pisa-analysis 3.0.3__tar.gz

pisa_analysis-3.0.3/PKG-INFO

@@ -0,0 +1,214 @@
+Metadata-Version: 2.4
+Name: pisa-analysis
+Version: 3.0.3
+Summary: This python package works with PISA to analyse data for macromolecular interfaces and interactions in assemblies.
+Author-email: Grisell Diaz Leines <gdiazleines@ebi.ac.uk>
+License: Apache 2.0
+Project-URL: Homepage, https://github.com/PDBe-KB/pisa-analysis
+Project-URL: Repository, https://github.com/PDBe-KB/pisa-analysis
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: gemmi>=0.7.3
+Requires-Dist: jsonschema>=4.25.1
+Requires-Dist: lxml>=6.0.2
+Requires-Dist: pandas>=2.3.3
+Requires-Dist: pydantic>=2.12.4
+Requires-Dist: xmlschema>=4.2.0
+Requires-Dist: xmltodict>=1.0.2
+
+# Assembly interfaces analysis
+
+## Basic information
+
+This python package works with PISA to analyze data for macromolecular interfaces and interactions in assemblies.
+
+The code consists of the module `pisa_analysis` that will:
+
+- Analyse macromolecular interfaces with PISA
+- Create a JSON dictionary with assembly interactions/interfaces information
+
+```
+git clone https://github.com/PDBe-KB/pisa-analysis
+
+cd pisa-analysis
+```
+## Dependencies
+
+The pisa_analysis process runs PISA as a subprocess and requires apriori compilation of PISA.
+
+To make your life easier when running the process, you can set two path environment variables for PISA:
+
+An environment variable to the `pisa` binary:
+
+```
+export PATH="$PATH:your_path_to_pisa/pisa/build"
+```
+
+A path to the setup directory of PISA:
+
+```
+export PISA_SETUP_DIR="/your_path_to_pisa/pisa/setup"
+```
+
+Additionally, it is required that PISA setup directory contains a pisa configuration template named [pisa_cfg_tmp](https://github.com/PDBe-KB/pisa/tree/main/setup/pisa_cfg_tmp)
+
+<!-- Comment that config for CCP4 install can also be used.  -->
+
+Other dependencies can be installed with:
+
+```
+pip install -r requirements.txt
+```
+See  [requirements.txt](https://github.com/PDBe-KB/pisa-analysis/blob/main/requirements.txt)
+
+
+For development:
+
+**pre-commit usage**
+
+```
+pip install pre-commit
+pre-commit
+pre-commit install
+```
+
+## Usage
+
+Follow below steps to install the module **pisa_analysis** :
+
+```
+cd pisa-analysis/
+
+python3 -m venv .venv
+source .venv/bin/activate
+
+python3 -m pip install .
+
+
+```
+
+To run the modules in command line:
+
+**pisa_analysis**:
+```
+pisa_analysis [-h] \
+  -i <INPUT_CIF_FILE> \
+  --pdb_id <PDB_ID> \
+  --assembly_id <ASSEMBLY_CODE> \
+  -o <OUTPUT_JSON> \
+  --output_xml <OUTPUT_XML>
+```
+
+Required arguments are :
+
+```
+--input_cif (-i)          :  Assembly CIF file (It can also read a PDB file). Optional if --gen_full_results is used and --assembly_id not specified.
+--pdb_id                  :  Entry ID
+--assembly_id             :  Assembly code
+--output_json (-o)        :  Output directory for JSON fille
+--output_xml              :  Output directory for XML files
+```
+
+
+Other optional arguments are:
+
+```
+--input_updated_cif       : Updated cif for pdbid entry
+--force                   : Always runs PISA calculation
+--pisa_setup_dir          : Path to the 'setup' directory in PISA
