protpy 1.0.8__tar.gz → 1.3.0__tar.gz

protpy-1.3.0/PKG-INFO

@@ -0,0 +1,556 @@
+Metadata-Version: 2.4
+Name: protpy
+Version: 1.3.0
+Summary: Python package for generating various biochemical, physicochemical and structural descriptors/features of protein sequences.
+Author-email: AJ McKenna <amckenna41@qub.ac.uk>
+Maintainer-email: AJ McKenna <amckenna41@qub.ac.uk>
+License: MIT
+Project-URL: Homepage, https://github.com/amckenna41/protPy
+Project-URL: Repository, https://github.com/amckenna41/protPy
+Project-URL: Bug Tracker, https://github.com/amckenna41/protpy/issues
+Project-URL: Download, https://github.com/amckenna41/protPy/archive/refs/heads/main.zip
+Keywords: bioinformatics,protein engineering,python,pypi,machine learning,aaindex,protein descriptors,physicochemical descriptors,biochemical descriptors,structural descriptors,pySAR
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: Intended Audience :: Information Technology
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: Implementation :: PyPy
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: aaindex>=1.2.0
+Requires-Dist: numpy>=2.4.4
+Requires-Dist: pandas>=3.0.2
+Requires-Dist: varname>=0.15.1
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Requires-Dist: pytest-flake8; extra == "test"
+Requires-Dist: pytest-timeout; extra == "test"
+Requires-Dist: biopython>=1.87; extra == "test"
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Dynamic: license-file
+
+
+<a id="TOP"></a>
+
+# protpy - Package for generating protein physicochemical, biochemical and structural descriptors using their constituent amino acids. #
+[![PyPI](https://img.shields.io/pypi/v/protpy)](https://pypi.org/project/protpy/)
+[![pytest](https://github.com/amckenna41/protpy/workflows/Building%20and%20Testing/badge.svg)](https://github.com/amckenna41/protpy/actions?query=workflowBuilding%20and%20Testing)
+[![Platforms](https://img.shields.io/badge/platforms-linux%2C%20macOS%2C%20Windows-green)](https://pypi.org/project/protpy/)
+[![PythonV](https://img.shields.io/pypi/pyversions/protpy?logo=2)](https://pypi.org/project/protpy/)
+[![codecov](https://codecov.io/gh/amckenna41/protPy/graph/badge.svg?token=H508M9J13W)](https://codecov.io/gh/amckenna41/protPy)
+[![License: MIT](https://img.shields.io/badge/License-MIT-red.svg)](https://opensource.org/licenses/MIT)
+[![Issues](https://img.shields.io/github/issues/amckenna41/protpy)](https://github.com/amckenna41/protpy/issues)
+<!-- [![Size](https://img.shields.io/github/repo-size/amckenna41/protpy)](https://github.com/amckenna41/protpy)
+[![Commits](https://img.shields.io/github/commit-activity/w/amckenna41/protpy)](https://github.com/amckenna41/protpy) -->
+<!-- <p align="center">
+<img src="https://images.newscientist.com/wp-content/uploads/2021/07/22155326/22-july_deepmind-proteome.jpg?width=300" alt="protpyLogo" height="200"/>
+</p> -->
+
+* 🧬 A <b>demo</b> of the software is available [here][demo]
+* 📝 A <b>Medium</b> article about `protPy` and its background is available [here][article]
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/amckenna41/protpy/main/images/protpy.png" alt="protpy" width="500"/>
+</p>
+
+Table of Contents
+-----------------
+
+  * [Introduction](#introduction)
+  * [Requirements](#requirements)
+  * [Installation](#installation)
+  * [Usage](#usage)
+  * [Documentation](#documentation)
+  * [Directories](#directories)
+  * [Tests](#tests)
+  * [Issues](#Issues)
+  * [Contact](#contact)
+  * [References](#references)
+
+Introduction
+------------
+`protpy` is a Python software package for generating a variety of physicochemical, biochemical and structural descriptors for proteins. All of these descriptors are calculated using sequence-derived or physicochemical features of the amino acids that make up the proteins. These descriptors have been highly studied and used in a series of Bioinformatic applications including protein engineering, SAR (sequence-activity-relationships), predicting protein structure & function, subcellular localization, protein-protein interactions, drug-target interactions etc. 
