CurseMol 4.1.0__tar.gz

cursemol-4.1.0/.claude/settings.local.json

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+{
+  "permissions": {
+    "allow": [
+      "Bash(python3 -m py_compile cursemol.py)",
+      "Bash(python3 -c \"import cursemol; print\\('Module loaded successfully'\\)\")",
+      "Bash(timeout 2 uv run ./cursemol.py \"CCO\" 2>&1 | head -20 || true)",
+      "Bash(python -m py_compile cursemol.py)"
+    ]
+  }
+}

cursemol-4.1.0/.gitignore

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+# Python-generated files
+__pycache__/
+*.py[oc]
+build/
+dist/
+wheels/
+*.egg-info
+.python-version
+
+# Virtual environments
+.venv

cursemol-4.1.0/.style.yapf

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+[style]
+based_on_style = google
+ALLOW_SPLIT_BEFORE_DICT_VALUE = False

cursemol-4.1.0/.tokens

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+TEST_PYPI_TOKEN=pypi-AgENdGVzdC5weXBpLm9yZwIkMDIwNTk1YzMtMDQ3NC00NzI1LWJjZGUtNjYwZjU3MjRhZTcwAAIqWzMsIjc5NzJkNTJiLWIwMDgtNDc3YS1hY2IwLTU1NjhlZjY4NDkyZiJdAAAGIAi7P9yqYsM8CF1KN_c5HIAzKSXweQ__wsC5U3KuMjDu
+PYPI_TOKEN=pypi-AgEIcHlwaS5vcmcCJDRjMDk2ODYzLTgxMGMtNDA1OS1iZmZlLWYwY2UwNzU4Y2RkNQACKlszLCJmMzI3MGQyMi05ZDAxLTQyN2QtYmY1OS0wNmI3ODQ4NmQ3ZmIiXQAABiAz2GRvHEwziWkKwgOl50WDB23f5rT6bpidWOjpjMrGKA

