Update render script and Makefile

terminal/pythonchemistry

@@ -1,4 +1,4 @@
-                Awesome Python Chemistry !Awesome (https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg) (https://github.com/sindresorhus/awesome)
+      Awesome Python Chemistry !Awesome (https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg) (https://github.com/sindresorhus/awesome)
 !License: CC BY 4.0 (https://img.shields.io/badge/License-CC%20BY%204.0-lightgrey.svg) (https://creativecommons.org/licenses/by/4.0/)
 
 A curated list of awesome Python frameworks, libraries, software and resources related to Chemistry.
@@ -17,7 +17,7 @@
   - Learning Resources (#learning-resources)
   - See Also (#see-also)
 
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 General Chemistry
 
@@ -25,11 +25,11 @@
 
 - AQME (https://github.com/jvalegre/aqme) - Ensemble of automated QM workflows that can be run through jupyter notebooks, command lines and yaml files.
 - aizynthfinder (https://github.com/MolecularAI/aizynthfinder) - A tool for retrosynthetic planning.
-- batchcalculator (http://lukaszmentel.com/batchcalculator/) - A GUI app based on wxPython for calculating the correct amount of reactants (batch) for a particular composition given by the molar ratio of its 
-components.
+- batchcalculator (http://lukaszmentel.com/batchcalculator/) - A GUI app based on wxPython for calculating the correct amount of reactants (batch) for a particular composition given by the 
+molar ratio of its components.
 - cctbx (https://cctbx.github.io/) - The Computational Crystallography Toolbox.
-- ChemFormula (https://github.com/molshape/ChemFormula) - ChemFormula provides a class for working with chemical formulas. It allows parsing chemical formulas, calculating formula weights, and generating 
-formatted output strings (e.g. in HTML, LaTeX, or Unicode).
+- ChemFormula (https://github.com/molshape/ChemFormula) - ChemFormula provides a class for working with chemical formulas. It allows parsing chemical formulas, calculating formula weights, 
+and generating formatted output strings (e.g. in HTML, LaTeX, or Unicode).
 - chemlib (https://chemlib.readthedocs.io/en/latest/) - A robust and easy-to-use package that solves a variety of chemistry problems.
 - chempy (http://pythonhosted.org/chempy/) - ChemPy is a package useful for chemistry (mainly physical/inorganic/analytical chemistry).
 - datamol (https://github.com/datamol-org/datamol): - Molecular Manipulation Made Easy. A light wrapper build on top of RDKit.
@@ -38,7 +38,8 @@
 - ionize (http://lewisamarshall.github.io/ionize/) - Calculates the properties of individual ionic species in aqueous solution, as well as aqueous solutions containing arbitrary sets of ions.
 - LModeA-nano (https://lmodea-nano.readthedocs.io/en/latest/) - Calculates the intrinsic chemical bond strength based on local vibrational mode theory in solids and molecules.
 - mendeleev (http://mendeleev.readthedocs.io/en/stable/) - A package that provides a python API for accessing various properties of elements from the periodic table of elements.
