biobb-io 4.1.0__py3-none-any.whl → 4.2.0__py3-none-any.whl

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Files changed (8) hide show
  1. biobb_io/__init__.py +1 -1
  2. biobb_io/api/common.py +3 -3
  3. {biobb_io-4.1.0.dist-info → biobb_io-4.2.0.dist-info}/METADATA +20 -13
  4. {biobb_io-4.1.0.dist-info → biobb_io-4.2.0.dist-info}/RECORD +8 -8
  5. {biobb_io-4.1.0.dist-info → biobb_io-4.2.0.dist-info}/WHEEL +1 -1
  6. {biobb_io-4.1.0.dist-info → biobb_io-4.2.0.dist-info}/LICENSE +0 -0
  7. {biobb_io-4.1.0.dist-info → biobb_io-4.2.0.dist-info}/entry_points.txt +0 -0
  8. {biobb_io-4.1.0.dist-info → biobb_io-4.2.0.dist-info}/top_level.txt +0 -0
biobb_io/__init__.py CHANGED
@@ -1,3 +1,3 @@
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  name = "biobb_io"
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  __all__ = ["api"]
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- __version__ = "4.1.0"
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+ __version__ = "4.2.0"
biobb_io/api/common.py CHANGED
@@ -100,7 +100,7 @@ def download_ligand(ligand_code, api_id, out_log=None, global_log=None):
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  url = "http://mmb.irbbarcelona.org/api/pdbMonomer/" + ligand_code.lower()
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  text = requests.get(url, verify=False).content.decode('utf-8')
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  elif api_id == 'pdbe':
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- url = "ftp://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/{0}/{1}/{1}_ideal.pdb".format(ligand_code.upper()[0], ligand_code.upper())
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+ url = "https://www.ebi.ac.uk/pdbe/static/files/pdbechem_v2/" + ligand_code.upper() + "_ideal.pdb"
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  text = urllib.request.urlopen(url).read().decode('utf-8')
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  fu.log("Downloading %s from: %s" % (ligand_code, url), out_log, global_log)
@@ -166,10 +166,10 @@ def download_ideal_sdf(ligand_code, api_id, out_log=None, global_log=None):
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  """
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  if api_id == 'pdb':
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- url = "https://files.rcsb.org/ligands/view/" + ligand_code.upper() + "_ideal.sdf"
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+ url = "https://files.rcsb.org/ligands/download/" + ligand_code.upper() + "_ideal.sdf"
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  text = requests.get(url, verify=False).content.decode('utf-8')
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  elif api_id == 'pdbe':
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- url = "ftp://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/{0}/{1}/{1}_ideal.sdf".format(ligand_code.upper()[0], ligand_code.upper())
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+ url = "https://www.ebi.ac.uk/pdbe/static/files/pdbechem_v2/" + ligand_code.upper() + "_ideal.sdf"
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  text = urllib.request.urlopen(url).read().decode('utf-8')
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  fu.log("Downloading %s from: %s" % (ligand_code, url), out_log, global_log)
{biobb_io-4.1.0.dist-info → biobb_io-4.2.0.dist-info}/METADATA RENAMED
@@ -1,11 +1,11 @@
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  Metadata-Version: 2.1
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  Name: biobb-io
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- Version: 4.1.0
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+ Version: 4.2.0
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  Summary: Biobb_io is the Biobb module collection to fetch data to be consumed by the rest of the Biobb building blocks.
