Merge branch 'master' into support_point_mutation

.codecov.yml

@@ -5,10 +5,12 @@ coverage:
     project:
       default:
         threshold: 50%
+ignore:
+  - "transformato/testsystems.py"  # ignore folders and all its contents
 comment:
   layout: "header"
   require_changes: false
   branches: null
   behavior: default
   flags: null
-  paths: null
+  paths: null

.github/workflows/CI.yaml

@@ -32,11 +32,24 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [macOS-latest, ubuntu-latest]
-        python-version: [3.8, 3.9]
+        # os: [macOS-latest, ubuntu-latest]
+        os: [ubuntu-latest]
+        python-version: [3.9]
+        include:
+          - os: ubuntu-latest
+            label: linux-64
+            # prefix: /usr/share/miniconda3/envs/openmm7.6
+            environment-file: devtools/conda-envs/fep_env.yaml
+            miniforge-variant: Mambaforge
+            miniforge-version: 4.9.2-4
+          #- os: macos-latest
+          #  label: osx-64
+          #  # prefix: /Users/runner/miniconda3/envs/openmm7.6
+          #  environment-file: devtools/conda-envs/openmm7.6.yaml
+          #  miniforge-variant: Mambaforge-pypy3
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v3
 
     - name: Additional info about the build
       shell: bash
@@ -50,7 +63,7 @@ jobs:
 
     - name: Make Cache (no worflow_dispatch)
       if: ${{ github.event_name != 'workflow_dispatch' }}
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       with:
         path: ~/conda_pkgs_dir # ${{ matrix.prefix }}
         # Increase the last number (0) to reset cache manually
@@ -70,12 +83,17 @@ jobs:
     - uses: conda-incubator/setup-miniconda@v2
       with:
         python-version: ${{ matrix.python-version }}
-        environment-file: devtools/conda-envs/fep_env.yaml
-
+        condarc-file: ${{ matrix.condarc-file }}
+        environment-file: ${{ matrix.environment-file }}
+        miniforge-variant: ${{ matrix.miniforge-variant }}
+        miniforge-version: ${{ matrix.miniforge-version }}
+        use-mamba: true
+        # mamba-version: "*"
+        # environment-file: devtools/conda-envs/fep_env.yaml
         channels: conda-forge,defaults
-
-        activate-environment: test
-        auto-update-conda: false
+        # channel-priority: true
+        activate-environment: fep
+        #auto-update-conda: false
         auto-activate-base: false
         #show-channel-urls: true
         use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
@@ -89,7 +107,11 @@ jobs:
       shell: bash -l {0}
       run: |
         python -m pip install . --no-deps
+        conda info
         conda list
+        conda config --show-sources
+        conda config --show
+        printenv | sort
 
 
     - name: Run tests

.github/workflows/lint_python.yml → .github/workflows/black.yml

@@ -1,4 +1,4 @@
-name: lint_python
+name: Black Formatter
 
 on: [pull_request, workflow_dispatch]
 
@@ -8,7 +8,7 @@ permissions:
 
 jobs:
   run-linters:
-    name: Run linters
+    name: Black Formatting
     runs-on: ubuntu-latest
 
     steps:
@@ -23,9 +23,10 @@ jobs:
       - name: Install Python dependencies
         run: pip install black
 
-      - name: Run linters
+      - name: Run Black formatting
         uses: wearerequired/lint-action@v2
         with:
+          repo-token: "${{ secrets.GITHUB_TOKEN }}"
           black: true
           black_dir: "transformato/"
           black_args: '--extend-exclude="(bin/*|scripts/*|_version.py)"'
@@ -35,12 +36,12 @@ jobs:
 #           flake8_args: "--exclude=scripts,bin,_version.py --max-line-length=88 --extend-ignore=E203 --exit-zero"
 