-- nmrglue (https://github.com/jjhelmus/nmrglue) - A package for working with nuclear magnetic resonance (NMR) data including functions for reading common binary file formats and processing NMR data.
+- nmrglue (https://github.com/jjhelmus/nmrglue) - A package for working with nuclear magnetic resonance (NMR) data including functions for reading common binary file formats and processing 
+NMR data.
 - Open Babel (http://openbabel.org/wiki/Main_Page) - A chemical toolbox designed to speak the many languages of chemical data.
 - periodictable (https://github.com/pkienzle/periodictable) - This package provides a periodic table of the elements with support for mass, density and xray/neutron scattering information.
 - propka (https://github.com/jensengroup/propka) - Predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.
@@ -75,13 +76,15 @@
 - MORFEUS (https://github.com/kjelljorner/morfeus) - Library for fast calculations of molecular features from 3D structures for machine learning with a focus on steric descriptors.
 - olorenchemengine (https://github.com/Oloren-AI/olorenchemengine) - Molecular property prediction with unified API for diverse models and respresentations,
   with integrated uncertainty quantification, interpretability, and hyperparameter/architecture tuning.
-- ROBERT (https://github.com/jvalegre/robert) - Ensemble of automated machine learning protocols that can be run sequentially through a single command line. The program works for regression and classification 
-problems.
+- ROBERT (https://github.com/jvalegre/robert) - Ensemble of automated machine learning protocols that can be run sequentially through a single command line. The program works for regression 
+and classification problems.
 - schnetpack (https://github.com/atomistic-machine-learning/schnetpack) - Deep Neural Networks for Atomistic Systems.
 - selfies (https://github.com/aspuru-guzik-group/selfies) - Self-Referencing Embedded Strings (SELFIES): A 100% robust molecular string representation.
 - Summit (https://github.com/sustainable-processes/summit) - Package for optimizing chemical reactions using machine learning (contains 10 algorithms + several benchmarks).
-- TDC (https://github.com/mims-harvard/TDC) - Therapeutics Data Commons (TDC) is the first unifying framework to systematically access and evaluate machine learning across the entire range of therapeutics.
-- XenonPy (https://github.com/yoshida-lab/XenonPy) - Library with several compositional and structural material descriptors, along with a few pre-trained neural network models of material properties.
+- TDC (https://github.com/mims-harvard/TDC) - Therapeutics Data Commons (TDC) is the first unifying framework to systematically access and evaluate machine learning across the entire range of
+therapeutics.
+- XenonPy (https://github.com/yoshida-lab/XenonPy) - Library with several compositional and structural material descriptors, along with a few pre-trained neural network models of material 
+properties.
 
