decode_description(description)

Parse the first line of a FASTA file using the specifications of several different database headers (in _DATABASES). description: The header line with the initial >removed.return`: A dictionary for which each key-value pair comprises a property specified by the database used and the value of that property given by the header. If the database is not recognized, the keys are given as 'desc-n' where n is the position of the property.

getdata(datapath, pdbid, color; resetview=false, lc=true)

gethighlights(string, sep, atomindicator)

Helper function to set highlights using string, sep, atom_indicator

Example

a,b = DashBioUtils.NglParser.get_highlights("Hello.app", ".", "a")

readfasta(datapathordatastring; isdatafile=true)

Read a file in FASTA format, either from a file or from a string of raw data.

datapath_or_datastring: Either the path to the FASTA file (can be relative or absolute), or a string corresponding to the content of a FASTA file (including newline characters).

is_datafile: Either true (default) if passing the filepath to the data, or false if passing a string of raw data.

return: A list of protein objects, each containing a description (based on the header line) and the amino acid sequence with, optionally, all non-amino-acid letters removed.

readxyz(datapathordatastring, isdatafile=true)

Read data in .xyz format, from either a file or a raw string. datapath_or_datastring: Either the path to the XYZ file (can be relative or absolute), or a string corresponding to the content of an XYZ file (including newline characters). is_datafile: Either True (default) if passing the filepath to the data, or False if passing a string of raw data. return: A list of the atoms in the order that they appear on the file, stored in objects with keys "symbol", "x", "y", and "z".

single_split(string, sep)

Helper function to split string into 2 sub string based on sep

Example

  a,b = DashBioUtils.NglParser.single_split("hello.app",".")