| import os |
|
|
| import subprocess |
|
|
| import logging |
| LOG = logging.getLogger(__name__) |
|
|
|
|
| def generate_pymol_image(pdb_path, chopping, image_out_path, path_to_script, |
| pymol_executable): |
| """ |
| This function generates a pymol script which describes how one protein should be visualized |
| and saved as a png file. Script is then executed via subprocess. |
| Delimit separate domains with commas , and discontinuous domains |
| with underscores _. Residue ranges separated by hyphens -, e.g. 1-100,101-200_300-340 |
| :param pdb_path: string which is the path to a .pdb file |
| :param bounds: domain boundaries expressed in residue author numbers in the pdb file e.g. 1-100,101-200_300-340 |
| :param path_to_script: where the pymol bash script is saved |
| :param pymol_executable: path to pymol executable |
| :return: None |
| """ |
| script_text = f""" |
| load {pdb_path}, structure |
| hide everything |
| bg_color white |
| as cartoon, structure |
| set ray_opaque_background,1 |
| color white, structure\n""" |
| color_list = ['green', 'red', 'cyan', 'magenta', 'blue', 'orange', 'dirtyviolet', 'olive', |
| 'limon', 'salmon', 'deepteal', 'yellow', 'sand', 'purpleblue', 'black'] |
| bounds = chopping.split(',') |
| for i, bound in enumerate(bounds): |
| if len(bound): |
| domain_color = color_list[i % len(color_list)] |
| for segment in bound.split('_'): |
| start, end = segment.split('-') |
| script_text += f"color {domain_color}, structure and resi {start}-{end}\n" |
| script_text += "orient\n" |
| script_text += f"png {image_out_path}, ray=1, width=20cm, dpi=300,\n" |
| script_text += f"save {image_out_path.split('.')[0] + '.pse'}\n" |
| with open(path_to_script, 'w') as filehandle: |
| filehandle.write(script_text) |
| bash_command = f"{pymol_executable} -c {path_to_script}" |
| status = subprocess.run(bash_command.split(), timeout=120) |
| os.remove(path_to_script) |
| return status |
|
|
|
|
