[Biopython-dev] [Bug 2943] MMCIFParser only handling a single model.

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2943





------- Comment #4 from TallPaulInJax at yahoo.com  2009-11-04 23:54 EST -------
Note: my testing of MMCIFParser.py depends on the changes I have made to
MMCIF2Dict.py which requires the new MMCIFlex.py I wrote completely in python
with no lex/flex/C support required. Peter, you should have copies of these?

To test MMCIFParser.py, download:
ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/mmCIF/be/2beg.cif.gz
and unzip it.

Run MMCIFParser in IDLE, etc. It will prompt you for a filename. Enter the path
and filename to the unzipped 2beg file you just downloaded. 2beg has 10 models
(1 thru 10), each with 5 chains, and each chain with 26 residues. You should
get:

<Model id=1>
<Chain id=A>
Found 26 residues.
<Chain id=B>
Found 26 residues.
<Chain id=C>
Found 26 residues.
<Chain id=D>
Found 26 residues.
<Chain id=E>
Found 26 residues.
<Model id=2>
<Chain id=A>
Found 26 residues.
<Chain id=B>
Found 26 residues.
<Chain id=C>
Found 26 residues.
<Chain id=D>
Found 26 residues.
<Chain id=E>
Found 26 residues.
<Model id=3>
<Chain id=A>
Found 26 residues.
<Chain id=B>
Found 26 residues.
<Chain id=C>
Found 26 residues.
<Chain id=D>
Found 26 residues.
<Chain id=E>
Found 26 residues.
<Model id=4>
<Chain id=A>
Found 26 residues.
<Chain id=B>
Found 26 residues.
<Chain id=C>
Found 26 residues.
<Chain id=D>
Found 26 residues.
<Chain id=E>
Found 26 residues.
<Model id=5>
<Chain id=A>
Found 26 residues.
<Chain id=B>
Found 26 residues.
<Chain id=C>
Found 26 residues.
<Chain id=D>
Found 26 residues.
<Chain id=E>
Found 26 residues.
<Model id=6>
<Chain id=A>
Found 26 residues.
<Chain id=B>
Found 26 residues.
<Chain id=C>
Found 26 residues.
<Chain id=D>
Found 26 residues.
<Chain id=E>
Found 26 residues.
<Model id=7>
<Chain id=A>
Found 26 residues.
<Chain id=B>
Found 26 residues.
<Chain id=C>
Found 26 residues.
<Chain id=D>
Found 26 residues.
<Chain id=E>
Found 26 residues.
<Model id=8>
<Chain id=A>
Found 26 residues.
<Chain id=B>
Found 26 residues.
<Chain id=C>
Found 26 residues.
<Chain id=D>
Found 26 residues.
<Chain id=E>
Found 26 residues.
<Model id=9>
<Chain id=A>
Found 26 residues.
<Chain id=B>
Found 26 residues.
<Chain id=C>
Found 26 residues.
<Chain id=D>
Found 26 residues.
<Chain id=E>
Found 26 residues.
<Model id=10>
<Chain id=A>
Found 26 residues.
<Chain id=B>
Found 26 residues.
<Chain id=C>
Found 26 residues.
<Chain id=D>
Found 26 residues.
<Chain id=E>
Found 26 residues.

Note on a different protein: 100d.ent identifies the models, chains, and
residues differently than it's counterpart 100d.cif!!! And I thought they came
from the same database!?


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