Bio.FSSP package

Module contents

Parser for FSSP files, used in a database of protein fold classifications.

This is a module to handle FSSP files. For now it parses only the header, summary and alignment sections.

See: Holm and Sander (1996) The FSSP database: fold classification based on structure-structure alignment of proteins.



reads an fssp file into the records. Returns a tuple of two instances.


returns a Biopython alignment object.

class Bio.FSSP.FSSPHeader

Bases: object

Store the FSSP file header’s properties.


Initialize the class.

fill_header(self, inline)

Fill in properties from line.

class Bio.FSSP.PosAlign(inStr)

Bases: object

Store the position alignments, AminoAcid plus Structure.

__init__(self, inStr)

Initialize the class.


Return position alignments as a string.

class Bio.FSSP.FSSPSumRec(in_str)

Bases: object

Store the summary records from SUMMARY Section of file.

__init__(self, in_str)

Initialize the class.


Return the text from the FSSP SUMMARY section.

class Bio.FSSP.FSSPAlignRec(in_fff_rec)

Bases: object

Store the Alignment records from ALIGNMENTS section of file.

__init__(self, in_fff_rec)

Initialize the class.

add_align_list(self, align_list)

Add the given alignment list to the structure.


Create a dictionary from the position alignment list.

The key is sequential starting on 1.

class Bio.FSSP.FSSPAlignDict

Bases: dict

Create a dict to access Alignment Records(FSSPAlignRec).

Key is the alignment record’s chain_id, plus residue name, plus PDB residue number

key = align_rec.chain_id + align_rec.res_name + str(align_rec.pdb_res_num

Also creates two indexes, one by PDB Residue Number, the other by absolute residue number, so you can access the data by either. pdb_res_dict: Key PDB residue number abs_res_dict: Key absolute residue number


Initialize the class.


Create the keys by residue number.

abs(self, num)

Given an absolute residue number & chain, returns the relevant fssp record.

pdb(self, num)

Given an PDB residue number & chain, returns the relevant fssp record.

sequence(self, num)

Return a sequence string.


Create a FASTA multi alignment record.

class Bio.FSSP.FSSPSumDict

Bases: dict

Create a dict to access summary records (FSSPSumRec).

The key is NR, Record Number.


Process a FSSP file and creates the classes containing its parts.


Contains the file header and its properties.


Contains the summary section.


Contains the alignments.