[FEATURE] New sandbox_path property

bioexcel · Jun 14, 2024 · 4872f99 · 4872f99
1 parent eb47782
commit 4872f99
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Showing 11 changed files with 50 additions and 27 deletions.
diff --git a/biobb_md/gromacs/editconf.py b/biobb_md/gromacs/editconf.py
@@ -28,6 +28,7 @@ class Editconf(BiobbObject):
             * **gmx_path** (*str*) - ("gmx") Path to the GROMACS executable binary.
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
+            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
             * **container_path** (*str*) - (None)  Path to the binary executable of your container.
             * **container_image** (*str*) - (None) Container Image identifier.
             * **container_volume_path** (*str*) - ("/data") Path to an internal directory in the container.
@@ -92,7 +93,8 @@ def launch(self) -> int:
         """Execute the :class:`Editconf <gromacs.editconf.Editconf>` object."""
 
         # Setup Biobb
-        if self.check_restart(): return 0
+        if self.check_restart():
+            return 0
         self.stage_files()
 
         # Create command line

diff --git a/biobb_md/gromacs/genion.py b/biobb_md/gromacs/genion.py
@@ -34,6 +34,7 @@ class Genion(BiobbObject):
             * **gmx_path** (*str*) - ("gmx") Path to the GROMACS executable binary.
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
+            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
             * **container_path** (*str*) - (None)  Path to the binary executable of your container.
             * **container_image** (*str*) - ("gromacs/gromacs:latest") Container Image identifier.
             * **container_volume_path** (*str*) - ("/data") Path to an internal directory in the container.
@@ -62,6 +63,7 @@ class Genion(BiobbObject):
             * name: EDAM
             * schema: http://edamontology.org/EDAM.owl
     """
+
     def __init__(self, input_tpr_path: str, output_gro_path: str, input_top_zip_path: str,
                  output_top_zip_path: str, input_ndx_path: str = None, properties: dict = None, **kwargs) -> None:
         properties = properties or {}
@@ -104,7 +106,8 @@ def launch(self) -> int:
         """Execute the :class:`Genion <gromacs.genion.Genion>` object."""
 
         # Setup Biobb
-        if self.check_restart(): return 0
+        if self.check_restart():
+            return 0
         self.stage_files()
 
         # Unzip topology to topology_out

diff --git a/biobb_md/gromacs/genrestr.py b/biobb_md/gromacs/genrestr.py
@@ -28,6 +28,7 @@ class Genrestr(BiobbObject):
             * **gmx_path** (*str*) - ("gmx") Path to the GROMACS executable binary.
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
+            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
             * **container_path** (*str*) - (None)  Path to the binary executable of your container.
             * **container_image** (*str*) - ("gromacs/gromacs:latest") Container Image identifier.
             * **container_volume_path** (*str*) - ("/data") Path to an internal directory in the container.
@@ -92,7 +93,8 @@ def launch(self) -> int:
         """Execute the :class:`Grompp <gromacs.grompp.Grompp>` object."""
 
         # Setup Biobb
-        if self.check_restart(): return 0
+        if self.check_restart():
+            return 0
         self.stage_files()
 
         self.cmd = ['echo', '\"'+self.restrained_group+'\"', '|',

diff --git a/biobb_md/gromacs/gmxselect.py b/biobb_md/gromacs/gmxselect.py
@@ -29,6 +29,7 @@ class Gmxselect(BiobbObject):
             * **gmx_lib** (*str*) - (None) Path set GROMACS GMXLIB environment variable.
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
+            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
             * **container_path** (*str*) - (None)  Path to the binary executable of your container.
             * **container_image** (*str*) - ("gromacs/gromacs:latest") Container Image identifier.
             * **container_volume_path** (*str*) - ("/data") Path to an internal directory in the container.
@@ -92,7 +93,8 @@ def launch(self) -> int:
         """Execute the :class:`Gmxselect <gromacs.gmxselect.Gmxselect>` object."""
 
         # Setup Biobb
-        if self.check_restart(): return 0
+        if self.check_restart():
+            return 0
         self.stage_files()
 
         self.cmd = [self.gmx_path, 'select',

diff --git a/biobb_md/gromacs/grompp.py b/biobb_md/gromacs/grompp.py
@@ -36,6 +36,7 @@ class Grompp(BiobbObject):
             * **gmx_path** (*str*) - ("gmx") Path to the GROMACS executable binary.
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
+            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
             * **container_path** (*str*) - (None)  Path to the binary executable of your container.
             * **container_image** (*str*) - ("gromacs/gromacs:latest") Container Image identifier.
             * **container_volume_path** (*str*) - ("/data") Path to an internal directory in the container.
@@ -121,7 +122,8 @@ def launch(self) -> int:
         """Execute the :class:`Grompp <gromacs.grompp.Grompp>` object."""
 
