# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
import MDAnalysis as mda
import pytim
from pytim.datafiles import *
u = mda.Universe(WATER_GRO)
g = u.select_atoms('name OW')
interface = pytim.GITIM(u, group=g, molecular=True, symmetry='planar',
alpha=2.5, cluster_cut=3.5, cluster_threshold_density='auto')
layers = interface.layers[:]
print(repr(layers))
interface.writepdb('gitim_flat.pdb', centered='middle')
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
import MDAnalysis as mda
import pytim
from pytim.datafiles import *
u = mda.Universe(MICELLE_PDB)
g = u.select_atoms('resname DPC')
radii = pytim_data.vdwradii(G43A1_TOP)
interface = pytim.GITIM(u, itim_group=g, molecular=False,
symmetry='spherical', alpha=2.5,)
layer = interface.layers[0]
interface.writepdb('gitim.pdb', centered=False)
print("selected one layer of " + str(len(layer)) +
" atoms out of a group of " + str(len(g)))