Merge pull request #11 from cch1999/use_hydrite

Use hydrite

.github/workflows/tests.yaml

@@ -41,21 +41,21 @@ jobs:
       - name: Install Extras
         run: pip install -r requirements.txt
 
-      - name: Install OpenBabel
-        run: mamba install -c conda-forge openbabel
+      # - name: Install OpenBabel
+      #   run: mamba install -c conda-forge openbabel
 
-      - name: Install reduce
-        run: mamba install -c speleo3 reduce
+      # - name: Install reduce
+      #   run: mamba install -c speleo3 reduce
 
       # Install coverage tool
       - name: Install Coverage
         run: pip install coverage
 
-      # # Run tests with coverage
-      # - name: Run unit tests and generate coverage report
-      #   run: |
-      #     coverage run --source=posecheck -m unittest discover -s tests -p "test_*.py"
-      #     coverage xml
+      # Run tests with coverage
+      - name: Run unit tests and generate coverage report
+        run: |
+          coverage run --source=posecheck -m unittest discover -s tests -p "test_*.py"
+          coverage xml
       
       # # Upload coverage to Codecov
       # - name: Upload coverage to Codecov

.gitignore

@@ -3,4 +3,5 @@
 posecheck/__pycache__/*.pyc
 */*/__pycache__/
 .vscode/*
-.DS_Store
+.DS_Store
+*.pyc

changelog.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## [1.3] - 20-08-2024
+
+### Changed
+- Changed protonation script from `reduce` to `hydride` to make app dependencies pip installable
+
 ## [1.2] - 25-07-2024
 
 ### Changed

posecheck/posecheck.py

@@ -43,9 +43,9 @@ def __init__(
         self.reduce_path = reduce_path
         self.clash_tolerance = clash_tolerance
 
-        # Check if reduce is installed
-        if not is_reduce_installed(reduce_path):
-            print_reduce_warning()
+        # # Check if reduce is installed
+        # if not is_reduce_installed(reduce_path):
+        #     print_reduce_warning()
 
     def load_protein_from_pdb(self, pdb_path: str) -> None:
         """Load a protein from a PDB file.

posecheck/utils/biopython.py

@@ -0,0 +1,113 @@
+
+from Bio.PDB import PDBParser, PDBIO
+from Bio.PDB.Structure import Structure
+
+def load_biopython_structure(pdb_path: str) -> Structure:
+    """
+    Load a structure from a PDB file using Biopython's PDBParser.
+    
+    Args:
+        pdb_path (str): The file path to the PDB file.
+        
+    Returns:
+        Bio.PDB.Structure.Structure: The structure parsed from the PDB file.
+    """
+    parser = PDBParser()
+    structure = parser.get_structure("PDB_structure", pdb_path)
+    return structure
+
+def save_biopython_structure(structure: Structure, pdb_path: str):
+    """
+    Save a structure to a PDB file using Biopython's PDBIO.
+    
+    Args:
+        structure (Bio.PDB.Structure.Structure): The structure to save.
+        pdb_path (str): The file path to save the PDB file to.
+    """
+    io = PDBIO()
+    io.set_structure(structure)
+    io.save(pdb_path)
+
+def ids_scriptly_increasing(structure: Structure) -> bool:
+    """
+    Check if the IDs of residues in a structure are strictly increasing.
+    
+    Args:
+        structure (Bio.PDB.Structure.Structure): The structure to check.
+        
+    Returns:
+        bool: True if the IDs are strictly increasing, False otherwise.
+    """
+    ids = []
+
+    for model in structure:
+        for chain in model:
+            for i, residue in enumerate(chain):
+                ids.append((chain.id, residue.id, i))
+
+    if ids != sorted(ids):
+        return False
+    return True
+
+def reorder_ids(structure: Structure) -> Structure:
+    """
+    Reorder the IDs of residues in a structure to be strictly increasing.
+    
+    Args:
+        structure (Bio.PDB.Structure.Structure): The structure to reorder.
+        
+    Returns:
+        Bio.PDB.Structure.Structure: The structure with reordered IDs.
+    """
+    for model in structure:
+        for chain in model:
+            chain_id = chain.id
+            # Extract residues from the chain
+            residues = [residue for residue in chain]
+            # Sort residues based on their id[1]
+            sorted_residues = sorted(residues, key=lambda residue: residue.id[1])
+            # Clear the chain of residues before adding them back in sorted order
+            # Iterate over a copy of the list of residues to safely remove them
+            for residue in residues:
+                chain.detach_child(residue.id)
+            for residue in sorted_residues:
+                # Prevent adding a residue that is already present
+                if not chain.has_id(residue.id):
+                    chain.add(residue)
+    return structure
+
+
+def remove_connect_lines(pdb_path):
+    """
+    Remove CONECT lines from a PDB file.
+    """
+
+    with open(pdb_path, "r") as f:
+        lines = f.readlines()
+    with open(pdb_path, "w") as f:
+        for line in lines:
+            if line.startswith("CONECT"):
+                continue
+            f.write(line)
+
+
+if __name__ == "__main__":
+    from posecheck.utils.constants import EXAMPLE_PDB_PATH
+    # import temp path 
+    import tempfile
+
+    structure = load_biopython_structure(EXAMPLE_PDB_PATH)
+
+    print(ids_scriptly_increasing(structure))
+
+    reordered_structure = reorder_ids(structure)
+
+    print(ids_scriptly_increasing(reordered_structure))
+
+    with tempfile.NamedTemporaryFile(suffix=".pdb") as temp:
+        print(temp.name)
+        save_biopython_structure(reordered_structure, temp.name)
+        print(load_biopython_structure(temp.name))
+
+
+