[FEATURE] New sandbox_path property

bioexcel · Jun 14, 2024 · 7bd589c · 7bd589c
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commit 7bd589c
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diff --git a/biobb_pmx/pmxbiobb/pmxanalyse.py b/biobb_pmx/pmxbiobb/pmxanalyse.py
@@ -41,6 +41,7 @@ class Pmxanalyse(BiobbObject):
             * **binary_path** (*str*) - ("pmx") Path to the PMX command line interface.
             * **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_pmx/pmxbiobb/pmxatom_mapping.py b/biobb_pmx/pmxbiobb/pmxatom_mapping.py
@@ -46,6 +46,7 @@ class Pmxatom_mapping(BiobbObject):
             * **timeout** (*int*) - (10) Maximum time (s) for an MCS search.
             * **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*) - ("/inout") Path to an internal directory in the container.

diff --git a/biobb_pmx/pmxbiobb/pmxcreate_top.py b/biobb_pmx/pmxbiobb/pmxcreate_top.py
@@ -31,6 +31,7 @@ class Pmxcreate_top(BiobbObject):
             * **mols** (*list*) - ([['Protein',1],['Ligand',1]]) Molecules to be included in the generated topology.
             * **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*) - ("/inout") Path to an internal directory in the container.

diff --git a/biobb_pmx/pmxbiobb/pmxgentop.py b/biobb_pmx/pmxbiobb/pmxgentop.py
@@ -30,6 +30,7 @@ class Pmxgentop(BiobbObject):
             * **binary_path** (*str*) - ("pmx") Path to the PMX command line interface.
             * **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*) - ("/inout") Path to an internal directory in the container.

diff --git a/biobb_pmx/pmxbiobb/pmxligand_hybrid.py b/biobb_pmx/pmxbiobb/pmxligand_hybrid.py
@@ -42,6 +42,7 @@ class Pmxligand_hybrid(BiobbObject):
             * **distance** (*float*) - (0.05) Distance (nm) between atoms to consider them morphable for alignment approach (Only used if input_pairs_path is not provided).
             * **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*) - ("/inout") Path to an internal directory in the container.

diff --git a/biobb_pmx/pmxbiobb/pmxmerge_ff.py b/biobb_pmx/pmxbiobb/pmxmerge_ff.py
@@ -27,6 +27,7 @@ class Pmxmerge_ff(BiobbObject):
         properties (dic):
             * **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*) - ("/inout") Path to an internal directory in the container.

diff --git a/biobb_pmx/pmxbiobb/pmxmutate.py b/biobb_pmx/pmxbiobb/pmxmutate.py
@@ -32,6 +32,7 @@ class Pmxmutate(BiobbObject):
             * **binary_path** (*str*) - ("pmx") Path to the PMX command line interface.
             * **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*) - ("/inout") Path to an internal directory in the container.