[med-svn] [Git][med-team/plip][master] 3 commits: New upstream version 2.2.2+dfsg

Nilesh Patra (@nilesh) gitlab at salsa.debian.org
Tue May 18 16:48:26 BST 2021 


Nilesh Patra pushed to branch master at Debian Med / plip


Commits:
df595f7b by Nilesh Patra at 2021-05-18T21:13:50+05:30
New upstream version 2.2.2+dfsg
- - - - -
f3ce8260 by Nilesh Patra at 2021-05-18T21:13:52+05:30
Update upstream source from tag 'upstream/2.2.2+dfsg'

Update to upstream version '2.2.2+dfsg'
with Debian dir c9441adde878ba3e08274035cf401b28239d37d1
- - - - -
8c8e6728 by Nilesh Patra at 2021-05-18T21:15:51+05:30
Interim changelog entry

- - - - -


8 changed files:

- CHANGES.txt
- DOCUMENTATION.md
- README.md
- debian/changelog
- plip/basic/config.py
- plip/exchange/report.py
- plip/plipcmd.py
- plip/test/test_command_line.py


Changes:

=====================================
CHANGES.txt
=====================================
@@ -1,5 +1,11 @@
 Changelog
 ---------
+# 2.2.2
+* fixes an issue that caused encoding errors to be thrown
+
+# 2.2.1
+* updates citation information to latest paper: https://doi.org/10.1093/nar/gkab294
+
 # 2.2.0
 * new minor release
 * increased detail level of report (individual atoms on protein side)


=====================================
DOCUMENTATION.md
=====================================
@@ -99,11 +99,12 @@ $ plip -i 1vsn 1osn 2reg -vx
 PLIP will create subdirectories for each given structure in the output folder. If in PDB ID mode (`-i`), the folder structure will be nested and based on the two middle characters of the PDB ID. The structure `1vsn` in batch processing will have its output files in `<outputfolder>/vs/1vsn`.
 
 ### Detection of Protein-Peptide Interactions
-For the detection of ligands, PLIP relies on the separation of `ATOM` and `HETATM` entries in the PDB file. The latter are searched for suitable ligands when running in normal mode. Peptide ligands, however, are usually deposited as `ATOM` entries in a separate chain. PLIP can not detect these entities automatically. To switch into protein-peptide interaction mode, start PLIP with the option `--peptide`, followed by the peptide chain of interest, e.g.:
+For the detection of ligands, PLIP relies on the separation of `ATOM` and `HETATM` entries in the PDB file. The latter are searched for suitable ligands when running in normal mode. Peptide ligands, however, are usually deposited as `ATOM` entries in a separate chain. PLIP can not detect these entities automatically. To switch into protein-peptide interaction mode, start PLIP with the option `--peptides`, followed by the peptide chain of interest, e.g.:
 
 ```bash
-$ plip -i 5hi4 --peptide I -vx
+$ plip -i 5hi4 --peptides I -vx
 ```
+This option can also be used to analyze interaction between different protein chains or nucleic acid strands and is therefore also available using the synonym `--inter`.
 
 ### Detection of Intra-Chain Interactions
 Intra-protein interactions are important for the stabilization of a structure and can give valuable insights for protein engineering and drug discovery. PLIP supports detection of interactions within one chain. o switch into intra-chain interaction mode, start PLIP with the option `--intra`, followed by the protein chain of interest, e.g.:
@@ -277,6 +278,7 @@ After assigning all target groups to one metal ions, the resulting set of angles
 | citation_information | How to cite PLIP |
 | mode | Documents if PLIP was started in default or any special mode (e.g. intra-protein interactions) |
 | pdbid | PDB identifier of the input file |
+| model | Number of the model in the PDB file on which analysis was done |
 | pdbfile | Name of the input PDB file |
 | pdbfixes | Were any fixes applied automatically to the input file? |
 | filename | Filename of the processed PDB file |


