From 572d2062838d0924695d4c71a9ee6fde36b1990d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mart=C3=AD=20Municoy?= Date: Wed, 13 Sep 2023 17:30:31 +0200 Subject: [PATCH 1/3] Do not shrink bonds and angles to 0.0 --- peleffy/topology/alchemistry.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/peleffy/topology/alchemistry.py b/peleffy/topology/alchemistry.py index 04f9ed3a..df07e2b8 100644 --- a/peleffy/topology/alchemistry.py +++ b/peleffy/topology/alchemistry.py @@ -283,12 +283,12 @@ def topology_from_lambda_set(self, lambda_set): for bond_idx, bond in enumerate(alchemical_topology.bonds): if bond_idx in self._exclusive_bonds: - bond.apply_lambda(["spring_constant", "eq_dist"], + bond.apply_lambda(["spring_constant", ], lambda_set.get_lambda_for_bonded(), reverse=False) if bond_idx in self._non_native_bonds: - bond.apply_lambda(["spring_constant", "eq_dist"], + bond.apply_lambda(["spring_constant", ], lambda_set.get_lambda_for_bonded(), reverse=True) @@ -309,12 +309,12 @@ def topology_from_lambda_set(self, lambda_set): for angle_idx, angle in enumerate(alchemical_topology.angles): if angle_idx in self._exclusive_angles: - angle.apply_lambda(["spring_constant", "eq_angle"], + angle.apply_lambda(["spring_constant", ], lambda_set.get_lambda_for_bonded(), reverse=False) if angle_idx in self._non_native_angles: - angle.apply_lambda(["spring_constant", "eq_angle"], + angle.apply_lambda(["spring_constant", ], lambda_set.get_lambda_for_bonded(), reverse=True) From 2eb33311d526a5cf0a89f86205e7599607268577 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mart=C3=AD=20Municoy?= Date: Thu, 16 Nov 2023 13:32:06 +0100 Subject: [PATCH 2/3] Update releasehistory.rst --- docs/releasehistory.rst | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/docs/releasehistory.rst b/docs/releasehistory.rst index 9adc751c..2974aea4 100644 --- a/docs/releasehistory.rst +++ b/docs/releasehistory.rst @@ -8,6 +8,16 @@ Releases follow the ``major.minor.micro`` scheme recommended by `PEP440 `_: bug fixes for alchemical topologies + + 1.4.4 - Corrections for alchemistry and new charge calculator ------------------------------------------------------------- From d0f3bd04809b3eb061a2920339937b6ce45c29ea Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mart=C3=AD=20Municoy?= Date: Thu, 16 Nov 2023 13:35:13 +0100 Subject: [PATCH 3/3] Define noarch generic package --- devtools/conda/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/devtools/conda/meta.yaml b/devtools/conda/meta.yaml index 1ed9e228..1064aded 100644 --- a/devtools/conda/meta.yaml +++ b/devtools/conda/meta.yaml @@ -10,6 +10,7 @@ source: build: script: python -m pip install . --no-deps number: 0 + noarch: python requirements: build: