Source code for graphein.protein.meshes

"""Functions to create protein meshes via pymol."""
# Graphein
# Author: Arian Jamasb <>
# License: MIT
# Project Website:
# Code Repository:
from __future__ import annotations

import importlib.util
import logging
import os
import time
from typing import List, NamedTuple, Optional, Tuple

from graphein.protein.config import ProteinMeshConfig
from graphein.utils.pymol import MolViewer
from graphein.utils.utils import import_message

log = logging.getLogger(__name__)

    from pytorch3d.structures import Meshes
except ImportError:
    message = import_message(

[docs]def check_for_pymol_installation(): """Checks for presence of a pymol installation""" spec = importlib.util.find_spec("pymol") if spec is None: log.error( "Please install pymol: conda install -c schrodinger pymol or conda install -c tpeulen pymol-open-source" )
[docs]def configure_pymol_session( config: Optional[ProteinMeshConfig] = None, ): """ Configures a PyMol session based on ``config.parse_pymol_commands``. Uses default parameters ``"-cKq"``. See: :param config: :class:`~graphein.protein.config.ProteinMeshConfig` to use. Defaults to ``None`` which uses default config. :type config: graphein.protein.config.ProteinMeshConfig """ pymol = MolViewer() pymol.delete("all") # delete all objects from other sessions if necessary. # If no config is provided, use default if config is None: config = ProteinMeshConfig() # Start PyMol session pymol.start([config.pymol_command_line_options])
[docs]def get_obj_file( pdb_file: Optional[str] = None, pdb_code: Optional[str] = None, out_dir: Optional[str] = None, config: Optional[ProteinMeshConfig] = None, ) -> str: """ Runs PyMol to compute surface/mesh for a given protein. :param pdb_file: path to ``pdb_file`` to use. Defaults to ``None``. :type pdb_file: str, optional :param pdb_code: 4-letter pdb accession code. Defaults to ``None``. :type pdb_code: str, optional :param out_dir: path to output. Defaults to ``None``. :type out_dir: str, optional :param config: :class:`~graphein.protein.config.ProteinMeshConfig` containing pymol commands to run. Default is ``None`` (``"show surface"``). :type config: graphein.protein.config.ProteinMeshConfig :raises: ValueError if both or neither ``pdb_file`` or ``pdb_code`` are provided. :return: returns path to ``.obj`` file (str) :rtype: str """ pymol = MolViewer() check_for_pymol_installation() # Check inputs if not pdb_code and not pdb_file: raise ValueError("Please pass either a pdb_file or pdb_code argument") if pdb_code and pdb_file: raise ValueError( "Please pass either a pdb_file or pdb_code argument. Not both" ) if out_dir is None: out_dir = "/tmp/" configure_pymol_session() # Load structure pymol.load(pdb_file) if pdb_file else pymol.fetch(pdb_code) # Create file_name file_name = ( f"{pdb_file[:-3]}obj" if pdb_file else out_dir + pdb_code + ".obj" ) if config is None: config = ProteinMeshConfig() commands = parse_pymol_commands(config) print(commands) run_pymol_commands(commands) # Save surface object as .obj"save {file_name}") log.debug(f"Saved {file_name}") return file_name
[docs]def parse_pymol_commands(config: ProteinMeshConfig) -> List[str]: """ Parses pymol commands from config. At the moment users can only supply a list of string commands. :param config: ProteinMeshConfig containing pymol commands to run in ``config.pymol_commands``. :type config: ProteinMeshConfig :return: list of pymol commands to run :rtype: List[str] """ if config is None: config = ProteinMeshConfig() # Todo parsing of individual pymol mesh calculation parameters. There's a lot of them so this is not a priority now. if config.pymol_commands is not None: return config.pymol_commands
[docs]def run_pymol_commands(commands: List[str]) -> None: """ Runs Pymol Commands. :param commands: List of commands to pass to PyMol. :type commands: List[str] """ pymol = MolViewer() for c in commands: log.debug(c)
[docs]def create_mesh( pdb_file: Optional[str] = None, pdb_code: Optional[str] = None, out_dir: Optional[str] = None, config: Optional[ProteinMeshConfig] = None, ) -> Tuple[torch.FloatTensor, NamedTuple, NamedTuple]: """ Creates a ``PyTorch3D`` mesh from a ``pdb_file`` or ``pdb_code``. :param pdb_file: path to ``pdb_file``. Defaults to ``None``. :type pdb_file: str, optional :param pdb_code: 4-letter PDB accession code. Defaults to None. :type pdb_code: str, optional :param out_dir: output directory to store ``.obj`` file. Defaults to ``None``. :type out_dir: str, optional :param config: :class:`~graphein.protein.config.ProteinMeshConfig` config to use. Defaults to default config in ``graphein.protein.config``. :type config: graphein.protein.config.ProteinMeshConfig :return: ``verts``, ``faces``, ``aux``. :rtype: Tuple[torch.Tensor, torch.Tensor, torch.Tensor] """ from import load_obj if config is None: config = ProteinMeshConfig() obj_file = get_obj_file( pdb_code=pdb_code, pdb_file=pdb_file, out_dir=out_dir, config=config ) # Wait for PyMol to finish while os.path.isfile(obj_file) is False: time.sleep(0.1) verts, faces, aux = load_obj(obj_file) return verts, faces, aux
[docs]def normalize_and_center_mesh_vertices( verts: torch.FloatTensor, ) -> torch.FloatTensor: """ We scale normalize and center the target mesh to fit in a sphere of radius 1 centered at ``(0,0,0)``. ``(scale, center)`` will be used to bring the predicted mesh to its original center and scale Note that normalizing the target mesh, speeds up the optimization but is not necessary! :param verts: Mesh vertices. :type verts: torch.FloatTensor :return: Normalized and centered vertices. :rtype: torch.FloatTensor """ center = verts.mean() verts = verts - center scale = max(verts.abs().max(0)[0]) verts = verts / scale return verts
[docs]def convert_verts_and_face_to_mesh( verts: torch.FloatTensor, faces: NamedTuple ) -> Meshes: """ Converts vertices and faces into a ``pytorch3d.structures`` Meshes object. :param verts: Vertices. :type verts: torch.FloatTensor :param faces: Faces. :type faces: NamedTuple :return: Meshes object. :rtype: pytorch3d.structures.Meshes """ faces_idx = faces.verts_idx return Meshes(verts=[verts], faces=[faces_idx])
if __name__ == "__main__": from graphein.protein.visualisation import plot_pointcloud config = ProteinMeshConfig( pymol_commands=[ "show surface", "set surface_solvent, on", "set solvent_radius, 10000", ] ) verts, faces, aux = create_mesh(pdb_code="3eiy", config=config) trg_mesh = convert_verts_and_face_to_mesh(verts, faces) plot_pointcloud(trg_mesh)