SAXS-EOM-FULL-ATOM

Convert EOM output to a full atom PDB files

Features

EOM v3.xx generates cif files that you can convert to full atom pdb files :

1 - Converts CIF files to PDB format using Open Babel.

2 - Creates peptide bonds and links C-alpha dummy atoms using PD2.

3 - Optimises side-chain conformations using Scwrl4.

Requirements

Python 3.x

Python packages:

1- Open Babel

conda install openbabel

2- tqdm

conda install tqdm

External programs:

1- PD2

https://github.com/jmacdona/pd2_public

To install PD2 you need:

For LINUX and MAC:

1- You need to update the SConstruct file and change all the print fonction

   example print("INFO: compiling with gprof flags")

2- you need to change the name of the liboost by removing the "-mt", because liboost change its name

For Mac M1,M2 ...:

1- In src/external/include/eigen replace the file by the last version on GitHub

       https://github.com/libigl/eigen

2- Modify the SConstruct

  add 

      import platform
      is_arm = platform.machine() == "arm64"
  
  and change the line 'gcc_cppflags='
  for 
      gcc_cppflags = ['-ffast-math', '-funroll-loops', '-pipe','-g', '-Wall', '-fmessage-length=0', '-std=c++17' ]
      if not is_arm:
      cxxflags.insert(0, '-msse3')  # On ajoute -msse3 uniquement sur x86_64

For LINUX and MAC:

   In your .bashrc add something like

       export PATH=$PATH:/location/of/PD2/bin
       export PD2_DB=/location/of/PD2/database

Scwrl4

http://dunbrack.fccc.edu/lab/scwrl

In your .bashrc add something like

export PATH=$PATH://location/of/Scwrl4 export SCWRL_DB=/location/of/Scwrl4.ini

USAGE

Ensure you set up properly the environment variables PD2_DB and SCWRL_DB to point to the respective database directories. Run the script by providing the path of the folder where the CiFS are and the sequence in fasta format as a command-line argument:

python script_name.py path_to_sequence.fasta path_to_CIFS_FOLDER

In the sequence file if the aa are in lower case they will be untouched by SCWRL4.

The script will convert CIF files to PDB format, perform protein structure refinement, optimize side-chain conformations, and generate output PDB files in the final_pdb/ directory.

2025 JMB