+
+This software is aimed at any researcher or developer using protein sequence/structural data, and was mainly created to use in my own project [`pySAR`](https://github.com/amckenna41/pySAR) which uses protein sequence data to identify Sequence Activity Relationships (SAR) using Machine Learning [[1]](#references). `protpy` is built and developed in Python 3.10.
+
+The descriptors available in `protpy` include:
+
+<details>
+<summary><b>Composition Descriptors (22)</b></summary>
+
+* **Amino Acid Composition (AAComp)**
+* **Dipeptide Composition (DPComp)**
+* **Tripeptide Composition (TPComp)**
+* **Grand Average of Hydropathy (GRAVY)**
+* **Aromaticity**
+* **Instability Index**
+* **Isoelectric Point**
+* **Molecular Weight**
+* **Charge Distribution**
+* **Hydrophobic/Polar/Charged Composition (HPC)**
+* **Secondary Structure Propensity (SSP)**
+* **k-mer Composition**
+* **Reduced Alphabet Composition**
+* **Motif Composition**
+* **Amino Acid Pair Composition**
+* **Aliphatic Index**
+* **Extinction Coefficient**
+* **Boman Index**
+* **Aggregation Propensity**
+* **Hydrophobic Moment**
+* **Shannon Entropy**
+* **Pseudo Amino Acid Composition (PAAComp)**
+* **Amphiphilic Amino Acid Composition (APAAComp)**
+
+</details>
+
+<details>
+<summary><b>Autocorrelation Descriptors (3)</b></summary>
+
+* **Moreaubroto Autocorrelation (MBAuto)**
+* **Moran Autocorrelation (MAuto)**
+* **Geary Autocorrelation (GAuto)**
+
+</details>
+
+<details>
+<summary><b>Conjoint Triad (1)</b></summary>
+
+* **Conjoint Triad (CTriad)**
+
+</details>
+
+<details>
+<summary><b>CTD Descriptors (4)</b></summary>
+
+* **CTD Composition**
+* **CTD Transition**
+* **CTD Distribution**
+* **CTD Combined**
+
+</details>
+
+<details>
+<summary><b>Sequence Order Descriptors (5)</b></summary>
+
+* **Sequence Order Coupling Number — single (SOCN)**
+* **Sequence Order Coupling Number — series**
+* **Sequence Order Coupling Number — all matrices**
+* **Quasi Sequence Order (QSO)**
+* **Quasi Sequence Order — all matrices**
+
+</details>
+
+More detail of each descriptor is listed in the markdown file: [`DESCRIPTORS.md`](https://github.com/amckenna41/protPy/blob/main/DESCRIPTORS.md)
+
+
+Requirements
+------------
+* [Python][python] >= 3.9
+* [aaindex][aaindex] >= 1.2.0
+* [numpy][numpy] >= 2.4.4
+* [pandas][pandas] >= 3.0.2
+* [varname][varname] >= 0.15.1
+* [biopython][biopython] >= 1.87 (only required for testing) 
+
+Installation 
+------------
+Install the latest version of `protpy` using pip:
+
+```bash
+pip3 install protpy --upgrade
+```
+
+Install by cloning repository:
+
+```bash
+git clone https://github.com/amckenna41/protpy.git
+python3 setup.py install
+```
+
+Usage
+-----
+### Import `protpy` after installation: 
+```python
+import protpy as protpy
+```
+
+### Import protein sequence from fasta:
+```python
+from Bio import SeqIO
+
+with open("test_fasta.fasta") as pro:
+    protein_seq = str(next(SeqIO.parse(pro,'fasta')).seq)
+```
+
+
+<details>
+<summary><b>Composition Descriptors Usage Examples</b></summary>
+
+Calculate Amino Acid Composition:
+```python
+amino_acid_composition = protpy.amino_acid_composition(protein_seq)
+# A      C      D      E      F ...
