Greg Landrum
81ee476fd7
Fixes #1118 ( #1119 )
2016-10-24 11:15:25 -04:00
Greg Landrum
7fa3cae4cd
clear up a bunch of windows warnings ( #1086 )
2016-10-04 06:46:07 -04:00
gedeck
e9af48ffd7
Issue1071/yapf ( #1078 )
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* Issue #1071 : add yapf configuration file
* yapf formatting of Code directory
* yapf formatting of Contrib directory
* yapf formatting of Data directory
* yapf formatting of Docs directory
* yapf formatting of External directory
* yapf formatting of Projects directory
* yapf formatting of Regress directory
* yapf formatting of Scripts directory
* yapf formatting of Web directory
* yapf formatting of rdkit directory
2016-09-23 04:58:46 +02:00
Greg Landrum
2907166444
Add a MultiFPBReader class ( #909 )
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* first pass at a MultiFPBReader in c++
includes initial tests
* first pass at multi-threading; untested
* add multi-threaded test
* multi-threaded tversky
* add multi-threaded contains searches
* allow FPBReader::init() to be called multiple times
* add a cleanup() method to clear out whatever memory we are using
* allow the init() call to be pushed to search-time;
this allows calls to the contained init() methods to be run in separate threads
* make ownership of FPBReader pointers optional
add addReader() method
* Add MultiFPBReader python wrapper
* support multi-threaded initOnSearch
* add a couple of more tests
2016-05-29 09:38:14 -04:00
Greg Landrum
c0f9be86c8
Get things building with gcc4.4 on centos6
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* 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
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* 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
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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
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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
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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
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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
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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