=====================================
README.md
=====================================
@@ -11,7 +11,7 @@ Analyze noncovalent protein-ligand interactions in 3D structures with ease.
 <img src="pliplogo.png"  alt="PLIP Logo" height="100">
 
 
-| Use Case                                                                  | [Web Server](https://projects.biotec.tu-dresden.de/plip-web/plip)         | Docker             | Singularity        | Python Module       |
+| Use Case                                                                  | [Web Server](https://plip-tool.biotec.tu-dresden.de)         | Docker             | Singularity        | Python Module       |
 |---------------------------------------------------------------------------|--------------------|--------------------|--------------------|--------------------|
 | "I want to analyze my protein-ligand complex!"                            | :heavy_check_mark: | :heavy_check_mark: | :yellow_circle:    | :x:                |
 | "I want to analyze *a billion* protein-ligand complexes!"                 | :x:                | :yellow_circle:    | :heavy_check_mark: | :yellow_circle:    |
@@ -22,6 +22,7 @@ Analyze noncovalent protein-ligand interactions in 3D structures with ease.
 
 ## Quickstart
 
+### Docker
 If you have Docker installed, you can run a PLIP analysis for the structure `1vsn` with the following shell command:
 
 On Linux / MacOS:
@@ -30,7 +31,7 @@ $ docker run --rm \
     -v ${PWD}:/results \
     -w /results \
     -u $(id -u ${USER}):$(id -g ${USER}) \
-    pharmai/plip:latest -i 1s3v -yv
+    pharmai/plip:latest -i 1vsn -yv
 ```
 
 On Windows:
@@ -39,8 +40,9 @@ $ docker run --rm \
     -v ${PWD}:/results \
     -w /results \
     -u $(id -u ${USER}):$(id -g ${USER}) \
-    pharmai/plip:latest -i 1s3v -yv
+    pharmai/plip:latest -i 1vsn -yv
 ```
+### Singularity
 
 The equivalent command for our pre-built [Singularity](https://singularity.lbl.gov/) image for Linux (available under [Releases](https://github.com/pharmai/plip/releases)) is as follows:
 
@@ -50,31 +52,41 @@ $ ./plip.simg -i 1vsn -yv
 
 Singularity allows to use PLIP with ease in HPC environments. Note that you need to have Singularity installed on your base system.
 
+---
+
 ## Usage
 
 This README provides instructions for setup and using basic functions of PLIP.
 For more details, see the [Documentation](DOCUMENTATION.md).
 
-### 1. (optional) Clone the repository
-
-Open a new system terminal and clone this repository using
-```bash
-$ git clone https://github.com/pharmai/plip.git
-```
-
-### 2. Install PLIP
+### 1. Install PLIP
 
 #### Containerized Image (recommended)
-:exclamation: We ship PLIP as a pre-built containers for multiple architectures (amd64/ARM), available on the [Docker Hub](https://hub.docker.com/r/pharmai/plip) or as pre-built Singularity image under [Releases](https://github.com/pharmai/plip/releases).
+:exclamation: We ship PLIP as pre-built containers for multiple architectures (amd64/ARM), available on the [Docker Hub](https://hub.docker.com/r/pharmai/plip) or as pre-built Singularity image under [Releases](https://github.com/pharmai/plip/releases). See the quickstart section above for usage instructions.
 
-#### From Source
+#### Dependencies
 If you cannot use the containerized bundle or want to use PLIP sources, make sure you have the following requirements installed:
 - Python >= 3.6.9
-- OpenBabel >= 3.0.0
+- [OpenBabel](#Installing-OpenBabel) >= 3.0.0 with [Python bindings](https://open-babel.readthedocs.io/en/latest/UseTheLibrary/PythonInstall.html)
 - PyMOL >= 2.3.0 with Python bindings (optional, for visualization only)
 - ImageMagick >= 6.9 (optional)
 