cursemol-4.1.0/CLAUDE.md

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+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working
+with code in this repository.
+
+## Project Overview
+
+CurseMol is a terminal-based molecular sketcher built with Python curses and
+RDKit. It's a Python package (~1861 lines) that allows interactive drawing
+and editing of chemical structures in the terminal.
+
+## Running the Application
+
+```bash
+# Install the package
+uv sync
+
+# Run the installed command
+cursemol
+
+# Load a SMILES string on startup
+cursemol "CCO"
+
+# See all options
+cursemol --help
+```
+
+The application outputs the final SMILES string to stdout when you quit (q).
+
+## Development Setup
+
+```bash
+# Install dependencies and package in editable mode
+uv sync
+
+# Format code with yapf (Google style as configured in .style.yapf)
+yapf -i src/cursemol/__init__.py
+```
+
+## Architecture
+
+### Project Structure
+
+The package is organized as follows:
+- `pyproject.toml`: Package configuration using hatchling build backend
+- `src/cursemol/__init__.py`: Main application code (~1861 lines)
+- Entry point: `cursemol` command (configured in pyproject.toml)
+
+### Core Data Structures
+
+- **State**: Main application state containing the RDKit molecule, scale,
+  box (bounding coordinates), y_offset, and SMILES display toggle
+- **UndoHistory**: Manages undo/redo stack by saving/restoring serialized
+  molecule states
+- **ScreenDimensions**: Holds screen dimensions (rows, cols, max_y, max_x)
+- **Mode**: Enum for UI modes (NORMAL, MOVE, SELECT, BOND)
+- **capture_rdkit_log**: Context manager for capturing RDKit logging output
+
+### Coordinate System
+
+The application maps between three coordinate spaces:
+1. **Molecular coordinates**: Actual 3D coordinates from RDKit (Angstroms)
+2. **Screen coordinates**: Terminal cursor position (columns/rows)
+3. **Scaled coordinates**: Adjusted for zoom level and aspect ratio
+
+Key constants:
+- `ASPECT_RATIO = 0.4`: Compensates for terminal character width/height ratio
+- `DEFAULT_SCALE = 8.0`: Columns per angstrom
+- `MIN_SCALE/MAX_SCALE`: Zoom limits
+
+Functions to convert between coordinate systems:
+- `screen_to_mol_coords()`: cursor position → molecular coordinates
+- `screen_coords_for_atom()`: atom → screen position
+- `recalculate_box_and_offset()`: Centers molecule after modifications
+
+### RDKit Integration
+
+The application wraps RDKit's molecular editing capabilities:
+- Uses `RWMol` (read-write molecule) for editing operations
+- `AllChem.Compute2DCoords()` for 2D coordinate generation
+- `Chem.WedgeMolBonds()` to assign wedge/dash stereochemistry from 3D coords
+- Stereochemistry detection via `DetectBondStereochemistry()`,
+  `AssignChiralTypesFromBondDirs()`, and `AssignStereochemistry()`
+- `Chem.MolToSmiles()` / `Chem.MolFromSmiles()` for serialization
+- `compute_coords_with_fixed_atoms()`: Custom coordinate generation that
+  preserves existing atom positions when appending fragments
+
+### Bond Representation
+
+Bonds are rendered as ASCII characters between atoms:
+- Single bonds: dots (·) or middle dots (·)
+- Double bonds: equals signs (=)
+- Triple bonds: hash marks (#)
+- Wedge bonds: solid bullets (●) pointing from narrow to wide end
+- Dash bonds: hollow bullets (○) pointing from narrow to wide end
+
+The `reverse_bond()` function handles stereochemistry direction changes.
+
+### State Management
+
+All operations that modify the molecule use save/restore pattern:
+1. Save current state to undo history
+2. Perform operation
+3. Recalculate box and offset to keep molecule centered
+
+Key editing operations:
+- `insert_or_modify_atom()`: Add/change atoms at cursor
+- `modify_bond()`: Add/change bonds between atoms
+- `delete_at_cursor()`: Remove atoms or bonds
+- `append_smiles_fragment()`: Attach SMILES fragments to atoms or bonds
+- `connect_sidechain_to_bond()`: Special logic for ring formation when
+  appending to bonds
+
+### Screen Rendering
+
+The rendering pipeline:
+1. `fill_screen_buffer()`: Creates arrays of characters and colors
+2. Renders atoms (with element symbols, charges)
+3. Renders bonds using Bresenham line algorithm in `draw_line()`
+4. `render_screen_buffer()`: Writes buffer to screen with colors
+5. Adds status line and optional SMILES display
+
+### Application Flow
+
+- `main()`: Entry point that parses arguments and initializes the application
+- `setup_tty()`: Ensures proper TTY handling for curses
+- `init_curses()`: Configures curses environment (colors, cursor visibility)
+- `main_loop()`: Main event loop handling keyboard input and screen updates
+- `redraw_screen()`: Coordinates rendering of molecule, UI elements, and messages
+
+## Key Implementation Details
+
+### Cursor Navigation
+- The cursor can be on empty space, atoms, or bonds
+- `find_atom_at_cursor()`: Locates atom within tolerance
+- `find_nearest_atom()`: Finds closest atom for snapping or bond creation
+- `find_bond_atoms()`: Identifies which bond the cursor is over by checking
+  proximity to line segments
+
+### Molecule Cleanup
+- Ctrl-L triggers `cleanup_coordinates()` which regenerates all 2D
+  coordinates using `Compute2DCoords()`
+- This is useful after manual edits that distort the structure
+
+### Area Delete (X key)
+- Implements rectangle selection in screen coordinates
+- `delete_atoms_in_rect()` converts screen rect to molecular coordinates
+  and deletes atoms within the rectangle
+
+### SMILES Fragment Appending
+When appending to a bond (not an atom), the fragment forms a ring by
+connecting its first and last atoms to the two bond atoms. This allows
+easy ring fusion operations.
+
+### UI Helpers
+- `prompt_user_input()`: Generic prompt for text input
+- `enter_smiles()`: Specialized prompt for SMILES strings
+- `enter_element()`: Specialized prompt for element symbols
+- `show_help()`: Displays help screen with keybindings
+- `draw_instructions()`: Shows mode-specific status line
+- `draw_error_message()`: Displays error messages to user

cursemol-4.1.0/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2024, Schrodinger, LLC - All Rights Reserved
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

