong with the SMILES string. Daylight won't accept it for
example: http://www.daylight.com/daycgi/depict?5b43405d3132335b4340405d34285b4340485d285b4e5d2843433543433529434333294329436333633163284f5b4340485d3243283d4f29434334296328636333294f294f

We should fix the segmentation fault though...

- Noel

On 5 March 2013 16:16, david.lagorce
<[hidden email]> wrote:

> Dear all
>
> I am in trouble with some molecules which are ending my script. When I run
> in a python interpreter with a sample molecule I get that message:
>
> Python 2.6.6 (r266:84292, Feb 11 2011, 09:52:37)
> [GCC 4.3.2] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>>>> import pybel
>>>> mol =
>>>> pybel.readstring("smi","[C@]123[C@@]4([C@H]([N](CC5CC5)CC3)C)Cc3c1c(O[C@H]2C(=O)CC4)c(cc3)O)O")
> Segmentation Fault
>
> Is someone can help me...?
>
> thanks for all
>
>
>
>
> --
> View this message in context: http://forums.openbabel.org/segmentation-fault-tp4656023.html
> Sent from the openbabel-devel mailing list archive at Nabble.com.
>
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Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the  
endpoint security space. For insight on selecting the right partner to
tackle endpoint security challenges, access the full report.
http://p.sf.net/sfu/symantec-dev2dev
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Re: segmentation fault

david.lagorce
Dear Noel,


I am still searching what is wrong with that kind of molecules.
I wrote the problematic molecule in "bug.sdf" and the smiles generated by pybel (the same by babel -i bug.sdf -o bug2.smi) in "bug.smi


The smiles is ok in depiction by Daylight:
http://www.daylight.com/daycgi/depict?5b43405d3132335b4340405d34285b4340485d284e284343332943433d4329436333633163284f5b4340485d3243283d4f29434334296328636333294f294f




Python 2.7.3 (default, Mar 21 2013, 14:15:19)
[GCC 4.3.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import pybel
>>> mol = pybel.readfile("sdf","bug.sdf").next()
>>> mol.write()
'[C@]123[C@@]4([C@H](N(CC3)CC=C)Cc3c1c(O[C@H]2C(=O)CC4)c(cc3)O)O\tNALOXONE\n'
>>>
>>>
>>> pybel.readstring('smi','[C@]123[C@@]4([C@H](N(CC3)CC=C)Cc3c1c(O[C@H]2C(=O)CC4)c(cc3)O)O')
Segmentation fault
>>> mol = pybel.readfile("smi","bug.smi").next()
Segmentation fault


Do you have an idea?

Thanks for all

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Re: segmentation fault

Noel O'Boyle
Administrator
Can you confirm that you're using OB 2.3.2? It works fine for me on Windows:

C:\Users\Noel>python
Python 2.7.1 (r271:86832, Nov 27 2010, 18:30:46) [MSC v.1500 32 bit (Intel)] on
win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import pybel
>>> pybel.readstring('smi','[C@]123[C@@]4([C@H](N(CC3)CC=C)Cc3c1c(O[C@H]2C(=O)CC
4)c(cc3)O)O')
<pybel.Molecule object at 0x02807810>
>>> mol = pybel.readstring('smi','[C@]123[C@@]4([C@H](N(CC3)CC=C)Cc3c1c(O[C@H]2C
>>> mol.write("smi")
'[C@]123[C@@]4([C@H](N(CC1)CC=C)Cc1c2c(O[C@H]3C(=O)CC4)c(cc1)O)O\t\n'
>>>

On 21 March 2013 14:43, david.lagorce
<[hidden email]> wrote:

> Dear Noel,
>
>
> I am still searching what is wrong with that kind of molecules.
> I wrote the problematic molecule in "bug.sdf" and the smiles generated by
> pybel (the same by babel -i bug.sdf -o bug2.smi) in "bug.smi
>
>
> The smiles is ok in depiction by Daylight:
> http://www.daylight.com/daycgi/depict?5b43405d3132335b4340405d34285b4340485d284e284343332943433d4329436333633163284f5b4340485d3243283d4f29434334296328636333294f294f
>
>
>
>
> Python 2.7.3 (default, Mar 21 2013, 14:15:19)
> [GCC 4.3.2] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>>>> import pybel
>>>> mol = pybel.readfile("sdf","bug.sdf").next()
>>>> mol.write()
> '[C@]123[C@@]4([C@H](N(CC3)CC=C)Cc3c1c(O[C@H]2C(=O)CC4)c(cc3)O)O\tNALOXONE\n'
>>>>
>>>>
>>>> pybel.readstring('smi','[C@]123[C@@]4([C@H](N(CC3)CC=C)Cc3c1c(O[C@H]2C(=O)CC4)c(cc3)O)O')
> Segmentation fault
>>>> mol = pybel.readfile("smi","bug.smi").next()
> Segmentation fault
>
>
> Do you have an idea?
>
> Thanks for all
>
>
>
>
>
> --
> View this message in context: http://forums.openbabel.org/segmentation-fault-tp4656023p4656087.html
> Sent from the openbabel-devel mailing list archive at Nabble.com.
>
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> Everyone hates slow websites. So do we.
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