Python Rst7.open Beispiele

Beispiel #1

Datei: uc_water.py Projekt: pjanowski/Pawel_PhD_Scripts

def get_U_invU(asu_rst7_file_name):
  rst7 = Rst7.open(asu_rst7_file_name)
  UCbox = rst7.box
  U, invU = raf.CompXfrm(UCbox)
  return U, invU, UCbox

Beispiel #2

#! /usr/bin/env python

import sander
from chemistry.amber.readparm import AmberParm, Rst7
import numpy as np

pdb = '3stl'
parm = AmberParm('4amber_%s.prmtop' % pdb)  #topo
rst = Rst7.open('4amber_%s.rst7' % pdb)  #box
sander.setup(parm, rst.coordinates, rst.box, sander.pme_input())
ene, frc = sander.energy_forces()
print ene.tot
print max(frc)

import code
code.interact(local=dict(globals(), **locals()))
sander.cleanup()

Beispiel #3

def get_U_invU(asu_rst7_file_name):
    rst7 = Rst7.open(asu_rst7_file_name)
    UCbox = rst7.box
    U, invU = raf.CompXfrm(UCbox)
    return U, invU, UCbox

Beispiel #4

Datei: phenix_sander_api.py Projekt: pjanowski/Pawel_PhD_Scripts

#! /usr/bin/env python

import sander
from chemistry.amber.readparm import AmberParm, Rst7
import numpy as np

pdb ='3stl'
parm = AmberParm('4amber_%s.prmtop' %pdb)  #topo
rst = Rst7.open('4amber_%s.rst7' %pdb)     #box
sander.setup(parm, rst.coordinates, rst.box, sander.pme_input())
ene, frc = sander.energy_forces()
print ene.tot
print max(frc)

import code; code.interact(local=dict(globals(), **locals()))
sander.cleanup()

Beispiel #5

Datei: sander_api.py Projekt: pjanowski/Pawel_PhD_Scripts

#! /usr/bin/env python

import sander
from chemistry.amber.readparm import AmberParm, Rst7
from chemistry.structure import Structure, read_PDB, write_PDB
import numpy as np


parm = AmberParm('4amber_1cby.prmtop')
pdb = read_PDB('new.pdb')
rst = Rst7.open('4amber_1cby.rst7')
xyz = pdb.pdbxyz[0]
sander.setup(parm,xyz, rst.box, sander.pme_input())

sander.set_positions(xyz)
ene, frc = sander.energy_forces()

#~ import code; code.interact(local=dict(globals(), **locals()))
sander.cleanup()