+--pisa_binary             : Binary file for PISA
+-h, --help                : Show help message
+```
+
+
+The process is as follows:
+
+For **pisa_analysis** module:
+
+1. The process first runs PISA in a subprocess and generates two xml files:
+   - interfaces.xml
+   - assembly.xml
+
+   The xml files are saved in the output directory defined by the `--output_xml` argument. If the xml files exist and are valid, the process will skip running PISA unless the `--force` is used in the arguments.
+
+2. Next, the process parses xml files generated by PISA and creates a dictionary that contains all assembly interfaces/interactions information.
+
+3. While creating the interfaces dictionary for the entry, the process reads UniProt accession and sequence numbers from an Updated CIF file using Gemmi.
+
+4. The process also parses xml file `assembly.xml` generated by PISA and creates a simplified dictionary with some assembly information.
+
+4. In the last steps, the process dumps the dictionaries into JSON files. The JSON files are saved in the output directory defined by the `-o` or `--output_json` arguments. The output json files are:
+
+     *xxxx-assemX_interfaces.json*  and  *xxxx-assemblyX.json*
+
+     where xxxx is the pdb id entry and X is the assembly code.
+
+
+## Expected JSON files
+
+Documentation on the assembly interfaces json file and schema can be found here:
+
+https://pisalite.docs.apiary.io/#reference/0/pisaqualifierjson/interaction-interface-data-per-pdb-assembly-entry
+
+The simplified assembly json output looks as follows:
+```
+{
+   "PISA": {
+      "pdb_id": "1d2s",
+      "assembly_id": "1",
+      "pisa_version": "2.0",
+      "assembly": {
+         "id": "1",
+         "size": "8",
+         "macromolecular_size": "2",
+         "dissociation_energy": -3.96,
+         "accessible_surface_area": 15146.45,
+         "buried_surface_area": 3156.79,
+         "entropy": 12.09,
+         "dissociation_area": 733.07,
+         "solvation_energy_gain": -41.09,
+         "number_of_uc": "0",
+         "number_of_dissociated_elements": "2",
+         "symmetry_number": "2",
+         "formula": "A(2)a(4)b(2)",
+         "composition": "A-2A[CA](4)[DHT](2)"
+      }
+   }
+}
+```
+
+## Setup with Docker
+
+Build the docker image with:
+```shell
+docker build -t pisa-analysis .
+```
+
+Run the docker container with:
+```
+docker run -v <HOST_DIR>:/data_dir \
+   pisa-analysis \
+   pisa_analysis \
+   --input_cif /data_dir/<INPUT_CIF> \
+   --pdb_id <PDB_ID> \
+   --assembly_id <ASSEMBLY_CODE> \
+   --output_json /data_dir/<OUTPUT_JSON> \
+   --output_xml /data_dir/<OUTPUT_XML>
+```
+
+## Versioning
+
+We use [SemVer](https://semver.org) for versioning.
+
+## Authors
+* [Grisell Diaz Leines](https://github.com/grisell) - Lead developer
+* [Stephen Anyango](otienoanyango) - Review and productionising
+* [Mihaly Varadi](https://github.com/mvaradi) - Review and management
+
+See all contributors [here](https://github.com/PDBe-KB/pisa-analysis/graphs/contributors).
+
+## License
+
+See  [LICENSE](https://github.com/PDBe-KB/pisa-analysis/blob/main/LICENSE)
+
+## Acknowledgements

