what is the '10' in result = pt.clustering_dataset(xyz[:, 0], 'clusters
10') ? Is it required final number of clusters or cutoff distance between
oxygen atoms when calculating the contact map?
On Mon, Aug 3, 2015 at 4:48 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> .Jose
> for the sake of completeness. You can use pytraj/cpptraj for this task (if
> I understand your goal and Jason's idea correctly)
>
> Since pytraj is not well-documented (yet), I wrote example here for demo.
>
> https://github.com/pytraj/pytraj/blob/master/examples/example_water_clustering.py
>
> import pytraj as pt
>
> # use `iterload` to save memory (same as `generator` (with fancy indexing)
> in python)
> # you can use `load`, which is similiar to `mdtraj`
> traj = pt.iterload("../tests/data/tz2.ortho.nc",
> "../tests/data/tz2.ortho.parm7")
> # get some info
> print(traj)
>
> # get new trajectory for specific waters (Oxygen atom only)
> wat_traj = traj[':100-500.O']
>
> # iterate every frame and do clustering
> for frame in wat_traj:
> xyz = frame.xyz
> # clustering for x-coordniates
> result = pt.clustering_dataset(xyz[:, 0], 'clusters 10')
>
> # cluster index for each atom
> print(result)
>
> Hai
>
> On Mon, Aug 3, 2015 at 3:21 PM, Jose Borreguero <borreguero.gmail.com>
> wrote:
>
> > I have created a graph for every frame. Nodes in the graph are the
> solvent
> > molecules, and two nodes are connected with and edge if the distance
> > between the associated solvent molecules is below a cutoff I chose. I
> have
> > systems with different solvation levels, some of then featuring "pockets"
> > of solvent molecules. These pockets are the clusters I'm interested in.
> > Algorithm networkx.connected_components
> > <
> >
> https://networkx.github.io/documentation/latest/reference/generated/networkx.algorithms.components.connected.connected_components.html
> > >can
> > find the connected clusters from a graph. To create the graph, I am using
> > MDAnalysis to obtain the contact map between solvent molecules. Regarding
> > time, it takes 2.2seconds to create a contact map for 4132 solvent
> > molecules, which I think is reasonable (unless you have many thousands of
> > frames)
> >
> > On Mon, Aug 3, 2015 at 1:17 PM, Jason Swails <jason.swails.gmail.com>
> > wrote:
> >
> > > On Mon, 2015-08-03 at 12:57 -0400, Jose Borreguero wrote:
> > > > Thanks a lot, Jason. I'll go along with python for the clustering
> > step. I
> > > > found module networkx which is very straighforward for clustering,
> and
> > > > quite fast.
> > >
> > > How are you using networkx for this? I've used it to define a bond
> > > graph in molecular topology before, but I don't see how networkx maps
> to
> > > clustering here. Do you have a fully connected graph whose edge
> weights
> > > are the distance between the nodes or something? That sounds like it
> > > would be an expensive graph to create. Keep in mind that the PBC will
> > > have an effect on the clusters, so how you pick the unit cell
> > > representation is likely important.
> > >
> > > I've used sklearn to cluster in the past, and I've found it to be
> pretty
> > > easy to use, for what that's worth.
> > >
> > > All the best,
> > > Jason
> > >
> > > --
> > > Jason M. Swails
> > > BioMaPS,
> > > Rutgers University
> > > Postdoctoral Researcher
> > >
> > >
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Received on Mon Aug 03 2015 - 15:00:03 PDT
