biobb-io 5.1.1__py3-none-any.whl → 5.2.0__py3-none-any.whl

biobb_io/__init__.py

@@ -2,4 +2,4 @@ from . import api
 
 name = "biobb_io"
 __all__ = ["api"]
-__version__ = "5.1.1"
+__version__ = "5.2.0"

biobb_io/api/mddb.py

@@ -169,6 +169,7 @@ mddb.__doc__ = MDDB.__doc__
 main = MDDB.get_main(
     mddb,
     "This class is a wrapper for downloading a trajectory / topology pair from the MDDB Database.",
+    custom_flags={"output_top_path": "-o", "output_trj_path": "-t"}
 )
 
 if __name__ == "__main__":

biobb_io/api/memprotmd_sim_list.py

@@ -15,7 +15,7 @@ class MemProtMDSimList(BiobbObject):
     | Wrapper for the `MemProtMD DB REST API <http://memprotmd.bioch.ox.ac.uk/>`_ to get all available membrane-protein systems (simulations).
 
     Args:
-        output_simulations (str): Path to the output JSON file. File type: output. `Sample file <https://github.com/bioexcel/biobb_io/raw/master/biobb_io/test/reference/api/output_sim_list.json>`_. Accepted formats: json (edam:format_3464).
+        output_simulations (str): Path to the output JSON file. File type: output. `Sample file <https://github.com/bioexcel/biobb_io/raw/master/biobb_io/test/reference/api/output_sim_list_schema_validator.json>`_. Accepted formats: json (edam:format_3464).
         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.

biobb_io/api/memprotmd_sim_search.py

@@ -16,7 +16,7 @@ class MemProtMDSimSearch(BiobbObject):
     | Wrapper for the `MemProtMD DB REST API <http://memprotmd.bioch.ox.ac.uk/>`_ to perform advanced searches.
 
     Args:
-        output_simulations (str): Path to the output JSON file. File type: output. `Sample file <https://github.com/bioexcel/biobb_io/raw/master/biobb_io/test/reference/api/output_sim_search.json>`_. Accepted formats: json (edam:format_3464).
+        output_simulations (str): Path to the output JSON file. File type: output. `Sample file <https://github.com/bioexcel/biobb_io/raw/master/biobb_io/test/reference/api/output_sim_search_schema_validator.json>`_. Accepted formats: json (edam:format_3464).
         properties (dic - Python dictionary object containing the tool parameters, not input/output files):
             * **collection_name** (*str*) - ("refs") Name of the collection to query.
             * **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.

biobb_io/api/pdb_cluster_zip.py

@@ -129,7 +129,7 @@ class PdbClusterZip(BiobbObject):
         fu.log("Zipping the pdb files to: %s" % self.output_pdb_zip_path)
         fu.zip_list(self.output_pdb_zip_path, file_list, out_log=self.out_log)
 
-        self.tmp_files.extend([unique_dir])
+        self.tmp_files.append(unique_dir)
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)

{biobb_io-5.1.1.dist-info → biobb_io-5.2.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: biobb_io
-Version: 5.1.1
+Version: 5.2.0
 Summary: Biobb_io is the Biobb module collection to fetch data to be consumed by the rest of the Biobb building blocks.
 Home-page: https://github.com/bioexcel/biobb_io
 Author: Biobb developers
@@ -9,15 +9,15 @@ Project-URL: Documentation, http://biobb-io.readthedocs.io/en/latest/
 Project-URL: Bioexcel, https://bioexcel.eu/
 Keywords: Bioinformatics Workflows BioExcel Compatibility
 Classifier: Development Status :: 5 - Production/Stable
-Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
 Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Operating System :: MacOS :: MacOS X
 Classifier: Operating System :: POSIX
 Classifier: Operating System :: Unix
-Requires-Python: >=3.9
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: biobb_common==5.1.1
+Requires-Dist: biobb_common==5.2.0
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier
@@ -36,7 +36,7 @@ Dynamic: summary
 [![](https://img.shields.io/conda/vn/bioconda/biobb_io?label=Conda)](https://anaconda.org/bioconda/biobb_io)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_io?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_io)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_io?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_io:5.1.1--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_io:5.2.0--pyhdfd78af_0)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_io)
 [![](https://img.shields.io/pypi/pyversions/biobb-io.svg?label=Python%20Versions)](https://pypi.org/project/biobb-io/)
@@ -74,7 +74,7 @@ The latest documentation of this package can be found in our readthedocs site:
 [latest API documentation](http://biobb-io.readthedocs.io/en/latest/).
 
