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8 Commits

Author SHA1 Message Date
Brian Kelley
a661489226 Fix/rgroup prefer matching nonhs over hs (#1707) 
* Tweak the scoring function to penalize non h matches considerably.  Only full H rgroups get a one.  Might need to tweak int the future

* Scale the hydrogens as 1/# mols unless they are a full group
 2018-01-09 05:56:37 +01:00
Greg Landrum
1efa8e696e another clang-format run 2017-10-12 06:42:15 +02:00
Greg Landrum
f94e277856 another pass of clang modernize 2017-10-12 06:35:51 +02:00
Greg Landrum
c0d3842df1 get the new code building with the old compiler (#1601) 2017-10-02 09:37:18 +02:00
Greg Landrum
db89172bf8 handle the heavy-atom degree queries differently (#1560) 
* handle the heavy-atom degree queries differently

* Fixes #1563

* add a test for the heavy atom degree option

* Support (and test) adjustHeavyDegree in the cartridge too.

* test results
 2017-09-12 16:10:15 -04:00
Brian Kelley
58ede0f81b Dev/rgroup decomp freefunction (#1557) 
* Adds RGroupDecomp free function and python wrapper

* Fixes subtle bug, adds new RGroupDecomp API

* Updates results for the subtle bug fix.  Verified results were correct.

* Removes smilesCaching.

* Changes RGroupDecompose ordering, adds docstrings and more tests
 2017-09-12 17:41:21 +02:00
Greg Landrum
5a06022704 R group improvements (#1552) 
* Fixes #1550

* might as well update properties on the r groups too

* add option to remove Hs from sidechains;
expose a few more parameters to python;
expose ctor with parameter object to python
 2017-09-08 07:49:05 -04:00
Greg Landrum
62150f7d80 Squashed commit of the following: 
commit 7f7b5268a62eecd260027e0918abbdf62b100034
Merge: 90e9fd3 6dd173d
Author: Greg Landrum <greg.landrum@gmail.com>
Date:   Tue Aug 8 01:19:15 2017 +0200

    merge back to master

commit 6dd173dec6
Merge: 45a94bd e11ad49
Author: Brian Kelley <fustigator@gmail.com>
Date:   Thu Aug 3 07:54:26 2017 -0400

    Merge pull request #8 from greglandrum/dev/rgroup-decomposition

    support using generic iterators in ctor;

commit e11ad49068
Author: Greg Landrum <greg.landrum@gmail.com>
Date:   Tue Aug 1 06:29:52 2017 +0200

    move notebooks to docs

commit 606c03c28f
Author: Greg Landrum <greg.landrum@gmail.com>
Date:   Thu Jul 27 05:13:13 2017 +0200

    support using generic iterators in ctor;
    general comment: this is a useful pattern that we could use elsewhere

commit 45a94bd663
Author: Brian Kelley <brian.kelley@novartis.com>
Date:   Wed Jul 26 13:30:23 2017 -0400

    Updates notebooks

commit 8f78ba97d3
Author: Brian Kelley <brian.kelley@novartis.com>
Date:   Wed Jul 26 09:00:42 2017 -0400

    Updates notebooks

commit 44728803ae
Merge: d67409d 4d0b00d
Author: Brian Kelley <fustigator@gmail.com>
Date:   Wed Jul 26 08:53:11 2017 -0400

    Merge pull request #7 from greglandrum/dev/rgroup-decomposition

    clean up a couple leaks and some compiler warnings

commit 4d0b00dd2e
Author: Greg Landrum <greg.landrum@gmail.com>
Date:   Wed Jul 26 07:47:56 2017 +0200

    clean up a couple leaks and some compiler warnings

commit d67409da0c
Author: Brian Kelley <brian.kelley@novartis.com>
Date:   Tue Jul 25 11:43:14 2017 -0400

    Makes the scoring system more sane

commit 1b5181dc2f
Author: Brian Kelley <brian.kelley@novartis.com>
Date:   Tue Jul 25 10:55:33 2017 -0400

    Finalizes enums

commit 7e9ee61556
Author: Brian Kelley <brian.kelley@novartis.com>
Date:   Tue Jul 25 10:55:18 2017 -0400

    Fixes constructor botched in the last commit

commit aed2a201bf
Author: Brian Kelley <brian.kelley@novartis.com>
Date:   Mon Jul 24 18:22:42 2017 -0400

    Cleans up some code

commit 95e82a1398
Author: Brian Kelley <brian.kelley@novartis.com>
Date:   Mon Jul 24 18:14:31 2017 -0400

    Removes unused variable

commit 0b1ed09316
Author: Brian Kelley <brian.kelley@novartis.com>
Date:   Mon Jul 24 18:14:23 2017 -0400

    Slight optimization by combining two loops

commit ed3340a516
Author: Brian Kelley <brian.kelley@novartis.com>
Date:   Mon Jul 24 13:53:06 2017 -0400

    Fixes post increments in for loops

commit 25b1678a58
Author: Brian Kelley <brian.kelley@novartis.com>
Date:   Mon Jul 24 13:52:53 2017 -0400

    Fixes memory leak and doesn’t call SmartsToMol twice

commit 86c8c42688
Author: Brian Kelley <brian.kelley@novartis.com>
Date:   Mon Jul 24 13:52:32 2017 -0400

    Adds header guards

commit b043e38d3a
Author: Brian Kelley <brian.kelley@novartis.com>
Date:   Mon Jul 24 13:52:25 2017 -0400

    Removes unused variable

commit 631aa77153
Author: Brian Kelley <brian.kelley@novartis.com>
Date:   Tue Jul 11 08:10:39 2017 -0400

    Fixes typo in filename

commit d6e0dc753a
Author: Brian Kelley <brian.kelley@novartis.com>
Date:   Mon Jul 10 14:48:04 2017 -0400

    Fixes c++11 style enums

commit b9a31eae9a
Author: Brian Kelley <brian.kelley@novartis.com>
Date:   Mon Jul 10 14:00:04 2017 -0400

    Adds RGroupDecomposition attempt
 2017-08-08 01:23:49 +02:00