pisa_analysis-3.0.3/README.md

@@ -0,0 +1,196 @@
+# Assembly interfaces analysis
+
+## Basic information
+
+This python package works with PISA to analyze data for macromolecular interfaces and interactions in assemblies.
+
+The code consists of the module `pisa_analysis` that will:
+
+- Analyse macromolecular interfaces with PISA
+- Create a JSON dictionary with assembly interactions/interfaces information
+
+```
+git clone https://github.com/PDBe-KB/pisa-analysis
+
+cd pisa-analysis
+```
+## Dependencies
+
+The pisa_analysis process runs PISA as a subprocess and requires apriori compilation of PISA.
+
+To make your life easier when running the process, you can set two path environment variables for PISA:
+
+An environment variable to the `pisa` binary:
+
+```
+export PATH="$PATH:your_path_to_pisa/pisa/build"
+```
+
+A path to the setup directory of PISA:
+
+```
+export PISA_SETUP_DIR="/your_path_to_pisa/pisa/setup"
+```
+
+Additionally, it is required that PISA setup directory contains a pisa configuration template named [pisa_cfg_tmp](https://github.com/PDBe-KB/pisa/tree/main/setup/pisa_cfg_tmp)
+
+<!-- Comment that config for CCP4 install can also be used.  -->
+
+Other dependencies can be installed with:
+
+```
+pip install -r requirements.txt
+```
+See  [requirements.txt](https://github.com/PDBe-KB/pisa-analysis/blob/main/requirements.txt)
+
+
+For development:
+
+**pre-commit usage**
+
+```
+pip install pre-commit
+pre-commit
+pre-commit install
+```
+
+## Usage
+
+Follow below steps to install the module **pisa_analysis** :
+
+```
+cd pisa-analysis/
+
+python3 -m venv .venv
+source .venv/bin/activate
+
+python3 -m pip install .
+
+
+```
+
+To run the modules in command line:
+
+**pisa_analysis**:
+```
+pisa_analysis [-h] \
+  -i <INPUT_CIF_FILE> \
+  --pdb_id <PDB_ID> \
+  --assembly_id <ASSEMBLY_CODE> \
+  -o <OUTPUT_JSON> \
+  --output_xml <OUTPUT_XML>
+```
+
+Required arguments are :
+
+```
+--input_cif (-i)          :  Assembly CIF file (It can also read a PDB file). Optional if --gen_full_results is used and --assembly_id not specified.
+--pdb_id                  :  Entry ID
+--assembly_id             :  Assembly code
+--output_json (-o)        :  Output directory for JSON fille
+--output_xml              :  Output directory for XML files
+```
+
+
+Other optional arguments are:
+
+```
+--input_updated_cif       : Updated cif for pdbid entry
+--force                   : Always runs PISA calculation
+--pisa_setup_dir          : Path to the 'setup' directory in PISA
+--pisa_binary             : Binary file for PISA
+-h, --help                : Show help message
+```
+
+
+The process is as follows:
+
+For **pisa_analysis** module:
+
+1. The process first runs PISA in a subprocess and generates two xml files:
+   - interfaces.xml
+   - assembly.xml
+
+   The xml files are saved in the output directory defined by the `--output_xml` argument. If the xml files exist and are valid, the process will skip running PISA unless the `--force` is used in the arguments.
+
+2. Next, the process parses xml files generated by PISA and creates a dictionary that contains all assembly interfaces/interactions information.
+
+3. While creating the interfaces dictionary for the entry, the process reads UniProt accession and sequence numbers from an Updated CIF file using Gemmi.
+
+4. The process also parses xml file `assembly.xml` generated by PISA and creates a simplified dictionary with some assembly information.
+
+4. In the last steps, the process dumps the dictionaries into JSON files. The JSON files are saved in the output directory defined by the `-o` or `--output_json` arguments. The output json files are:
+
+     *xxxx-assemX_interfaces.json*  and  *xxxx-assemblyX.json*
+
+     where xxxx is the pdb id entry and X is the assembly code.
+
+
+## Expected JSON files
+
+Documentation on the assembly interfaces json file and schema can be found here:
+
+https://pisalite.docs.apiary.io/#reference/0/pisaqualifierjson/interaction-interface-data-per-pdb-assembly-entry
+
+The simplified assembly json output looks as follows:
+```
+{
+   "PISA": {
+      "pdb_id": "1d2s",
+      "assembly_id": "1",
+      "pisa_version": "2.0",
+      "assembly": {
+         "id": "1",
+         "size": "8",
+         "macromolecular_size": "2",
+         "dissociation_energy": -3.96,
+         "accessible_surface_area": 15146.45,
+         "buried_surface_area": 3156.79,
+         "entropy": 12.09,
+         "dissociation_area": 733.07,
+         "solvation_energy_gain": -41.09,
+         "number_of_uc": "0",
+         "number_of_dissociated_elements": "2",
+         "symmetry_number": "2",
+         "formula": "A(2)a(4)b(2)",
+         "composition": "A-2A[CA](4)[DHT](2)"
+      }
+   }
+}
+```
+
+## Setup with Docker
+
+Build the docker image with:
+```shell
+docker build -t pisa-analysis .
+```
+
+Run the docker container with:
+```
+docker run -v <HOST_DIR>:/data_dir \
+   pisa-analysis \
+   pisa_analysis \
+   --input_cif /data_dir/<INPUT_CIF> \
+   --pdb_id <PDB_ID> \
+   --assembly_id <ASSEMBLY_CODE> \
+   --output_json /data_dir/<OUTPUT_JSON> \
+   --output_xml /data_dir/<OUTPUT_XML>
+```
+
+## Versioning
+
+We use [SemVer](https://semver.org) for versioning.
+
+## Authors
+* [Grisell Diaz Leines](https://github.com/grisell) - Lead developer
+* [Stephen Anyango](otienoanyango) - Review and productionising
+* [Mihaly Varadi](https://github.com/mvaradi) - Review and management
+
+See all contributors [here](https://github.com/PDBe-KB/pisa-analysis/graphs/contributors).
+
+## License
+
+See  [LICENSE](https://github.com/PDBe-KB/pisa-analysis/blob/main/LICENSE)
+
+## Acknowledgements

