Merge pull request #158 from nostrumbiodiscovery/devel

Release of 1.6.0b6

docs/build_docs/source/analysis/index.rst

@@ -132,6 +132,10 @@ class Analysis
             Path to the topology file, if using XTC trajectories.
         cpus: int (optional, default = 1)
             Number of CPUs to use.
+        water_ids_to_track : List (optional, default = [])
+            List of IDs of water molecules to cluster. Each water ID is defined by
+            a tuple that contains the PDB chain and the residue number, e.g.
+            ``water_ids_to_track = [("A", 234), ("A", 235)]``
 
 .. code-block:: python
 

docs/build_docs/source/environment/index.rst

@@ -5,50 +5,111 @@ Mandatory variables
 -------------------
 
 They must be defined for the pele_platform to work correctly:
-	- PELE: path to PELE installation
-	- SCHRODINGER: path to Schrodinger installation
 
-	Examples:
+    - PELE: path to PELE installation
+    - SCHRODINGER: path to Schrodinger installation
 
-	.. code-block:: bash
+    Examples:
 
-		export PELE=/path/to/PELE-1.X/
-		export SCHRODINGER=/path/to/schoringer/20XX/
+    .. code-block:: bash
+
+        export PELE=/path/to/PELE-1.X/
+        export SCHRODINGER=/path/to/schoringer/20XX/
 
 Optional variables
 ------------------
-    - PELE_LICENSE:
 
-    	Licenses can be configured in several ways (from highest to lowest precedence):
+PELE_EXEC:
+++++++++++
+
+    The PELE executable can be configured in several ways (from highest to lowest precedence):
+
+      1. Can be specified by input.yaml flag:
+
+      .. code-block:: yaml
+
+        pele_exec: "/home/pele/bin/Pele_mpi"
+
+      2. Can be specified by environment variable:
+
+      .. code-block:: bash
+
+          export PELE_EXEC=/home/pele/bin/Pele_mpi
+
+      3. If no path is specified, the PELE executable must be ``/path/to/PELE-1.X/bin/Pele_mpi`` (according to the path specified by the environment variable PELE).
+
+PELE_DATA:
+++++++++++
+
+    The PELE data folder can be configured in several ways (from highest to lowest precedence):
+
+      1. Can be specified by input.yaml flag:
+
+      .. code-block:: yaml
+
+        pele_data: "/home/pele/Data/"
+
+      2. Can be specified by environment variable:
+
+      .. code-block:: bash
+
+        export PELE_DATA=/home/pele/Data/
+
+      3. If no path is specified, the PELE data folder must be ``/path/to/PELE-1.X/Data`` (according to the path specified by the environment variable PELE).
+
+PELE_DOCUMENTS:
++++++++++++++++
+
+    The PELE documents folder can be configured in several ways (from highest to lowest precedence):
+
+      1. Can be specified by input.yaml flag:
+
+      .. code-block:: yaml
+
+        pele_documents: "/home/pele/Documents/"
+
+      2. Can be specified by environment variable:
+
+      .. code-block:: bash
+
+        export PELE_DOCUMENTS=/home/pele/Documents/
+
+      3. If no path is specified, the PELE documents folder must be ``/path/to/PELE-1.X/Documents`` (according to the path specified by the environment variable PELE).
+
+PELE_LICENSE:
++++++++++++++
+
+    Licenses can be configured in several ways (from highest to lowest precedence):
 
-    	  1. Can be specified by input.yaml flag: 
+      1. Can be specified by input.yaml flag:
 
-    	  .. code-block:: yaml
+      .. code-block:: yaml
 
-    	  	license: /path/to/licenses/folder/
+        license: /path/to/licenses/folder/
 
-    	  2. Can be specified by environment variable:
+      2. Can be specified by environment variable:
 
-    	  .. code-block:: bash
+      .. code-block:: bash
 
-    	  	export PELE_LICENSE=/path/to/licenses/folder/
+        export PELE_LICENSE=/path/to/licenses/folder/
 
-          3. If no path is specified, licenses must be under /path/to/PELE-1.X/licenses/ (according to the path specified by the environment variable PELE)
+      3. If no path is specified, licenses must be under ``/path/to/PELE-1.X/licenses/`` (according to the path specified by the environment variable PELE).
 
 
-    - SINGULARITY_EXEC:
+SINGULARITY_EXEC:
++++++++++++++++++
 
-    	Path of the singularity container that contains the PELE executable. It can be configured in two ways:
+    Path of the singularity container that contains the PELE executable. It can be configured in two ways:
 
-    	  1. Can be specified by input.yaml flag
+      1. Can be specified by input.yaml flag:
 
-    	  .. code-block:: yaml
+      .. code-block:: yaml
 
-    	  	singularity_exec: /path/to/singularity/container/
+        singularity_exec: /path/to/singularity/container/
 
 
-    	  2. Can be specified by environment variable:
+      2. Can be specified by environment variable:
 
-    	  .. code-block:: bash
+      .. code-block:: bash
 
-    		export SINGULARITY_EXEC=/path/to/singularity/container/
+        export SINGULARITY_EXEC=/path/to/singularity/container/

pele_platform/Adaptive/simulation.py

@@ -45,7 +45,7 @@ def run_adaptive(args):
             adaptiveSampling.main(parameters.ad_ex_temp)
             parameters.logger.info("Simulation run successfully (:\n\n")
 
