Add PDB voxelization visualization script#1
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Reviewer's GuideAn example script has been added to parse PDB files, discretize atomic coordinates into a padded 3D voxel grid, and visualize the occupied voxels with matplotlib. Class diagram for voxelization and visualization scriptclassDiagram
class voxelize {
+voxelize(coords, voxel_size=1.0, padding=2.0)
}
class load_atoms {
+load_atoms(pdb_file)
}
class visualize {
+visualize(voxels)
}
class main {
+main()
}
main --> load_atoms : calls
main --> voxelize : calls
main --> visualize : calls
Flow diagram for PDB voxelization and visualization processflowchart TD
A[Start: User runs script with PDB file] --> B[Parse PDB file and extract atomic coordinates]
B --> C[Discretize coordinates into 3D voxel grid]
C --> D[Visualize occupied voxels in 3D]
D --> E[Show plot to user]
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Hey @yeonsungk1m - I've reviewed your changes - here's some feedback:
- The voxelize function returns both
originandvoxel_sizebut these aren’t used downstream—consider removing them or using them to correctly position or label the grid in the visualization. - Right now atoms are treated as point samples; you might improve the volume rendering by accounting for atomic radii or using a Gaussian kernel to better approximate occupied space.
- Voxel grids can grow very large for small voxel sizes or big structures—consider adding a CLI warning or limit for grid dimensions to prevent excessive memory usage.
Prompt for AI Agents
Please address the comments from this code review:
## Overall Comments
- The voxelize function returns both `origin` and `voxel_size` but these aren’t used downstream—consider removing them or using them to correctly position or label the grid in the visualization.
- Right now atoms are treated as point samples; you might improve the volume rendering by accounting for atomic radii or using a Gaussian kernel to better approximate occupied space.
- Voxel grids can grow very large for small voxel sizes or big structures—consider adding a CLI warning or limit for grid dimensions to prevent excessive memory usage.
## Individual Comments
### Comment 1
<location> `example/voxelize_view.py:46` </location>
<code_context>
+ return voxels, min_c, voxel_size
+
+
+def visualize(voxels):
+ fig = plt.figure()
+ ax = fig.add_subplot(111, projection='3d')
</code_context>
<issue_to_address>
No axis scaling or aspect ratio adjustment in visualization.
Setting axis limits or aspect ratio can help ensure the 3D plot accurately represents the voxel grid's proportions.
</issue_to_address>
<suggested_fix>
<<<<<<< SEARCH
def visualize(voxels):
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
ax.voxels(voxels, edgecolor='k', facecolors='cyan', alpha=0.7)
ax.set_xlabel('X')
ax.set_ylabel('Y')
ax.set_zlabel('Z')
plt.tight_layout()
plt.show()
=======
def visualize(voxels):
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
ax.voxels(voxels, edgecolor='k', facecolors='cyan', alpha=0.7)
ax.set_xlabel('X')
ax.set_ylabel('Y')
ax.set_zlabel('Z')
# Set axis limits based on voxel grid shape
shape = voxels.shape
ax.set_xlim(0, shape[0])
ax.set_ylim(0, shape[1])
ax.set_zlim(0, shape[2])
# Set aspect ratio to match voxel grid proportions
max_range = max(shape)
ax.set_box_aspect((shape[0]/max_range, shape[1]/max_range, shape[2]/max_range))
plt.tight_layout()
plt.show()
>>>>>>> REPLACE
</suggested_fix>
### Comment 2
<location> `example/voxelize_view.py:60` </location>
<code_context>
+def main():
+ parser = argparse.ArgumentParser(description='Voxelize PDB and visualize.')
+ parser.add_argument('pdb', help='Input PDB file')
+ parser.add_argument('--size', type=float, default=1.0, help='Voxel size in angstroms')
+ args = parser.parse_args()
+
</code_context>
<issue_to_address>
No validation for non-positive voxel size.
Validate that voxel_size is positive to prevent failures or unexpected behavior when users provide invalid values.
</issue_to_address>Help me be more useful! Please click 👍 or 👎 on each comment and I'll use the feedback to improve your reviews.
Comment on lines
+46
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+54
| def visualize(voxels): | ||
| fig = plt.figure() | ||
| ax = fig.add_subplot(111, projection='3d') | ||
| ax.voxels(voxels, edgecolor='k', facecolors='cyan', alpha=0.7) | ||
| ax.set_xlabel('X') | ||
| ax.set_ylabel('Y') | ||
| ax.set_zlabel('Z') | ||
| plt.tight_layout() | ||
| plt.show() |
There was a problem hiding this comment.
suggestion: No axis scaling or aspect ratio adjustment in visualization.
Setting axis limits or aspect ratio can help ensure the 3D plot accurately represents the voxel grid's proportions.
Suggested change
| def visualize(voxels): | |
| fig = plt.figure() | |
| ax = fig.add_subplot(111, projection='3d') | |
| ax.voxels(voxels, edgecolor='k', facecolors='cyan', alpha=0.7) | |
| ax.set_xlabel('X') | |
| ax.set_ylabel('Y') | |
| ax.set_zlabel('Z') | |
| plt.tight_layout() | |
| plt.show() | |
| def visualize(voxels): | |
| fig = plt.figure() | |
| ax = fig.add_subplot(111, projection='3d') | |
| ax.voxels(voxels, edgecolor='k', facecolors='cyan', alpha=0.7) | |
| ax.set_xlabel('X') | |
| ax.set_ylabel('Y') | |
| ax.set_zlabel('Z') | |
| # Set axis limits based on voxel grid shape | |
| shape = voxels.shape | |
| ax.set_xlim(0, shape[0]) | |
| ax.set_ylim(0, shape[1]) | |
| ax.set_zlim(0, shape[2]) | |
| # Set aspect ratio to match voxel grid proportions | |
| max_range = max(shape) | |
| ax.set_box_aspect((shape[0]/max_range, shape[1]/max_range, shape[2]/max_range)) | |
| plt.tight_layout() | |
| plt.show() |
| def main(): | ||
| parser = argparse.ArgumentParser(description='Voxelize PDB and visualize.') | ||
| parser.add_argument('pdb', help='Input PDB file') | ||
| parser.add_argument('--size', type=float, default=1.0, help='Voxel size in angstroms') |
There was a problem hiding this comment.
issue (bug_risk): No validation for non-positive voxel size.
Validate that voxel_size is positive to prevent failures or unexpected behavior when users provide invalid values.
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Summary by Sourcery
New Features: