ncbi · prameshsharma25 · May 5, 2026 · May 5, 2026 · May 5, 2026 · May 5, 2026
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,78 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+*.manifest
+*.spec
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# IDE
+.vscode/
+.idea/
+*.swp
+*.swo
+*~
+.DS_Store
+
+# Project specific
+examples/*/results/
+blind_prediction/
+successed_prediction/
+failed_prediction/
+multimer_prediction/
+test_data/
+msa_folder/
+structures_all.csv
+
+# Foldseek
+pdb*
+pdb_*
+tmp/
diff --git a/Data/Fold-switch_hits-SPEACH_AF/pdb_pairs.csv b/Data/Fold-switch_hits-SPEACH_AF/pdb_pairs.csv
diff --git a/Install/install_colabbatch_linux_101624.sh b/Install/install_colabbatch_linux_101624.sh
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -0,0 +1,4 @@
+include README.md
+include LICENSE.md
+recursive-include cf_random/data *
+recursive-include examples *
diff --git a/README.md b/README.md
@@ -1,52 +1,27 @@
 # Data and code for CF-random
-General installation and usage guidance of CF-random for predicting the alternative conformation and fold-switching proteins.<br>
-To run CF-random in a Colab notebook, please use following [link](https://colab.research.google.com/drive/16pD2tUMkUx1gwDxZXcSr9WOosYp0ZU6j?authuser=0).<br><br>
+
+General installation and usage guidance of CF-random for predicting the alternative conformation and fold-switching proteins.
+
+To run CF-random in a Colab notebook, please use following [link](https://colab.research.google.com/drive/16pD2tUMkUx1gwDxZXcSr9WOosYp0ZU6j?authuser=0).
+
 <a target="_blank" href="https://colab.research.google.com/drive/16pD2tUMkUx1gwDxZXcSr9WOosYp0ZU6j?authuser=0">
  <img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open CF-random Colab"/>
 </a>
 
-
 # Installation
-CF-random uses the [localcolabfold](https://github.com/YoshitakaMo/localcolabfold) and [Foldseek](https://github.com/steineggerlab/foldseek) under linux environment.<br>
-For more details about localcolabfold, please visit [here.](https://github.com/YoshitakaMo/localcolabfold) <br>
-We currently not support the Windows and MacOS environment.<br>
-
-Installation process including localcolabfold, dependencies, and Foldseek is done with following commands.
-```
-wget https://raw.githubusercontent.com/YoshitakaMo/localcolabfold/main/install_colabbatch_linux.sh
-bash install_colabbatch_linux.sh
-
-** Or use a bash script in install folder 
-bash install_colabbatch_linux.sh
-```
-<br>
-
 
-After the installation of localcolabfold, add the localcolabfold path to your .bashrc file:.<br>
-```
-export PATH="/path/to/your/localcolabfold/colabfold-conda/bin:$PATH"
-```
-<br>
+CF-random uses [ColabFold](https://github.com/sokrypton/ColabFold) (for structure prediction) and [Foldseek](https://github.com/steineggerlab/foldseek) (for structure search) under Linux environment.
 
-Then reactivate your .bashrc file <br>
+**For installation details, see [INSTALL.md](INSTALL.md)**
 
-Now create a conda new conda environment: 
-```
-conda create --name CF-random python=3.10
-conda activate CF-random
-pip install textalloc tmtools adjustText thefuzz mdtraj biopython seaborn MDAnalysis
-conda install conda-forge::pymol-open-source
-pip3 install -U scikit-learn
-```
-Once the dependencies are installed, install Foldseek.
-<br>
-```
+Quick start:
+```bash
+conda create --name cf-random python=3.10 -y
+conda activate cf-random
+pip install -e ".[colabfold]"
 conda install -c conda-forge -c bioconda foldseek
 foldseek databases PDB pdb tmp
 ```
-<br>
-
-### We recommend running the foldseek databases command in a directory where the libraries can be stored. <br>
 
 
 # Usage
@@ -65,7 +40,7 @@ foldseek databases PDB pdb tmp
  --type  ####    |  can choose the model type of Colabfold. e.g.) ptm, monomer, and multimer
  --options ###   |  AC: predicting alternative conformations of protein with references, FS: predicting the fold-switching protein with references, and blind: predicting the alternative conformations or fold-switching proteins without reference PDB files.
 ```
-* In default mode (fold-switching and alternative conformation), CF-ramdon produces the results of TM-scores (csv and png files), plDDT, and information of selected random MSA. If CF-random predicts the both folds, generated prediction files are deposited under successed_prediction/pdb1_name and additional_sampling/pdb1_name . If not, it would not generate anything. <br>
+* In default mode (fold-switching and alternative conformation), CF-random produces the results of TM-scores (csv and png files), plDDT, and information of selected random MSA. If CF-random predicts the both folds, generated prediction files are deposited under successed_prediction/pdb1_name and additional_sampling/pdb1_name . If not, it would not generate anything. <br>
 * Before running the default mode of fold-switching, setting the "range_fs_pairs_all.txt" file is required. The name of reference PDB files, residue ranges of reference pdb files, and residue ranges of prediction files. ColabFold generates the residue index starting from 1, so please choose the residue range of fold-switching region correctly. CF-random reads the residue index in PDB file, make sure that selection of residue range is correct. <br>
  examples) pdb1, pdb2, XXX-XXX, XXX-XXX, XXX-XXX, XXX-XXX (residue range of reference 1, residue range of reference 2, residue range of prediction1, resodie range of prediction2) <br>
 * --nMSA can be applied for all options, but --nESN cannot be used for blind mode.

diff --git a/cf_random/__init__.py b/cf_random/__init__.py
@@ -0,0 +1,18 @@
+"""
+CF-random: Predicting alternative conformations and fold-switching proteins
+
+A package for identifying and analyzing protein fold-switching and alternative conformations
+using AlphaFold predictions and structural analysis tools.
+"""
+
+__version__ = "0.1.0"
+__author__ = "Myeongsang (Samuel) Lee"
+__all__ = [
+    "main",
+]
+
+# Import main modules for easier access
+try:
+    from .core import main
+except ImportError:
+    pass
diff --git a/...AFcluster/CRKL/2bzy_B_tmscores_fs_all.csv → cf_random/analysis/__init__.py b/...AFcluster/CRKL/2bzy_B_tmscores_fs_all.csv → cf_random/analysis/__init__.py