from ligandparam.parametrization import Recipe
from ligandparam.stages import *
[docs]
class BuildLigand(Recipe):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.nproc = kwargs.get("nproc", 12)
self.mem = kwargs.get("mem", "60GB")
self.net_charge = kwargs.get("net_charge", 0)
self.atom_type = kwargs.get("atom_type", "gaff2")
self.leaprc = kwargs.get("leaprc", None)
self.target_pdb = kwargs.get("target_pdb")
self.force_gaussian_rerun = kwargs.get("force_gaussian_rerun", False)
"""
def setup(self):
self.stages = [
StageInitialize("Initialize",,,
StageNormalizeCharge("Normalize1",,,
GaussianMinimize("Minimize", inputoptions=self.inputoptions),
StageGaussianRotation("Rotate",,,
StageGaussiantoMol2("GrabGaussianCharge",,,
StageMultiRespFit("MultiRespFit",,,
StageUpdateCharge("UpdateCharge",,,
StageNormalizeCharge("Normalize2",,,
StageUpdate("UpdateNames",,,
StageUpdate("UpdateTypes",,,
StageParmChk("ParmChk",,,
StageLeap("Leap",,,
StageBuild("BuildGas", build_type='gas', inputoptions=self.inputoptions),
StageBuild("BuildAq", build_type='aq', concentration=0.14, inputoptions=self.inputoptions),
StageBuild("BuildTarget", build_type='target', inputoptions=self.inputoptions)
]
"""