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57 Commits

Author SHA1 Message Date
Greg Landrum
d63f44cc0c Add cartridge support for adjustQueryProperties() (#949) 
* backup commit

* Change the names and meanings of MolOps::AdjustQueryWhichFlags
What was there before was not flexible enough and was extremely confusing. This should clear that up.

NOTE: this does break backwards compatibility with code that uses this enum, but given that this is new and has not been
widely promoted, I suspect it should not affect that many people. The default behavior of MolOps::adjustQueryProperties()
remains the same.

* adjust to the new AdjustQueryWhichFlags

* add mol_adjust_query_properties tests to the cartridge
 2016-06-21 14:38:32 -04:00
Paolo Tosco
95ad08f934 - added a PGDLLEXPORT to _PG_init(void) to avoid "unrecognized 
configuration parameter" errors on Windows with PostgreSQL 9.1
- added a dummy RDKit cartridge function call at the beginning of the
  reaction.sql test to avoid "unrecognized configuration parameter" errors
  with PostgreSQL 9.1
- modified reaction.out to reflect the change in reaction.sql
 2016-03-31 22:04:42 +01:00
Greg Landrum
dab873fc4d support providing InChI (or InChI key) generation options in cartridge 2016-02-06 05:50:23 +01:00
Greg Landrum
1692914b6e Fixes #525 2015-10-28 06:01:46 +01:00
Greg Landrum
c924b36c9a Merge branch 'master' into Issue525 2015-10-28 03:19:17 +01:00
Greg Landrum
d905e07f20 support new descrs in cartridge 2015-09-21 16:31:36 +02:00
Greg Landrum
49f55e76ed add test for the issue 2015-06-23 07:01:16 +02:00
Greg Landrum
1b195e0146 Fixes #499 2015-05-03 08:53:27 +02:00
Greg Landrum
d3d362a702 merge master 2015-04-03 07:23:23 +02:00
Greg Landrum
d7474cd621 Merge branch 'Issue469' 2015-04-03 07:14:39 +02:00
Greg Landrum
a0b9b94f34 check empty string handling in the cartridge too 2015-04-02 11:15:33 +02:00
Greg Landrum
f0d4cf1ec6 first pass at a solution for #469 2015-04-02 10:10:22 +02:00
Jan Holst Jensen
d0b3f9e84e Add code to accept blank SMILES input. 
No-Structures are saved to database dumps as blank strings ''.
This patch allows dumps with No-Structures to be read back in.
 2015-04-01 16:54:12 +02:00
Greg Landrum
9fd56d66f6 Fixes: #455 2015-03-16 08:48:04 +01:00
Riccardo Vianello
e1ab15e94c fix some minor inconsistencies in the naming of a few guc variables 2014-10-27 22:11:39 +01:00
Schneider
2b05873136 ChemReactionUtils: remove unused/specialized functions from interface 
- specialized utils functions only used in the pgsql cartridge were removed
  from the interface
 2014-08-25 16:30:09 +02:00
Schneider
5f9a241b8b PGSQL cartridge: Add new reaction functionalities to cartridge 
- Supports reaction type
- Input reaction as SMILES, SMARTS or ctab
- Supports GiST-index substucture/superstructure scans
- Supports reaction fingerprints
 2014-08-19 13:13:57 +02:00
Greg Landrum
d4fe3825b1 initial pass at adding avalon fps to cartridge. needs more testing 2014-08-16 06:31:01 +02:00
Greg Landrum
ea6263008d add tests for indexing on maccs 2014-05-09 18:17:27 +02:00
Greg Landrum
5a6c1c6a12 Fixes: #259 
Fixes: #260
 2014-05-09 12:39:21 +02:00
Greg Landrum
3762b0bd7a rename fmla->formula 2014-03-12 05:37:04 +01:00
Jan Holst Jensen
