MDANCE
About
MDANCE: Molecular Dynamics Analysis with
N
-ary Clustering Ensembles
Getting Started
Examples
Learn NANI in 60 seconds!
Preprocessing of Molecular Dynamics Data
Cluster Analysis
Clustering Results Postprocessing
MDANCE's Tutorials
k
-means NANI Tutorial
eQual - Extended Quality Clustering
PRIME Tutorial
SHINE tutorial
HELM - Hierarchical Extended Linkage Method
MDANCE's API
mdance.cluster
mdance.cli
mdance.data
mdance.inputs
mdance.outputs
mdance.prime
mdance.tools
MDANCE
Index
Index
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
K
|
L
|
M
|
N
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
|
Z
_
__call__() (mdance.tools.esim.SimilarityIndex method)
A
ac_nw() (mdance.tools.esim.SimilarityIndex method)
ac_w() (mdance.tools.esim.SimilarityIndex method)
align_traj() (in module mdance.tools.bts)
B
bub_nw() (mdance.tools.esim.SimilarityIndex method)
bub_w() (mdance.tools.esim.SimilarityIndex method)
C
calc() (mdance.cluster.helm.HELM method)
calc_comp_sim() (in module mdance.tools.esim)
calc_medoid() (in module mdance.tools.esim)
calc_outlier() (in module mdance.tools.esim)
calculate_best_frames() (mdance.cluster.equal.ExtendedQuality method)
calculate_comp_sim() (in module mdance.tools.bts)
(in module mdance.tools.isim)
calculate_counters() (in module mdance.tools.esim)
(in module mdance.tools.isim)
calculate_isim() (in module mdance.tools.isim)
calculate_max_key() (in module mdance.prime.rep_frames)
calculate_medoid() (in module mdance.tools.bts)
(in module mdance.tools.isim)
(mdance.prime.sim_calc.FrameSimilarity method)
calculate_outlier() (in module mdance.tools.bts)
(in module mdance.tools.isim)
(mdance.prime.sim_calc.FrameSimilarity method)
calculate_pairwise() (mdance.prime.sim_calc.FrameSimilarity method)
calculate_populations() (mdance.cluster.equal.ExtendedQuality method)
calculate_union() (mdance.prime.sim_calc.FrameSimilarity method)
centers (mdance.cluster.nani.KmeansNANI attribute)
cluster_dict (mdance.cluster.nani.KmeansNANI attribute)
comp_sim_seeds() (mdance.cluster.equal.ExtendedQuality method)
compute_scores() (in module mdance.cluster.equal)
(in module mdance.cluster.helm)
(in module mdance.cluster.nani)
(mdance.cluster.nani.KmeansNANI method)
create_cluster_dict() (mdance.cluster.nani.KmeansNANI method)
ct1_nw() (mdance.tools.esim.SimilarityIndex method)
ct1_w() (mdance.tools.esim.SimilarityIndex method)
ct2_nw() (mdance.tools.esim.SimilarityIndex method)
ct2_w() (mdance.tools.esim.SimilarityIndex method)
ct3_nw() (mdance.tools.esim.SimilarityIndex method)
ct3_w() (mdance.tools.esim.SimilarityIndex method)
ct4_nw() (mdance.tools.esim.SimilarityIndex method)
ct4_w() (mdance.tools.esim.SimilarityIndex method)
D
diversity_selection() (in module mdance.tools.bts)
E
equil_align() (in module mdance.tools.bts)
execute_kmeans_all() (mdance.cluster.nani.KmeansNANI method)
extended_comparison() (in module mdance.tools.bts)
ExtendedQuality (class in mdance.cluster.equal)
F
fai_nw() (mdance.tools.esim.SimilarityIndex method)
fai_w() (mdance.tools.esim.SimilarityIndex method)
find_best_frames_indices() (mdance.cluster.equal.ExtendedQuality method)
find_medoids() (mdance.cluster.equal.ExtendedQuality method)
FrameSimilarity (class in mdance.prime.sim_calc)
G
gen_all_methods_max() (in module mdance.prime.rep_frames)
gen_cluster_dists() (mdance.cluster.helm.HELM method)
gen_link_matrix() (mdance.cluster.helm.HELM method)
gen_msdmatrix() (mdance.cluster.shine.Shine method)
gen_new_cluster() (mdance.cluster.helm.HELM method)
gen_one_method_max() (in module mdance.prime.rep_frames)
gen_sim_dict() (in module mdance.tools.esim)
(in module mdance.tools.isim)
