[global]
top = 1cqz_sample_topology.pdb
trj = 1cqz_sample_10ns.nc

[traceable_residues]
scope = name CA
scope_convexhull = True
object = (resname WAT) and (sphzone 6.0 (resnum 99 or resnum 147 or resnum 231 or resnum 261 or resnum 289))

[raw_paths]
clear_in_object_info = False

[separate_paths]
sort_by_id = True
apply_smoothing = False
apply_soft_smoothing = True
discard_short_paths = 1
auto_barber = protein

[smooth]
method = dwin_mss
step = 4.2
window = 4.2

[inlets_clusterization]
recluster_outliers = True
detect_outliers = Auto
singletons_outliers = 2
create_master_paths = True

[clusterization]
method = meanshift
cluster_all = True
bandwidth = Auto
recursive_clusterization = clusterization
recursive_threshold = >0.9

[reclusterization]
method = meanshift
cluster_all = False
bandwidth = Auto

[analysis]
dump_config = True

[visualize]
all_paths_raw = True
all_paths_smooth = True
all_paths_split = True
all_paths_raw_io = True
all_paths_smooth_io = True
paths_raw = True
paths_smooth = True
paths_states = True
paths_raw_io = True
paths_smooth_io = True
ctypes_raw = True
ctypes_smooth = True
inlets_clusters = True
show_molecule = protein
show_molecule_frames = 0
show_chull = name CA
show_chull_frames = 0
show_object = name * and (sphzone 6.0 (resnum 99 or resnum 147 or resnum 231 or resnum 261 or resnum 289))
show_object_frames = 0