bd982fb66d Adds sum formula function to PG cartridge. 
* Function signature equivalent to Python interface's CalcMolFormula().
	* Only defined for Postgres 9.x but should work on 8.x too.
 2014-03-08 21:04:55 +01:00
Jan Holst Jensen
fa9198046a Add mol_to_ctab(mol, bool default true) to Postgres cartridge. 
* Tested on Postgres 9.x only. Should however work on 8.x too.
	* Tests require fix for issue #229 to complete successfully.
 2014-03-05 21:05:22 +01:00
Greg Landrum
bd9e624977 Fixes #216 2014-02-08 07:14:44 +01:00
Greg Landrum
cd0365350b add support for tversky similarity to cartridge 2013-10-05 15:18:34 +02:00
Greg Landrum
c2ba91fcdc cartridge changes: 
- add support for chiral SSS
 - add substruct_count operation
 2013-04-01 05:00:38 +00:00
Greg Landrum
ae6b87ccb3 update tests; 
fix github issue 9
 2013-03-29 06:11:52 +00:00
Greg Landrum
f16b517943 add cartridge support for MACCS fingerprints 2013-02-09 16:47:14 +00:00
Greg Landrum
904e34f47d add support for pre v9.1 versions of postgres back into the cartridge 2013-01-14 11:31:31 +00:00
Greg Landrum
bd2ada6202 support connectivity descriptors in the cartridge 2013-01-10 04:36:01 +00:00
Greg Landrum
0ea6d0ce33 remove support for versions of postgresql <9.1 2012-12-16 06:40:46 +00:00
Greg Landrum
42d1fba7eb cartridge murcko updates 2012-12-04 09:25:34 +00:00
Greg Landrum
aca71e7fc2 add MurckoScaffold support to cartridge 2012-12-04 08:56:29 +00:00
Greg Landrum
e34ba72849 at this point fingerprints to/from bytea should work; I am still somewhat concerned about a potential memory leak 2012-08-25 03:48:42 +00:00
Greg Landrum
7e803e071e version bump for the extension; add tests for the mol_{to,from}_pkl funcs 2012-08-22 08:30:19 +00:00
Greg Landrum
aa352dbceb add mol_to_{smiles,smarts} 2012-07-09 04:18:25 +00:00
Greg Landrum
17a4d25e88 further refinement 2012-07-07 13:22:10 +00:00
Greg Landrum
c01f271562 get that returning null thing right 2012-07-07 13:13:12 +00:00
Greg Landrum
aa40419d39 work around an order-dependence thing in the cartridge tests 2012-05-31 05:44:43 +00:00
Greg Landrum
7e36c8296b add mol_from_smarts and mol_from_smiles 2012-03-04 16:24:44 +00:00
Greg Landrum
0778f13107 add all_values_{gt,lt}; further build system cleanups 2011-10-27 05:41:24 +00:00
Greg Landrum
d3c9d3bdd8 switch to a single Makefile and further build-system rationalizations 2011-10-25 05:22:55 +00:00
Greg Landrum
f14812bbf6 add knn integration for bfps (from Adrian Schreyer) 2011-10-25 04:24:08 +00:00
Greg Landrum
6e77f86edb get this working with postgresql 9.1; thanks to Adrian Schreyer for a lot of the work 2011-10-23 14:14:52 +00:00
Greg Landrum
955786ec8d add default arguments for morgan and featmorganfps 
add support for constructing molecules from ctabs
 2011-07-18 05:27:53 +00:00
Greg Landrum
84f2da3323 add inchi support to cartridge 2011-07-02 05:29:43 +00:00
Greg Landrum
62b4290b04 add some tests for adding and subtracting fingerprints 2011-06-20 09:33:53 +00:00
Greg Landrum
403a669ac8 add some additional descriptors to the cartridge 2011-03-19 04:25:48 +00:00
Greg Landrum
f619c0bbe1 add rotatable bonds function 2011-03-10 05:14:32 +00:00
Greg Landrum
e6dee34976 add a couple more tests 2010-12-30 10:22:34 +00:00