pisa_analysis-3.0.3/pisa_analysis.egg-info/PKG-INFO

@@ -0,0 +1,214 @@
+Metadata-Version: 2.4
+Name: pisa-analysis
+Version: 3.0.3
+Summary: This python package works with PISA to analyse data for macromolecular interfaces and interactions in assemblies.
+Author-email: Grisell Diaz Leines <gdiazleines@ebi.ac.uk>
+License: Apache 2.0
+Project-URL: Homepage, https://github.com/PDBe-KB/pisa-analysis
+Project-URL: Repository, https://github.com/PDBe-KB/pisa-analysis
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: gemmi>=0.7.3
+Requires-Dist: jsonschema>=4.25.1
+Requires-Dist: lxml>=6.0.2
+Requires-Dist: pandas>=2.3.3
+Requires-Dist: pydantic>=2.12.4
+Requires-Dist: xmlschema>=4.2.0
+Requires-Dist: xmltodict>=1.0.2
+
+# Assembly interfaces analysis
+
+## Basic information
+
+This python package works with PISA to analyze data for macromolecular interfaces and interactions in assemblies.
+
+The code consists of the module `pisa_analysis` that will:
+
+- Analyse macromolecular interfaces with PISA
+- Create a JSON dictionary with assembly interactions/interfaces information
+
+```
+git clone https://github.com/PDBe-KB/pisa-analysis
+
+cd pisa-analysis
+```
+## Dependencies
+
+The pisa_analysis process runs PISA as a subprocess and requires apriori compilation of PISA.
+
+To make your life easier when running the process, you can set two path environment variables for PISA:
+
+An environment variable to the `pisa` binary:
+
+```
+export PATH="$PATH:your_path_to_pisa/pisa/build"
+```
+
+A path to the setup directory of PISA:
+
+```
+export PISA_SETUP_DIR="/your_path_to_pisa/pisa/setup"
+```
+
+Additionally, it is required that PISA setup directory contains a pisa configuration template named [pisa_cfg_tmp](https://github.com/PDBe-KB/pisa/tree/main/setup/pisa_cfg_tmp)
+
+<!-- Comment that config for CCP4 install can also be used.  -->
+
+Other dependencies can be installed with:
+
+```
+pip install -r requirements.txt
+```
+See  [requirements.txt](https://github.com/PDBe-KB/pisa-analysis/blob/main/requirements.txt)
+
+
+For development:
+
+**pre-commit usage**
+
+```
+pip install pre-commit
+pre-commit
+pre-commit install
+```
+
+## Usage
+
+Follow below steps to install the module **pisa_analysis** :
+
+```
+cd pisa-analysis/
+
+python3 -m venv .venv
+source .venv/bin/activate
+
+python3 -m pip install .
+
+
+```
+
+To run the modules in command line:
+
+**pisa_analysis**:
+```
+pisa_analysis [-h] \
+  -i <INPUT_CIF_FILE> \
+  --pdb_id <PDB_ID> \
+  --assembly_id <ASSEMBLY_CODE> \
+  -o <OUTPUT_JSON> \
+  --output_xml <OUTPUT_XML>
+```
+
+Required arguments are :
+
+```
+--input_cif (-i)          :  Assembly CIF file (It can also read a PDB file). Optional if --gen_full_results is used and --assembly_id not specified.
+--pdb_id                  :  Entry ID
+--assembly_id             :  Assembly code
+--output_json (-o)        :  Output directory for JSON fille
+--output_xml              :  Output directory for XML files
+```
+
+
+Other optional arguments are:
+
+```
+--input_updated_cif       : Updated cif for pdbid entry
+--force                   : Always runs PISA calculation
+--pisa_setup_dir          : Path to the 'setup' directory in PISA
+--pisa_binary             : Binary file for PISA
+-h, --help                : Show help message
+```
+
+
+The process is as follows:
+
+For **pisa_analysis** module:
+
+1. The process first runs PISA in a subprocess and generates two xml files:
+   - interfaces.xml
+   - assembly.xml
+
+   The xml files are saved in the output directory defined by the `--output_xml` argument. If the xml files exist and are valid, the process will skip running PISA unless the `--force` is used in the arguments.
+
+2. Next, the process parses xml files generated by PISA and creates a dictionary that contains all assembly interfaces/interactions information.
+
+3. While creating the interfaces dictionary for the entry, the process reads UniProt accession and sequence numbers from an Updated CIF file using Gemmi.
+
+4. The process also parses xml file `assembly.xml` generated by PISA and creates a simplified dictionary with some assembly information.
+
+4. In the last steps, the process dumps the dictionaries into JSON files. The JSON files are saved in the output directory defined by the `-o` or `--output_json` arguments. The output json files are:
+
+     *xxxx-assemX_interfaces.json*  and  *xxxx-assemblyX.json*
+
+     where xxxx is the pdb id entry and X is the assembly code.
+
+
+## Expected JSON files
+
+Documentation on the assembly interfaces json file and schema can be found here:
+
+https://pisalite.docs.apiary.io/#reference/0/pisaqualifierjson/interaction-interface-data-per-pdb-assembly-entry
+
+The simplified assembly json output looks as follows:
+```
+{
+   "PISA": {
+      "pdb_id": "1d2s",
+      "assembly_id": "1",
+      "pisa_version": "2.0",
+      "assembly": {
+         "id": "1",
+         "size": "8",
+         "macromolecular_size": "2",
+         "dissociation_energy": -3.96,
+         "accessible_surface_area": 15146.45,
+         "buried_surface_area": 3156.79,
+         "entropy": 12.09,
+         "dissociation_area": 733.07,
+         "solvation_energy_gain": -41.09,
+         "number_of_uc": "0",
+         "number_of_dissociated_elements": "2",
+         "symmetry_number": "2",
+         "formula": "A(2)a(4)b(2)",
+         "composition": "A-2A[CA](4)[DHT](2)"
+      }
+   }
+}
+```
+
+## Setup with Docker
+
+Build the docker image with:
+```shell
+docker build -t pisa-analysis .
+```
+
+Run the docker container with:
+```
+docker run -v <HOST_DIR>:/data_dir \
+   pisa-analysis \
+   pisa_analysis \
+   --input_cif /data_dir/<INPUT_CIF> \
+   --pdb_id <PDB_ID> \
+   --assembly_id <ASSEMBLY_CODE> \
+   --output_json /data_dir/<OUTPUT_JSON> \
+   --output_xml /data_dir/<OUTPUT_XML>
+```
+
+## Versioning
+
+We use [SemVer](https://semver.org) for versioning.
+
+## Authors
+* [Grisell Diaz Leines](https://github.com/grisell) - Lead developer
+* [Stephen Anyango](otienoanyango) - Review and productionising
+* [Mihaly Varadi](https://github.com/mvaradi) - Review and management
+
+See all contributors [here](https://github.com/PDBe-KB/pisa-analysis/graphs/contributors).
+
+## License
+
+See  [LICENSE](https://github.com/PDBe-KB/pisa-analysis/blob/main/LICENSE)
+
+## Acknowledgements

