WillardChandler

Module: willard-chandler

class pytim.willard_chandler.WillardChandler(universe, group=None, alpha=2.0, radii_dict=None, mesh=2.0, symmetry='spherical', cluster_cut=None, include_zero_radius=False, cluster_threshold_density=None, extra_cluster_groups=None, centered=False, warnings=False, autoassign=True, **kargs)[source]

Identifies the dividing surface using the Willard-Chandler method NOTE that this method does not identify surface atoms

(Willard, A. P.; Chandler, D. J. Phys. Chem. B 2010, 114, 1954–1958)

Parameters:

  • universe (Object) – The MDAnalysis Universe, MDTraj trajectory or OpenMM Simulation objects.

  • group (AtomGroup) – An AtomGroup, or an array-like object with the indices of the atoms in the group. Will identify the interfacial molecules from this group

  • alpha (float) – The width of the Gaussian kernel

  • mesh (float) – The grid spacing for the density calculation

  • group – Compute the density using this group

  • radii_dict (dict) – Dictionary with the atomic radii of the elements in the group. If None is supplied, the default one (from GROMOS 43a1) will be used.

  • cluster_cut (float) – Cutoff used for neighbors or density-based cluster search (default: None disables the cluster analysis)

  • cluster_threshold_density (float) – Number density threshold for the density-based cluster search. ‘auto’ determines the threshold automatically. Default: None uses simple neighbors cluster search, if cluster_cut is not None

  • extra_cluster_groups (Object) – Additional groups, to allow for mixed interfaces

  • include_zero_radius (bool) – if false (default) exclude atoms with zero radius from the surface analysis (they are always included in the cluster search, if present in the relevant group) to avoid some artefacts.

  • centered (bool) – Center the group

  • warnings (bool) – Print warnings

Example:

>>> 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)
>>>
>>> inter= pytim.WillardChandler(u, group=g, alpha=3.0, fast=True)
>>> R, _, _, _ = pytim.utilities.fit_sphere(inter.triangulated_surface[0])
>>> print ("Radius={:.3f}".format(R))
Radius=19.970
property layers

The method does not identify layers.

Example:

>>> import MDAnalysis as mda
>>> import pytim
>>> from pytim.datafiles import *
>>>
>>> u = mda.Universe(MICELLE_PDB)
>>> g = u.select_atoms('resname DPC')
>>> inter= pytim.WillardChandler(u, group=g, alpha=3.0, fast=True)
>>> inter.layers
<AtomGroup with 0 atoms>
property autoassign

(bool) assign layers every time a frame changes

property include_zero_radius

(bool) include atoms with zero radius in the analysis (excluded by default)

writecube(filename='pytim.cube', group=None, sequence=False)[source]

Write to cube files (sequences) the volumentric density and the atomic positions.

Parameters:

  • filename (str) – the file name

  • sequence (bool) – if true writes a sequence of files adding the frame to the filename

>>> import MDAnalysis as mda
>>> import pytim
>>> from pytim.datafiles import MICELLE_PDB
>>> u = mda.Universe(MICELLE_PDB)
>>> g = u.select_atoms('resname DPC')
>>> inter= pytim.WillardChandler(u, group=g, alpha=3.0, mesh=2.0)
>>> inter.writecube('dens.cube') # writes on dens.cube
>>> inter.writecube('dens.cube',group=g) # writes also  particles
>>> inter.writecube('dens.cube',sequence=True) # dens.<frame>.cube
writeobj(filename='pytim.obj', sequence=False)[source]

Write to wavefront obj files (sequences) the triangulated surface

Parameters:

  • filename (str) – the file name

  • sequence (bool) – if true writes a sequence of files adding the frame to the filename

>>> import MDAnalysis as mda
>>> import pytim
>>> from pytim.datafiles import MICELLE_PDB
>>> u = mda.Universe(MICELLE_PDB)
>>> g = u.select_atoms('resname DPC')
>>> inter= pytim.WillardChandler(u, group=g, alpha=3.0, mesh=2.0)
>>> inter.writeobj('surf.obj') # writes on surf.obj
>>> inter.writeobj('surf.obj',sequence=True) # surf.<frame>.obj
property analysis_group

