py2Dmol 1.0.0__tar.gz

py2dmol-1.0.0/LICENSE

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+/*
+ * ----------------------------------------------------------------------------
+ * "THE BEER-WARE LICENSE" (Revision 42):
+ * <so3@mit.edu> wrote this file.  As long as you retain this notice you
+ * can do whatever you want with this stuff. If we meet some day, and you think
+ * this stuff is worth it, you can buy me a beer in return.  Sergey Ovchinnikov
+ * ----------------------------------------------------------------------------
+ */

py2dmol-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: py2Dmol
+Version: 1.0.0
+Summary: A Python library for visualizing protein structures in 2D.
+Home-page: https://github.com/sokrypton/py2Dmol
+Author: sokrypton
+Author-email: so3@mit.edu
+License: BEER-WARE
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.6
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: ipython
+Requires-Dist: gemmi
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+A Python library for visualizing protein structures in 2D.

py2dmol-1.0.0/README.md

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+# py2Dmol
+
+A Python library for visualizing protein structures in 2D, designed for use in Google Colab and Jupyter environments.
+
+## Installation
+
+You can install `py2Dmol` directly from GitHub:
+
+```bash
+pip install git+https://github.com/sokrypton/py2Dmol.git
+```
+
+## Usage
+
+Here are a few examples of how to use `py2Dmol`.
+
+### Basic Usage
+
+To create a viewer, simply import the package and instantiate the `view` class:
+
+```python
+import py2Dmol
+viewer = py2Dmol.view()
+```
+
+### Loading a Structure from a PDB or CIF File
+
+You can load a structure directly from a PDB or CIF file using the `from_pdb` method. This will automatically extract the C-alpha atoms for proteins and all heavy atoms for ligands. If the file contains multiple models, they will be loaded as an animation.
+
+```python
+import py2Dmol
+viewer = py2Dmol.view()
+viewer.from_pdb('my_protein.pdb')
+```
+
+You can also specify which chains to display:
+
+```python
+viewer.from_pdb('my_protein.pdb', chains=['A', 'B'])
+```
+
+### Manually Adding Data
+
+You can also add data to the viewer using the `add` method. This is useful for visualizing custom trajectories or molecular data.
+
+```python
+import numpy as np
+
+# Example data
+coords = np.random.rand(100, 3) * 50  # 100 atoms with random coordinates
+plddts = np.random.rand(100) * 100    # Random pLDDT scores
+chains = ['A'] * 50 + ['B'] * 50      # Two chains
+atom_types = ['P'] * 100              # All protein atoms
+
+# Create a viewer and display the initial data
+viewer = py2Dmol.view()
+viewer.display(coords, plddts, chains, atom_types)
+
+# Update the viewer with new data to create an animation
+for _ in range(10):
+    new_coords = coords + np.random.rand(100, 3) * 5
+    viewer.add(new_coords)
+```
+
+## Data Format
+
+The viewer distinguishes between two types of atoms:
+
+*   **P (Protein):** Represents the C-alpha atom of a protein residue.
+*   **L (Ligand):** Represents a heavy atom of a non-protein, non-water molecule.
+
+### Chains
+
+Chains are automatically extracted from the PDB or CIF file. When loading a structure, you can choose to display all chains or specify a subset of chains to visualize.

py2dmol-1.0.0/py2Dmol/__init__.py

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+from .viewer import view