+# 6.693  3.108  5.817  3.347  6.614 ...
+```
+
+Calculate Dipeptide Composition:
+```python
+dipeptide_composition = protpy.dipeptide_composition(protein_seq)
+# AA    AC    AD   AE    AF ...
+# 0.72  0.16  0.48  0.4  0.24 ...
+```
+
+Calculate Tripeptide Composition:
+```python
+tripeptide_composition = protpy.tripeptide_composition(protein_seq)
+# AAA  AAC  AAD  AAE  AAF ...
+# 1    0    0    2    0 ...
+```
+
+Calculate GRAVY (Grand Average of Hydropathy):
+```python
+gravy = protpy.gravy(protein_seq)
+# GRAVY
+# -0.045
+```
+
+Calculate Aromaticity:
+```python
+aromaticity = protpy.aromaticity(protein_seq)
+# Aromaticity
+# 0.118
+```
+
+Calculate Instability Index:
+```python
+instability = protpy.instability_index(protein_seq)
+# InstabilityIndex
+# 31.836
+```
+
+Calculate Isoelectric Point:
+```python
+pi = protpy.isoelectric_point(protein_seq)
+# IsoelectricPoint
+# 5.412
+```
+
+Calculate Molecular Weight:
+```python
+mw = protpy.molecular_weight(protein_seq)
+# MolecularWeight (Da)
+# 139122.355
+```
+
+Calculate Charge Distribution:
+```python
+charge = protpy.charge_distribution(protein_seq)
+#using default parameters: ph=7.4
+
+# PositiveCharge  NegativeCharge  NetCharge
+# 99.526          114.956         -15.43
+```
+
+Calculate Hydrophobic/Polar/Charged Composition:
+```python
+hpc = protpy.hydrophobic_polar_charged_composition(protein_seq)
+# Hydrophobic  Polar   Charged
+# 44.542       32.669  18.247
+```
+
+Calculate Secondary Structure Propensity:
+```python
+ssp = protpy.secondary_structure_propensity(protein_seq)
+# Helix  Sheet  Coil
+# 0.983  1.05   1.043
+```
+
+Calculate k-mer Composition:
+```python
+kmer = protpy.kmer_composition(protein_seq)
+#using default parameters: k=2
+
+# AA     AC     AD  ...
+# 0.797  0.159  ... ...
+```
+
+Calculate Reduced Alphabet Composition:
+```python
+reduced = protpy.reduced_alphabet_composition(protein_seq)
+#using default parameters: alphabet_size=6
+
+# Group_1  Group_2  Group_3  Group_4  Group_5  Group_6
+# 25.339   34.741   9.163    9.084    10.837   10.837
+```
+
+Calculate Motif Composition:
+```python
+motif = protpy.motif_composition(protein_seq)
+# NxST_glycosylation  RGD_integrin  KDEL_retention  ...
+# 23                  0             0               ...
+```
+
+Calculate Amino Acid Pair Composition:
+```python
+aapair = protpy.amino_acid_pair_composition(protein_seq)
+# AA_Hydrophobic-Hydrophobic  AA_Hydrophobic-Polar  ...
+# 0.797                       0.159                 ...