 ### Version
-v5.1.1 2025.1
+v5.2.0 2025.2
 
 ### Installation
 Using PIP:
@@ -100,12 +100,12 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_io:5.1.1--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_io:5.2.0--pyhdfd78af_0
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_io:5.1.1--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_io:5.2.0--pyhdfd78af_0 <command>
 
 
 The command list and specification can be found at the [Command Line documentation](https://biobb-io.readthedocs.io/en/latest/command_line.html).
@@ -117,7 +117,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:5.1.1--pyhdfd78af_0
+        singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:5.2.0--pyhdfd78af_0
 
 
 * Usage:

{biobb_io-5.1.1.dist-info → biobb_io-5.2.0.dist-info}/RECORD

@@ -1,4 +1,4 @@
-biobb_io/__init__.py,sha256=yuyKuMxXekhEdVhlQAADYrFWmGfm2YyXpYKUdIDHuvc,77
+biobb_io/__init__.py,sha256=Xvx_Rj0RAAmZIhyokvORbIxSt6YB6ylDI6ziG0z8U84,77
 biobb_io/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biobb_io/api/__init__.py,sha256=s4K59-8EX7yX2qBtB8717ynIEjQ0lVNTp0BDSoc_raM,558
 biobb_io/api/alphafold.py,sha256=EsUHtbypku6rNtMaDrnKf3KLoanuOOB0LOZOnenmoP0,4371
@@ -7,19 +7,19 @@ biobb_io/api/canonical_fasta.py,sha256=ohuVq410Vk_OvnMVYxReb9QUuce3Ki3FFhV_DJhKZ
 biobb_io/api/common.py,sha256=KY3ayHCaGBe9zTLDdDc_wK13xXeIaEHTegeWPR2t02M,15766
 biobb_io/api/ideal_sdf.py,sha256=BKpFIPcZ8vV6ayQXCmP3Kt_rcQf3ltQCRTtcCqGHriE,4566
 biobb_io/api/ligand.py,sha256=pMd5wvYqYNlVYT5MatrX346whVfwYY58B2RR_FqEwhE,4610
-biobb_io/api/mddb.py,sha256=J5qgudIQEeE9-UXwjFPQAiFkc7aHXVMMG7Z_j2Dj3yI,7067
+biobb_io/api/mddb.py,sha256=RWw1MgTTUpvdV-k7ZGNxBr4_wMXf29kGMZKdDj9UTYA,7135
 biobb_io/api/memprotmd_sim.py,sha256=UKgc4UJPukjmBwelVcKbFqGqQhA9BOtfrlJiHf_aW5Q,4120
-biobb_io/api/memprotmd_sim_list.py,sha256=WOg4YqWfMvIAgz_19oZ-8asKJnFv8MmRfz0t5ZQhUZo,4059
-biobb_io/api/memprotmd_sim_search.py,sha256=vWfBxNYCmGwGyzTpHnmnuwQ39ZXWO8T0MhdjGjGgZr4,6419
+biobb_io/api/memprotmd_sim_list.py,sha256=aF4bXr--GZ8byK3ydtvrIL1OesvPLeTERAHsZ5r6AeE,4076
+biobb_io/api/memprotmd_sim_search.py,sha256=VkbHE_qVoQov3iJQFaOy43ZSahCqOHy-7F2s9idcXxE,6436
 biobb_io/api/mmcif.py,sha256=M8Tlto6d2hLTUwZGo6zIUGO5bzN6ZwMqYoiMMu1b-rM,4628
 biobb_io/api/pdb.py,sha256=uRCMPSvuOSUObMsxlRC513wJ2bmFEh9P8FPtG30yfp0,4975
-biobb_io/api/pdb_cluster_zip.py,sha256=9s_HXWep7X3h-kNq1cYbadXgDmsAlG8_Sat0q0snyDA,6633
+biobb_io/api/pdb_cluster_zip.py,sha256=2Ps9R2QhBvTflrRjyz3k6x1CzDnF57E76ng8SguvGjk,6631
 biobb_io/api/pdb_variants.py,sha256=BGIbsHl64IANiq2R39dycIxBRGPjm3u1oGpTyeWQ2nA,6707
 biobb_io/api/structure_info.py,sha256=aoh_Do7QipPgsse7ay-nlddeGCrK-YEjUHbg1Q21HgE,4443
 biobb_io/test/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-biobb_io-5.1.1.dist-info/licenses/LICENSE,sha256=z8d0m5b2O9McPEK1xHG_dWgUBT6EfBDz6wA0F7xSPTA,11358
-biobb_io-5.1.1.dist-info/METADATA,sha256=LTPhHWFk9SzHSC-AxEUmkmrGU8wdoAvhSlTRHJfFxxc,7049
-biobb_io-5.1.1.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-biobb_io-5.1.1.dist-info/entry_points.txt,sha256=dDYvVClLKe_Aa3HaMm-7WuS2d16FKGxlnKl816Cf5T4,644
-biobb_io-5.1.1.dist-info/top_level.txt,sha256=1VPldlX2AnFaqODGFJK10WN8AOQuulpX88bLSaQdoS8,9
-biobb_io-5.1.1.dist-info/RECORD,,
+biobb_io-5.2.0.dist-info/licenses/LICENSE,sha256=z8d0m5b2O9McPEK1xHG_dWgUBT6EfBDz6wA0F7xSPTA,11358
+biobb_io-5.2.0.dist-info/METADATA,sha256=B3RCQFlwvu7FMRM1StyFKIKxmbGZ5LCUmfjc6Wt9URk,7051
+biobb_io-5.2.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+biobb_io-5.2.0.dist-info/entry_points.txt,sha256=dDYvVClLKe_Aa3HaMm-7WuS2d16FKGxlnKl816Cf5T4,644
+biobb_io-5.2.0.dist-info/top_level.txt,sha256=1VPldlX2AnFaqODGFJK10WN8AOQuulpX88bLSaQdoS8,9
+biobb_io-5.2.0.dist-info/RECORD,,

{biobb_io-5.1.1.dist-info → biobb_io-5.2.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (78.1.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any