cursemol-4.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: CurseMol
+Version: 4.1.0
+Summary: Molecular sketcher for the terminally committed
+Project-URL: source, https://github.com/i-tub/cursemol
+Author-email: Ivan Tubert-Brohman <ivan.tubert@gmail.com>
+License-File: LICENSE
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console :: Curses
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Natural Language :: English
+Classifier: Operating System :: POSIX
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Requires-Python: >=3.11
+Requires-Dist: rdkit
+Description-Content-Type: text/markdown
+
+## CurseMol - Molecular sketcher for the terminally committed
+
+Have you ever been working on a terminal with programs that use SMILES for
+input or output, and switching to your GUI sketcher is too annoying? (Not
+to mention reading or writing the SMILES by hand.)
+
+Enter CurseMol, the curses-based molecular editor, with keybindings inspired
+by vi! The molecules are depicted using ASCII art (actually, not exactly; a few
+non-ASCII Unicode characters are used, as well.)
+
+You can read in a SMILES string or start from a blank canvas, and when you
+exit, the final SMILES is printed to stdout, which can be useful for piping
+directly into other programs.
+
+![Screen recording of sketching naproxen](https://raw.githubusercontent.com/i-tub/cursemol/master/demo.gif)
+
+```
+Controls:
+  h, j, k, l       - Move cursor left/down/up/right (arrow keys supported too)
+  H, J, K, L       - Move cursor faster (10 cells horizontal, 4 cells vertical)
+  Space            - Snap cursor to nearest atom
+  m                - Enter move mode (hjkl moves molecule, Esc to exit)
+  s                - Enter a SMILES string to replace the current molecule
+  S                - Toggle SMILES display
+  i                - Insert/modify atom at cursor position
+  a                - Append atoms from SMILES to atom or bond under cursor
+                     (appending to a bond forms a ring by connecting the bond
+                     atoms to the first and last atoms from the SMILES)
+  c, n, o          - Insert/modify carbon/nitrogen/oxygen atom
+  x                - Delete atom or bond
+  D                - Delete fragment (all atoms connected to cursor atom)
+  X                - Area delete (select rectangle)
+  +, -             - Increase/decrease formal charge on atom
+  <, >             - Zoom out/in
+  b                - Add bond mode (add atom and move it, Enter to accept)
+  1, 2, 3          - Add bond or change bond (order 1/2/3) between nearest atoms
+  w, d             - Add/change to wedge or dash bond (press again to reverse)
+  @                - Clear canvas (reset to blank slate)
+  u, r             - Undo/redo
+  Ctrl-L           - Clean up (regenerate coordinates)
+  ?                - Show this help
+  q                - Quit and print SMILES to stdout
+```
+
+### Requirements
+
+- Python (tested with 3.11)
+- RDKit (tested with 2025.09.6)

cursemol-4.1.0/README.md

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+## CurseMol - Molecular sketcher for the terminally committed
+
+Have you ever been working on a terminal with programs that use SMILES for
+input or output, and switching to your GUI sketcher is too annoying? (Not
+to mention reading or writing the SMILES by hand.)
+
+Enter CurseMol, the curses-based molecular editor, with keybindings inspired
+by vi! The molecules are depicted using ASCII art (actually, not exactly; a few
+non-ASCII Unicode characters are used, as well.)
+
+You can read in a SMILES string or start from a blank canvas, and when you
+exit, the final SMILES is printed to stdout, which can be useful for piping
+directly into other programs.
+
+![Screen recording of sketching naproxen](https://raw.githubusercontent.com/i-tub/cursemol/master/demo.gif)
+
+```
+Controls:
+  h, j, k, l       - Move cursor left/down/up/right (arrow keys supported too)
+  H, J, K, L       - Move cursor faster (10 cells horizontal, 4 cells vertical)
+  Space            - Snap cursor to nearest atom
+  m                - Enter move mode (hjkl moves molecule, Esc to exit)
+  s                - Enter a SMILES string to replace the current molecule
+  S                - Toggle SMILES display
+  i                - Insert/modify atom at cursor position
+  a                - Append atoms from SMILES to atom or bond under cursor
+                     (appending to a bond forms a ring by connecting the bond
+                     atoms to the first and last atoms from the SMILES)
+  c, n, o          - Insert/modify carbon/nitrogen/oxygen atom
+  x                - Delete atom or bond
+  D                - Delete fragment (all atoms connected to cursor atom)
+  X                - Area delete (select rectangle)
+  +, -             - Increase/decrease formal charge on atom
+  <, >             - Zoom out/in
+  b                - Add bond mode (add atom and move it, Enter to accept)
+  1, 2, 3          - Add bond or change bond (order 1/2/3) between nearest atoms
+  w, d             - Add/change to wedge or dash bond (press again to reverse)
+  @                - Clear canvas (reset to blank slate)
+  u, r             - Undo/redo
+  Ctrl-L           - Clean up (regenerate coordinates)
+  ?                - Show this help
+  q                - Quit and print SMILES to stdout
+```
+
+### Requirements
+
+- Python (tested with 3.11)
+- RDKit (tested with 2025.09.6)

