Adding new/updated polnet_pdb-to-pns_0.0.2

solutions/polnet/pdb-to-pns/CHANGELOG.md

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+# Changelog
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.0.2] - 2024-08-11
+Remove defaults

solutions/polnet/pdb-to-pns/solution.py

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+###album catalog: cellcanvas
+
+from album.runner.api import setup, get_data_path, get_args
+
+env_file = """
+channels:
+  - conda-forge
+dependencies:
+  - python=3.10
+  - biopython
+  - scipy
+  - numpy
+"""
+
+def run():
+    import numpy as np
+    from Bio.PDB import PDBParser
+    from Bio.PDB.PDBList import PDBList
+    from scipy.spatial import distance
+    import os
+
+    def fetch_pdb_file(pdb_id):
+        pdbl = PDBList()
+        pdbl.retrieve_pdb_file(pdb_id, file_format='pdb', pdir='.')
+        return f"./pdb{pdb_id.lower()}.ent"
+
+    def read_pdb_file(pdb_file):
+        parser = PDBParser(QUIET=True)
+        structure = parser.get_structure('', pdb_file)
+        atoms = []
+        for model in structure:
+            for chain in model:
+                for residue in chain:
+                    for atom in residue:
+                        atoms.append(atom.coord)
+        return np.array(atoms)
+
+    def generate_grid(atoms, grid_resolution, grid_spacing):
+        min_coord = atoms.min(axis=0) - grid_spacing
+        max_coord = atoms.max(axis=0) + grid_spacing
+        grid_shape = np.ceil((max_coord - min_coord) / grid_resolution).astype(int)
+
+        grid = np.zeros(grid_shape)
+
+        for ix in range(grid_shape[0]):
+            for iy in range(grid_shape[1]):
+                for iz in range(grid_shape[2]):
+                    point = min_coord + np.array([ix, iy, iz]) * grid_resolution
+                    distances = distance.cdist([point], atoms, 'euclidean').min()
+                    grid[ix, iy, iz] = 1 / (distances + 1e-12)
+
+        return grid, min_coord
+
+    def save_grid(grid, min_coord, grid_resolution, output_file):
+        with open(output_file, 'w') as f:
+            for ix in range(grid.shape[0]):
+                for iy in range(grid.shape[1]):
+                    for iz in range(grid.shape[2]):
+                        point = min_coord + np.array([ix, iy, iz]) * grid_resolution
+                        value = grid[ix, iy, iz]
+                        f.write(f"{point[0]:.3f} {point[1]:.3f} {point[2]:.3f} {value:.5f}\n")
+
+    args = get_args()
+    pdb_id = args.pdb_id
+    grid_resolution = args.grid_resolution
+    grid_spacing = args.grid_spacing
+    output_file = args.output_file
+
+    pdb_file = fetch_pdb_file(pdb_id)
+    atoms = read_pdb_file(pdb_file)
+    grid, min_coord = generate_grid(atoms, grid_resolution, grid_spacing)
+    save_grid(grid, min_coord, grid_resolution, output_file)
+
+    os.remove(pdb_file)
+    print(f"PNS file saved as {output_file}")
+
+setup(
+    group="polnet",
+    name="pdb-to-pns",
+    version="0.0.2",
+    title="Generate a PNS density image from PDB ID",
+    description="Generate a Point Normal Surface (PNS) file from a PDB ID.",
+    solution_creators=["Kyle Harrington"],
+    cite=[{"text": "Cellcanvas and copick teams", "url": "https://cellcanvas.org/"}],
+    tags=["PDB", "grid", "surface", "structural biology", "pns"],
+    license="MIT",
+    covers=[],
+    album_api_version="0.5.1",
+    args=[
+        {"name": "pdb_id", "type": "string", "required": True, "description": "PDB ID of the structure."},
+        {"name": "output_file", "type": "string", "required": True, "description": "Path to the output PNS file."},
+        {"name": "grid_resolution", "type": "float", "required": False, "description": "Grid resolution for the PNS.", "default": 10.0},
+        {"name": "grid_spacing", "type": "float", "required": False, "description": "Grid spacing around the structure.", "default": 50.0},
+    ],
+    run=run,
+    dependencies={
+        "environment_file": env_file
+    },
+)

solutions/polnet/pdb-to-pns/solution.yml

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+album_api_version: 0.5.1
+args:
+- description: PDB ID of the structure.
+  name: pdb_id
+  required: true
+  type: string
+- description: Path to the output PNS file.
+  name: output_file
+  required: true
+  type: string
+- default: 10.0
+  description: Grid resolution for the PNS.
+  name: grid_resolution
+  required: false
+  type: float
+- default: 50.0
+  description: Grid spacing around the structure.
+  name: grid_spacing
+  required: false
+  type: float
+changelog: Remove defaults
+cite:
+- text: Cellcanvas and copick teams
+  url: https://cellcanvas.org/
+covers: []
+description: Generate a Point Normal Surface (PNS) file from a PDB ID.
+group: polnet
+license: MIT
+name: pdb-to-pns
+solution_creators:
+- Kyle Harrington
+tags:
+- PDB
+- grid
+- surface
+- structural biology
+- pns
+timestamp: '2024-08-11T10:27:13.085412'
+title: Generate a PNS density image from PDB ID
+version: 0.0.2