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  Home-page: https://github.com/bioexcel/biobb_io
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  Author: Biobb developers
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  Author-email: pau.andrio@bsc.es
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- Project-URL: Documentation, http://biobb_io.readthedocs.io/en/latest/
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+ Project-URL: Documentation, http://biobb-io.readthedocs.io/en/latest/
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  Project-URL: Bioexcel, https://bioexcel.eu/
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  Keywords: Bioinformatics Workflows BioExcel Compatibility
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  Classifier: Development Status :: 3 - Alpha
@@ -18,14 +18,14 @@ Classifier: Operating System :: POSIX
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  Requires-Python: >=3.8
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  Description-Content-Type: text/markdown
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  License-File: LICENSE
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- Requires-Dist: biobb-common (==4.1.0)
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+ Requires-Dist: biobb-common ==4.2.0
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  [![](https://img.shields.io/github/v/tag/bioexcel/biobb_io?label=Version)](https://GitHub.com/bioexcel/biobb_io/tags/)
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  [![](https://img.shields.io/pypi/v/biobb-io.svg?label=Pypi)](https://pypi.python.org/pypi/biobb-io/)
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  [![](https://img.shields.io/conda/vn/bioconda/biobb_io?label=Conda)](https://anaconda.org/bioconda/biobb_io)
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  [![](https://img.shields.io/conda/dn/bioconda/biobb_io?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_io)
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  [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_io?tab=tags)
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- [![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_io:4.1.0--pyhdfd78af_0)
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+ [![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_io:4.2.0--pyhdfd78af_0)
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  [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_io)
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  [![](https://img.shields.io/pypi/pyversions/biobb-io.svg?label=Python%20Versions)](https://pypi.org/project/biobb-io/)
@@ -44,6 +44,13 @@ Requires-Dist: biobb-common (==4.1.0)
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  [![](https://img.shields.io/github/last-commit/bioexcel/biobb_io?label=Last%20Commit)](https://github.com/bioexcel/biobb_io/commits/master)
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  [![](https://img.shields.io/github/issues/bioexcel/biobb_io.svg?color=brightgreen&label=Issues)](https://GitHub.com/bioexcel/biobb_io/issues/)
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+ [![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu)
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+ [![](https://www.bestpractices.dev/projects/8847/badge)](https://www.bestpractices.dev/projects/8847)
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+
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+ [](https://bestpractices.coreinfrastructure.org/projects/8847/badge)
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+
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+ [//]: # (The previous line invisible link is for compatibility with the howfairis script https://github.com/fair-software/howfairis-github-action/tree/main wich uses the old bestpractices URL)
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+
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  # biobb_io
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  ### Introduction
@@ -53,10 +60,10 @@ Biobb (BioExcel building blocks) packages are Python building blocks that
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  create new layer of compatibility and interoperability over popular
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  bioinformatics tools.
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  The latest documentation of this package can be found in our readthedocs site:
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- [latest API documentation](http://biobb_io.readthedocs.io/en/latest/).
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+ [latest API documentation](http://biobb-io.readthedocs.io/en/latest/).
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  ### Version
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- v4.1.0 2023.3
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+ v4.2.0 2024.1
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  ### Installation
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  Using PIP:
@@ -65,7 +72,7 @@ Using PIP:
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  * Installation:
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- pip install "biobb_io==4.1.0"
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+ pip install "biobb_io==4.2.0"
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  * Usage: [Python API documentation](https://biobb-io.readthedocs.io/en/latest/modules.html)
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@@ -73,7 +80,7 @@ Using ANACONDA:
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  * Installation:
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- conda install -c bioconda "biobb_io==4.1.0"
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+ conda install -c bioconda "biobb_io==4.2.0"
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  * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-io.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-io.readthedocs.io/en/latest/command_line.html)
@@ -82,12 +89,12 @@ Using DOCKER:
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  * Installation:
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- docker pull quay.io/biocontainers/biobb_io:4.1.0--pyhdfd78af_0
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+ docker pull quay.io/biocontainers/biobb_io:4.2.0--pyhdfd78af_0
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  * Usage:
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- docker run quay.io/biocontainers/biobb_io:4.1.0--pyhdfd78af_0 <command>
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+ docker run quay.io/biocontainers/biobb_io:4.2.0--pyhdfd78af_0 <command>
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  The command list and specification can be found at the [Command Line documentation](https://biobb-io.readthedocs.io/en/latest/command_line.html).
@@ -99,7 +106,7 @@ Using SINGULARITY:
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  * Installation:
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- singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:4.1.0--pyhdfd78af_0
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+ singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:4.2.0--pyhdfd78af_0
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  * Usage:
@@ -114,8 +121,8 @@ The command list and specification can be found at the [Command Line documentati
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  ### Copyright & Licensing
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  This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).
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- * (c) 2015-2023 [Barcelona Supercomputing Center](https://www.bsc.es/)
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- * (c) 2015-2023 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
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+ * (c) 2015-2024 [Barcelona Supercomputing Center](https://www.bsc.es/)
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+ * (c) 2015-2024 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
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  Licensed under the
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  [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.
