Topology fingerprint¶

A fingerprint is the label-independent key of a bonded graph: one rooted neighbourhood class per atom, the histogram of those classes, the primitive ring census, and a frame key over all of it. Relabelled copies of the same bonded graph share the key.

CLI¶

seams fingerprint mW_cubic.lammpstrj --type 1 --hops 2
seams fingerprint mW_cubic.lammpstrj --type 1 --hops 2 --colour-types
seams fingerprint mW_cubic.lammpstrj --type 1 --hops 2 --emit-library Ic > ic.keys
seams fingerprint hydrate.lammpstrj --type 2 --hops 3 --library ic.keys
seams fingerprint hydrate.lammpstrj --type 2 --hops 3 --library ic3.keys,ic2.keys

--hops is the number of bonds from the centre in each local key (default 2). --colour-types colours vertices by LAMMPS type so species never match across types. --emit-library LABEL prints the frame's distinct keys as library lines under LABEL. --library FILE names atoms of a frame by that library. A comma-separated list of libraries built at different --hops names each atom by the deepest library that knows its key. An atom whose wide neighbourhood is disturbed still takes a name from its inner shells. The output adds the count named at each depth. Python classify_topology and Lua dseams.classify_topology take a sequence of libraries the same way. DSEAMS_CAGES LIBRARY splits on commas too.

The bond graph follows --graph. seeded is two graphs, so the fingerprint falls back to the cutoff list. Use --graph knn or --graph knn-union for a k-nearest graph.

Python¶

from pydseams import Frame
from pydseams import yoda

frame = Frame.from_file("mW_cubic.lammpstrj", atom_type=1)
fp = frame.fingerprint(hops=2, colour_types=False)
print(fp.key, fp.method, fp.classes)

lib = frame.topology_library("Ic", hops=2)
print(yoda.writeLibrary(lib))

named = frame.classify_topology(lib, hops=2)
print(named.matched, named.counts)

deep = frame.topology_library("Ic", hops=3)
both = frame.classify_topology([deep, lib])
print(both.matched, both.depth[:8])

fingerprint returns a FrameFingerprint: key, atomKeys, classes, ringCensus, and method ("nauty" when the engine links nauty, else "wl"). topology_library adds this frame's keys under a label. classify_topology names every analysed atom; unmatched atoms carry "". Given a sequence of libraries at different hop counts it names each atom by the deepest that knows it. depth is the hops of the library that named the atom (0 when none).

Lua¶

dseams.fingerprint takes neighbour-list rows by index.

local dseams = require("dseams")
local cloud = dseams.read("mW_cubic.lammpstrj", {type = 1})
local rows = dseams.core.neighbourListByIndex(
    cloud, dseams.neighbors(cloud, {cutoff = 3.5, type = 1}))
local fp = dseams.fingerprint(rows, {hops = 2})
local lib = dseams.topology_library(rows, "Ic", {hops = 2})
local named = dseams.classify_topology(rows, lib, {hops = 2})
local both = dseams.classify_topology(rows, { lib, dseams.topology_library(rows, "Ic", {hops = 3}) })
print(fp.key, named.matched, both.depth[1])

o.colours is an optional list of one integer class per row.

Book: seams CLI.