def test_merge_system(): # take a protein from chemlab.io import datafile from chemlab.graphics import display_system from chemlab.db import ChemlabDB water = ChemlabDB().get("molecule", "example.water") prot = datafile("tests/data/3ZJE.pdb").read("system") # Take a box of water NWAT = 50000 bsize = 20.0 pos = np.random.random((NWAT, 3)) * bsize wat = water.copy() s = System.empty(NWAT, NWAT * 3, box_vectors=np.eye(3) * bsize) for i in range(NWAT): wat.move_to(pos[i]) s.add(wat) prot.r_array += 10 s = merge_systems(s, prot, 0.5) display_system(s, 'ball-and-stick')
def test_merge_system(): # take a protein from chemlab.io import datafile from chemlab.graphics import display_system from chemlab.db import ChemlabDB water = ChemlabDB().get("molecule", "example.water") prot = datafile("tests/data/3ZJE.pdb").read("system") # Take a box of water NWAT = 50000 bsize = 20.0 pos = np.random.random((NWAT, 3)) * bsize wat = water.copy() s = System.empty(NWAT, NWAT*3, box_vectors=np.eye(3)*bsize) for i in range(NWAT): wat.move_to(pos[i]) s.add(wat) prot.r_array += 10 s = merge_systems(s, prot, 0.5) display_system(s, 'ball-and-stick')