+```
+
+Calculate Aliphatic Index:
+```python
+aliphatic = protpy.aliphatic_index(protein_seq)
+# AliphaticIndex
+# 82.725
+```
+
+Calculate Extinction Coefficient:
+```python
+extinction = protpy.extinction_coefficient(protein_seq)
+# ExtCoeff_Reduced  ExtCoeff_Oxidized
+# 140960            143335
+```
+
+Calculate Boman Index:
+```python
+boman = protpy.boman_index(protein_seq)
+# BomanIndex
+# 0.119
+```
+
+Calculate Aggregation Propensity:
+```python
+aggregation = protpy.aggregation_propensity(protein_seq)
+# AggregProneRegions  AggregProneFraction
+# 58                  11.793
+```
+
+Calculate Hydrophobic Moment:
+```python
+hm = protpy.hydrophobic_moment(protein_seq)
+#using default parameters: window=11, angle=100
+
+# HydrophobicMoment_Mean  HydrophobicMoment_Max
+# 0.272                   0.813
+```
+
+Calculate Shannon Entropy:
+```python
+se = protpy.shannon_entropy(protein_seq)
+# ShannonEntropy
+# 4.163
+```
+
+Calculate Pseudo Composition:
+```python
+pseudo_composition = protpy.pseudo_amino_acid_composition(protein_seq)
+#using default parameters: lamda=30, weight=0.05, properties=[]
+
+# PAAC_1  PAAC_2  PAAC_3  PAAC_4  PAAC_5 ...
+# 0.127   0.059   0.111   0.064   0.126 ...
+```
+
+Calculate Amphiphilic Composition:
+```python
+amphiphilic_composition = protpy.amphiphilic_pseudo_amino_acid_composition(protein_seq)
+#using default parameters: lamda=30, weight=0.5, properties=[hydrophobicity_, hydrophilicity_]
+
+# APAAC_1  APAAC_2  APAAC_3  APAAC_4  APAAC_5 ...
+# 6.624    3.076    5.757    3.032    5.988 ...
+```
+
+</details>
+
+<details>
+<summary><b>Autocorrelation Descriptors Usage Examples</b></summary>
+
+Calculate MoreauBroto Autocorrelation:
+```python
+moreaubroto_autocorrelation = protpy.moreaubroto_autocorrelation(protein_seq)
+#using default parameters: lag=30, properties=["CIDH920105", "BHAR880101", "CHAM820101", "CHAM820102", "CHOC760101", "BIGC670101", "CHAM810101", "DAYM780201"], normalize=True
+
+# MBAuto_CIDH920105_1  MBAuto_CIDH920105_2  MBAuto_CIDH920105_3  MBAuto_CIDH920105_4  MBAuto_CIDH920105_5 ...  
+# -0.052               -0.104               -0.156               -0.208               0.246 ...
+```
+
+Calculate Moran Autocorrelation:
+```python
+moran_autocorrelation = protpy.moran_autocorrelation(protein_seq)
+#using default parameters: lag=30, properties=["CIDH920105", "BHAR880101", "CHAM820101", "CHAM820102", "CHOC760101", "BIGC670101", "CHAM810101", "DAYM780201"], normalize=True
+
+# MAuto_CIDH920105_1  MAuto_CIDH920105_2  MAuto_CIDH920105_3  MAuto_CIDH920105_4  MAuto_CIDH920105_5 ...
+# -0.07786            -0.07879            -0.07906            -0.08001            0.14911 ...
+```
+
+Calculate Geary Autocorrelation:
+```python
+geary_autocorrelation = protpy.geary_autocorrelation(protein_seq)
+#using default parameters: lag=30, properties=["CIDH920105", "BHAR880101", "CHAM820101", "CHAM820102", "CHOC760101", "BIGC670101", "CHAM810101", "DAYM780201"], normalize=True
+
+# GAuto_CIDH920105_1  GAuto_CIDH920105_2  GAuto_CIDH920105_3  GAuto_CIDH920105_4  GAuto_CIDH920105_5 ...
+# 1.057               1.077               1.04                1.02                1.013 ...