-Set your `PYTHONPATH` environment variable to the root directory of this repository.
+**Python:** If you are on a system where Python 3 is executed using `python3` instead of just `python`, replace the `python` and `pip` commands in the following steps with `python3` and `pip3` accordingly.
+
+**OpenBabel:** Many users have trouble setting up OpenBabel with Python bindings correctly. We therefore provide some [installation help for OpenBabel](#Installing-OpenBabel) below.
+
+#### From Source
+
+Open a terminal and clone this repository using
+```bash
+$ git clone https://github.com/pharmai/plip.git
+```
+
+Either set your `PYTHONPATH` environment variable to the root directory of your PLIP repository or run the following command in it
+
+```bash
+$ python setup.py install
+```
 
 #### Via PyPi
 We deploy the PLIP package to [PyPi](https://pypi.org/project/plip/). You can install PLIP as Python module with:
@@ -83,9 +95,9 @@ We deploy the PLIP package to [PyPi](https://pypi.org/project/plip/). You can in
 $ pip install plip
 ```
 
-**Note:** Be aware that you still have to install all other dependencies and link them correctly.
+**Note:** Be aware that you still have to install the above mentioned dependencies and link them correctly.
 
-### 3. Run PLIP
+### 2. Run PLIP
 
 #### Command Line Tool
 
@@ -94,8 +106,10 @@ Run the `plipcmd.py` script inside the PLIP folder to detect, report, and visual
 **Note:** If you have installed PLIP with `python setup.py install` or PyPi, you will not have to set an alias for the `plip` command.
 
 ```bash
-$ alias plip='python ~/pliptool/plip/plipcmd.py'
+# Set an alias to make your life easier and create and enter /tmp/1vsn
+$ alias plip='python ~/plip/plip/plipcmd.py'
 $ mkdir /tmp/1vsn && cd /tmp/1vsn
+# Run PLIP for 1vsn and open the resulting visualization in PyMOL
 $ plip -i 1vsn -yv
 $ pymol 1VSN_NFT_A_283.pse
 ```
@@ -124,7 +138,7 @@ my_interactions = my_mol.interaction_sets[my_bsid] # Contains all interaction da
 print([pistack.resnr for pistack in my_interactions.pistacking]) # Prints [84, 129]
 ```
 
-### 4. Investigate the Results
+### 3. Investigate the Results
 PLIP offers various output formats, ranging from renderes images and PyMOL session files to human-readable text files and XML files. By default, all files are deposited in the working directory unless and output path is provided. For a full documentation of running options and output formats, please refer to the [Documentation](DOCUMENTATION.md).
 
 ## Versions and Branches
@@ -137,9 +151,10 @@ For production environments, you should use the latest tagged commit from the `m
 - Alexandre Mestiashvili | [github.com/mestia](https://github.com/mestia)
 - Christoph Leberecht  | [github.com/cleberecht](https://github.com/cleberecht)
 - Florian Kaiser  | [github.com/fkaiserbio](https://github.com/fkaiserbio)
+- Katja Linnemann | [github.com/kalinni](https://github.com/kalinni)
 
 ## PLIP Web Server
-Visit our PLIP Web Server on [plip.biotec.tu-dresden.de/plip-web](https://plip.biotec.tu-dresden.de/plip-web).
+Visit our PLIP Web Server on [plip-tool.biotec.tu-dresden.de](https://plip-tool.biotec.tu-dresden.de).
 
 ## License Information
 PLIP is published under the GNU GPLv2. For more information, please read the `LICENSE.txt` file.
@@ -147,6 +162,11 @@ Using PLIP in your commercial or non-commercial project is generally possible wh
 
 ## Citation Information
 If you are using PLIP in your work, please cite
+> Adasme,M. et al. PLIP 2021: expanding the scope of the protein-ligand interaction profiler to DNA and RNA.
+> Nucl. Acids Res. (05 May 2021), gkab294. doi: 10.1093/nar/gkab294
+ 
+or
+
 > Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler.
 > Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi: 10.1093/nar/gkv315
 
@@ -155,8 +175,8 @@ If you are using PLIP in your work, please cite
 > ValueError: [...] is not a recognised Open Babel descriptor type
 >
 Make sure OpenBabel is correctly installed. This error can occur if the installed Python bindings don't match the OpenBabel version on your machine.
-We don't offer technical support for installation of third-party packages.
-For an instruction how to install Open Babel, please refer to their [website](https://openbabel.org/docs/dev/Installation/install.html).
+We don't offer technical support for installation of third-party packages but added some [installation help for OpenBabel](#Installing-OpenBabel) below.
+Alternatively you can refer to their [website](https://openbabel.org/docs/dev/Installation/install.html).
 
