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Convert RadiallySymmetricRestraint Forces to CV Forces #365

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merged 8 commits into from
Aug 2, 2018
Merged

Convert RadiallySymmetricRestraint Forces to CV Forces #365

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05f1bdc
Convert HarmonicRestraint Forces to CV Forces
Lnaden Jul 31, 2018
fdc41d5
Fix typo in meta.yaml
Lnaden Jul 31, 2018
8726101
Make it way more clear about backwards compatibility breaking.
Lnaden Jul 31, 2018
e36b593
Start trying to make serialization more stable.
Lnaden Aug 1, 2018
66d86c6
Update the forces to be restorable correctly.
Lnaden Aug 1, 2018
3c7ba04
Fix unneeded import
Lnaden Aug 1, 2018
7686d1f
Stupid. netcdf. stupid
Lnaden Aug 1, 2018
77c6ac8
AHG!
Lnaden Aug 1, 2018
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7 changes: 1 addition & 6 deletions devtools/appveyor/install.ps1
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Original file line number Diff line number Diff line change
Expand Up @@ -7,11 +7,7 @@ $MINICONDA_URL = "http://repo.continuum.io/miniconda/"

function DownloadMiniconda ($python_version, $platform_suffix) {
$webclient = New-Object System.Net.WebClient
if ($python_version -match "3.4") {
$filename = "Miniconda3-3.7.3-Windows-" + $platform_suffix + ".exe"
} else {
$filename = "Miniconda-3.7.3-Windows-" + $platform_suffix + ".exe"
}
$filename = "Miniconda3-4.5.4-Windows-" + $platform_suffix + ".exe"
$url = $MINICONDA_URL + $filename

$basedir = $pwd.Path + "\"
Expand Down Expand Up @@ -86,7 +82,6 @@ function UpdateConda ($python_home) {
Start-Process -FilePath "$conda_path" -ArgumentList $args -Wait -Passthru
}


function main () {
InstallMiniconda $env:PYTHON_VERSION $env:PYTHON_ARCH $env:PYTHON
UpdateConda $env:PYTHON
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4 changes: 3 additions & 1 deletion devtools/conda-recipe/meta.yaml
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Expand Up @@ -27,10 +27,12 @@ requirements:
- numpy
- scipy
- six
- openmm
- openmm >=7.2
- parmed
- mdtraj
# NetCDF4 on windows conda has DLL issues, so pin libnetcdf
- netcdf4
- libnetcdf ==4.6.1=h183b1a9_3 # [win]
- pyyaml


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15 changes: 15 additions & 0 deletions docs/releasehistory.rst
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Expand Up @@ -15,6 +15,9 @@ New features
control global variables (`#363 <https://github.com/choderalab/openmmtools/pull/363>`_).
- Allow restraint force classes to be controlled by a parameter other than ``lambda_restraints``. This will enable
multi-restraints simulations (`#363 <https://github.com/choderalab/openmmtools/pull/363>`_).
- ``RadiallySymmetricRestraintForce`` and all subclasses are now a ``CustomCVForce`` subclass wrapping their
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We should warn that this may be an API-breaking change in the changelog!

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I did?

RadiallySymmetricRestraintForce and all subclasses are now a CustomCVForce subclass wrapping their respective CustomBondForce and CustomCentroidBondForce objects. This breaks backwards compatibility, but enables tracking the restraint distances through the new SamplerSate collective variable features.

Emphasis mine

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Just meant that there might be a "Warnings" section rather than burying this in the "Features" (since it may break your program, which may not be a "feature").

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Fair point. I'll make this more visible

respective ``CustomBondForce`` and ``CustomCentroidBondForce`` objects. This breaks backwards compatibility, but
enables tracking the restraint distances through the new ``SamplerSate`` collective variable features.

Deprecated
----------
Expand All @@ -24,6 +27,18 @@ Deprecated
- Deprecated ``update_alchemical_charges`` in ``AlchemicalState`` in anticipation of the new implementation of the
exact PME that will be based on the ``NonbondedForce`` offsets rather than ``updateParametersInContext()``.

Compatibility Warnings
----------------------
- ``RadiallySymmetricRestraintForce``'s conversion to ``CustomCVForce``'s break the backwards compatibility with older
codes which implement subclasses of it. The largest change is how the Energy Function is implemented, and subclass
hierarchy. E.g. All these classes are now ``CustomCVForce``'s instead of ``CustomBondForce`` and
``CustomCentroidBondForce`` objects.

- This affects ``RadiallySymmetricRestraintForce``,
``RadiallySymmetricCentroidRestraintForce``, ``RadiallySymmetricBondRestraintForce``,
``HarmonicRestraintForceMixIn``, ``HarmonicRestraintForce``, ``HarmonicRestraintBondForce``,
``FlatBottomRestraintForceMixIn``, ``FlatBottomRestraintForce``, and ``FlatBottomRestraintBondForce``.


0.15.0 - Restraint forces
=========================
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