[FEATURE] New sandbox_path property

bioexcel · Jun 14, 2024 · 3a7722b · 3a7722b
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commit 3a7722b
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diff --git a/biobb_gromacs/gromacs/editconf.py b/biobb_gromacs/gromacs/editconf.py
@@ -28,6 +28,7 @@ class Editconf(BiobbObject):
             * **binary_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.

diff --git a/biobb_gromacs/gromacs/genion.py b/biobb_gromacs/gromacs/genion.py
@@ -33,6 +33,7 @@ class Genion(BiobbObject):
             * **binary_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_gromacs/gromacs/genrestr.py b/biobb_gromacs/gromacs/genrestr.py
@@ -28,6 +28,7 @@ class Genrestr(BiobbObject):
             * **binary_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_gromacs/gromacs/gmxselect.py b/biobb_gromacs/gromacs/gmxselect.py
@@ -28,6 +28,7 @@ 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.

diff --git a/biobb_gromacs/gromacs/grompp.py b/biobb_gromacs/gromacs/grompp.py
@@ -36,6 +36,7 @@ class Grompp(BiobbObject):
             * **binary_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_gromacs/gromacs/grompp_mdrun.py b/biobb_gromacs/gromacs/grompp_mdrun.py
@@ -50,6 +50,7 @@ class GromppMdrun(BiobbObject):
             * **binary_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_gromacs/gromacs/make_ndx.py b/biobb_gromacs/gromacs/make_ndx.py
@@ -27,6 +27,7 @@ class MakeNdx(BiobbObject):
             * **binary_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_gromacs/gromacs/mdrun.py b/biobb_gromacs/gromacs/mdrun.py
@@ -42,6 +42,7 @@ class Mdrun(BiobbObject):
             * **binary_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.

diff --git a/biobb_gromacs/gromacs/pdb2gmx.py b/biobb_gromacs/gromacs/pdb2gmx.py
@@ -31,6 +31,7 @@ class Pdb2gmx(BiobbObject):
             * **binary_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_gromacs/gromacs/solvate.py b/biobb_gromacs/gromacs/solvate.py
@@ -30,6 +30,7 @@ class Solvate(BiobbObject):
             * **binary_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_gromacs/gromacs/trjcat.py b/biobb_gromacs/gromacs/trjcat.py
@@ -28,6 +28,7 @@ class Trjcat(BiobbObject):
             * **binary_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.

diff --git a/biobb_gromacs/gromacs_extra/append_ligand.py b/biobb_gromacs/gromacs_extra/append_ligand.py
@@ -27,6 +27,7 @@ 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::