from ligandparam.parametrization import Recipe
from ligandparam.stages import *
[docs]
class RNALigand(Recipe):
def __init__(self, *args, **kwargs):
""" This is a recipe for doing a parametrization of an RNA-based 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):
raise NotImplementedError("This class is not yet implemented.")
self.stages = [
StageInitialize("Initialize", base_cls=self),
"""
StageNormalizeCharge("Normalize1", base_cls=self,
orig_mol2=self.base_name+".antechamber.mol2",
new_mol2=self.base_name+".antechamber.mol2"),
StageGaussian("Minimize", base_cls=self),
StageLazyResp("LazyResp", base_cls=self),
StageNormalizeCharge("Normalize2", base_cls=self,
orig_mol2=self.base_name+".resp.mol2",
new_mol2=self.base_name+".resp.mol2"),
StageUpdate("UpdateNames", base_cls=self,
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),
StageParmChk("ParmChk", base_cls=self),
StageLeap("Leap", base_cls=self)
"""
]