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Changes in CS should also lead to automatic updates of NRG-CING related entries. #283

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
Clear

Original issue reported on code.google.com by jurge...@gmail.com on 7 Feb 2011 at 12:38

GoogleCodeExporter commented 9 years ago 
There's a problem with this in that the time stamps from the BMRB rsynced files 
differ from the rev date inside the file.

Worrying is also that 5509 entries were modified on March 5th, 2011. We can't 
redo all NRG-CING entries triggered by such a large number automatically. We'll 
have to do this manually. Eldon, could you propose an alternative for this? 
What should trigger an update of NRG-CING for the BMRB CS?

What should be automatically doable is to include the weekly new ones. Any time 
we get a BMRB entry for which the NRG-CING RDB doesn't have a CS count for we 
should add the CS. Of course that would infinitely loop the entries for which 
we fail to process the CS to NRG-CING.

Original comment by jurge...@gmail.com on 11 Apr 2011 at 12:49

GoogleCodeExporter commented 9 years ago 
I'll try to update 

$CINGROOT/python/cing/NRG/matchBmrbPdb.py

to run weekly but this might have to slip to the next milestone.

Original comment by jurge...@gmail.com on 11 Apr 2011 at 12:55

GoogleCodeExporter commented 9 years ago 
Looks easy as per below. 
Increased # of matches from 3339 to 3450.

=======================================================
Reusing existing data dir /Users/jd/wattosTestingPlatform/bmrb/matchBmrbPdb
Read 6795 BMRB entries from DB dump
Found 18 entries on file but not in DB: [15919, 16267, 16298, 16312, 16336, 
16338, 16347, 16352, 16353, 16364, 16370, 16372, 16373, 16385, 20010, 20011, 
20024, 20025]
Found 3 entries in DB but not on file: [16355, 16927, 17086]
Skipped: 19 obsolete PDB entries from score_many2one ['1lnp', '1bqv', '1bxj', 
'1ymj', '1ym6', '1ck9', '1cn9', '1cn8', '1ck8', '1ck5', '2new', '1jyp', '1n4t', 
'1n9d', '1xm0', '1uw2', '1xo9', '1xaq', '1yl2']
Skipped: 0 obsolete BMRB entries from score_many2one []
Accepted from old list 1689 matches
DEBUG: Already found 1vj6 in PDB; consider updating the manual list.
Skipped: 2 double entries from pdbIdAditList ['2kmp', '2kh9']
Skipped: 182 obsolete  PDB entries from adit0 ['1a3k', '1abj', '1alp', '1aox', 
'1ass', '1ayf', '1b9c', '1b9k', '1bq8', '1bqv', '1bxj', '1d5k', '1d8c', '1dki', 
'1dpj', '1dqe', '1e0r', '1e96', '1ehk', '1emv', '1ew4', '1ezk', '1f5w', '1fbt', 
'1fio', '1g6l', '1gaj', '1gyu', '1h0x', '1h40', '1h70', '1hco', '1hg6', '1hur', 
'1hzq', '1hzr', '1i45', '1igd', '1iof', '1ird', '1irn', '1iwo', '1iya', '1j9d', 
'1jiw', '1jjl', '1jjq', '1jsb', '1jyp', '1k04', '1k16', '1kdd', '1khc', '1kil', 
'1kjo', '1krk', '1l2v', '1laz', '1lks', '1lsk', '1m2y', '1m4o', '1mh1', '1mjf', 
'1mms', '1mu4', '1n3v', '1n4t', '1n9d', '1naq', '1nvh', '1nzt', '1o0z', '1omp', 
'1oob', '1oqj', '1oun', '1p38', '1p67', '1pin', '1plq', '1q8e', '1qaw', '1qot', 
'1r40', '1r83', '1ril', '1rp6', '1sfc', '1spz', '1sv7', '1tgq', '1uav', '1uea', 
'1uec', '1uiu', '1upo', '1utx', '1uv0', '1vie', '1vk7', '1wjh', '1x6k', '1xaq', 
'1xo4', '1xo9', '1xyf', '1yl2', '1ywz', '1yzo', '1z3b', '1zs1', '1zwq', '2a2h', 
'2a4y', '2aic', '2asw', '2auf', '2b0n', '2b2m', '2bar', '2cth', '2dhw', '2di1', 
'2end', '2f2y', '2fjj', '2g8p', '2gpg', '2gx3', '2h33', '2h7u', '2hc6', '2hnm', 
'2hnp', '2jmt', '2jp4', '2jrn', '2js8', '2jsu', '2jth', '2jud', '2juq', '2jur', 
'2jus', '2jut', '2jux', '2jvp', '2jw3', '2jy3', '2jy4', '2jzu', '2k0h', '2k0i', 
'2k1c', '2k82', '2k83', '2kab', '2kao', '2kci', '2ki1', '2knw', '2kps', '2ks7', 
'2ks8', '2ksx', '2non', '2nyo', '2om4', '2p60', '2p7w', '2qkz', '2rls', '2rn6', 
'2rnc', '2rof', '2rpg', '2rq3', '2uz7', '3mbp', '3paz', '4azu']
Skipped: 0 obsolete BMRB entries from adit0 []
Accepted from adit0 1653 for a total of 3342 matches
Skipped: 1 obsolete  PDB entries from adit1 ['2kjs']
Skipped: 3 obsolete BMRB entries from adit1 ['16355', '16927', '17086']
Accepted from adit1 107 for a total of 3449 matches
Accepted from manual list 1 for a total of 3450 matches
Accepted unique 3450 PDB and 3099 BMRB entries
Will write 3450 nrows and 2 ncols to newMany2OneTable.csv

