coFeatures

Cofactor-dependent feature generation for protiens

Clone Repository

git clone https://github.com/ESPhoenix/coFeatures

Create and Activate Conda Environment

conda create -n coFeaturesEnv python=3.7.12
conda activate coFeaturesEnv

Install Required Python Packages

pip install argpass==0.0.2 numpy==1.21.6 pandas==1.3.5 tqdm==4.66.1

Edit Config File or Create Your Own

import numpy as np        
def inputs():
       ## LOCATION OF YOUR PDB FILES
       inputDir = "/home/esp/featureGenerationMethods/coFeatures/test_pdbs"       
       ## WHERE DO YOU WANT YOUR OUTPUTS
       outDir = "/home/esp/featureGenerationMethods/coFeatures/features"          
       ## LOCATION OF AA PROPERTIES
       aminoAcidTable="/home/esp/featureGenerationMethods/coFeatures/amino_acid_properties.txt" 
       # cofactor information
       ## LIST OF COFACTOR NAMES IN YOUR PDB FILES
       cofactorNames = ["FAD", "FMN"]
       ## DICT CONTAINING: RESIDUE_NAME:[ATOM1,ATOM2...]
       ## WILL BE USED TO GENERATE NEAREST 1 and NEAREST 3 RESIDUES FEATURES
       keyAtomsDict = {
               "FMN":["N1","N3","N5"],
               "FAD":["N1","N3","N5"]
               }
       ## DICT CONTAINING: RESIDUE_NAME:[ATOM1,ATOM2...]
       ## WILL BE USED TO DEFINE CENTER OF ORB REGION 
       orbAtomsDict = {
               "FMN":["N10","C10","C4A","N5","C5A","C9A"],
               "FAD":["N10","C10","C4X","N5","C5X","C9A"]
                       }
       ## DICT CONTAINING: RESIDUE_NAME:[ATOM1,ATOM2...]
       ## WILL BE USED TO DEFINE ATOMS TO CONTRUCT CLOUD REGION                 
       cloudAtomsDict = {
               "FMN":["N10","C9A","C9","C8","C8M","C7","C7M","C6","C5A","N5",
                       "C4A","C4","O4","N3","HN3","C2","O2","N1","C10"],
               "FAD":["N10","C9A","C9","C8","C8M","C7","C7M","C6","C5X","N5",
                       "C4X","C4","O4","N3","HN3","C2","O2","N1","C10"]
                       }
       ## LIST OF RADII FOR ORB REGION
       orbRange = list(np.arange(6, 10))
       ## LIST OF RADII FOR CLOUD REGION
       cloudRange = list(np.arange(3, 7))                      

       return (inputDir, outDir, aminoAcidTable, cofactorNames, keyAtomsDict,
                   orbAtomsDict, cloudAtomsDict, orbRange, cloudRange)

Useage

From the coFeatures directory, run the following in the command line:

python coFeatures.py --config config.py

You may want to change the name of config.py to your own config file