+```
+
+</details>
+
+<details>
+<summary><b>Conjoint Triad Descriptors Usage Examples</b></summary>
+
+Calculate Conjoint Triad:
+```python
+conjoint_triad = protpy.conjoint_triad(protein_seq)
+# 111  112  113  114  115 ...
+# 7    17   11   3    6 ...
+```
+
+</details>
+
+<details>
+<summary><b>CTD Descriptors Usage Examples</b></summary>
+
+Calculate CTD:
+```python
+ctd = protpy.ctd(protein_seq)
+#using default parameters: property="hydrophobicity", all_ctd=True
+
+# hydrophobicity_CTD_C_01  hydrophobicity_CTD_C_02  hydrophobicity_CTD_C_03  normalized_vdwv_CTD_C_01 ...
+# 0.279                    0.386                    0.335                    0.389 ...                   
+```
+
+</details>
+
+<details>
+<summary><b>Sequence Order Descriptors Usage Examples</b></summary>
+
+Calculate Sequence Order Coupling Number (SOCN):
+```python
+socn = protpy.sequence_order_coupling_number_(protein_seq)
+#using default parameters: d=1, distance_matrix="schneider-wrede"
+
+#401.387        
+```
+
+Calculate all SOCN's per distance matrix:
+```python
+#using default parameters: lag=30, distance_matrix="schneider-wrede"
+socn_all = protpy.sequence_order_coupling_number(protein_seq)
+
+# SOCN_SW1  SOCN_SW2  SOCN_SW3  SOCN_SW4  SOCN_SW5 ...
+# 401.387    409.243    376.946    393.042    396.196 ...  
+
+#using custom parameters: lag=10, distance_matrix="grantham"
+socn_all = protpy.sequence_order_coupling_number(protein_seq, lag=10, distance_matrix="grantham")      
+
+# SOCN_Grant1  SOCN_Grant_2  SOCN_Grant_3  SOCN_Grant_4  SOCN_Grant_5 ...
+# 399.125    402.153    387.820    393.111    409.096 ...  
+```
+
+Calculate Quasi Sequence Order (QSO):
+```python
+#using default parameters: lag=30, weight=0.1, distance_matrix="schneider-wrede"
+qso = protpy.quasi_sequence_order(protein_seq)
+
+# QSO_SW1   QSO_SW2   QSO_SW3   QSO_SW4   QSO_SW5 ...
+# 0.005692  0.002643  0.004947  0.002846  0.005625 ...  
+
+#using custom parameters: lag=10, weight=0.2, distance_matrix="grantham"
+qso = protpy.quasi_sequence_order(protein_seq, lag=10, weight=0.2, distance_matrix="grantham")
+
+# QSO_Grant1   QSO_Grant2   QSO_Grant3   QSO_Grant4   QSO_Grant5 ...
+# 0.123287  0.079967  0.04332  0.039983  0.013332 ...  
+```
+
+</details>
+
+Documentation
+-------------
+The documentation for `protpy` is hosted on **ReadTheDocs** and is available [here][readthedocs].
+
+Directories
+-----------
+* `/tests` - unit and integration tests for `protpy` package.
+* `/protpy` - source code and all required external data files for package.
+* `/docs` - `protpy` documentation.
+* `/examples` - example notebook for protpy
+
+Tests
+-----
+To run all tests, from the main `protpy` folder run:
+```
+python3 -m unittest discover tests -v
+-v: verbose output flag
+```
+
+Contact
+-------
+If you have any questions or comments, please contact amckenna41@qub.ac.uk or raise an issue on the [Issues][Issues] tab.