Original comment by jurge...@gmail.com on 11 Apr 2011 at 2:24

GoogleCodeExporter commented 9 years ago 
Addressed in r967. It would be good to improve on this list but I'll leave that 
for another time.

Final result today:

Recreating data dir /Users/jd/wattosTestingPlatform/bmrb/matchBmrbPdb from SVN 
/Users/jd/workspace35/cing/data/NRG/bmrbPdbMatch
Will write 3078 nrows and 2 ncols to adit_nmr_matched_pdb_bmrb_entry_ids.csv
Read 6795 BMRB entries from DB dump
Found 18 entries on file but not in DB: [15919, 16267, 16298, 16312, 16336, 
16338, 16347, 16352, 16353, 16364, 16370, 16372, 16373, 16385, 20010, 20011, 
20024, 20025]
Found 3 entries in DB but not on file: [16355, 16927, 17086]
Will write 8847 nrows and 1 ncols to pdbNmrTable.csv
Skipped: 19 obsolete PDB entries from score_many2one ['1lnp', '1bqv', '1bxj', 
'1ymj', '1ym6', '1ck9', '1cn9', '1cn8', '1ck8', '1ck5', '2new', '1jyp', '1n4t', 
'1n9d', '1xm0', '1uw2', '1xo9', '1xaq', '1yl2']
Skipped: 0 obsolete BMRB entries from score_many2one []
Accepted from old list 1689 matches
Using manual mapping of 1vj6 in PDB with BMRB 6060 in manual list instead of 
BMRB 5131 in current list.
First removing match at idx 834 in current list.
Skipped: 2 double entries from pdbIdAditList ['2kmp', '2kh9']
Skipped: 71 obsolete  PDB entries from adit0 ['1c9s', '1cje', '1eul', '1foe', 
'1hh8', '1j9d', '1jjl', '1k05', '1l2v', '1laz', '1lku', '1lsk', '1oob', '1q8e', 
'1qts', '1r40', '1rp6', '1tip', '1uav', '1uiv', '1vas', '1vk7', '1z3b', '1zs1', 
'1zwq', '2asw', '2auf', '2b0n', '2bar', '2di1', '2f2y', '2g8p', '2gpg', '2gx3', 
'2h7u', '2hnm', '2igd', '2kjs', '2kuy', '2kx2', '2l5c', '2l5d', '2l61', '2l62', 
'2l73', '2l7b', '2l7f', '2l7l', '2l7m', '2l7w', '2l7z', '2l87', '2l8b', '2l8k', 
'2l97', '2l9b', '2l9c', '2l9k', '2l9s', '2la1', '2lag', '2lak', '2lan', '2lb9', 
'2lbb', '2lbo', '2lbu', '2non', '2om4', '2p7w', '2xv9']
Skipped: 0 obsolete BMRB entries from adit0 []
Accepted from adit0 1929 for a total of 3618 matches
Skipped: 1 obsolete  PDB entries from adit1 ['2kjs']
Skipped: 3 obsolete BMRB entries from adit1 ['16355', '16927', '17086']
Accepted from adit1 11 for a total of 3629 matches
Accepted from manual list 1 for a total of 3630 matches
Accepted unique 3630 PDB and 3280 BMRB entries
Using 78 BMRB entries that match two or more PDB entries.
Will write 3630 nrows and 2 ncols to newMany2OneTable.csv

Original comment by jurge...@gmail.com on 12 Apr 2011 at 1:48