I am using Python to access the database. So far I have come across an issue I cannot solve:

Occupancy of an atom is not accessible. Whenever I try to access it, I get the following error: AttributeError: 'Atom' object has no attribute 'occupancy'. However, this attribute has been specified in Molecule API documentation. Everything works well for other attributes, e.g. mymolecule.atoms[0].label gives me the label etc., but mymolecule.atoms[0].occupancy returns error.

Additional question: How to understand from stereochemistry point of view atom chirality flag valued 'Mixed'? 

 

Thanks in advance,

T.

 

Dear Toms,

Can you show me an example script where atom.occupancy gives you an error?  The occupancy attribute may be None if the atom has no coordinates, that is for an implicit hydrogen.

I can use it perfectly normally in, for example:

from ccdc import io
csd = io.EntryReader('csd')
mol = csd.molecule('ABABUB')
print('\n'.join('%s: %.4f' % (a, a.occupancy) for a in mol.atoms))

The value 'Mixed' is returned when the algorithm used to determine chirality is unable to come up with an answer.  This can occur when the chiral atom has more than four bonds, for example, atom U1 of AAPUNI.

Best wishes
Richard

Thanks!

I keep getting the same error using the code specified above, but it should be system-related issue then. I am running everything on Arch Linux (Manjaro) for which the product has not been tested. I should switch to another distribution. Interesting, however, that .occupancy seems to be the only one not being recognized, as every other attribute tested returns the corresponding value without any problem.

Hi Toms,

can you let me know what the error message is when you try to access the occupancy attribute, and give me details of your Manjaro operating system?  I'd like to investigate this if I can find an appropriate vagrant virtualbox for it.

Thanks

Richard

Code sample from the terminal:

>>> entry.molecule.atoms[0].label
u'S1'
>>> entry.molecule.atoms[0].occupancy
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
AttributeError: 'Atom' object has no attribute 'occupancy'

I am using the following:

LSB Version: n/a
Distributor ID: ManjaroLinux
Description: Manjaro Linux
Release: 18.0.2
Codename: Illyria

 

Best regards,

Toms

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