Source code for pysisyphus.wrapper.packmol

import subprocess
import tempfile

from jinja2 import Template

from pysisyphus.config import get_cmd


TPL = """tolerance {{ tolerance }}
output {{ output_fn }}
filetype pdb

{% if solute_fn %}
# Solute
structure {{ solute_fn }}
 number {{ solute_num }}
 {% if solute_num == 1 %}
     fixed 0. 0. 0. 0. 0. 0.
     centerofmass
 {% endif %}
end structure
{% endif %}

# Solvent
structure {{ solvent_fn }}
 number {{ solvent_num }}
 inside sphere 0. 0. 0. {{ sphere_radius }}
end structure
"""




def make_input(
    output_fn,
    solvent_fn,
    solvent_num,
    sphere_radius,
    solute_fn=None,
    solute_num=None,
    tolerance=2.0,
):
    tpl = Template(TPL)
    rendered = tpl.render(
        tolerance=tolerance,
        output_fn=output_fn,
        solute_fn=solute_fn,
        solute_num=solute_num,
        solvent_fn=solvent_fn,
        solvent_num=solvent_num,
        sphere_radius=sphere_radius,
    )
    return rendered





def call_packmol(inp):
    packmol_cmd = get_cmd("packmol")

    with tempfile.NamedTemporaryFile(mode="w", dir=".") as tmp:
        tmp.write(inp)
        tmp.flush()
        cmd = f"{packmol_cmd} < {tmp.name}"
        proc = subprocess.run(
            cmd,
            shell=True,
            stdout=subprocess.PIPE,
            # stderr=subprocess.PIPE,
            text=True,
        )
    # out = proc.stdout
    # err = proc.stderr

    return proc