+
+References
+----------
+\[1\]: Mckenna, A., & Dubey, S. (2022). Machine learning based predictive model for the analysis of sequence activity relationships using protein spectra and protein descriptors. Journal of Biomedical Informatics, 128(104016), 104016. https://doi.org/10.1016/j.jbi.2022.104016 <br>
+\[2\]: Shuichi Kawashima, Minoru Kanehisa, AAindex: Amino Acid index database, Nucleic Acids Research, Volume 28, Issue 1, 1 January 2000, Page 374, https://doi.org/10.1093/nar/28.1.374 <br>
+\[3\]: Dong, J., Yao, ZJ., Zhang, L. et al. PyBioMed: a python library for various molecular representations of chemicals, proteins and DNAs and their interactions. J Cheminform 10, 16 (2018). https://doi.org/10.1186/s13321-018-0270-2 <br>
+\[4\]: Reczko, M. and Bohr, H. (1994) The DEF data base of sequence based protein
+fold class predictions. Nucleic Acids Res, 22, 3616-3619. <br>
+\[5\]: Hua, S. and Sun, Z. (2001) Support vector machine approach for protein
+subcellular localization prediction. Bioinformatics, 17, 721-728. <br>
+\[6\]: Broto P, Moreau G, Vandicke C: Molecular structures: perception,
+autocorrelation descriptor and SAR studies. Eur J Med Chem 1984, 19: 71–78. <br>
+\[7\]: Ong, S.A., Lin, H.H., Chen, Y.Z. et al. Efficacy of different protein
+descriptors in predicting protein functional families. BMC Bioinformatics
+8, 300 (2007). https://doi.org/10.1186/1471-2105-8-300 <br>
+\[8\]: Inna Dubchak, Ilya Muchink, Stephen R.Holbrook and Sung-Hou Kim. Prediction
+of protein folding class using global description of amino acid sequence.
+Proc.Natl. Acad.Sci.USA, 1995, 92, 8700-8704. <br>
+\[9\]: Juwen Shen, Jian Zhang, Xiaomin Luo, Weiliang Zhu, Kunqian Yu, Kaixian Chen,
+Yixue Li, Huanliang Jiang. Predicting proten-protein interactions based only
+on sequences inforamtion. PNAS. 2007 (104) 4337-4341. <br>
+\[10\]: Kuo-Chen Chou. Prediction of Protein Subcellar Locations by Incorporating
+Quasi-Sequence-Order Effect. Biochemical and Biophysical Research
+Communications 2000, 278, 477-483. <br>
+\[11\]: Kuo-Chen Chou. Prediction of Protein Cellular Attributes Using
+Pseudo-Amino Acid Composition. PROTEINS: Structure, Function, and
+Genetics, 2001, 43: 246-255. <br>
+\[12\]: Kuo-Chen Chou. Using amphiphilic pseudo amino acid composition to predict enzyme
+subfamily classes. Bioinformatics, 2005,21,10-19.
+
+Support
+-------
+[<img src="https://img.shields.io/github/stars/amckenna41/protpy?color=green&label=star%20it%20on%20GitHub" width="132" height="20" alt="Star it on GitHub">](https://github.com/amckenna41/protpy)
+
+
+<a href="https://www.buymeacoffee.com/amckenna41" target="_blank"><img src="https://cdn.buymeacoffee.com/buttons/default-orange.png" alt="Buy Me A Coffee" height="41" width="174"></a>
+
+[Back to top](#TOP)
+
+<!-- Links -->
+[python]: https://www.python.org/downloads/release/python-360/
+[protpy]: https://github.com/amckenna41/protpy
+[aaindex]: https://github.com/amckenna41/aaindex
+[varname]: https://pypi.org/project/varname/
+[biopython]: https://biopython.org/
+[numpy]: https://numpy.org/
+[pandas]: https://pandas.pydata.org/
+[PyPi]: https://pypi.org/project/protpy/
+[demo]: https://colab.research.google.com/drive/12E3ayovpZOf6Gv-8ILwkN1zReKslEksB?usp=sharing
+[article]: https://medium.com/@ajmckenna69/protpy-05f02f821baa
+[Issues]: https://github.com/amckenna41/protpy/issues
+[readthedocs]: https://protpy.readthedocs.io/en/latest