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
49
|
from ost.mol import mm
from PyQt5 import QtCore
"""
MM - Demo
!!!Requires OpenStructure to be compiled with MM-Support!!!
This demo should show the setup of a simple simulation using implicit solvent.
The script can directly be started from within DNG.
"""
class Anim(QtCore.QTimer):
def __init__(self,sim,ent,go):
QtCore.QTimer.__init__(self)
self.ent=ent
self.sim=sim
self.go = go
self.ed = ent.EditXCS(ost.mol.BUFFERED_EDIT)
self.timeout.connect(self.OnTimer)
def OnTimer(self):
self.sim.Steps(5)
self.sim.UpdatePositions()
self.go.UpdatePositions()
prot=ost.mol.CreateEntityFromView(io.LoadPDB('1CRN.pdb').Select('peptide=true'),True)
settings = mm.Settings()
settings.integrator = mm.LangevinIntegrator(310,1,0.002)
settings.add_gbsa = True
settings.forcefield = mm.LoadCHARMMForcefield()
settings.platform = mm.Platform.CPU
settings.nonbonded_method = mm.NonbondedMethod.CutoffNonPeriodic
sim = mm.Simulation(prot,settings)
sim.ApplyLBFGS(tolerance = 1.0, max_iterations = 200)
sim.UpdatePositions()
ent = sim.GetEntity()
go = gfx.Entity("crambin",ent)
scene.Add(go)
anim = Anim(sim,ent,go)
anim.start(1)
|