 Generative Molecular Design
 
@@ -98,10 +101,12 @@
 
 - alchemlyb (https://github.com/alchemistry/alchemlyb) - Makes alchemical free energy calculations easier by leveraging the full power and flexibility of the PyData stack.
 - atomate2 (https://github.com/materialsproject/atomate2) - atomate2 is a library of computational materials science workflows.
-- Atomic Silumation Environment (ASE) (https://wiki.fysik.dtu.dk/ase/index.html) - Is a set of tools and modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations.
-- basis_set_exchange (https://github.com/MolSSI-BSE/basis_set_exchange) - A library containing basis sets for use in quantum chemistry calculations. In addition, this library has functionality for manipulation 
-of basis set data.
-- CACTVS (https://www.xemistry.com/academic/) - Cactvs is a universal, scriptable cheminformatics toolkit, with a large collection of modules for property computation, chemistry data file I/O and other tasks.
+- Atomic Silumation Environment (ASE) (https://wiki.fysik.dtu.dk/ase/index.html) - Is a set of tools and modules for setting up, manipulating, running, visualizing and analyzing atomistic 
+simulations.
+- basis_set_exchange (https://github.com/MolSSI-BSE/basis_set_exchange) - A library containing basis sets for use in quantum chemistry calculations. In addition, this library has 
+functionality for manipulation of basis set data.
+- CACTVS (https://www.xemistry.com/academic/) - Cactvs is a universal, scriptable cheminformatics toolkit, with a large collection of modules for property computation, chemistry data file I/O
+and other tasks.
 - CalcUS (https://github.com/cyllab/CalcUS) - Quantum chemisttry web platform that brings all the necessary tools to perform quantum chemistry in a user-friendly web interface.
 - cantera (https://github.com/Cantera/cantera) - A collection of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and transport processes.
 - CatKit (https://github.com/SUNCAT-Center/CatKit) - General purpose tools for high-throughput catalysis.
@@ -110,9 +115,11 @@
 - cinfony (http://cinfony.github.io/) - A common API to several cheminformatics toolkits (Open Babel, RDKit, the CDK, Indigo, JChem, OPSIN and cheminformatics webservices).
 - chemlab (http://chemlab.readthedocs.io/en/latest/index.html) - Is a library that can help the user with chemistry-relevant calculations.
 - emmet (https://github.com/materialsproject/emmet) - A package to 'build' collections of materials properties from the output of computational materials calculations.
-- fromage (https://github.com/Crespo-Otero-group/fromage/) - The "FRamewOrk for Molecular AGgregate Excitations" enables localised QM/QM' excited state calculations in a solid state environment.
+- fromage (https://github.com/Crespo-Otero-group/fromage/) - The "FRamewOrk for Molecular AGgregate Excitations" enables localised QM/QM' excited state calculations in a solid state 
+environment.
 - GPAW (https://wiki.fysik.dtu.dk/gpaw/) - Is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE).
-- horton (http://theochem.github.io/horton/2.0.1/index.html) - Helpful Open-source Research TOol for N-fermion system, a quantum-chemistry program that can perform computations involving model Hamiltonians.
+- horton (http://theochem.github.io/horton/2.0.1/index.html) - Helpful Open-source Research TOol for N-fermion system, a quantum-chemistry program that can perform computations involving 
+model Hamiltonians.
 - HTMD (https://github.com/Acellera/htmd) - High-Throughput Molecular Dynamics: Programming Environment for Molecular Discovery.
 - Indigo (https://github.com/epam/Indigo) - Universal cheminformatics libraries, utilities and database search tools.
 - Jarvis-tools (https://github.com/usnistgov/jarvis) - An open-access software package for atomistic data-driven materials design
@@ -124,19 +131,21 @@
 - oddt (https://github.com/oddt/oddt) - Open Drug Discovery Toolkit, a modular and comprehensive toolkit for use in cheminformatics, molecular modeling etc.
 - OPEM (https://github.com/ECSIM/opem) - Open source PEM (Proton Exchange Membrane) fuel cell simulation tool.
 - openmmtools (https://github.com/choderalab/openmmtools) - A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
-- overreact (https://github.com/geem-lab/overreact) - A library and command-line tool for building and analyzing complex homogeneous microkinetic models from quantum chemistry calculations, with support for 
-quasi-harmonic thermochemistry, quantum tunnelling corrections, molecular symmetries and more.
+- overreact (https://github.com/geem-lab/overreact) - A library and command-line tool for building and analyzing complex homogeneous microkinetic models from quantum chemistry calculations, 
+with support for quasi-harmonic thermochemistry, quantum tunnelling corrections, molecular symmetries and more.
 - ParmEd (https://github.com/ParmEd/ParmEd) -  Parameter/topology editor and molecular simulator with visualization capability.
