Bio.FSSP package¶
Module contents¶
Parser for FSSP files, used in a database of protein fold classifications (DEPRECATED).
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.
Functions¶
- read_fssp(file_handle)
reads an fssp file into the records. Returns a tuple of two instances.
- mult_align
returns a Biopython alignment object.
-
class
Bio.FSSP.
FSSPHeader
¶ Bases:
object
Store the FSSP file header’s properties.
-
__init__
(self)¶ 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.
-
__repr__
(self)¶ 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.
-
__repr__
(self)¶ 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.
-
pos_align_list2dict
(self)¶ 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
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__init__
(self)¶ Initialize the class.
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build_resnum_list
(self)¶ Create the keys by residue number.
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abs
(self, num)¶ Given an absolute residue number & chain, returns the relevant fssp record.
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pdb
(self, num)¶ Given an PDB residue number & chain, returns the relevant fssp record.
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sequence
(self, num)¶ Return a sequence string.
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fasta_mult_align
(self)¶ Create a FASTA multi alignment record.
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-
class
Bio.FSSP.
FSSPSumDict
¶ Bases:
dict
Create a dict to access summary records (FSSPSumRec).
The key is NR, Record Number.
-
Bio.FSSP.
read_fssp
(fssp_handle)¶ Process a FSSP file and creates the classes containing its parts.
- Returns:
- header
Contains the file header and its properties.
- sum_dict
Contains the summary section.
- align_dict
Contains the alignments.