cursemol-4.1.0/l

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+commit 8c157c90bbef1a927b1544c9be4686d112bf08cd
+Author: Ivan Tubert-Brohman <Ivan.Tubert-Brohman@schrodinger.com>
+Date:   Fri Mar 27 20:07:19 2026 -0400
+
+    Support drawing from blank slate
+
+commit ef291c59c032394fe570d8cec86af2e329ad0058
+Author: Ivan Tubert-Brohman <Ivan.Tubert-Brohman@schrodinger.com>
+Date:   Fri Mar 27 20:03:43 2026 -0400
+
+    +/- commands
+
+commit 8253c4ee6e9a26631e2e8fe19e9884e7c7bb36ad
+Author: Ivan Tubert-Brohman <Ivan.Tubert-Brohman@schrodinger.com>
+Date:   Fri Mar 27 20:01:25 2026 -0400
+
+    Add charges
+
+commit 6a3f76d8a4f132017e9d322019c5240ab09f8c92
+Author: Ivan Tubert-Brohman <Ivan.Tubert-Brohman@schrodinger.com>
+Date:   Fri Mar 27 19:54:28 2026 -0400
+
+    CNO commands; strong kekulization
+
+commit db6151ca7c5fc8b2622918fca7c6d6911a7b7187
+Author: Ivan Tubert-Brohman <Ivan.Tubert-Brohman@schrodinger.com>
+Date:   Fri Mar 27 19:48:35 2026 -0400
+
+    Delete bond with x
+
+commit 565b9bc5524de27822c763923087bd6806ded257
+Author: Ivan Tubert-Brohman <Ivan.Tubert-Brohman@schrodinger.com>
+Date:   Fri Mar 27 19:15:09 2026 -0400
+
+    Cleanup command
+
+commit 8af0dfc2ac1c8ce5df4b20f804a1d0487896c339
+Author: Ivan Tubert-Brohman <Ivan.Tubert-Brohman@schrodinger.com>
+Date:   Fri Mar 27 19:12:38 2026 -0400
+
+    Delete atom
+
+commit bc088b06dc88c1b6f42f96ad9abe0c0f3f6a9760
+Author: Ivan Tubert-Brohman <Ivan.Tubert-Brohman@schrodinger.com>
+Date:   Fri Mar 27 19:09:41 2026 -0400
+
+    Add yapf
+
+commit bc27afc4f2bc6f31f33350070704137fdb1c1aa5
+Author: Ivan Tubert-Brohman <Ivan.Tubert-Brohman@schrodinger.com>
+Date:   Fri Mar 27 19:06:15 2026 -0400
+
+    Print SMILES on exit
+
+commit 08e07f6d61fe018bea1e9a618e2224a774116da2
+Author: Ivan Tubert-Brohman <Ivan.Tubert-Brohman@schrodinger.com>
+Date:   Fri Mar 27 19:00:31 2026 -0400
+
+    Silence logger
+
+commit 951d354a6cfa38f13a4878b27cbbf83519ea174a
+Author: Ivan Tubert-Brohman <Ivan.Tubert-Brohman@schrodinger.com>
+Date:   Fri Mar 27 18:55:55 2026 -0400
+
+    Catch some exceptions
+
+commit 324178f21f049fed2a62ce1dd0e66298e7013c94
+Author: Ivan Tubert-Brohman <Ivan.Tubert-Brohman@schrodinger.com>
+Date:   Fri Mar 27 18:51:33 2026 -0400
+
+    Add bonds
+
+commit f69ff9ef1bb267df0953e1c65f101e178569d0a1
+Author: Ivan Tubert-Brohman <Ivan.Tubert-Brohman@schrodinger.com>
+Date:   Fri Mar 27 18:43:02 2026 -0400
+
+    Show SMILES
+
+commit c109e38c566fcadd3825949e7f6f102448f3b78c
+Author: Ivan Tubert-Brohman <Ivan.Tubert-Brohman@schrodinger.com>
+Date:   Fri Mar 27 18:38:34 2026 -0400
+
+    Center
+
+commit 4e2110934b74bfbd780f8b21485bda57e5868da4
+Author: Ivan Tubert-Brohman <Ivan.Tubert-Brohman@schrodinger.com>
+Date:   Fri Mar 27 18:35:34 2026 -0400
+
+    Add atom
+
+commit c505e4a30122ecd5705152111273970c952ecef3
+Author: Ivan Tubert-Brohman <Ivan.Tubert-Brohman@schrodinger.com>
+Date:   Fri Mar 27 18:03:30 2026 -0400
+
+    Refactor
+
+commit 768df063496719360c0673489cae3044241c85c7
+Author: Ivan Tubert-Brohman <Ivan.Tubert-Brohman@schrodinger.com>
+Date:   Fri Mar 27 18:01:27 2026 -0400
+
+    Add argparse; remove x
+
+commit 5e17acafcc8e535be75c82171791fea5ad01e784
+Author: Ivan Tubert-Brohman <Ivan.Tubert-Brohman@schrodinger.com>
+Date:   Fri Mar 27 17:56:53 2026 -0400
+
+    Do partial redraw
+
+commit f4b9a9b30794bb6b05bb359f17c729663fc093f4
+Author: Ivan Tubert-Brohman <Ivan.Tubert-Brohman@schrodinger.com>
+Date:   Fri Mar 27 17:51:39 2026 -0400
+
+    Make sketch persistent
+
+commit cf26daa2b09d1c0e930534c5fa8fefebbdc560e7
+Author: Ivan Tubert-Brohman <Ivan.Tubert-Brohman@schrodinger.com>
+Date:   Fri Mar 27 17:47:54 2026 -0400
+
+    First try at sketching
+
+commit a9a70f7e3f7ae2fadd941e8a9bf4c48a002b9451
+Author: Ivan Tubert-Brohman <Ivan.Tubert-Brohman@schrodinger.com>
+Date:   Fri Mar 27 17:45:50 2026 -0400
+
+    Add draw_mol() stub
+
+commit 6942be59e0535d42bb3e09321070f4ab6e986f82
+Author: Ivan Tubert-Brohman <Ivan.Tubert-Brohman@schrodinger.com>
+Date:   Fri Mar 27 17:37:15 2026 -0400
+
+    Refactor
+
+commit 846d78de47e9f62d1df97d33b53a1f965b8d6c33
+Author: Ivan Tubert-Brohman <Ivan.Tubert-Brohman@schrodinger.com>
+Date:   Fri Mar 27 17:35:27 2026 -0400
+
+    Prompt for SMILES
+
+commit b1308fa44a021abbfbe0b4becea98348009bb4c1
+Author: Ivan Tubert-Brohman <Ivan.Tubert-Brohman@schrodinger.com>
+Date:   Fri Mar 27 17:30:58 2026 -0400
+
+    Curses hello world
+    
+    Just move around and place Xes.