(AtomGroup) the group, the surface of which should be computed

is_buried(pos)

Checks wether an array of positions are located below the first interfacial layer

label_planar_sides()

Assign to all layers a label (the beta tempfactor) that can be used in pdb files. Additionally, set the new layers and sides.

prepare_box()

Before the analysis, pack every molecule into the box. Keep the original positions for latter use.

reset_labels()

Reset labels before interfacial analysis

property surface_cluster_cut

(float) distance cut to calculate the surface clusters

writepdb(filename='layers.pdb', centered='no', group='all', multiframe=True, tempfactors=None)

Write the frame to a pdb file, marking the atoms belonging to the layers with different beta factors.

Parameters:

  • filename (str) – the output file name

  • centered (str) – ‘origin’, ‘middle’, or ‘no’

  • group (AtomGroup) – if ‘all’ is passed, use universe

  • multiframe (bool) – append to pdb file if True

  • tempfactors (ndarray) – use this array as temp (beta) factors

Example: save the positions (centering the interface in the cell)

without appending

>>> import pytim
>>> import pytim.datafiles
>>> import MDAnalysis as mda
>>> from pytim.datafiles import WATER_GRO
>>> u = mda.Universe(WATER_GRO)
>>> interface = pytim.ITIM(u)
>>> interface.writepdb('layers.pdb',multiframe=False)
Example: save the positions without centering the interface. This

will not shift the atoms from the original position (still, they will be put into the basic cell). The multiframe option set to False will overwrite the file

>>> interface.writepdb('layers.pdb',centered='no')

Note that if GITIM is used, and the symmetry option is different from planar, the centered='origin' option is equivalent to centered='middle'.

class pytim.willard_chandler.Writevtk(interface)[source]
density(filename='pytim_dens.vtk', sequence=False)[source]

Write to vtk files the volumetric density.

Parameters:

  • filename (str) – the file name

  • sequence (bool) – if true writes a sequence of files adding the frame to the filename

>>> import MDAnalysis as mda
>>> import pytim
>>> from pytim.datafiles import MICELLE_PDB
>>> u = mda.Universe(MICELLE_PDB)
>>> g = u.select_atoms('resname DPC')
>>> inter= pytim.WillardChandler(u, group=g, alpha=3.0, mesh=2.0)

>>> inter.writevtk.density('dens.vtk') # writes on dens.vtk
>>> inter.writevtk.density('dens.vtk',sequence=True) # dens.<n>.vtk
particles(filename='pytim_part.vtk', group=None, sequence=False)[source]

Write to vtk files the particles in a group.

Parameters:

  • filename (str) – the file name

  • sequence (bool) – if true writes a sequence of files adding the frame to the filename

  • group (AtomGroup) – if None, writes the whole universe

>>> import MDAnalysis as mda
>>> import pytim
>>> from pytim.datafiles import MICELLE_PDB
>>> u = mda.Universe(MICELLE_PDB)
>>> g = u.select_atoms('resname DPC')
>>> inter= pytim.WillardChandler(u, group=g, alpha=3.0, mesh=2.0)

>>> # writes on part.vtk
>>> inter.writevtk.particles('part.vtk')
>>> # writes on part.<frame>.vtk
>>> inter.writevtk.particles('part.vtk',sequence=True)
surface(filename='pytim_surf.vtk', sequence=False)[source]

Write to vtk files the triangulated surface.

Parameters:

  • filename (str) – the file name

  • sequence (bool) – if true writes a sequence of files adding the frame to the filename

>>> import MDAnalysis as mda
>>> import pytim
>>> from pytim.datafiles import MICELLE_PDB
>>> u = mda.Universe(MICELLE_PDB)
>>> g = u.select_atoms('resname DPC')
>>> inter= pytim.WillardChandler(u, group=g, alpha=3.0, mesh=2.0)
>>> inter.writevtk.surface('surf.vtk') # writes on surf.vtk
>>> inter.writevtk.surface('surf.vtk',sequence=True) # surf.<n>.vtk