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088256bfb13d14f998f6325669c2cfbabc498308
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181 Commits

Author SHA1 Message Date
Greg Landrum
c0f9be86c8 Get things building with gcc4.4 on centos6 
* Fixes exposing shared_ptr<const T> to python

* remove some of the pragmas for pre 4.5 versions of gcc

* get things working with centos6 and gcc4.4
 2016-04-17 11:48:35 -04:00
Greg Landrum
2d78b7f710 FPB Reader documentation update 2016-04-12 06:21:18 +02:00
Greg Landrum
249146afaa Dev/containing nbrs in python 
* expose GetContainingNeighbors() to python

* add another contains test from python
 2016-04-11 13:09:18 -04:00
Paolo Tosco
f18b12b2dc Merge remote-tracking branch 'upstream/master' into origmaster 
Conflicts:
	Code/GraphMol/MolDraw2D/Wrap/CMakeLists.txt
 2016-03-24 10:05:36 +00:00
Greg Landrum
b9ba12f8f9 Remove extra calls to python::register_exception_translator 2016-03-01 06:36:54 +01:00
Paolo Tosco
ae55c83fc2 - fixed a typo in Code/DataStructs/BitOps.cpp which caused the build 
to fail on Windows 64-bit
 2016-02-22 22:08:16 +00:00
Paolo Tosco
c27a2a317b - as the __popcnt64 builtin is not present on 32-bit Windows, the build 
failed; this commit fixes the problem using the __popcnt builtin on
  32-bit Windows
 2016-02-21 21:31:41 +00:00
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