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80a72c3 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 | 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
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