The Proteins package is an application of the ChemMW package. The Proteins object returns the mass of a protein, with its appropriate significant digits, by either parsing a string of a protein sequence, or by parsing a FASTA-formatted file. This is applied in the Codons module for genome-scale biology and bioengineering.

Proteins

This class determines the MW of a protein sequence, after the initial parameters are specified:

import chemw
protein_mass = chemw.Proteins(verbose = False, printing = True)

  • verbose & printing bool: specifies whether troubleshooting information or MW results will be printed, respectively.

Returns protein_mass float: The mass of the parameterized protein sequence to the appropriate significant digitsthat are alloted by those of the elemental masses.

mass()

The parameterized data is fitted to the Hill equation, with the following arguments and their default values:

protein.mass(protein_sequence = None,  fasta_path = None, fasta_link = None  # providing the link to a FASTA file as a string = None)

  • protein_sequence str: The protein sequence, with any combination of upper-case or lower-case letters, for which the MW is desired. The acceptable formats for the formula are quite broad, which are exemplified in the following formulae:

Example sequence

Format option

'LFCTHGLERVVZCLWHKRCCSTRLKSLLLRGCABC*'

A single string of the one-letter amino acid codes. A trailing “*” is acceptable.

'gly-gln-his-ala-arg-asn-phe-pro-thr'

A sequence of three-letter amino acid codes must be delimited with hyphens.

  • fasta_path & fasta_link str: The path and URL link, respectively, to a FASTA file that contains the sequence, or multiple sequences, of the protein(s) for which the MW is desired. Each sequence must commence with a > as the first character of the description line.

Accessible content

The Proteins object retains numerous components that are accessible to the user:

  • protein_mass str: The protein mass with the appropriate quantity of significant digits, which should be used for printing and storing the mass value.

  • raw_protein_mass float: The protein mass without consideration of significant digits, which should be used for calculations.

  • fasta_protein_masses dict: A dictionary of each sequence from processing a FASTA file, where the value is the corresponding sequence’s mass.

  • amino_acid_masses dict: A dictionary of all natural amino acids, and their masses to the appropriate number of significant digits.

  • fasta_lines list: The raw list of lines that constitute the loaded FASTA file, which can be used for post-processing.

  • sigfigs float: The number of sigfigs that are defined for each protein.

  • chem_mw ChemMW: An instance of the ChemMW object is loaded, which allows the user to access the ChemMW module through the PHREEQdb module.