         # Setup Biobb
-        if self.check_restart(): return 0
+        if self.check_restart():
+            return 0
         self.stage_files()
 
         # Unzip topology to topology_out
@@ -146,13 +148,13 @@ def launch(self) -> int:
             top_file = str(Path(self.container_volume_path).joinpath(Path(top_dir).name, Path(top_file).name))
 
         self.cmd = [self.gmx_path, 'grompp',
-               '-f', self.output_mdp_path,
-               '-c', self.stage_io_dict["in"]["input_gro_path"],
-               '-r', self.stage_io_dict["in"]["input_gro_path"],
-               '-p', top_file,
-               '-o', self.stage_io_dict["out"]["output_tpr_path"],
-               '-po', 'mdout.mdp',
-               '-maxwarn', self.maxwarn]
+                    '-f', self.output_mdp_path,
+                    '-c', self.stage_io_dict["in"]["input_gro_path"],
+                    '-r', self.stage_io_dict["in"]["input_gro_path"],
+                    '-p', top_file,
+                    '-o', self.stage_io_dict["out"]["output_tpr_path"],
+                    '-po', 'mdout.mdp',
+                    '-maxwarn', self.maxwarn]
 
         if self.stage_io_dict["in"].get("input_cpt_path") and Path(self.stage_io_dict["in"]["input_cpt_path"]).exists():
             self.cmd.append('-t')

diff --git a/biobb_md/gromacs/grompp_mdrun.py b/biobb_md/gromacs/grompp_mdrun.py
@@ -49,6 +49,7 @@ class GromppMdrun(BiobbObject):
             * **gmx_path** (*str*) - ("gmx") Path to the GROMACS executable binary.
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
+            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
             * **container_path** (*str*) - (None)  Path to the binary executable of your container.
             * **container_image** (*str*) - ("gromacs/gromacs:latest") Container Image identifier.
             * **container_volume_path** (*str*) - ("/data") Path to an internal directory in the container.

diff --git a/biobb_md/gromacs/make_ndx.py b/biobb_md/gromacs/make_ndx.py
@@ -28,6 +28,7 @@ class MakeNdx(BiobbObject):
             * **gmx_path** (*str*) - ("gmx") Path to the GROMACS executable binary.
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
+            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
             * **container_path** (*str*) - (None)  Path to the binary executable of your container.
             * **container_image** (*str*) - ("gromacs/gromacs:latest") Container Image identifier.
             * **container_volume_path** (*str*) - ("/data") Path to an internal directory in the container.
@@ -53,6 +54,7 @@ class MakeNdx(BiobbObject):
             * name: EDAM
             * schema: http://edamontology.org/EDAM.owl
     """
+
     def __init__(self, input_structure_path: str, output_ndx_path: str, input_ndx_path: str = None,
                  properties: dict = None, **kwargs) -> None:
         properties = properties or {}
@@ -89,15 +91,16 @@ def launch(self) -> int:
         """Execute the :class:`MakeNdx <gromacs.make_ndx.MakeNdx>` object."""
 
         # Setup Biobb
-        if self.check_restart(): return 0
+        if self.check_restart():
+            return 0
         self.stage_files()
 
         # Create command line
         self.cmd = ['echo', '-e', '\'' + self.selection + '\\nq' + '\'', '|',
-               self.gmx_path, 'make_ndx',
-               '-f', self.stage_io_dict["in"]["input_structure_path"],
-               '-o', self.stage_io_dict["out"]["output_ndx_path"]
-               ]
+                    self.gmx_path, 'make_ndx',
+                    '-f', self.stage_io_dict["in"]["input_structure_path"],
+                    '-o', self.stage_io_dict["out"]["output_ndx_path"]
+                    ]
 
         if self.stage_io_dict["in"].get("input_ndx_path")\
                 and Path(self.stage_io_dict["in"].get("input_ndx_path")).exists():

diff --git a/biobb_md/gromacs/mdrun.py b/biobb_md/gromacs/mdrun.py
@@ -43,6 +43,7 @@ class Mdrun(BiobbObject):
             * **gmx_path** (*str*) - ("gmx") Path to the GROMACS executable binary.
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
+            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
             * **container_path** (*str*) - (None)  Path to the binary executable of your container.
             * **container_image** (*str*) - (None) Container Image identifier.
             * **container_volume_path** (*str*) - ("/data") Path to an internal directory in the container.
@@ -128,7 +129,8 @@ def launch(self) -> int:
         """Execute the :class:`Mdrun <gromacs.mdrun.Mdrun>` object."""
 
         # Setup Biobb
-        if self.check_restart(): return 0
+        if self.check_restart():
+            return 0
         self.stage_files()
 
         self.cmd = [self.gmx_path, 'mdrun',
@@ -182,7 +184,7 @@ def launch(self) -> int:
             self.cmd.append('-ntomp_pme')
             self.cmd.append(self.num_threads_omp_pme)
         # GMX gpu properties
-        if self.use_gpu: 
+        if self.use_gpu:
             fu.log('Adding GPU specific settings adds: -nb gpu -pme gpu', self.out_log)
             self.cmd += ["-nb", "gpu", "-pme", "gpu"]
         if self.gpu_id:
@@ -194,7 +196,6 @@ def launch(self) -> int:
             self.cmd.append('-gputasks')
             self.cmd.append(self.gpu_tasks)
 