 - pGrAdd (https://github.com/VlachosGroup/PythonGroupAdditivity) - A library for estimating thermochemical properties of molecules and adsorbates using group additivity.
 - phonopy (http://atztogo.github.io/phonopy/) - An open source package for phonon calculations at harmonic and quasi-harmonic levels.
-- PLAMS (https://github.com/SCM-NV/PLAMS) - Python Library for Automating Molecular Simulation: input preparation, job execution, file management, output processing and building data workflows.
+- PLAMS (https://github.com/SCM-NV/PLAMS) - Python Library for Automating Molecular Simulation: input preparation, job execution, file management, output processing and building data 
+workflows.
 - pMuTT (https://vlachosgroup.github.io/pMuTT/) - A library for ab-initio thermodynamic and kinetic parameter estimation.
 - PorePy (https://github.com/pmgbergen/porepy) - A Simulation Tool for Fractured and Deformable Porous Media.
 - ProDy (http://prody.csb.pitt.edu/) - An open source package for protein structural dynamics analysis with a flexible and responsive API.
 - ProLIF (https://github.com/chemosim-lab/ProLIF) - Interaction Fingerprints for protein-ligand complexes and more.
 - Psi4 (http://psicode.org) - A hybrid Python/C++ open-source package for quantum chemistry.
 - Psi4NumPy (https://github.com/psi4/psi4numpy/) - Psi4-based reference implementations and Jupyter notebook-based tutorials for foundational quantum chemistry methods.
-- pyEMMA (http://www.emma-project.org/latest/) - Library for the estimation, validation and analysis Markov models of molecular kinetics and other kinetic and thermodynamic models from molecular dynamics data.
+- pyEMMA (http://www.emma-project.org/latest/) - Library for the estimation, validation and analysis Markov models of molecular kinetics and other kinetic and thermodynamic models from 
+molecular dynamics data.
 - pygauss (https://pygauss.readthedocs.io/en/stable/index.html) - An interactive tool for supporting the life cycle of a computational molecular chemistry investigations.
 - PyQuante (http://pyquante.sourceforge.net/) - Is an open-source suite of programs for developing quantum chemistry methods.
 - pysic (https://github.com/thynnine/pysic) - A calculator incorporating various empirical pair and many-body potentials.
@@ -159,8 +168,8 @@
 - FitSNAP (https://github.com/FitSNAP/FitSNAP) - A Package For Training SNAP Interatomic Potentials for use in the LAMMPS molecular dynamics package.
 - fftool (https://github.com/paduagroup/fftool) - Tool to build force field input files for molecular simulation.
 - FLARE (https://github.com/mir-group/flare) - A package for creating fast and accurate interatomic potentials.
-- global-chem (https://github.com/Sulstice/global-chem) - A Chemical Knowledge Graph and Toolkit, writting in IUPAC/SMILES/SMARTS, for common small molecules from diverse communities to aid users in selecting 
-compounds for forcefield parametirization.
+- global-chem (https://github.com/Sulstice/global-chem) - A Chemical Knowledge Graph and Toolkit, writting in IUPAC/SMILES/SMARTS, for common small molecules from diverse communities to aid 
+users in selecting compounds for forcefield parametirization.
 - matbench-discovery (https://github.com/janosh/matbench-discovery) - A benchmark for ML-guided high-throughput materials discovery.
 - NeuralForceField (https://github.com/learningmatter-mit/NeuralForceField) - Neural Network Force Field based on PyTorch.
 - openff-toolkit (https://github.com/openforcefield/openff-toolkit) - The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools.
@@ -176,8 +185,8 @@
 - moleculekit (https://github.com/Acellera/moleculekit) - A molecule manipulation library.
 - nglview (https://github.com/arose/nglview) - A Jupyter (https://jupyter.org/) widget to interactively view molecular structures and trajectories.
 - PyMOL (https://pymol.org/) - A user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger.
-- pymoldyn (https://pgi-jcns.fz-juelich.de/portal/pages/pymoldyn-main.html) - A viewer for atomic clusters, crystalline and amorphous materials in a unit cell corresponding to one of the seven 3D Bravais 
-lattices.
+- pymoldyn (https://pgi-jcns.fz-juelich.de/portal/pages/pymoldyn-main.html) - A viewer for atomic clusters, crystalline and amorphous materials in a unit cell corresponding to one of the 
+seven 3D Bravais lattices.
 - sumo (http://sumo.readthedocs.io/en/latest/) - A toolkit for plotting and analysis of ab initio solid-state calculation data.
 - surfinpy (https://surfinpy.readthedocs.io/en/latest/) - A library for the analysis, plotting and visualisation of ab initio surface calculation data.
 - trident-chemwidgets (https://github.com/tridentbio/trident-chemwidgets) - Jupyter Widgets to interact with molecular datasets.
@@ -187,7 +196,8 @@
 Providing a python layer for accessing chemical databases
 