 
-      #- name: Setup flake8 annotations
-      #  uses: rbialon/flake8-annotations@v1
-      #- name: Lint with flake8
-      #  run: |
-      #    pip install flake8 pep8-naming
-      #    # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-      #    flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+#       - name: Setup flake8 annotations
+#        uses: rbialon/flake8-annotations@v1
+#       - name: Lint with flake8
+#        run: |
+#          pip install flake8 pep8-naming
+#          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+#          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
 
 

devtools/conda-envs/fep_env.yaml

@@ -17,11 +17,13 @@ dependencies:
   - matplotlib
   - networkx
   - tqdm
+  - pip
   - seaborn
     # Testing
   - pytest
   - pytest-cov
   - 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

docs/index.rst

@@ -3,23 +3,21 @@
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.
  
-Welcome to the documentation for |trafo|!
+Welcome to the documentation for transformato!
 =========================================================
 
-The python package |trafo| is an implementation of the Common Core / Serial-Atom-Insertion
-(CC-SAI) approach\ [1]_ for calculating free energy differences\.
+The python package transformato (**T**\ ool **R**\ unning MD **A**\ g\ **N**\ o\ **S**\ tic Calculations **FOR** **M**\ ultistate Serial **ATO**\ m Insertion) is an implementation of the Common Core / Serial-Atom-Insertion
+(CC-SAI) approach [1]_ for calculating free energy differences\.
 It does so by connecting the physical endstates of two molecules via alchemical pathways.
 
 It requires very little set-up time and is designed to work directly with output from
 `CHARMM - GUI <http://www.charmm-gui.org>`_\. Currently either **relative solvation free energies** (RSFE) [2]_
 or **relative binding free energies** (RBFE) [3]_ can be calculated. For the production runs either
-`CHARMM <https://academiccharmm.org/>`_\ or `openMM <https://openmm.org/>`_\ are required.
+`CHARMM <https://academiccharmm.org/>`_\  or `openMM <https://openmm.org/>`_\  are required.
 
 If you'd like to take a look at the code,
 head over to our `github repository <https://github.com/wiederm/transformato>`_\ .
 
-Das ist jetzt aber der letzte test
-
 
 .. toctree::
   :maxdepth: 2
@@ -41,7 +39,7 @@ Das ist jetzt aber der letzte test
  
 .. [2] Wieder, M., Fleck, M., Braunsfeld, B., and Boresch, S. (2022). *Alchemical free energy simulations without speed limits. A generic framework to calculate free energy differences independent of the underlying molecular dynamics program.* J. Comput. Chem. 43, 1151–1160, `DOI ⤶ <https://doi.org/10.1002/jcc.26877>`_
  
-.. [3] Karwounopoulos, J., Wieder, M., and Boresch, S. (2022). *Relative binding free energy calculations with Transformato: a molecular dynamics engine-independent tool.* Front. Mol. Biosic., *submitted*.
+.. [3] Karwounopoulos, J., Wieder, M., and Boresch, S. (2022). *Relative binding free energy calculations with Transformato: a molecular dynamics engine-independent tool.* Front. Mol. Biosic. 9:954638, `DOI ⤶ <https://doi.org/10.3389/fmolb.2022.954638>`_
  
 .. rubric:: Maintainers
 

transformato/analysis.py

@@ -292,7 +292,6 @@ def _parse_CHARMM_energy_output(path: str, env: str) -> list:
         return pot_energies
 
     def calculate_dG_using_mbar(self, u_kn: np.array, N_k: dict, env: str):
-
         logger.debug("#######################################")
         logger.debug("Pairwise Free Energy Estimate")
         logger.debug("#######################################")
@@ -453,7 +452,6 @@ def energy_at_lambda(
         energies = []
 