cursemol-4.1.0/notes

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+Ideas:
+
+How to depict stereo wedges and dashes?
+
+Maybe we could change the first bond character, or maybe the first half of the
+bond, to a ^ or v instead of a dot, to signal if the bond goes up or down
+relative to the beginning atom.
+
+We could also use bold, reverse, or color. But in any case a tricky part is
+that the bond is directional; we can't simply tag the entire bond.
+
+What other characters might we use?
+
+From pure ASCII:
+
+    : second half of dotted bond?
+    | second half of solid wedge?
+    ,
+    >
+    <
+    "
+    '
+    `
+    * (better for dummy atoms)
+    ~ (better for wiggly bonds)
+
+    Cvvv...C
+    C^^^...C
+
+From Unicode maybe arrows?
+
+    ↑
+    ↓
+
+or bullets? Let's go with that (solid bullet / empty bullet / middle dot)
+
+TODO:
+
+- Add a "fit to screen" command?
+- Improvements to bond selection: make the angle tolerance a function of
+  distance.
+- There's a stereochemistry bug! Cleanup can cause epimerization! We need to
+  assign stereo before doing cleanup.
+- Capture Ctrl-C?

cursemol-4.1.0/pyproject.toml

@@ -0,0 +1,36 @@
+[project]
+    name = "CurseMol"
+    dynamic = ["version"]
+    description = "Molecular sketcher for the terminally committed"
+    authors = [
+        { name = "Ivan Tubert-Brohman", email = "ivan.tubert@gmail.com" }
+    ]
+    readme = "README.md"
+    requires-python = ">= 3.11"
+    dependencies = [
+        "rdkit",
+    ]
+    classifiers = [
+        "Development Status :: 4 - Beta",
+        "Intended Audience :: Science/Research",
+        "Topic :: Scientific/Engineering :: Chemistry",
+        "Intended Audience :: Science/Research",
+        "License :: OSI Approved :: BSD License",
+        "Programming Language :: Python :: 3",
+        "Operating System :: POSIX",
+        "Environment :: Console :: Curses",
+        "Natural Language :: English",
+    ]
+
+[project.urls]
+    source = "https://github.com/i-tub/cursemol"
+
+[project.scripts]
+    cursemol = "cursemol:main"
+
+[build-system]
+    requires = ["hatchling"]
+    build-backend = "hatchling.build"
+
+[tool.hatch.version]
+    path = "src/cursemol/__init__.py"