protinspect 0.1.0__py3-none-any.whl

protinspect/analyzer.py

@@ -0,0 +1,140 @@
+from .parser import load_structure
+
+
+def count_chains(file_path):
+    """
+    Count number of chains.
+    """
+
+    structure = load_structure(file_path)
+
+    chains = list(structure.get_chains())
+
+    return {
+        "chain_count": len(chains),
+        "chain_ids": [c.id for c in chains]
+    }
+
+
+def get_resolution(file_path):
+    """
+    Get experimental resolution.
+    """
+
+    structure = load_structure(file_path)
+
+    resolution = structure.header.get(
+        "resolution"
+    )
+
+    return resolution
+
+
+def detect_ligands(file_path):
+    """
+    Detect ligands in structure.
+    """
+
+    structure = load_structure(file_path)
+
+    ligands = []
+
+    excluded = [
+        "HOH",
+        "WAT"
+    ]
+
+    for model in structure:
+        for chain in model:
+            for residue in chain:
+
+                if residue.id[0] != " ":
+
+                    ligand_name = residue.resname
+
+                    if ligand_name not in excluded:
+                        ligands.append(
+                            ligand_name
+                        )
+
+    unique_ligands = list(
+        set(ligands)
+    )
+
+    return {
+        "ligand_present":
+            len(unique_ligands) > 0,
+
+        "ligands":
+            unique_ligands
+    }
+
+
+def get_ligand_ids(file_path):
+    """
+    Return ligand IDs with chain and position.
+    """
+
+    structure = load_structure(file_path)
+
+    ligand_data = []
+
+    excluded = [
+        "HOH",
+        "WAT"
+    ]
+
+    for model in structure:
+        for chain in model:
+            for residue in chain:
+
+                if residue.id[0] != " ":
+
+                    ligand = residue.resname
+
+                    if ligand not in excluded:
+
+                        ligand_data.append({
+                            "id": ligand,
+                            "chain": chain.id,
+                            "position":
+                                residue.id[1]
+                        })
+
+    return ligand_data
+
+
+def get_missing_residues(file_path):
+    """
+    Parse REMARK 465 section.
+    """
+
+    missing_residues = []
+
+    with open(file_path, "r") as file:
+
+        lines = file.readlines()
+
+    for line in lines:
+
+        if line.startswith("REMARK 465"):
+
+            parts = line.split()
+
+            if len(parts) >= 5:
+
+                try:
+                    residue = parts[2]
+                    chain = parts[3]
+                    position = int(parts[4])
+
+                    missing_residues.append({
+                        "residue": residue,
+                        "chain": chain,
+                        "position": position
+                    })
+
+                except:
+                    continue
+
+    return missing_residues

protinspect/cli.py

@@ -0,0 +1,73 @@
+import typer
+
+from .analyzer import (
+    count_chains,
+    get_resolution,
+    detect_ligands,
+    get_missing_residues
+)
+
+from .utils import (
+    show_chain_table,
+    show_resolution,
+    show_ligands,
+    show_missing_residues
+)
+
+app = typer.Typer()
+
+
+@app.command()
+def chains(file: str):
+
+    data = count_chains(file)
+
+    show_chain_table(data)
+
+
+@app.command()
+def resolution(file: str):
+
+    data = get_resolution(file)
+
+    show_resolution(data)
+
+
+@app.command()
+def ligands(file: str):
+
+    data = detect_ligands(file)
+
+    show_ligands(data)
+
+
+@app.command()
+def missing(file: str):
+
+    data = get_missing_residues(file)
+
+    show_missing_residues(data)
+
+
+@app.command()
+def all(file: str):
+
+    show_chain_table(
+        count_chains(file)
+    )
+
+    show_resolution(
+        get_resolution(file)
+    )
+
+    show_ligands(
+        detect_ligands(file)
+    )
+
+    show_missing_residues(
+        get_missing_residues(file)
+    )
+
+
+if __name__ == "__main__":
+    app()

protinspect/parser.py

@@ -0,0 +1,12 @@
+from Bio.PDB import PDBParser
+
+
+def load_structure(file_path):
+    parser = PDBParser(QUIET=True)
+
+    structure = parser.get_structure(
+        "protein",
+        file_path
+    )
+
+    return structure

