Tim Stevens wrote:
>> I have a set of chemAtomSets and a set of atomSets What is the most
>> efficient way to get from the chemAtomsSets to the relevant atomSets. Is
>> it via munging relevant keywords or traversing hierachies in parallel
>>
>
> Not sure what you mean by munging. Anyhow, this is what I'd do:
>
> lookup = {}
>
> for atomSet in atomSets:
> atom = atomSet.findFirstAtom()
> chemAtomSet = atom.chemAtom.chemAtomSet
>
> if chemAtomSet:
> lookup[chemAtomSet] = lookup.get(chemAtomSet, []) + atomSet
>
> chemAtomSet2 = chemAtomSet.chemAtomSet: # E.g ValHg*
> if chemAtomSet2:
> lookup[chemAtomSet2] = lookup.get(chemAtomSet2, []) + atomSet
>
> for chemAtomSet in myChemAtomSets:
> atomSets = lookup.get(chemAtomSet, [])
> ...
>
>
>
>
>> in explanation this is a problem to do with measuring distances on
>> structure which i believe I can ge via getAtomSetsDistance (atomSets1,
>> atomSets2, structure, coordSet=0, method='noe')...
>>
>
> That's the right function, although one should always take care with
> ambiguous prochirals. Depending on what you're doing, sometimes the 'min'
> method is more informative than 'noe'. :-)
>
>
many thanks!
def: munging()
print 'to chew up into a terrible mess'
regards
gary
> T.
>
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> Dr Tim Stevens Email: [log in to unmask]
> Department of Biochemistry [log in to unmask]
> University of Cambridge Phone: +44 1223 766018 (office)
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> -------------------------------------------------------------------------------
> ------ +NH3CH(CH(CH3)OH)C(O)NHCH(CH(CH3)CH2CH3)C(O)NHCH(CH2CH2SCH3)CO2- -------
> -------------------------------------------------------------------------------
>
> .
>
>
--
-------------------------------------------------------------------
Dr Gary Thompson
Astbury Centre for Structural Molecular Biology,
University of Leeds, Astbury Building,
Leeds, LS2 9JT, West-Yorkshire, UK Tel. +44-113-3433024
email: [log in to unmask] Fax +44-113-2331407
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