From 61efee481239aecfca99387f6720bf929e6af687 Mon Sep 17 00:00:00 2001 From: Pau Andrio Date: Fri, 14 Jun 2024 17:20:17 +0200 Subject: [PATCH] [FEATURE] New sandbox_path property --- biobb_io/api/alphafold.py | 1 + biobb_io/api/api_binding_site.py | 1 + biobb_io/api/canonical_fasta.py | 1 + biobb_io/api/drugbank.py | 1 + biobb_io/api/ideal_sdf.py | 1 + biobb_io/api/ligand.py | 1 + biobb_io/api/memprotmd_sim.py | 1 + biobb_io/api/memprotmd_sim_list.py | 1 + biobb_io/api/memprotmd_sim_search.py | 1 + biobb_io/api/mmcif.py | 1 + biobb_io/api/pdb.py | 1 + biobb_io/api/pdb_cluster_zip.py | 1 + biobb_io/api/pdb_variants.py | 1 + biobb_io/api/structure_info.py | 1 + 14 files changed, 14 insertions(+) diff --git a/biobb_io/api/alphafold.py b/biobb_io/api/alphafold.py index 0bc91f0..9c23ceb 100755 --- a/biobb_io/api/alphafold.py +++ b/biobb_io/api/alphafold.py @@ -20,6 +20,7 @@ class AlphaFold(BiobbObject): * **uniprot_code** (*str*) - (None) Uniprot code. * **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:: diff --git a/biobb_io/api/api_binding_site.py b/biobb_io/api/api_binding_site.py index 3692f5c..3dd5c01 100755 --- a/biobb_io/api/api_binding_site.py +++ b/biobb_io/api/api_binding_site.py @@ -22,6 +22,7 @@ class ApiBindingSite(BiobbObject): * **pdb_code** (*str*) - (None) RSCB PDB code. * **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:: diff --git a/biobb_io/api/canonical_fasta.py b/biobb_io/api/canonical_fasta.py index d4608f6..735d2c4 100755 --- a/biobb_io/api/canonical_fasta.py +++ b/biobb_io/api/canonical_fasta.py @@ -21,6 +21,7 @@ class CanonicalFasta(BiobbObject): * **api_id** (*str*) - ("pdbe") Identifier of the PDB REST API from which the PDB structure will be downloaded. Values: pdbe (`PDB in Europe REST API `_), pdb (`RCSB PDB REST API `_), mmb (`MMB PDB mirror API `_). * **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:: diff --git a/biobb_io/api/drugbank.py b/biobb_io/api/drugbank.py index 0779f4f..063f1d1 100755 --- a/biobb_io/api/drugbank.py +++ b/biobb_io/api/drugbank.py @@ -20,6 +20,7 @@ class Drugbank(BiobbObject): * **drugbank_id** (*str*) - (None) Drugbank component id. * **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:: diff --git a/biobb_io/api/ideal_sdf.py b/biobb_io/api/ideal_sdf.py index d58e720..9bb409c 100755 --- a/biobb_io/api/ideal_sdf.py +++ b/biobb_io/api/ideal_sdf.py @@ -21,6 +21,7 @@ class IdealSdf(BiobbObject): * **api_id** (*str*) - ("pdbe") Identifier of the PDB REST API from which the SDF structure will be downloaded. Values: pdbe (`PDB in Europe REST API `_), pdb (`RCSB PDB REST API `_). * **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:: diff --git a/biobb_io/api/ligand.py b/biobb_io/api/ligand.py index 1b21ca9..4c03295 100755 --- a/biobb_io/api/ligand.py +++ b/biobb_io/api/ligand.py @@ -21,6 +21,7 @@ class Ligand(BiobbObject): * **api_id** (*str*) - ("mmb") Identifier of the PDB REST API from which the PDB structure will be downloaded. Values: pdbe (`PDB in Europe REST API `_), mmb (`MMB PDB mirror API `_). * **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:: diff --git a/biobb_io/api/memprotmd_sim.py b/biobb_io/api/memprotmd_sim.py index 48814f7..8472b3a 100755 --- a/biobb_io/api/memprotmd_sim.py +++ b/biobb_io/api/memprotmd_sim.py @@ -20,6 +20,7 @@ class MemProtMDSim(BiobbObject): * **pdb_code** (*str*) - (None) RSCB PDB code. * **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:: diff --git a/biobb_io/api/memprotmd_sim_list.py b/biobb_io/api/memprotmd_sim_list.py index 1b434c7..e7aa1ce 100755 --- a/biobb_io/api/memprotmd_sim_list.py +++ b/biobb_io/api/memprotmd_sim_list.py @@ -19,6 +19,7 @@ class MemProtMDSimList(BiobbObject): properties (dic - Python dictionary object containing the tool parameters, not input/output files): * **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:: diff --git a/biobb_io/api/memprotmd_sim_search.py b/biobb_io/api/memprotmd_sim_search.py index b66aea9..f91a60b 100755 --- a/biobb_io/api/memprotmd_sim_search.py +++ b/biobb_io/api/memprotmd_sim_search.py @@ -21,6 +21,7 @@ class MemProtMDSimSearch(BiobbObject): * **keyword** (*str*) - (None) String