         for lambda_state in range(1, self.nr_of_states + 1):
-
             if not multiple_runs:
                 dcd_path = f"{self.base_path}/intst{lambda_state}/{conf_sub['intermediate-filename']}.dcd"
             else:
@@ -518,7 +516,6 @@ def _analyse_results_using_mda(
         multiple_runs: int,
         in_memory: bool = False,
     ):
-
         logger.info(f"Evaluating with {engine}, using {num_proc} CPUs")
         if not os.path.isdir(self.base_path):
             sys.exit(f"{self.base_path} does not exist")
@@ -579,7 +576,6 @@ def _analyse_results_using_mdtraj(
         save_results: bool,
         engine: str,
     ):
-
         logger.debug(f"Evaluating with {engine}")
 
         if engine == "openMM":
@@ -599,7 +595,7 @@ def _analyse_results_using_mdtraj(
         elif engine == "CHARMM":
             confs = []
             # write out traj in self.base_path
-            for (dcd, psf) in self.traj_files[env]:
+            for dcd, psf in self.traj_files[env]:
                 traj = mdtraj.load(
                     f"{dcd}",
                     top=f"{psf}",
@@ -801,7 +797,7 @@ def plot_free_energy_overlap(self, env: str):
         plt.close()
 
     def plot_free_energy(self, env: str):
-        plt.figure(figsize=[4, 4], dpi=300)
+        plt.figure(figsize=[8, 8], dpi=300)
         if env == "vacuum":
             x = [
                 a
@@ -865,7 +861,6 @@ def end_state_free_energy_difference(self):
             raise RuntimeError()
 
     def show_summary(self):
-
         if (
             self.configuration["simulation"]["free-energy-type"] == "rsfe"
             or self.configuration["simulation"]["free-energy-type"] == "asfe"
@@ -886,7 +881,6 @@ def show_summary(self):
         )
 
     def detailed_overlap(self, env):
-
         mbar_matrix = self.free_energy_overlap(env=env)
         upper = np.diagonal(mbar_matrix, offset=1)
         lower = np.diagonal(mbar_matrix, offset=-1)

transformato/annihilation.py

@@ -8,7 +8,6 @@
 
 
 def calculate_order_of_LJ_mutations_asfe(central_atoms: list, G: nx.Graph) -> list:
-
     ordered_LJ_mutations = []
     root = central_atoms[0]
 
@@ -18,7 +17,6 @@ def calculate_order_of_LJ_mutations_asfe(central_atoms: list, G: nx.Graph) -> li
     G_dummy = G.copy()
 
     while len(G_dummy.nodes()) > 0:
-
         G_origweights = G_dummy.copy()
 
         # dijkstra

transformato/charmm_factory.py

@@ -9,7 +9,6 @@ class CharmmFactory:
     """Class to build the string needed to create a CHARMM input and streaming file"""
 
     def __init__(self, configuration: dict, structure: str) -> None:
-
         self.configuration = configuration
         self.structure = structure
         prms = self._get_simulations_parameters()
@@ -24,7 +23,6 @@ def _get_simulations_parameters(self):
         return prms
 
     def generate_CHARMM_postprocessing_files(self, env: str) -> str:
-
         charmm_postprocessing_script = self._get_CHARMM_postprocessing_header(env)
         if env == "vacuum":
             charmm_postprocessing_script += self._get_CHARMM_vacuum_postprocessing_body(
@@ -499,7 +497,6 @@ def _get_CHARMM_waterbox_production_body(self, env):
         return body
 
     def _get_CHARMM_postprocessing_header(self, env: str) -> str:
-
         intermediate_filename = self.configuration["system"][self.structure][env][
             "intermediate-filename"
         ]

transformato/constants.py

@@ -32,7 +32,6 @@ def initialize_NUM_PROC(n_proc):
 
 
 def change_platform_to_test_platform(configuration: dict, engine: str):
-
     if engine == "openMM":
         change_to = test_platform_openMM
     elif engine == "CHARMM":
@@ -51,7 +50,6 @@ def change_platform_to_test_platform(configuration: dict, engine: str):
 
 
 def change_platform_to(configuration: dict, change_to: str):
-
     if change_to.upper() == "GPU":
         configuration["simulation"]["GPU"] = True
         print("Setting platform to GPU")