 > I'm unsure on how to run PLIP and don't have much Linux experience.
 >
@@ -173,9 +193,56 @@ Due to the non-deterministic nature on how hydrogen atoms can be added to the in
 >
 By default PLIP uses the first model it sees in a PDB file. You can change this behavior with the flag `--model`.
 
+## Installing OpenBabel
+As many users encounter problems with installing the required OpenBabel tools, we want to provide some help here. However, we cannot offer technical support. Comprehensive information about the installation of OpenBabel for Windows, Linux, and macOS can be found in the [OpenBabel wiki](http://openbabel.org/wiki/Category:Installation) and the [OpenBabel Docs](https://open-babel.readthedocs.io/en/latest/Installation/install.html).
+Information about the installation of [OpenBabel Python bindings](https://open-babel.readthedocs.io/en/latest/UseTheLibrary/PythonInstall.html) can also be found there.
+
+### Using Conda, HomeBrew or the binary Windows Installer
+
+Install OpenBabel using the [binary from GitHub](https://github.com/openbabel/openbabel/releases/latest) or with
+```bash
+# For Conda users
+$ conda install openbabel -c conda-forge
+# On macOS
+$ brew install open-babel
+```
+Install the Python bindings with
+```bash
+$ pip install openbabel
+```
+**Note:** If you have trouble, make sure the OpenBabel version matches the one for the python bindings!
+
+### Using your Package Manager (Example for Ubuntu 20.04)
+
+```bash
+$ apt-get update && apt-get install -y \
+    libopenbabel-dev \
+    libopenbabel6 \
+    python3-openbabel \
+    openbabel
+```
+### From Source (Example for Ubuntu 18.04)
+Clone the OpenBabel repository into the /src directory
+```bash
+$ git clone -b openbabel-3-0-0 \
+https://github.com/openbabel/openbabel.git
+```
+
+Within /src/openbabel create end enter a directory /build and configure the build using
+```bash
+$ cmake .. \
+-DPYTHON_EXECUTABLE=/usr/bin/python3.6 \
+-DPYTHON_BINDINGS=ON \
+-DCMAKE_INSTALL_PREFIX=/usr/local \
+-DRUN_SWIG=ON
+```
+From within the same directory (/src/openbabel/build) compile and install using
+```bash
+$ make -j$(nproc --all) install
+```
 ## Contact / Maintainer
 As of April 2020 PLIP is now officially maintained by [PharmAI GmbH](https://pharm.ai). Do you have feature requests, found a bug or want to use  PLIP in your project? Commercial support is available upon request.
 
  ![](https://www.pharm.ai/wp-content/uploads/2020/04/PharmAI_logo_color_no_slogan_500px.png)
- 
+
  Please get in touch: `hello at pharm.ai`


=====================================
debian/changelog
=====================================
@@ -1,6 +1,6 @@
-plip (2.2.0+dfsg-1) UNRELEASED; urgency=medium
+plip (2.2.2+dfsg-1) UNRELEASED; urgency=medium
 