to search for in the database metadata. Examples are families like gpcr or porin. Values: porin, outer membrane protein, membrane protein, gpcr (7-transmembrane domain receptors transducing extracellular signals into cells), ion channels, rhodopsin (The most famous GPCRs), abc, mip (Major Intrinsic Protein (MIP)/FNT superfamily: specific for the transport of water and small neutral solutes), ligand-gated (Ligand-dependent signal conversion from chemical signals to electric signals), ammonia (Regulating transepithelial ammonia secretion), mapeg (Eicosanoid and Glutathione metabolism proteins), transmembrane (Heme biosynthesis), protein, kinase (Tyrosine-protein kinases: regulate central nervous system; gene transcription and cell differentiation), glycoprotein (Expression of TCR complex), immunoglobulin (Recognition; binding and adhesion process of cells), integrin (Bridges for cell-cell and cell-extracellular matrix interaction), bnip3 (BNip3 protein family: protect cell from apoptosis), bcl-2 (Regulating cell-death; either induce apoptotic or inhibit apoptosis), atpase (ATPase regulators; P-P-bond hydrolysis-driven transporter), cytochrome (Terminal oxidase enzyme in electron transfer chain), nadp (Transmembrane proteins with NAD(P)-binding Rossmann-fold domains: monoamine oxidase; deaminates norepinephrine; epinephrine; serotonin and dopamine), a4 (Amyloid beta A4 protein; involved in alzheimer's diseases), lysosome (Lysosome-associated membrane glycoprotein: specific to lysosomes; CD107), necrosis (Tumor necrosis factor recepto: binding with TNF and NGF; interacting with a variety of signal molecules; highly associated with apoptosis), oxidoreductase (DHODH; biosynthesis of orotate), ceramidase (Neutral/alkaline ceramidase: converting sphingolipid to sphingosine), dehydrogenase (Aldehyde dehydrogenase:ALDH; Oxidation of aldehydes), mitochondrial, plastid. * **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:: diff --git a/biobb_io/api/mmcif.py b/biobb_io/api/mmcif.py index 967746e..51a0afc 100755 --- a/biobb_io/api/mmcif.py +++ b/biobb_io/api/mmcif.py @@ -21,6 +21,7 @@ class Mmcif(BiobbObject): * **api_id** (*str*) - ("pdbe") Identifier of the PDB REST API from which the MMCIF structure will be downloaded. Values: pdbe (`PDB in Europe REST API `_), pdb (`RCSB PDB REST API `_), mmb (`MMB PDB mirror API `_). * **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:: diff --git a/biobb_io/api/pdb.py b/biobb_io/api/pdb.py index d2ec31a..9aeb917 100755 --- a/biobb_io/api/pdb.py +++ b/biobb_io/api/pdb.py @@ -22,6 +22,7 @@ class Pdb(BiobbObject): * **api_id** (*str*) - ("pdbe") Identifier of the PDB REST API from which the PDB structure will be downloaded. Values: pdbe (`PDB in Europe REST API `_), pdb (`RCSB PDB REST API `_), mmb (`MMB PDB mirror API `_). * **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:: diff --git a/biobb_io/api/pdb_cluster_zip.py b/biobb_io/api/pdb_cluster_zip.py index 35b431c..01fc752 100755 --- a/biobb_io/api/pdb_cluster_zip.py +++ b/biobb_io/api/pdb_cluster_zip.py @@ -25,6 +25,7 @@ class PdbClusterZip(BiobbObject): * **api_id** (*str*) - ("pdbe") Identifier of the PDB REST API from which the PDB structure will be downloaded. Values: pdbe (`PDB in Europe REST API `_), pdb (`RCSB PDB REST API `_), mmb (`MMB PDB mirror API `_). * **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:: diff --git a/biobb_io/api/pdb_variants.py b/biobb_io/api/pdb_variants.py index 1c5545a..3be2e34 100755 --- a/biobb_io/api/pdb_variants.py +++ b/biobb_io/api/pdb_variants.py @@ -23,6 +23,7 @@ class PdbVariants(BiobbObject): * **pdb_code** (*str*) - (None) RSCB PDB four letter code. * **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 PdbVariants module from Python diff --git a/biobb_io/api/structure_info.py b/biobb_io/api/structure_info.py index f9382eb..48b2d42 100755 --- a/biobb_io/api/structure_info.py +++ b/biobb_io/api/structure_info.py @@ -20,6 +20,7 @@ class StructureInfo(BiobbObject): * **pdb_code** (*str*) - (None) RSCB PDB structure code. * **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::