-    elif not parameters.only_analysis:
+    elif not parameters.only_analysis and not parameters.restart:
         parameters.logger.info(
             "System: {}; Platform Functionality: {}\n\n".format(
                 parameters.residue, parameters.software))
@@ -334,6 +334,13 @@ def run_adaptive(args):
             adaptive.run()
             parameters.logger.info("Simulation run successfully (:\n\n")
 
+    elif parameters.restart:
+        # Start simulation from scratch (unlike adaptive_restart) but use files created in debug mode
+        parameters.logger.info(f"Launching simulation from {parameters.pele_dir}")
+        adaptive = ad.SimulationBuilder(parameters.ad_ex_temp, parameters.pele_exit_temp, parameters.topology)
+        adaptive.run()
+        parameters.logger.info("Simulation run successfully (:\n\n")
+
     # Run analysis
     if parameters.analyse and not parameters.debug:
         from pele_platform.analysis import Analysis

pele_platform/Checker/main.py

@@ -20,10 +20,10 @@ def check_variables(self, args: yp.YamlParser) -> None:
 
     def _generate_env_variables(self, args: yp.YamlParser) -> list:
         self.env_variables = [
-        en.EnvVariable("pele_data", args.pele_data, os.path.join(cs.PELE, "Data"), "--pele_data /path/to/data/folder/", "export PELE=/path/to/PELE-1.X/"),
-        en.EnvVariable("pele_documents", args.pele_documents, os.path.join(cs.PELE, "Documents"), "--pele_documents /path/to/documents/folder", "export PELE=/path/to/PELE-1.X/"),
-        en.EnvVariable("pele_exec", args.pele_exec, os.path.join(cs.PELE, "bin/Pele_mpi"), "--pele_exec /path/to/PELE_exec", "export PELE=/path/to/PELE-1.X/"),
-        en.EnvVariable("pele_license", args.pele_license, cs.DEFAULT_PELE_LICENSE, "--pele_license /path/to/licenses", "export PELE=/path/to/PELE-1.X/"),
+        en.EnvVariable("pele_data", args.pele_data, cs.DEFAULT_PELE_DATA, "--pele_data /path/to/data/folder/", "export PELE_DATA=/path/to/PELE-Data/folder"),
+        en.EnvVariable("pele_documents", args.pele_documents, cs.DEFAULT_PELE_DOCUMENTS, "--pele_documents /path/to/documents/folder", "export PELE_DOCUMENTS=/path/to/PELE-Documents/folder"),
+        en.EnvVariable("pele_exec", args.pele_exec, cs.DEFAULT_PELE_EXEC, "--pele_exec /path/to/PELE_exec", "export PELE_EXEC=/path/to/PELE-1.X/binary"),
+        en.EnvVariable("pele_license", args.pele_license, cs.DEFAULT_PELE_LICENSE, "--pele_license /path/to/licenses", "export PELE_LICENSE=/path/to/PELE-License/folder"),
         en.EnvVariable("schrodinger", args.schrodinger, cs.SCHRODINGER, "--schrodinger /path/to/schrodinger-20XX/", "export SCHRODINGER=/path/to/schrodinger-20XX/")
         ]
         return self.env_variables

pele_platform/PPI/main.py

@@ -41,9 +41,10 @@ def run_ppi(parsed_yaml: dict) -> (pv.ParametersBuilder, pv.ParametersBuilder):
 
     # no waters in the first simulation
     parsed_yaml.water_arg = None
+    parsed_yaml.use_peleffy = parsed_yaml.use_peleffy if parsed_yaml.use_peleffy is not None else False
 
     # remove chains except for "protein" flag
-    protein_file = prepare_structure(protein_file, ligand_pdb, chain, True)
+    protein_file = prepare_structure(protein_file, ligand_pdb, chain, True, peleffy=parsed_yaml.use_peleffy)
     parsed_yaml.system = protein_file
 
     # start simulation 1 - induced fit

pele_platform/PPI/preparation.py

@@ -4,7 +4,7 @@
 from pele_platform.constants import constants
 
 
-def prepare_structure(protein_file, ligand_pdb, chain, remove_water=False):
+def prepare_structure(protein_file, ligand_pdb, chain, remove_water=False, peleffy=False):
 
     to_remove = []
 
@@ -41,9 +41,10 @@ def prepare_structure(protein_file, ligand_pdb, chain, remove_water=False):
         for line in ligand:
             file.write(line)
 
-    # Run through Schrodinger again to add CONECT lines.
-    schrodinger_path = os.path.join(constants.SCHRODINGER, "utilities/prepwizard")
-    command_pdb = f"{schrodinger_path} -nohtreat -noepik -noprotassign -noimpref -noccd -NOJOBID {protein} {new_protein_file}"
-    subprocess.call(command_pdb.split(), shell=True)
+    if peleffy:
+        # Run through Schrodinger again to add CONECT lines.
+        schrodinger_path = os.path.join(constants.SCHRODINGER, "utilities/prepwizard")
+        command_pdb = f"{schrodinger_path} -nohtreat -noepik -noprotassign -noimpref -noccd -NOJOBID {protein_file} {new_protein_file}"
+        subprocess.call(command_pdb.split(), shell=True)
 
     return new_protein_file

pele_platform/Utilities/Helpers/helpers.py

@@ -382,7 +382,7 @@ def check_remove_folder(*output_folders):
     """
     for folder in output_folders:
         if os.path.exists(folder):
-            shutil.rmtree(folder)
+            shutil.rmtree(folder, ignore_errors=True)
 
 
 def get_atom_indices(ids, pdb, pdb_atom_name=None):