ModelSEED model parsing and early PyPI package logic

.ipynb_checkpoints/README-checkpoint.md

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+# dGPredictor
+
+==================================
+### Requirements:
+
+1. Python 3.8.10
+2. RDkit (http://www.rdkit.org/)
+3. pandas (https://pandas.pydata.org/)
+4. matplotlib (https://matplotlib.org/stable/users/installing.html)
+5. Scikit-learn (https://scikit-learn.org/stable/)
+6. Streamlit (https://streamlit.io/)
+7. Openbabel (https://anaconda.org/openbabel/openbabel)
+8. ChemAxon's Marvin >= 5.11 
+9. Pulp
+
+Installation
+1. Python 3.8.10 (https://www.python.org/downloads/windows/)
+Recommended- 
+- Create anaconda environment using command "conda create -n dGPredictor python=3.8 ipython"
+- activate the env using command "conda activate dGPredictor" or "source activate dGPredictor"
+2. RDkit
+- type command "conda install -c conda-forge rdkit" in your dGPredictor env to install rdkit
+3. Pandas
+- "conda install pandas"
+4. matplotlib
+- "conda install -c conda-forge matplotlib"
+5. Scikit-learn
+- use command "pip install -U scikit-learn"
+6. Streamlit 
+- use command "pip install -U streamlit"
+7. Openbabel
+- run "conda install -c conda-forge openbabel" 
+- Installation via "pip" may require a wheel binary from this site https://www.lfd.uci.edu/~gohlke/pythonlibs/#openbabel, since the PyPI version may yield a "SWIG failed" installation error.
+8. ChemAxon's Marvin (PkA value estimation)
+- Marvin is only required for adding structures of novel metabolites/compounds that are not in the KEGG database
+- instructions (https://chemaxon.com/products/marvin/download)
+- add "cxcalc.bat (macOS) /cxcalc.exe (Windows)" to PATH and also in "./CC/chemaxon.py" file
+- you will need to get a license to use ChemAxon (it is free for academic use)
+9. Pulp
+- use command "pip install -U pulp"
+
+
+
+
+==================================
+### Running web-interface loacally using streamlit
+
+- Model generation: Run "model_gen.py" using "python model_gen.py" once to create dGPredictor model file :- (Running this might take some time)
+- run "streamlit run ./streamlit/main.py" from dGPredictor folder
+- running KEGG reaction (doesn't require ChemAxon's Marvin) : copy paste the reaction equation into reaction section and click search
+
+### Gibbs free energy prediction use automated group decomposition method
+
+- Step 1: decompose the metabolites based on smiles files (see function decompse_ac in decompose_groups.py or notebook )
+- Step 2: create group changes vectors (i.e. reaction rules) based on group changes in metabolites of reactions (see get_rxn_rule in decompose_groups.py)
+- Step 3: linear regression, Ridge Regression and Bayesian Ridge Regression in "predict.py"
+- Step 4: Multiple regression models in notebook "analysis_dGPredictor.ipynb"
+
+### Pathway design using novoStoic
+- Run "mini_novoStoic.py" to see an example to design pathways for Isobutanol synthesis
+
+
+# demo
+![dGPredictor Demo](figures/dg_demo_py3.gif)
+