174 Commits

Author	SHA1	Message	Date
Greg Landrum	f6db4aaab8	switch to using builtin_popcountll	2016-01-22 16:07:28 -05:00
Greg Landrum	9e9eaa729c	make it possible to turn off the use of popcnt	2016-01-22 03:49:04 -05:00
Greg Landrum	2179db09e0	switch dice and tversky to popcntl too	2016-01-19 05:05:27 -05:00
Greg Landrum	2c4964eed3	switch to popcntl	2016-01-19 01:54:21 -05:00
Greg Landrum	55c96db67e	first pass at block reads	2016-01-19 01:24:32 -05:00
Greg Landrum	6e6c200bd3	add Tversky code to the python wrapper	2016-01-18 10:57:48 +01:00
Greg Landrum	6581b4db7f	docs	2016-01-18 10:57:20 +01:00
Greg Landrum	37234afa62	passes tests	2016-01-18 10:42:04 +01:00
Greg Landrum	c0a820fb87	tversky basics work; still need better testing at the FPB level	2016-01-18 10:15:05 +01:00
Greg Landrum	38ece3aa62	backup, does not work	2016-01-18 04:23:07 +01:00
Greg Landrum	f08ceff556	report unrecognized chunks	2016-01-12 12:12:50 +01:00
Greg Landrum	de1192efe4	switch to a shared_array	2016-01-12 12:12:50 +01:00
Greg Landrum	d56a9d38b5	get this building on windows	2016-01-12 12:12:46 +01:00
Greg Landrum	6b06bccf3f	clean up the uses of casts in the new code	2016-01-12 12:09:56 +01:00
Greg Landrum	90f142cf11	a bit more documentaiton	2016-01-12 12:09:56 +01:00
Greg Landrum	3130578930	additional tests	2016-01-12 12:09:56 +01:00
Greg Landrum	9e7b6a7409	add lazy id reading on the other paths (also not checked)	2016-01-12 12:09:56 +01:00
Greg Landrum	606ae353ca	stop reading in all Ids when in lazy mode	2016-01-12 12:09:56 +01:00
Greg Landrum	700c59ff37	Add doxygen docs ... Add ExplicitBitVect versions of a few of the methods Update a couple of copyrights	2016-01-12 12:09:56 +01:00
Greg Landrum	4ae3318e45	speed up UpdateBitVectFromFPSText	2016-01-12 12:09:55 +01:00
Greg Landrum	438c1b217b	add fingerprint contains searches (to support SSS screening)	2016-01-12 12:09:55 +01:00
Greg Landrum	7c0d4bdd89	add bitmap version of AllProbeBitsMatch()	2016-01-12 12:09:55 +01:00
Greg Landrum	8aae258e3c	move responsibility for memory management out of extractBytes	2016-01-12 12:09:55 +01:00
Greg Landrum	9d26882286	comments	2016-01-12 12:09:55 +01:00
Greg Landrum	88826aea7b	add (and test) functions for converting byte arrays to bitsets and back	2016-01-12 12:09:55 +01:00
Greg Landrum	16dc0cdc27	fix a typo when builtin_popcount is not being used	2016-01-12 12:09:55 +01:00
Greg Landrum	a6f2aba9b5	remove some printing	2016-01-12 12:09:55 +01:00
Greg Landrum	5af208a1e4	add a lazy mode that does not need to read in the whole database	2016-01-12 12:09:54 +01:00
Greg Landrum	0532faee70	builds and passes tests on windows	2016-01-12 12:09:54 +01:00
Greg Landrum	9ae728ef5c	remove the topN arg since it isn't being used and won't save time anyway	2016-01-12 12:09:54 +01:00
Greg Landrum	dea28eb2fc	add tests for the bitmap bitops	2016-01-12 12:09:54 +01:00
Greg Landrum	50e925a478	further lessening of memory management stupidity	2016-01-12 12:09:54 +01:00
Greg Landrum	5e7a7e0238	get a bit smarter about passing around pointers. still lots to do here, but it probably should wait for the c++14 version	2016-01-12 12:09:54 +01:00
Greg Landrum	8722043df8	add nBits() method ... add getTanimotoNeighbors() method	2016-01-12 12:09:54 +01:00
Greg Landrum	72ab79508e	add CalcBitmapPopcount()	2016-01-12 12:09:54 +01:00
Greg Landrum	08ce5a287d	crude initial python wrapper	2016-01-12 12:09:54 +01:00
Greg Landrum	2e9063964e	add getBytes(), test tanimoto	2016-01-12 12:09:53 +01:00
Greg Landrum	0015f853ac	systematize use of popcnt	2016-01-12 12:09:53 +01:00
Greg Landrum	6bd2c20ac0	all tests pass	2016-01-12 12:09:53 +01:00
Greg Landrum	ca8ef113d4	parse popcounts and make them accessible	2016-01-12 12:09:53 +01:00
Greg Landrum	3813e9c802	we can now also read IDs	2016-01-12 12:09:53 +01:00
Greg Landrum	d17f4ca8f1	fingerprints are now properly read in	2016-01-12 12:09:53 +01:00
Greg Landrum	773f6b0432	backup	2016-01-12 12:09:53 +01:00
Greg Landrum	4cc2d46d49	initial commit, doesn't really do anything useful yet	2016-01-12 12:09:52 +01:00
Greg Landrum	79e1f8b1fa	compiles without numpy warnings, all tests pass on ubuntu 15.04 with numpy 1.10	2015-11-28 06:49:34 +01:00
Greg Landrum	e08e0d16d8	first pass, using google style	2015-11-14 14:58:11 +01:00
Greg Landrum	80bb809b31	back out one of those changes	2015-11-14 14:13:36 +01:00
Greg Landrum	2a75463959	get rid of some more warnings	2015-11-14 09:21:05 +01:00
Greg Landrum	9b437d0099	switch off pragmas for gcc<4.2	2015-11-14 08:53:50 +01:00
Greg Landrum	e37296d7c7	post review	2015-11-14 08:08:14 +01:00