allpy
annotate test/test.py @ 151:675b402094be
day commit -- a lot of changes
fasta.py:
universal save_fasta()
determine_long_line -- for determine length of fasta sequence string
in user input
everywhere: standart long_line=60 --> 70
blocK.sequences_chains: returns sequences in order as in project
added monomer pdb_secstr to store secondary structure
pdb adding: some improvements and fixes
fix in from_pdb_chain: use all peptides, not only first
Sequence.pdb_files added to store information about pdb file for each chain
dssp bindings to get secondary structure
/sec_str -- tool to map secondary structure on each sequence of alignment
| author | boris (netbook) <bnagaev@gmail.com> |
|---|---|
| date | Tue, 26 Oct 2010 00:40:36 +0400 |
| parents | 89de20cda19c |
| children | fb3164f03984 |
| rev | line source |
|---|---|
| bnagaev@98 | 1 import sys |
| bnagaev@83 | 2 |
| bnagaev@83 | 3 from allpy.lib.project import Project |
| bnagaev@121 | 4 from allpy.lib.block import Block |
| bnagaev@83 | 5 |
| bnagaev@122 | 6 p = Project(open('test.fasta')) |
| bnagaev@83 | 7 print "alignment length: %i" % len(p) |
| bnagaev@110 | 8 print "sequence: %s" % str(p.sequences[0]) |
| bnagaev@83 | 9 |
| bnagaev@120 | 10 p.sequences[0].pdb_chain_add(open('1jcc.pdb'), '1jcc', 'B') |
| bnagaev@120 | 11 p.sequences[1].pdb_chain_add(open('1kfm.pdb'), '1kfm', 'A') |
| bnagaev@120 | 12 |
| bnagaev@121 | 13 b = Block(p) |
| bnagaev@130 | 14 GCs = b.geometrical_cores(ac_new_atoms=0.00, ac_count=-1) |
| bnagaev@128 | 15 b.save_fasta(sys.stdout) |
| bnagaev@134 | 16 for i, GC in enumerate(GCs): |
| bnagaev@134 | 17 GC.save_xstring(sys.stdout, i) |
| bnagaev@121 | 18 |
| bnagaev@110 | 19 #~ p.muscle_align() |
| bnagaev@110 | 20 #~ p.save_fasta(sys.stdout) |