The example in this folder shows you have to parse a BPSEQ format file and produce the files necessary to run NAST and C2A.
Input: A file name without the .bpseq suffix. Make sure the file with the suffix exists in your folder.
Output: Three files:
    *.seq -- A primary sequence file for use with NAST
    *-helix.txt -- A helix definition file for use with NAST
    *-FD.txt -- A fragment definition file for use with C2A
You can also check your answers against the files contained in the "Results" folder.

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To run the example:
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"python parseBPseq.py NDB_00015"

You should get the following output text:

Opened NDB_00015.bpseq to parse secondary structure
Wrote the following files:
NDB_00015.seq -- Primary sequence file for use with NAST to start from an unfolded sequence
NDB_00015-helix.txt -- Secondary structure file for use with NAST to constrain secondary structure
NDB_00015-FD.txt --  Fragment definintion file based on secondary structure for use with C2A
If you wish to constrain tertiary contacts in NAST, you still need to write this file yourself
To check the fragments defined in the -FD.txt file, run "python parseFD.py NDB_00015-FD.txt"


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To test the -FD.txt output:
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"python parseFD.py NDB_00015-FD.txt"

You should get the following output text:

Helix H2
5' end  [4, 5, 6, 7]
3' end  [21, 20, 19, 18]

Helix H3
5' end  [8, 9, 10, 11]
3' end  [16, 15, 14, 13]

Helix H1
5' end  [1, 2]
3' end  [23, 22]

Loop L1
5' end  [8, 9, 10, 11]
loop           [12]
3' end  [16, 15, 14, 13]

Junction J1
5' end  [1, 2]
junction         [3]
3' end  [4, 5, 6, 7]

Junction J2
5' end  [13, 14, 15, 16]
junction         [17]
3' end  [18, 19, 20, 21]

End E1
end [24]
overlapping helix     [22, 23]