pisa_analysis-3.0.3/pisa_analysis.egg-info/SOURCES.txt

@@ -0,0 +1,23 @@
+README.md
+pyproject.toml
+pisa_analysis.egg-info/PKG-INFO
+pisa_analysis.egg-info/SOURCES.txt
+pisa_analysis.egg-info/dependency_links.txt
+pisa_analysis.egg-info/entry_points.txt
+pisa_analysis.egg-info/requires.txt
+pisa_analysis.egg-info/top_level.txt
+pisa_utils/__init__.py
+pisa_utils/analyze.py
+pisa_utils/constants.py
+pisa_utils/covariations_int.py
+pisa_utils/dictionaries.py
+pisa_utils/parsers.py
+pisa_utils/run.py
+pisa_utils/run_pisa.py
+pisa_utils/utils.py
+tests/test_analyze.py
+tests/test_covariations_int.py
+tests/test_dictionaries.py
+tests/test_models.py
+tests/test_parsers.py
+tests/test_utils.py

pisa_analysis-3.0.3/pisa_analysis.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

pisa_analysis-3.0.3/pisa_analysis.egg-info/entry_points.txt

@@ -0,0 +1,3 @@
+[console_scripts]
+pisa_analysis = pisa_utils.run:main
+pisa_analysis_service = pisa_utils.run:service

pisa_analysis-3.0.3/pisa_analysis.egg-info/requires.txt

@@ -0,0 +1,7 @@
+gemmi>=0.7.3
+jsonschema>=4.25.1
+lxml>=6.0.2
+pandas>=2.3.3
+pydantic>=2.12.4
+xmlschema>=4.2.0
+xmltodict>=1.0.2

pisa_analysis-3.0.3/pisa_analysis.egg-info/top_level.txt

@@ -0,0 +1 @@
+pisa_utils