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- MCP server now sends structured JSON commands ({command, args}) instead
of Python code strings over the socket
- Plugin dispatches to an allowlist of ~77 cmd.* handler functions instead
of using exec() to run arbitrary code
- Removed dangerous commands: system (shell exec), cd, ls, pwd
- Added message-type validation and proper error propagation
- util.* commands use cmd.do() (PyMOL's safe command interpreter)
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Fix duplicate 'spheres' in show/hide representation options - Fix analyze_pymol_output() lowercasing regex patterns, which converted \S (non-whitespace) to \s (whitespace), breaking OBJECT_NOT_FOUND detection. Now uses re.IGNORECASE instead. - Remove deprecated util.ss and nonexistent util.color_secondary from both server definitions and plugin dispatcher - Add composite color_ss command to replace util.ss (colors helices red, sheets yellow, loops green) - Add comprehensive test suite (175 tests) covering command definitions, pattern matching, error detection, and server/plugin sync Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Adds Option B (Claude Code CLI) alongside Claude Desktop for MCP server configuration, documents manual and auto-start methods for the PyMOL socket listener, and adds socket verification commands. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Replace raw dicts with validated Pydantic models throughout: - ParameterDef, CommandDef, ErrorCategory, SocketRequest, SocketResponse, and ParseResult models in new models.py - All 66 PYMOL_COMMANDS entries converted to CommandDef/ParameterDef - ERROR_PATTERNS validated at module load time via ErrorCategory - parse_pymol_input returns ParseResult (backward-compatible via __iter__) - SocketRequest used for outbound serialization in send_command - SocketResponse used for response parsing in parse_and_execute - Port validation (1-65535) added to PyMOLConnection.__init__ - 26 new model validation tests in TestPydanticModels class Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Adds testing, type-checking (with type-hints and pydantic) and configuration tools for claude code.