Merge pull request #117 from wiederm/update_to_new_packages

adapt some packages

README.md

@@ -8,7 +8,7 @@ Transformato
 [![GH Pages](https://github.com/wiederm/transformato/actions/workflows/build_page.yaml/badge.svg)](https://github.com/wiederm/transformato/actions/workflows/build_page.yaml)
 [![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/transformato.svg)](https://anaconda.org/conda-forge/transformato)
 
-Transformato is a package that helps to set up relative alchemical free energy calculations of small molecules with a common core scaffold, either for solvation free energy[^1] or binding free energy[^2] estimates. The package is designed to be used with output generated by [CHARMM-GUI](https://charmm-gui.org/).
+Transformato is a package that helps to set up relative alchemical free energy calculations of small molecules with a common core scaffold, either for relative solvation free energy[^1], absolute solvation free energy[^2] or binding free energy[^3] estimates. The package is designed to be used with output generated by [CHARMM-GUI](https://charmm-gui.org/).
 
 ## Installation
 
@@ -29,7 +29,7 @@ For more information on how to use transformato please visit the [documentation]
 
 ### Copyright
 
-:copyright: 2022, Marcus Wieder, Johannes Karwounopoulos, Stefan Boresch
+:copyright: 2023, Marcus Wieder, Johannes Karwounopoulos, Stefan Boresch
 
 
 #### Acknowledgements
@@ -39,5 +39,6 @@ Project based on the
 
 
 [^1]:  Wieder, M., Fleck, M., Braunsfeld, B., Boresch, S., *J. Comput. Chem.* 2022, 1. [DOI](https://doi.org/10.1002/jcc.26877)
-[^2]:  Karwounopoulos, J., Wieder, M., Boresch, S., *Front. Mol. Biosci.* 2022, 9, 954638 [DOI](https://doi.org/10.3389/fmolb.2022.954638
+[^2]:  Karwounopoulos, J.,Kaupang, A., Wieder, M., Boresch, S., *JCTC* 2023, 9, 954638 [DOI](https://doi.org/10.1021/acs.jctc.3c00691)
+[^3]:  Karwounopoulos, J., Wieder, M., Boresch, S., *Front. Mol. Biosci.* 2022, 9, 954638 [DOI](https://doi.org/10.3389/fmolb.2022.954638
 )

devtools/conda-envs/fep_env.yaml

@@ -8,7 +8,7 @@ dependencies:
   - openmmtools
   - numpy
   - ipython
-  - pymbar=3
+  - pymbar
   - rdkit
   - parmed
   - pyyaml
@@ -25,5 +25,4 @@ dependencies:
   - codecov
   - pip:
     - git+https://github.com/wiederm/tf_routes.git
-    - git+https://github.com/ParmEd/ParmEd.git
     - git+https://github.com/wiederm/transformato_testsystems.git

transformato/analysis.py

@@ -301,8 +301,12 @@ def calculate_dG_using_mbar(self, u_kn: np.array, N_k: dict, env: str):
             nr_of_snapshots = N_k[env][d] + N_k[env][d + 1]
             u_kn_ = u_kn[d : d + 2 :, start : start + nr_of_snapshots]
             m = mbar.MBAR(u_kn_, N_k[env][d : d + 2])
-            logger.debug(m.getFreeEnergyDifferences(return_dict=True)["Delta_f"][0, 1])
-            logger.debug(m.getFreeEnergyDifferences(return_dict=True)["dDelta_f"][0, 1])
+            logger.debug(
+                m.compute_free_energy_differences(return_dict=True)["Delta_f"][0, 1]
+            )
+            logger.debug(
+                m.compute_free_energy_differences(return_dict=True)["dDelta_f"][0, 1]
+            )
 
             start += N_k[env][d]
 
@@ -690,9 +694,9 @@ def _load_mbar_results(file: str):
     def free_energy_differences(self, env="vacuum"):
         """matrix of free energy differences"""
         try:
-            r = self.mbar_results[env].getFreeEnergyDifferences(return_dict=True)[
-                "Delta_f"
-            ]
+            r = self.mbar_results[env].compute_free_energy_differences(
+                return_dict=True
+            )["Delta_f"]
         except KeyError:
             raise KeyError(f"Free energy difference not obtained for : {env}")
         return r
@@ -709,9 +713,9 @@ def free_energy_overlap(self, env="vacuum"):
     def free_energy_difference_uncertainties(self, env="vacuum"):
         """matrix of asymptotic uncertainty-estimates accompanying free energy differences"""
         try:
-            r = self.mbar_results[env].getFreeEnergyDifferences(return_dict=True)[
-                "dDelta_f"
-            ]
+            r = self.mbar_results[env].compute_free_energy_differences(
+                return_dict=True
+            )["dDelta_f"]
         except KeyError:
             raise KeyError(f"Free energy uncertanties not obtained for : {env}")
         return r

transformato/tests/test_restraints.py

@@ -230,7 +230,8 @@ def test_integration():
     )
 
     simulation.minimizeEnergy(
-        tolerance=inputs.mini_Tol * kilojoule / mole, maxIterations=10
+        tolerance=inputs.mini_Tol * kilojoule / (openmm.unit.nanometer * mole),
+        maxIterations=10,
     )
     logger.info(
         f"Potential energy after 1-iter minimization {simulation.context.getState(getEnergy=True).getPotentialEnergy()}"