[Biopython-dev] Additions to SeqUtils

Yair Benita Y.Benita at pharm.uu.nl
Wed Aug 6 03:04:55 EDT 2003

Here is an update to the molecular weight functions in ProtParam:
   # Calculate MW from Protein sequence
    def molecular_weight (self):
        # make local dictionary for speed
        MwDict = {}
        # remove a molecule of water from the amino acid weights.
        for i in IUPACData.protein_weights.keys():
            MwDict[i] = IUPACData.protein_weights[i] - 18.02
        MW = 18.02 # add just one water molecule for the whole sequence.
        for i in self.sequence:
            MW += MwDict[i]
        return MW

on 4/8/03 16:16, Yair Benita at Y.Benita at pharm.uu.nl wrote:

> Hi All,
> As promised a few days ago I submit code to be added to the SeqUtils module.
> The modules include:
> Codon adaptation index -> for DNA sequence
> Protein analysis methods such as isoelectric point, molecular weight and
> more. Take a look.
> You just have to change the import statement at the top to fit the location
> you use for the module.
> I would appreciate any comments or feedback.
> Thanks,
> Yair

Yair Benita
Pharmaceutical Proteomics
Faculty of Pharmacy
Utrecht University

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