{biobb_io-4.1.0.dist-info → biobb_io-4.2.0.dist-info}/RECORD RENAMED
@@ -1,9 +1,9 @@
1
- biobb_io/__init__.py,sha256=vuFC6oQPwINtvLqQX-ZEF9b5zynN5bTgZkE0ExdalcE,58
1
+ biobb_io/__init__.py,sha256=v_3RWCfkq-jiX5D34gUZbzVIxmDlYwyoMSXFhEVVl3Y,58
2
2
  biobb_io/api/__init__.py,sha256=5jF02xLDXfTBDU2Pie2NTOwoB71lEv-Dikt1WK9s72Y,243
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  biobb_io/api/alphafold.py,sha256=qSnJHUjbgd6p0tTszbl4fNPLKjOOGrrV4-KxCWoS8CE,5082
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  biobb_io/api/api_binding_site.py,sha256=wOT2S6FspS7hVh8e8t4tfwI6vcEDxU-lhbWyUKOwQxY,5527
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  biobb_io/api/canonical_fasta.py,sha256=rMaomcSY91b3BlwyphQp6kFNpDhKcc4EF81mLny59WM,5474
6
- biobb_io/api/common.py,sha256=NO529jXyRsNDq0OVGJhsOlMJnu7OpHX7a5Vb6FoftM4,13139
6
+ biobb_io/api/common.py,sha256=7tcV25MpeUaeC-4Ll07YXTVI3_RukmQ4qFUJN2Qt3Xc,13075
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  biobb_io/api/drugbank.py,sha256=adxIVX7BH734zoEv_Y9OYKKzrPWatniXP7Xhk8vMGk0,4942
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  biobb_io/api/ideal_sdf.py,sha256=KmoNT9_J4Ilubn0iejOgcs-ST6d0DsCeNeg8z8ca94s,5282
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  biobb_io/api/ligand.py,sha256=HTO9bCxPQ3bhwBKzRR1eDxh1SrjRqIUIrLIYl8pLgVI,5332
@@ -16,9 +16,9 @@ biobb_io/api/pdb_cluster_zip.py,sha256=gV3QubG9Vqz9TxunLPTB5TwFGHgaKzMNa8kkPqs6G
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  biobb_io/api/pdb_variants.py,sha256=kmV_BvXFNTY-REFgZJj2vXmbOjv9RvbrzPXvJb7WJSc,6948
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  biobb_io/api/structure_info.py,sha256=_hPSOfBhQZ1cCA1LovitsI4wVMw_lskXHhcsyZTW3V8,5190
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  biobb_io/test/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- biobb_io-4.1.0.dist-info/LICENSE,sha256=z8d0m5b2O9McPEK1xHG_dWgUBT6EfBDz6wA0F7xSPTA,11358
20
- biobb_io-4.1.0.dist-info/METADATA,sha256=OTJHIhBh_EtVJWJND9H0KxT-khvtS8aMzxG4CYq3EYA,6224
21
- biobb_io-4.1.0.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
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- biobb_io-4.1.0.dist-info/entry_points.txt,sha256=oksijOyG3dbONd1oOcNd5VDcGaHufkIk11ubPka8fJg,652
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- biobb_io-4.1.0.dist-info/top_level.txt,sha256=1VPldlX2AnFaqODGFJK10WN8AOQuulpX88bLSaQdoS8,9
24
- biobb_io-4.1.0.dist-info/RECORD,,
19
+ biobb_io-4.2.0.dist-info/LICENSE,sha256=z8d0m5b2O9McPEK1xHG_dWgUBT6EfBDz6wA0F7xSPTA,11358
20
+ biobb_io-4.2.0.dist-info/METADATA,sha256=RF5keYBiN7zU528eZHac-KHGoPgw7r_fLZtoYSapDhQ,6761
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+ biobb_io-4.2.0.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
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+ biobb_io-4.2.0.dist-info/entry_points.txt,sha256=oksijOyG3dbONd1oOcNd5VDcGaHufkIk11ubPka8fJg,652
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+ biobb_io-4.2.0.dist-info/top_level.txt,sha256=1VPldlX2AnFaqODGFJK10WN8AOQuulpX88bLSaQdoS8,9
24
+ biobb_io-4.2.0.dist-info/RECORD,,
{biobb_io-4.1.0.dist-info → biobb_io-4.2.0.dist-info}/WHEEL RENAMED
@@ -1,5 +1,5 @@
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  Wheel-Version: 1.0
2
- Generator: bdist_wheel (0.38.4)
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+ Generator: bdist_wheel (0.41.2)
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  Root-Is-Purelib: true
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  Tag: py3-none-any
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