From cd9647292529fc17b22db8c2ca3f7ccb2019742e Mon Sep 17 00:00:00 2001 From: David Mobley Date: Wed, 28 Feb 2018 21:08:14 -0800 Subject: [PATCH 1/4] Update with hydroxyl hydrogen version (sans generics). --- smirnoff99Frosst/smirnoff99Frosst.ffxml | 642 ++++++++++++------------ 1 file changed, 319 insertions(+), 323 deletions(-) diff --git a/smirnoff99Frosst/smirnoff99Frosst.ffxml b/smirnoff99Frosst/smirnoff99Frosst.ffxml index 2515f9c..88160e1 100755 --- a/smirnoff99Frosst/smirnoff99Frosst.ffxml +++ b/smirnoff99Frosst/smirnoff99Frosst.ffxml @@ -1,344 +1,340 @@ - Date: Nov. 28, 2017 + Date: Feb. 27, 2018 C. I. Bayly, OpenEye/UC Irvine; C. C. Bannan, UC Irvine; D. L. Mobley, UC Irvine - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From d53536ecd3aa0497df26c076fef363c26e1be3dc Mon Sep 17 00:00:00 2001 From: David Mobley Date: Wed, 28 Feb 2018 21:09:10 -0800 Subject: [PATCH 2/4] Rename .ffxml to .offxml --- setup.py | 2 +- .../{smirnoff99Frosst.ffxml => smirnoff99Frosst.offxml} | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename smirnoff99Frosst/{smirnoff99Frosst.ffxml => smirnoff99Frosst.offxml} (100%) diff --git a/setup.py b/setup.py index fb33697..dd9d49f 100644 --- a/setup.py +++ b/setup.py @@ -1,5 +1,5 @@ """ -Setup script to install the smirnoff99Frosst.ffxml as a python package +Setup script to install the smirnoff99Frosst.offxml as a python package """ import sys,os diff --git a/smirnoff99Frosst/smirnoff99Frosst.ffxml b/smirnoff99Frosst/smirnoff99Frosst.offxml similarity index 100% rename from smirnoff99Frosst/smirnoff99Frosst.ffxml rename to smirnoff99Frosst/smirnoff99Frosst.offxml From 57af46f2b3e8edf3bc779bde32731346e9bad107 Mon Sep 17 00:00:00 2001 From: David Mobley Date: Wed, 28 Feb 2018 21:11:20 -0800 Subject: [PATCH 3/4] Update README. --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index d537af4..855778a 100644 --- a/README.md +++ b/README.md @@ -68,6 +68,7 @@ Please see the smarty issue tracker for details. - [Version 1.0.6](https://doi.org/10.5281/zenodo.1093346): Added monovalent ion parameters (Joung/Cheatham) for TIP3P as default. Added angle parameters for cyclobutyl groups. Replaced `R` decorators with `x` to guarantee compatibility between OpenEye toolkits and RDKit SMIRKS parsing. **Not yet in a version**: +- Add hydroxyl hydrogen radii (as per SMIRNOFF initial paper); remove generics with pure wildcards (not even elemental types). ## Contributors @@ -76,4 +77,4 @@ Contributors to the relevant ffxml file include: - Caitlin C. Bannan (UC Irvine) - David L. Mobley (UC Irvine) -Special thanks go to John D. Chodera (MSKCC) for his initial implementation of `smarty.forcefield`. +Special thanks go to John D. Chodera (MSKCC) for his initial implementation of `smarty.forcefield`, which later migrated to `openforcefield` and the SMIRNOFF format. From 94ad7ab72ac0f2e3be54656e252b441cc79553bc Mon Sep 17 00:00:00 2001 From: David Mobley Date: Wed, 28 Feb 2018 21:12:39 -0800 Subject: [PATCH 4/4] Update for 1.0.7 --- README.md | 5 +++-- setup.py | 2 +- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 855778a..6df881c 100644 --- a/README.md +++ b/README.md @@ -66,13 +66,14 @@ Please see the smarty issue tracker for details. - [Version 1.0.4](http://doi.org/10.5281/zenodo.348165): Bug fixes -- #11: Fix the parm@Frosst-derived C-OS bond length so it does not also match (and thus override) C-OH, switching from SMIRKS of `[#6X3:1](=[#8X1])-[#8X2:2]` to `[#6X3:1](=[#8X1])-[#8X2H0:2]`, which avoids overriding `[#6X3:1]-[#8X2H1:2]`. And then add back in a generic which should have been present (#15, fixing a bug introduced by #11) - [Version 1.0.5](http://doi.org/10.5281/zenodo.495249): Substantially improved coverage of chemical space via more general generics as well as a variety of new parameters introduced via generalization/estimation from other force fields such as GAFF/GAFF2. This release, this version covers an internal set of molecules from DrugBank filtered to remove metal atoms and to contain only compounds with less than 200 heavy atoms. Full documentation of changes is available [here](https://github.com/openforcefield/smarty/pull/232). - [Version 1.0.6](https://doi.org/10.5281/zenodo.1093346): Added monovalent ion parameters (Joung/Cheatham) for TIP3P as default. Added angle parameters for cyclobutyl groups. Replaced `R` decorators with `x` to guarantee compatibility between OpenEye toolkits and RDKit SMIRKS parsing. +- Version 1.0.7: Add hydroxyl hydrogen radii (as per SMIRNOFF initial paper); remove generics with pure wildcards (not even elemental types). **Not yet in a version**: -- Add hydroxyl hydrogen radii (as per SMIRNOFF initial paper); remove generics with pure wildcards (not even elemental types). + ## Contributors -Contributors to the relevant ffxml file include: +Contributors to the relevant .offxml file include: - Christopher I. Bayly (OpenEye Software/UC Irvine) - Caitlin C. Bannan (UC Irvine) - David L. Mobley (UC Irvine) diff --git a/setup.py b/setup.py index dd9d49f..27e36f5 100644 --- a/setup.py +++ b/setup.py @@ -26,7 +26,7 @@ def find_package_data(data_root, package_root): setup( name = 'smirnoff99frosst', - version = '1.0.6', + version = '1.0.7', description = 'SMIRNOFF Forcefield parameters', long_description = descr, url = 'https://github.com/openforcefield/smirnoff99Frosst',