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Added new openmmdl simulation files

openmmdl/openmmdl_simulation/cleaning_procedures.py

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+import os
+import shutil
+from typing import List
+
+
+class FileManager:
+    """
+    A class for file and directory management operations such as
+    creating directories, copying files, and organizing files.
+    """
+
+    @staticmethod
+    def create_directory_if_not_exists(directory_path):
+        """Create a directory if it doesn't exist, or overwrite it if already does.
+
+        Args:
+            directory_path (str): Path of the directory that you want to create.
+
+        Returns:
+            None
+        """
+        if not os.path.exists(directory_path):
+            os.mkdir(directory_path)
+        else:
+            shutil.rmtree(directory_path)
+            os.mkdir(directory_path)
+
+    @staticmethod
+    def copy_file(src, dest):
+        """Copy a file to the destination path.
+
+        Args:
+            src (str): Path of the file that needs to be copied.
+            dest (str): Path of destination where the file needs to be copied to.
+
+        Returns:
+            None
+        """
+        if os.path.exists(src):
+            shutil.copy(src, dest)
+
+    @staticmethod
+    def organize_files(source_files, destination):
+        """Organizes the files and moves them from the source to the destination directory.
+
+        Args:
+            source_files (List[str]): List of paths of the files that need to be moved.
+            destination (str): Path of destination where the files need to be moved to.
+
+        Returns:
+            None
+        """
+        for file in source_files:
+            if os.path.exists(file):
+                os.rename(file, os.path.join(destination, os.path.basename(file)))
+
+
+class Cleanup:
+    """
+    A class for cleaning up simulation files.
+    """
+
+    @staticmethod
+    def cleanup_files(protein_name):
+        """Cleans up the PDB Reporter Output File and MDTraj Files of the performed simulation.
+
+        Args:
+            protein_name (str): Name of the protein PDB.
+
+        Returns:
+            None
+        """
+        print("Cleaning Up :)")
+        try:
+            os.remove(f"output_{protein_name}")
+            os.remove(f"centered_old_coordinates.pdb")
+            os.remove(f"centered_old_coordinates.dcd")
+        except FileNotFoundError:
+            print("One or more files not found. Cleanup skipped.")
+        print("Cleanup is done.")
+
+
+class PostMDProcessor:
+    """
+    A class for organizing and moving files after MD simulation.
+    """
+
+    @staticmethod
+    def post_md_file_movement(
+        protein_name: str,
+        prmtop: str = None,
+        inpcrd: str = None,
+        ligands: List[str] = None,
+    ):
+        """Organizes and moves the files after the MD simulation to their respective directories.
+
+        Args:
+            protein_name (str): Name of the protein PDB.
+            prmtop (str, optional): Path to the AMBER topology file.
+            inpcrd (str, optional): Path to the AMBER coordinate file.
+            ligands (List[str], optional): List of paths to the ligand files.
+
+        Returns:
+            None
+        """
+        # Create necessary directories
+        dirs = [
+            "Input_Files",
+            "MD_Files",
+            "MD_Files/Pre_MD",
+            "MD_Files/Minimization_Equilibration",
+            "MD_Files/MD_Output",
+            "MD_Postprocessing",
+            "Final_Output",
+            "Final_Output/All_Atoms",
+            "Final_Output/Prot_Lig",
+            "Checkpoints",
+        ]
+
+        for directory in dirs:
+            FileManager.create_directory_if_not_exists(directory)
+
+        # Move input files
+        if ligands:
+            FileManager.copy_file(ligands, "Input_Files")
+            FileManager.copy_file(ligands, "Final_Output/All_Atoms")
+            FileManager.copy_file(ligands, "Final_Output/Prot_Lig")
+
+        FileManager.copy_file(protein_name, "Input_Files")
+        if prmtop:
+            FileManager.copy_file(prmtop, "Input_Files")
+        if inpcrd:
+            FileManager.copy_file(inpcrd, "Input_Files")
+
+        # Organize pre-MD files
+        source_pre_md_files = [
+            "prepared_no_solvent_",
+            "solvent_padding_",
+            "solvent_absolute_",
+            "membrane_",
+        ]
+        destination_pre_md = "MD_Files/Pre_MD"
+        FileManager.organize_files(
+            [f"{prefix}{protein_name}" for prefix in source_pre_md_files],
+            destination_pre_md,
+        )
+
+        # Organize topology files after minimization and equilibration
+        source_topology_files = ["Energyminimization_", "Equilibration_"]
+        destination_topology = "MD_Files/Minimization_Equilibration"
+        FileManager.organize_files(
+            [f"{prefix}{protein_name}" for prefix in source_topology_files],
+            destination_topology,
+        )
+
+        # Organize simulation output files
+        FileManager.organize_files(
+            [f"output_{protein_name}", "trajectory.dcd"], "MD_Files/MD_Output"
+        )
+
+        # Organize MDtraj and MDAnalysis files
+        postprocessing_files = [
+            "centered_old_coordinates_top.pdb",
+            "centered_old_coordinates.dcd",
+            "centered_old_coordinates_top.gro",
+            "centered_old_coordinates.xtc",
+            "centered_traj_unaligned.dcd",
+            "centered_traj_unaligned.xtc",
+            "prot_lig_traj_unaligned.dcd",
+            "prot_lig_traj_unaligned.xtc",
+        ]
+        FileManager.organize_files(postprocessing_files, "MD_Postprocessing")
+
+        all_atoms_files = [
+            "centered_top.pdb",
+            "centered_traj.dcd",
+            "centered_top.gro",
+            "centered_traj.xtc",
+        ]
+        FileManager.organize_files(all_atoms_files, "Final_Output/All_Atoms")
+
+        prot_lig_files = [
+            "prot_lig_top.pdb",
+            "prot_lig_traj.dcd",
+            "prot_lig_top.gro",
+            "prot_lig_traj.xtc",
+        ]
+        FileManager.organize_files(prot_lig_files, "Final_Output/Prot_Lig")
+
+        # Organize checkpoint files
+        checkpoint_files = [
+            "checkpoint.chk",
+            "10x_checkpoint.chk",
+            "100x_checkpoint.chk",
+        ]
+        FileManager.organize_files(checkpoint_files, "Checkpoints")