from ligandparam.parametrization import Recipe
from ligandparam.stages import *
[docs]
class FreeLigand(Recipe):
def __init__(self, *args, **kwargs):
""" This is a recipe for doing a parametrization of a ligand using the RESP method with multi-state fitting.
This recipe has a default list of stages that are run, and the stages can be disable by passing a dictionary of stages to disable to the disable stages method defined
in the Recipe class.
default_stage_list = {
"Initialize": True,
"Normalize1": True,
"Minimize": True,
"Rotate": True,
"GrabGaussianCharge": True,
"MultiRespFit": True,
"UpdateCharge": True,
"Normalize2": True,
"UpdateNames": True,
"UpdateTypes": True,
"ParmChk": True,
"Leap": True,
}
"""
super().__init__(*args, **kwargs)
return
[docs]
def setup(self):
self.stages = [
StageInitialize("Initialize", inputoptions=self.inputoptions),
StageNormalizeCharge("Normalize1", inputoptions=self.inputoptions,
orig_mol2=self.base_name+".antechamber.mol2",
new_mol2=self.base_name+".antechamber.mol2"),
StageGaussian("Minimize", inputoptions=self.inputoptions),
StageGaussianRotation("Rotate", inputoptions=self.inputoptions,
alpha=[0, 30, 60, 90, 120, 150, 180],
beta=[0, 30, 60, 90],
gamma=[0]),
StageGaussiantoMol2("GrabGaussianCharge", inputoptions=self.inputoptions),
StageMultiRespFit("MultiRespFit", inputoptions=self.inputoptions),
StageUpdateCharge("UpdateCharge", inputoptions=self.inputoptions,
orig_mol2=self.base_name+".antechamber.mol2",
new_mol2=self.base_name+".resp.mol2",
charge_source="multistate"),
StageNormalizeCharge("Normalize2", inputoptions=self.inputoptions,
orig_mol2=self.base_name+".resp.mol2",
new_mol2=self.base_name+".resp.mol2"),
StageUpdate("UpdateNames", inputoptions=self.inputoptions,
orig_mol2=self.base_name+'.antechamber.mol2',
to_update=self.base_name+'.resp.mol2',
new_mol2=self.base_name+'.resp.mol2',
update_names=True,
update_types=False,
update_resname=True),
StageUpdate("UpdateTypes", inputoptions=self.inputoptions,
orig_mol2=self.base_name+'.log.mol2',
to_update=self.base_name+'.resp.mol2',
new_mol2=self.base_name+'.resp.mol2',
update_names=False,
update_types=True),
StageParmChk("ParmChk", inputoptions=self.inputoptions),
StageLeap("Leap", inputoptions=self.inputoptions)
]