J. Clifford Dyer wrote:
>> OK...
>>
>> from the start.
>>
>> im trying to develop a simple command line application for determining
>> the degree of substitution (DS) on a polymer backbone from elemental
>> analysis, i.e., the % weights of different elements in the
>> monomer-substituent compound ( i want each element to give a result and
>> heaviest atoms give the most accurate results).
>>
>> most basic comp chem programs use input files but i dont know anything
>> about file iteration yet and want the program to be as user friendly as
>> possible..i.e. command line prompt. GUI would be great but too much for
>> me at this stage
>>
>> at the start of the script i have 2 dictionaries 1) containing every
>> atom in the periodic table with associated isotopic average masses 2)
>> containing the molecular forumla of the monomer unit...eg for cellulose
>> AGU {'C': 6, 'H': 10, 'O': 5}.
>>
>> the basic steps are
>>
>> 1. calculate the weight percentage values for each atom in the monomer
>> 2. iterate into dictionaries from DS=0 - DS=15 (0.00005 step) the
>> projected % values for the monomer plus substituent, for EACH atom in
>> the compound.
>> 3. find the (local) minimum from each dictionary/atom to give the
>> appropriate DS value.
>>
>> *Note* I have to iterate ALL the values as there is a non-linear
>> relationship between % values and DS due to the different atomic weights
>> The computer seems to cope with this in about 10 seconds with the above
>> parameters and about 8 elements for the iteration step
>>
>>
>
> Since you have a parallel structure for each element, consider using a
> dictionary with the element names as keys:
>
> >>> atomicdata = {}
> >>> for element in 'C','H','U':
> ... atomicdata[element] = getAtomVars(element)
> ...
> >>> print atomicdata
> { 'C': (1, 2), 'H': (4, 5), 'U': (78, 20) }
>
> The first value of each tuple will be your Xaa, and the second value
> will be Xma. Do you really need to keep the names Caa, Cma, Haa, Hma
> around? Instead of Caa, you have atomicdata['C'][0] and Cma becomes
> atomicdata['C'][1]. Completely unambiguous. A bit more verbose,
> perhaps, but you don't have to try to sneak around the back side of the
> language to find the data you are looking for. That's very much against
> the tao. If you really want the names, nest dicts, but don't try to get
> the element name into the keys, because you already have that:
>
> >>> atomicdata = { 'C': { 'aa': 1,
> ... 'ma': 2},
> ... 'H': { 'aa': 4
> ... 'ma': 5},
> ... 'U': { 'aa': 78
> ... 'ma': 20} }
>
> and to get from there to storing all your data for all however many
> steps, change the value of each entry in atomic data from a tuple (or
> dict) to a list of tuples (or dicts).
>
>
> >>> atomicdata = { 'C': [ (1,2), (4,6), (7,8), (20,19) ],
> ... 'H': [ (5,7), (2,986), (3,4) ] }
> >>> atomicdata['H'].append((5,9))
> >>> atomicdata
> { 'C': [ (1, 2), (4, 6), (7, 8), (20, 19) ], 'H': [ (5, 7), (2, 986),
> (3, 4), (5, 9) ] }
>
> You can build up those lists with nested for loops. (one tells you which
> element you're working on, the other which iteration).
>
> The indexes of your lists, of course, will not correspond to the DS
> values, but to the step number. To get back to the DS number, of
> course, let the index number be i, and calculate DS = i * 0.00005
>
> That should get you off and running now. Happy pythoning!
>
> Cheers,
> Cliff
>
Thanks Cliff,
this is what i need, it seems to make much more sense to do this way. I
think once i learn to include datastructures within each other im gonna
try to make up this 3D 'array' (i think this is a word from C, is there
a python equivalent?) of further iterations within each iteration to
take into account the excess water. For this i think ill have to add
another 100 values onto the values i already have, i.e. 1.8x10**8
entries in total and god knows how many calculations in potentially one
datastructure. Could my computer cope with this or should i try a series
of refinement iterations? Does anyone knows of a simple way of
determining how much processer time it takes to do these calculations?
thanks
a
--
Dr. Alistair King
Research Chemist,
Laboratory of Organic Chemistry,
Department of Chemistry,
Faculty of Science
P.O. Box 55 (A.I. Virtasen aukio 1)
FIN-00014 University of Helsinki
Tel. +358 9 191 50392, Mobile +358 (0)50 5279446
Fax +358 9 191 50366
--
http://mail.python.org/mailman/listinfo/python-list