-  * New upstream version 2.2.0+dfsg
+  * New upstream version 2.2.2+dfsg
 
  -- Nilesh Patra <nilesh at debian.org>  Mon, 19 Apr 2021 17:10:53 +0530
 


=====================================
plip/basic/config.py
=====================================
@@ -1,5 +1,7 @@
-__version__ = '2.2.0'
+__version__ = '2.2.2'
 __maintainer__ = 'PharmAI GmbH (2020-2021) - www.pharm.ai - hello at pharm.ai'
+__citation_information__ = "Adasme,M. et al. PLIP 2021: expanding the scope of the protein-ligand interaction profiler to DNA and RNA. " \
+                           "Nucl. Acids Res. (05 May 2021), gkab294. doi: 10.1093/nar/gkab294"
 
 import logging
 


=====================================
plip/exchange/report.py
=====================================
@@ -28,8 +28,7 @@ class StructureReport:
         date_of_creation = et.SubElement(report, 'date_of_creation')
         date_of_creation.text = time.strftime("%Y/%m/%d")
         citation_information = et.SubElement(report, 'citation_information')
-        citation_information.text = "Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler. " \
-                                    "Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi: 10.1093/nar/gkv315"
+        citation_information.text = config.__citation_information__
 
         maintainer_information = et.SubElement(report, 'maintainer_information')
         maintainer_information.text = config.__maintainer__
@@ -69,8 +68,7 @@ class StructureReport:
         textlines.append("=" * len(textlines[0]))
         textlines.append('Created on %s using PLIP v%s\n' % (time.strftime("%Y/%m/%d"), __version__))
         textlines.append('If you are using PLIP in your work, please cite:')
-        textlines.append('Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler.')
-        textlines.append('Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi: 10.1093/nar/gkv315\n')
+        textlines.append(config.__citation_information__)
         if len(self.excluded) != 0:
             textlines.append('Excluded molecules as ligands: %s\n' % ','.join([lig for lig in self.excluded]))
         if config.DNARECEPTOR:


=====================================
plip/plipcmd.py
=====================================
@@ -25,11 +25,10 @@ from plip.exchange.webservices import fetch_pdb
 from plip.structure.preparation import create_folder_if_not_exists, extract_pdbid
 from plip.structure.preparation import tilde_expansion, PDBComplex
 
-description = f"The Protein-Ligand Interaction Profiler (PLIP) {__version__}" \
+description = f"The Protein-Ligand Interaction Profiler (PLIP) Version {__version__} " \
               "is a command-line based tool to analyze interactions in a protein-ligand complex. " \
               "If you are using PLIP in your work, please cite: " \
-              "Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler. " \
-              "Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi:10.1093/nar/gkv315" \
+              f"{config.__citation_information__} " \
               f"Supported and maintained by: {config.__maintainer__}"
 
 
@@ -124,7 +123,7 @@ def run_analysis(inputstructs, inputpdbids):
     # Print title and version
     logger.info(f'Protein-Ligand Interaction Profiler (PLIP) {__version__}')
     logger.info(f'brought to you by: {config.__maintainer__}')
-    logger.info(f'please cite: https://www.doi.org/10.1093/nar/gkv315')
+    logger.info(f'please cite: {config.__citation_information__}')
     output_prefix = config.OUTPUTFILENAME
 
     if inputstructs is not None:  # Process PDB file(s)


=====================================
plip/test/test_command_line.py
=====================================
@@ -57,3 +57,8 @@ class CommandLineTest(unittest.TestCase):
         exitcode = subprocess.call(f'{sys.executable} ../plipcmd.py -t -f ./pdb/1eve.pdb -O', shell=True)
         self.assertEqual(exitcode, 0)
 
+    def test_help(self):
+        """A PDB ID with no valid PDB record is provided."""
+        exitcode = subprocess.call(f'{sys.executable} ../plipcmd.py -h', shell=True)
+        self.assertEqual(exitcode, 0)
+



View it on GitLab: https://salsa.debian.org/med-team/plip/-/compare/cdf3ace90672432387f5a06aa0b5d0b86b544d03...8c8e67280e95e52c343aca8cf63ec747ad398b8c

-- 
View it on GitLab: https://salsa.debian.org/med-team/plip/-/compare/cdf3ace90672432387f5a06aa0b5d0b86b544d03...8c8e67280e95e52c343aca8cf63ec747ad398b8c
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20210518/f34d359f/attachment-0001.htm>

More information about the debian-med-commit mailing list