protinspect/utils.py

@@ -0,0 +1,101 @@
+from rich.console import Console
+from rich.table import Table
+
+console = Console()
+
+
+def show_chain_table(data):
+
+    table = Table(
+        title="Chain Information"
+    )
+
+    table.add_column(
+        "Chain Count",
+        justify="center"
+    )
+
+    table.add_column(
+        "Chain IDs",
+        justify="center"
+    )
+
+    table.add_row(
+        str(data["chain_count"]),
+        ", ".join(data["chain_ids"])
+    )
+
+    console.print(table)
+
+
+def show_resolution(resolution):
+
+    table = Table(
+        title="Resolution"
+    )
+
+    table.add_column(
+        "Resolution (Å)",
+        justify="center"
+    )
+
+    table.add_row(
+        str(resolution)
+    )
+
+    console.print(table)
+
+
+def show_ligands(data):
+
+    table = Table(
+        title="Ligands"
+    )
+
+    table.add_column(
+        "Ligand Present"
+    )
+
+    table.add_column(
+        "Ligand IDs"
+    )
+
+    ligands = ", ".join(
+        data["ligands"]
+    )
+
+    table.add_row(
+        str(data["ligand_present"]),
+        ligands
+    )
+
+    console.print(table)
+
+
+def show_missing_residues(data):
+
+    table = Table(
+        title="Missing Residues"
+    )
+
+    table.add_column(
+        "Residue"
+    )
+
+    table.add_column(
+        "Chain"
+    )
+
+    table.add_column(
+        "Position"
+    )
+
+    for item in data:
+
+        table.add_row(
+            item["residue"],
+            item["chain"],
+            str(item["position"])
+        )
+
+    console.print(table)

protinspect-0.1.0.dist-info/METADATA

@@ -0,0 +1,59 @@
+Metadata-Version: 2.4
+Name: protinspect
+Version: 0.1.0
+Summary: 
+Author: rkarishma27
+Author-email: anukarishma.27@gmail.com
+Requires-Python: >=3.13
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Requires-Dist: biopython (>=1.87,<2.0)
+Requires-Dist: rich (>=15.0.0,<16.0.0)
+Requires-Dist: typer (>=0.25.1,<0.26.0)
+Description-Content-Type: text/markdown
+
+# ProtInspect
+
+ProtInspect is a Python package for protein structure analysis using PDB files.
+
+## Features
+
+- Detect missing residues
+- Count protein chains
+- Find experimental resolution
+- Detect ligands
+- Return ligand IDs
+
+## Installation
+
+```bash
+pip install protinspect
+```
+
+## Usage
+
+Analyze a protein structure:
+
+```bash
+protinspect all path/to/file.pdb
+```
+
+Example:
+
+```bash
+protinspect all examples/1crn.pdb
+```
+
+## Tech Stack
+
+- Python
+- Poetry
+- Biopython
+- Typer
+- Rich
+- Pytest
+
+## License
+
+MIT

protinspect-0.1.0.dist-info/RECORD

@@ -0,0 +1,9 @@
+protinspect/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+protinspect/analyzer.py,sha256=dO_TYMKVyIgrrSt_O9i-U7Aa8VeoZqVtzJ4d6KhALCw,2831
+protinspect/cli.py,sha256=ToWC80E0FYt0Eynq5mRohir5Kmd0j6B-qoy6gM-xYs0,1052
+protinspect/parser.py,sha256=0vYuIDp-jomrM3iHMldFlvWSPyVlcpubdPI6pGfZ9ek,212
+protinspect/utils.py,sha256=J5PE5nESEI7stPwvyBLirztSzNUNNVvZ7wltj_22QtE,1540
+protinspect-0.1.0.dist-info/entry_points.txt,sha256=IEIE9-z5V9gxZqYxYryiVDaN8NFmj_DkbyEw-gWYnJs,51
+protinspect-0.1.0.dist-info/METADATA,sha256=xxY1W1BjNOJaQEdz9L1Q8vSWV8YrpyS90C6hf7fxErk,967
+protinspect-0.1.0.dist-info/WHEEL,sha256=EGEvSphFYqXKs23-kQBeyNoJP1nrT8ZJKQoi5p5DYL8,88
+protinspect-0.1.0.dist-info/RECORD,,

protinspect-0.1.0.dist-info/WHEEL

@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: poetry-core 2.4.0
+Root-Is-Purelib: true
+Tag: py3-none-any

protinspect-0.1.0.dist-info/entry_points.txt

@@ -0,0 +1,3 @@
+[console_scripts]
+protinspect=protinspect.cli:app
+