-
         if self.gmx_lib:
             self.environment = os.environ.copy()
             self.environment['GMXLIB'] = self.gmx_lib
@@ -257,7 +258,7 @@ def main():
     # Specific call of each building block
     mdrun(input_tpr_path=args.input_tpr_path, output_trr_path=args.output_trr_path,
           output_gro_path=args.output_gro_path, output_edr_path=args.output_edr_path,
-          output_log_path=args.output_log_path, input_cpt_path=args.input_cpt_path, 
+          output_log_path=args.output_log_path, input_cpt_path=args.input_cpt_path,
           output_xtc_path=args.output_xtc_path, output_cpt_path=args.output_cpt_path,
           output_dhdl_path=args.output_dhdl_path, properties=properties)
 

diff --git a/biobb_md/gromacs/pdb2gmx.py b/biobb_md/gromacs/pdb2gmx.py
@@ -31,6 +31,7 @@ class Pdb2gmx(BiobbObject):
             * **gmx_path** (*str*) - ("gmx") Path to the GROMACS executable binary.
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
+            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
             * **container_path** (*str*) - (None)  Path to the binary executable of your container.
             * **container_image** (*str*) - ("gromacs/gromacs:latest") Container Image identifier.
             * **container_volume_path** (*str*) - ("/data") Path to an internal directory in the container.
@@ -72,8 +73,8 @@ def __init__(self, input_pdb_path: str, output_gro_path: str, output_top_zip_pat
         }
 
         # Properties specific for BB
-        self.internal_top_name = properties.get('internal_top_name', 'p2g.top') # Excluded from documentation for simplicity
-        self.internal_itp_name = properties.get('internal_itp_name', 'posre.itp') # Excluded from documentation for simplicity
+        self.internal_top_name = properties.get('internal_top_name', 'p2g.top')  # Excluded from documentation for simplicity
+        self.internal_itp_name = properties.get('internal_itp_name', 'posre.itp')  # Excluded from documentation for simplicity
         self.water_type = properties.get('water_type', 'spce')
         self.force_field = properties.get('force_field', 'amber99sb-ildn')
         self.ignh = properties.get('ignh', False)
@@ -100,7 +101,8 @@ def launch(self) -> int:
         """Execute the :class:`Pdb2gmx <gromacs.pdb2gmx.Pdb2gmx>` object."""
 
         # Setup Biobb
-        if self.check_restart(): return 0
+        if self.check_restart():
+            return 0
         self.stage_files()
 
         internal_top_name = fu.create_name(prefix=self.prefix, step=self.step, name=self.internal_top_name)

diff --git a/biobb_md/gromacs/solvate.py b/biobb_md/gromacs/solvate.py
@@ -31,6 +31,7 @@ class Solvate(BiobbObject):
             * **gmx_path** (*str*) - ("gmx") Path to the GROMACS executable binary.
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
+            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
             * **container_path** (*str*) - (None)  Path to the binary executable of your container.
             * **container_image** (*str*) - ("gromacs/gromacs:latest") Container Image identifier.
             * **container_volume_path** (*str*) - ("/data") Path to an internal directory in the container.
@@ -59,6 +60,7 @@ class Solvate(BiobbObject):
             * name: EDAM
             * schema: http://edamontology.org/EDAM.owl
     """
+
     def __init__(self, input_solute_gro_path: str, output_gro_path: str, input_top_zip_path: str,
                  output_top_zip_path: str, input_solvent_gro_path: str = None, properties: dict = None, **kwargs) -> None:
         properties = properties or {}
@@ -100,7 +102,8 @@ def launch(self) -> int:
         """Execute the :class:`Solvate <gromacs.solvate.Solvate>` object."""
 
         # Setup Biobb
-        if self.check_restart(): return 0
+        if self.check_restart():
+            return 0
         self.stage_files()
 
         # Unzip topology to topology_out

diff --git a/biobb_md/gromacs_extra/append_ligand.py b/biobb_md/gromacs_extra/append_ligand.py
@@ -26,6 +26,7 @@ class AppendLigand(BiobbObject):
             * **posres_name** (*str*) - ("POSRES_LIGAND") String to be included in the ifdef clause.
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
+            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
 
     Examples:
         This is a use example of how to use the building block from Python::
@@ -70,7 +71,8 @@ def __init__(self, input_top_zip_path: str, input_itp_path: str, output_top_zip_
     def launch(self) -> int:
         """Execute the :class:`AppendLigand <gromacs_extra.append_ligand.AppendLigand>` object."""
         # Setup Biobb
-        if self.check_restart(): return 0
+        if self.check_restart():
+            return 0
 
         # Unzip topology
         top_file = fu.unzip_top(zip_file=self.io_dict['in'].get("input_top_zip_path"), out_log=self.out_log)
@@ -176,7 +178,7 @@ def main():
     args = parser.parse_args()
     config = args.config if args.config else None
     properties = settings.ConfReader(config=config).get_prop_dic()
-    
+
     # Specific call of each building block
     append_ligand(input_top_zip_path=args.input_top_zip_path, input_itp_path=args.input_itp_path,
                   output_top_zip_path=args.output_top_zip_path, input_posres_itp_path=args.input_posres_itp_path,