(mdance.tools.esim.SimilarityIndex method)
gen_traj_numpy() (in module mdance.inputs.preprocess)
get_new_index_n() (in module mdance.tools.bts)
gle_nw() (mdance.tools.esim.SimilarityIndex method)
gle_w() (mdance.tools.esim.SimilarityIndex method)
greedy_seeds() (mdance.cluster.equal.ExtendedQuality method)
group_consecutive_indices() (mdance.cluster.shine.Shine method)
grow_clusters() (mdance.cluster.equal.ExtendedQuality method)
H
HELM (class in mdance.cluster.helm)
I
initial_pairwise_matrix() (mdance.cluster.helm.HELM method)
initiate_kmeans() (mdance.cluster.nani.KmeansNANI method)
J
ja0_nw() (mdance.tools.esim.SimilarityIndex method)
ja0_w() (mdance.tools.esim.SimilarityIndex method)
ja_nw() (mdance.tools.esim.SimilarityIndex method)
ja_w() (mdance.tools.esim.SimilarityIndex method)
jt_nw() (mdance.tools.esim.SimilarityIndex method)
jt_w() (mdance.tools.esim.SimilarityIndex method)
K
kmeans_clustering() (mdance.cluster.nani.KmeansNANI method)
KmeansNANI (class in mdance.cluster.nani)
L
labels (mdance.cluster.nani.KmeansNANI attribute)
labels() (mdance.cluster.equal.ExtendedQuality method)
(mdance.cluster.shine.Shine method)
link_matrix_to_cluster_dict() (mdance.cluster.helm.HELM method)
M
main() (in module mdance.cli.prime_rep)
(in module mdance.cli.prime_sim)
mdance.cli.prime_rep
module
mdance.cli.prime_sim
module
mdance.cluster.equal
module
mdance.cluster.helm
module
mdance.cluster.nani
module
mdance.cluster.shine
module
mdance.outputs.postprocess
module
mdance.prime.rep_frames
module
mdance.prime.sim_calc
module
mdance.tools.bts
module
mdance.tools.esim
module
mdance.tools.isim
module
mean_sq_dev() (in module mdance.tools.bts)
mini_batch_kmeans_seeds() (mdance.cluster.equal.ExtendedQuality method)
module
mdance.cli.prime_rep
mdance.cli.prime_sim
mdance.cluster.equal
mdance.cluster.helm
mdance.cluster.nani
mdance.cluster.shine
mdance.outputs.postprocess
mdance.prime.rep_frames
mdance.prime.sim_calc
mdance.tools.bts
mdance.tools.esim
mdance.tools.isim
msd_condensed() (in module mdance.tools.bts)
N
n_iter (mdance.cluster.nani.KmeansNANI attribute)
normalize_file() (in module mdance.inputs.preprocess)
numpy_array_to_crd_traj() (in module mdance.outputs.postprocess)
P
plot() (mdance.cluster.shine.Shine method)
process_trajs() (mdance.cluster.shine.Shine method)
Q
quota_sampling() (in module mdance.tools.bts)
R
refine_dis_matrix() (in module mdance.tools.bts)
rep_sample() (in module mdance.tools.bts)
rr_nw() (mdance.tools.esim.SimilarityIndex method)
rr_nw_nw() (mdance.tools.esim.SimilarityIndex method)
rr_w() (mdance.tools.esim.SimilarityIndex method)
rt_nw() (mdance.tools.esim.SimilarityIndex method)
rt_w() (mdance.tools.esim.SimilarityIndex method)
run() (mdance.cluster.equal.ExtendedQuality method)
(mdance.cluster.helm.HELM method)
(mdance.cluster.shine.Shine method)
S
Shine (class in mdance.cluster.shine)
SimilarityIndex (class in mdance.tools.esim)
sm_nw() (mdance.tools.esim.SimilarityIndex method)
sm_nw_nw() (mdance.tools.esim.SimilarityIndex method)
sm_w() (mdance.tools.esim.SimilarityIndex method)
ss1_nw() (mdance.tools.esim.SimilarityIndex method)
ss1_w() (mdance.tools.esim.SimilarityIndex method)
ss2_nw() (mdance.tools.esim.SimilarityIndex method)
ss2_w() (mdance.tools.esim.SimilarityIndex method)
T
trim_clusters() (mdance.cluster.helm.HELM method)
trim_outliers() (in module mdance.tools.bts)
U
unnormalize_data() (in module mdance.outputs.postprocess)
V
vanilla_seeds() (mdance.cluster.equal.ExtendedQuality method)
W
weight_dict() (in module mdance.prime.sim_calc)
write_centroids() (mdance.cluster.nani.KmeansNANI method)
Z
z_matrix() (in module mdance.cluster.helm)