New Command

new_command is a new API-only feature which exposes an user defined Python function as a command to other users.

In a brief

from pathlib import Path
from pprint import pprint
from typing import Any, Optional
from enum import Enum

from pymol import cmd
from pymol_new_command import new_command


class CoolFlag(Enum):
    STRUCTURE = 1
    SEQUENCE = 2

## Supported only on Python 3.11+
#from enum import StrEnum
#class Method(StrEnum):
#    SINGLE = "single"
#    COMPLETE = "complete"
#    WARD = "ward"

Point = tuple[float, float, float]

@new_command
def nice_tool(
    # Regular types are supported
    title: str,
    my_var: int | float,
    extended_calculation: bool,
    
    # Simple composite types
    a_point: Point,
    other_point: tuple[int, int, int] = (0, 0, 0),
    this_list: Optional[list[bool]] = None,

    # Support for Enum types
    flag: CoolFlag = CoolFlag.STRUCTURE,
 #   method: Method = Method.WARD,

    # Arbitrary types that allows initialization with str values
    dirname: Path = Path('~'),

    # Special arguments
    old_style: Any = "anything as string", # raw unparsed str
    quiet: bool = True,  # automatic 'quiet=1' on command-line
    _self=cmd  # used in multi-threaded applications
    
):
    pprint(locals())

These code block ahead are sample usage of the above function.

PyMOL> nice_tool Have a nice tool, 10, False, 0.1 2.3 4.5, this_list=true 0 yes 0, flag=SEQUENCE

{'_self': <module 'pymol.cmd' from '/home/peu/Desktop/pymol-open-source/modules/pymol/cmd.py'>,
 'a_point': (0.1, 2.3, 4.5),
 'dirname': PosixPath('~'),
 'extended_calculation': False,
 'flag': <CoolFlag.SEQUENCE: 2>,
 'method': <Method.WARD: 'ward'>,
 'my_var': 10,
 'old_style': 'anything as string',
 'other_point': (0, 0, 0),
 'quiet': False,
 'this_list': [True, False, True, False],
 'title': 'Have a nice tool'}

If you need more examples, here a non exhaustive list of examples [1]. Look for and inspect cmd.do() calls and because they contain code exactly as they would be written into command line.

Installation

The PyMOL open-source builtin new_command doesn't support all features listed here. To use the full featured version, you may install and test it through my implementation experimental proposal.

pip install https://github.com/pslacerda1/pymol_new_command/archive/refs/heads/main.zip

If you have Propietary PyMOL, it's recommended to run the previous pip command on the console. Otherwise, use any standard Python package installation method you want.

Advantages

It improves on extend, the standard command definition mechanism. It works by parsing the arguments given at command-line by users, enforcing correct types at runtime, and ensuring typing strictness. It is also advantageous for developers consuming the function/command directly by the API because types can also be enforced statically by MyPy.

Zero-overhead with direct access

Before parsing arguments, this feature introspects quickly if it was called by the PyMOL parser and so can further benefit from parsing refinement, or if it was called by another function and this feature is not necessary. The introspection mechanism is a simple observation on the caller stack frame filename, which can be a slowness factor. Because of this, we also provide direct access with zero overhead for developers by the .func attribute.

# works the same for developers
>>> nice_tool('Have a nice tool', 10, False, [0.1, 2.3, 4.5], this_list=[True, False, True, False], flag=CoolFlag.SEQUENCE)
>>> nice_tool.func('Have a nice tool', 10, False, [0.1, 2.3, 4.5], this_list=[True, False, True, False], flag=CoolFlag.SEQUENCE)

Here a quick benchmark (remove the print statement before trying it).

# 2.5x improvement for 1000000 calls
>>> from timeit import timeit
>>> timeit("nice_tool('Have a nice tool', 10, False, [0.1, 2.3, 4.5], this_list=[True, False, True, False], flag=CoolFlag.SEQUENCE)", globals=locals())
0.374392487006844
>>> timeit("nice_tool.func('Have a nice tool', 10, False, [0.1, 2.3, 4.5], this_list=[True, False, True, False], flag=CoolFlag.SEQUENCE)", globals=locals())
0.12843744499696186