### Install Required Packages Source: https://github.com/gao666999/ssbondpredict/blob/master/PreDisulfideBond/README.md Installs the necessary Python packages for PreDisulfideBond. Ensure NumPy version is less than 1.17. ```bash pip install scipy==1.4.1 pip install chardet==3.0.4 pip install pandas==1.0.1 pip install rmsd pip install Biopython pip install openpyxl pip install numpy==1.16(notice that the version of numpy should less than 1.17 ) ``` -------------------------------- ### Example: Predict Disulfide Bonds for 1crn.pdb Source: https://github.com/gao666999/ssbondpredict/blob/master/PreDisulfideBond/README.md An example command to predict disulfide bonds for '1crn.pdb' and save the results in the specified output directory. ```bash python predict.py /Users/ssb/Desktop/1crn.pdb /Users/ssb/Desktop ./ ``` -------------------------------- ### Example Prediction Output Format Source: https://github.com/gao666999/ssbondpredict/blob/master/README.md This snippet shows the format of the predicted output, indicating residue pairs, their formation probability, and changes in entropy and energy after mutations. ```text CYSA4-ARGA10 0.997 -24.4450 -1.8942 ``` -------------------------------- ### Example: Predict Pairs and Probabilities for 1crn.pdb Source: https://github.com/gao666999/ssbondpredict/blob/master/PreDisulfideBond/README.md Demonstrates how to use the `predict_pairs` function to obtain only residue pairs and their associated probabilities for a given PDB file. ```python # Make a prediction for 1crn.pdb and get the result which only contain residue pairs and probability form PreDisulfideBond import predict result = predict.predict_pairs('/Users/ssb/Desktop/1crn.pdb','/Users/ssb/Desktop') ``` -------------------------------- ### Example: Predict Disulfide Bonds and Generate Mutated PDBs Source: https://github.com/gao666999/ssbondpredict/blob/master/PreDisulfideBond/README.md Predicts disulfide bonds and generates mutated PDB files for further analysis. The output includes an Excel file and a folder with mutated PDBs. ```bash python predict.py /Users/ssb/Desktop/1crn.pdb /Users/ssb/Desktop /Users/ssb/Data/ --generate ``` -------------------------------- ### Set Environment Variable for Library Linking Source: https://github.com/gao666999/ssbondpredict/blob/master/PreDisulfideBond/README.md Sets the KMP_DUPLICATE_LIB_OK environment variable to TRUE to avoid dynamic library link errors, particularly with Anaconda installations. ```bash export KMP_DUPLICATE_LIB_OK=TRUE ``` -------------------------------- ### Predict Disulfide Bond Pairs using the predict_pairs function Source: https://github.com/gao666999/ssbondpredict/blob/master/PreDisulfideBond/README.md Uses the `predict_pairs` function from the `PreDisulfideBond.predict` module to get residue pairs and their probabilities. This function does not return entropy or energy changes. ```python from PreDisulfideBond import predict result = predict.predict_pairs('objectfile','the path contains PreDisulfideBond') ``` -------------------------------- ### Run CNN Training Script Source: https://github.com/gao666999/ssbondpredict/blob/master/AuxiliaryCode/traincode/README.md Execute the script for training and testing a convolutional neural network. Use the --help flag to see all available parameters. ```bash python noSG_cnn_train_test.py you can run python noSG_cnn_train_test.py --help Will display all parameters and features. ``` -------------------------------- ### Run FNN Training Script Source: https://github.com/gao666999/ssbondpredict/blob/master/AuxiliaryCode/traincode/README.md Execute the script for training and testing a fully connected neural network. Use the --help flag to see all available parameters. ```bash python noSG_fnn_train_test.py you can run python noSG_fnn_train_test.py --help Will display all parameters and features. ``` -------------------------------- ### Run SSBONDPredict for Disulfide Bond Prediction Source: https://github.com/gao666999/ssbondpredict/blob/master/PreDisulfideBond/README.md Executes the SSBONDPredict program to predict residue pairs that can form disulfide bonds. Provide the PDB file, the path to SSBONDPredict, and the output directory. ```bash python predict.py PDB_file the_path_of_SSBONDPredict output_path ``` -------------------------------- ### Create TensorFlow Records Source: https://github.com/gao666999/ssbondpredict/blob/master/AuxiliaryCode/datacode/README.md Converts positive and negative sample maps into TensorFlow data format. Use --help to see all parameters. ```python python create_tfrecords.py ``` ```python python create_tfrecords.py --help ``` -------------------------------- ### Download PDB Files Source: https://github.com/gao666999/ssbondpredict/blob/master/AuxiliaryCode/datacode/README.md Downloads PDB files from the Protein Data Bank. Requires the path to a cullpdb file and a dataset path for saving. ```python python Download_PDB.py cullpath datasetpath ``` -------------------------------- ### Create Negative Atom Position Matrix Source: https://github.com/gao666999/ssbondpredict/blob/master/AuxiliaryCode/datacode/README.md Extracts atom position matrices for negative samples from PDB files. Saves the resulting array in .npy format. ```python python create_negative_map.py pdbpath resultpath resultfilename ``` -------------------------------- ### Create Positive Atom Position Matrix Source: https://github.com/gao666999/ssbondpredict/blob/master/AuxiliaryCode/datacode/README.md Extracts atom position matrices for positive samples from PDB files. Saves the resulting array in .npy format. ```python python create_positive_map.py pdbpath resultpath resultfilename ``` -------------------------------- ### Create Distance Map from Atom Positions Source: https://github.com/gao666999/ssbondpredict/blob/master/AuxiliaryCode/datacode/README.md Converts atom position arrays (positive or negative) into a distance map. Saves the result in .npy format. ```python python ssbond_distance_map.py AtomPositionfile resultpath resultfilename ``` -------------------------------- ### Generate Mutated Residue Information Source: https://github.com/gao666999/ssbondpredict/blob/master/PreDisulfideBond/README.md Utilizes the `generate_mutated_residue` function to create information for a residue mutated into Cysteine. Requires PDB file, wildtype name, sequence number, and chain ID. ```python from PreDisufideBond import generate_mutated_residue NewResidueInformation = generate_mutated_residue.GenerateMutatedResidue(pdbfile,wildtype_name,AAsequenceNum,chainid) ``` === COMPLETE CONTENT === This response contains all available snippets from this library. No additional content exists. Do not make further requests.