 - ccdc (https://downloads.ccdc.cam.ac.uk/documentation/API/index.html) - An API for the Cambridge Structural Database System.
-- ChemSpiPy (http://chemspipy.readthedocs.io/en/latest/) - ChemSpider (http://www.chemspider.com/) wrapper, that allows chemical searches, chemical file downloads, depiction and retrieval of chemical properties.
+- ChemSpiPy (http://chemspipy.readthedocs.io/en/latest/) - ChemSpider (http://www.chemspider.com/) wrapper, that allows chemical searches, chemical file downloads, depiction and retrieval of 
+chemical properties.
 - CIRpy (http://cirpy.readthedocs.io/en/latest/) - An interface for the Chemical Identifier Resolver (CIR) by the CADD Group at the NCI/NIH.
 - pubchempy (http://pubchempy.readthedocs.io/en/latest/) - PubChemPy provides a way to interact with PubChem in Python.
 - chembl-downloader (https://github.com/cthoyt/chembl-downloader) - Automate downloading and querying the latest (or a given) version of ChEMBL (https://www.ebi.ac.uk/chembl/)
@@ -197,24 +207,25 @@
 
 Resources for learning to apply python to chemistry.
 
-- An Introduction to Applied Bioinformatics (https://github.com/applied-bioinformatics/iab2) - A Jupyter book demonstrating working with biochemical data using the scikit-bio library for tasks such as sequence 
-alignment and calculating Hamming distances.
-- Computational Thermodynamics (https://kyleniemeyer.github.io/computational-thermo/content/intro.html) - This collection of Jupyter notebooks demonstrates solutions to a range of thermodynamic problems 
-including solving chemical equilibria, comparing real versus ideal gas behavior, and calculating the temperature and composition of a combustion reaction.
-- SciCompforChemists (https://github.com/weisscharlesj/SciCompforChemists) - Scientific Computing for Chemists with Python is a Jupyter book teaching basic python in chemistry skills, including relevant 
-libraries, and applies them to solving chemical problems.
+- An Introduction to Applied Bioinformatics (https://github.com/applied-bioinformatics/iab2) - A Jupyter book demonstrating working with biochemical data using the scikit-bio library for 
+tasks such as sequence alignment and calculating Hamming distances.
+- Computational Thermodynamics (https://kyleniemeyer.github.io/computational-thermo/content/intro.html) - This collection of Jupyter notebooks demonstrates solutions to a range of 
+thermodynamic problems including solving chemical equilibria, comparing real versus ideal gas behavior, and calculating the temperature and composition of a combustion reaction.
+- SciCompforChemists (https://github.com/weisscharlesj/SciCompforChemists) - Scientific Computing for Chemists with Python is a Jupyter book teaching basic python in chemistry skills, 
+including relevant libraries, and applies them to solving chemical problems.
 
 Miscellaneous Awesome
 
-- Colorful Nuclide Chart (https://people.physics.anu.edu.au/~ecs103/chart/) - A beatuful, interactive visualization of nuclides with access to a varirty of nuclear properties and allows saving high quality 
-images for publications, presentations and outreach.
+- Colorful Nuclide Chart (https://people.physics.anu.edu.au/~ecs103/chart/) - A beatuful, interactive visualization of nuclides with access to a varirty of nuclear properties and allows 
+saving high quality images for publications, presentations and outreach.
 
 See Also
 
 - awesome-cheminformatics (https://github.com/hsiaoyi0504/awesome-cheminformatics) Another list focuses on Cheminformatics, including tools not only in Python.
-- awesome-small-molecule-ml (https://github.com/benb111/awesome-small-molecule-ml) A collection of papers, datasets, and packages for small-molecule drug discovery. Most links to code are in Python.
+- awesome-small-molecule-ml (https://github.com/benb111/awesome-small-molecule-ml) A collection of papers, datasets, and packages for small-molecule drug discovery. Most links to code are in 
+Python.
 - awesome-molecular-docking (https://github.com/yangnianzu0515/awesome-molecular-docking) A curated list of molecular docking software, datasets, and papers.
-- jarvis (https://jarvis.nist.gov/) Joint Automated Repository for Various Integrated Simulations is a repository designed to automate materials discovery and optimization using classical force-field, density 
-functional theory, machine learning calculations and experiments.
-- polypharmacy-ddi-synergy-survey (https://github.com/AstraZeneca/polypharmacy-ddi-synergy-survey) A collection of research papers (with Python implementations) focusing on drug-drug interactions, synergy and 
-polypharmacy.
+- jarvis (https://jarvis.nist.gov/) Joint Automated Repository for Various Integrated Simulations is a repository designed to automate materials discovery and optimization using classical 
+force-field, density functional theory, machine learning calculations and experiments.
+- polypharmacy-ddi-synergy-survey (https://github.com/AstraZeneca/polypharmacy-ddi-synergy-survey) A collection of research papers (with Python implementations) focusing on drug-drug 
+interactions, synergy and polypharmacy.