Index

A

AdaptiveSampling (class in fast.sampling.core) analysis_folder (fast.analysis.contacts.ContactsWrap property) (fast.analysis.distances.DistWrap property) (fast.analysis.minimize.MinimizeWrap property) (fast.analysis.pockets.PocketWrap property) (fast.analysis.rmsd.RMSDWrap property)

B

base_output_name (fast.analysis.contacts.ContactsWrap property) (fast.analysis.distances.DistWrap property) (fast.analysis.minimize.MinimizeWrap property) (fast.analysis.pockets.PocketWrap property) (fast.analysis.rmsd.RMSDWrap property)

base_ranking (class in fast.sampling.rankings) best_hummer_q() (in module fast.analysis.contacts)

C

check_clustering() (fast.msm_gen.clustering.ClusterWrap method) check_pid() (in module fast.submissions.os_sub) check_save_states() (fast.msm_gen.save_states.SaveWrap method) chunks() (in module fast.msm_gen.save_states) class_name (fast.analysis.contacts.ContactsWrap property) (fast.analysis.distances.DistWrap property) (fast.analysis.minimize.MinimizeWrap property) (fast.analysis.pockets.PocketWrap property) (fast.analysis.rmsd.RMSDWrap property) (fast.md_gen.gromax.Gromax property) (fast.md_gen.gromax.GromaxProcessing property) (fast.msm_gen.clustering.ClusterWrap property) (fast.msm_gen.save_states.SaveWrap property) (fast.sampling.core.AdaptiveSampling property) (fast.sampling.rankings.counts property) (fast.sampling.rankings.evens property) (fast.sampling.rankings.FAST property) (fast.sampling.rankings.page_ranking property) (fast.sampling.rankings.string property) (fast.sampling.scalings.feature_scale property) (fast.submissions.lsf_subs.LSFSub property) (fast.submissions.lsf_subs.LSFWrap property) (fast.submissions.os_sub.OSWrap property) (fast.submissions.os_sub.SPSub property) (fast.submissions.slurm_subs.SlurmSub property) (fast.submissions.slurm_subs.SlurmWrap property)

ClusterWrap (class in fast.msm_gen.clustering) config (fast.analysis.contacts.ContactsWrap property) (fast.analysis.distances.DistWrap property) (fast.analysis.minimize.MinimizeWrap property) (fast.analysis.pockets.PocketWrap property) (fast.analysis.rmsd.RMSDWrap property) (fast.md_gen.gromax.Gromax property) (fast.md_gen.gromax.GromaxProcessing property) (fast.msm_gen.clustering.ClusterWrap property) (fast.msm_gen.save_states.SaveWrap property) (fast.sampling.core.AdaptiveSampling property) (fast.sampling.rankings.counts property) (fast.sampling.rankings.evens property) (fast.sampling.rankings.FAST property) (fast.sampling.rankings.page_ranking property) (fast.sampling.rankings.string property) (fast.sampling.scalings.feature_scale property) (fast.submissions.lsf_subs.LSFSub property) (fast.submissions.lsf_subs.LSFWrap property) (fast.submissions.os_sub.OSWrap property) (fast.submissions.os_sub.SPSub property) (fast.submissions.slurm_subs.SlurmSub property) (fast.submissions.slurm_subs.SlurmWrap property) ContactsWrap (class in fast.analysis.contacts) counts (class in fast.sampling.rankings)

D

DistWrap (class in fast.analysis.distances)

E

evens (class in fast.sampling.rankings)

F

FAST (class in fast.sampling.rankings) fast.analysis.contacts module fast.analysis.distances module fast.analysis.minimize module fast.analysis.pockets module fast.analysis.rmsd module fast.md_gen.gromax module fast.msm_gen.clustering module

fast.msm_gen.save_states module fast.sampling.core module fast.sampling.rankings module fast.sampling.scalings module fast.submissions.lsf_subs module fast.submissions.os_sub module fast.submissions.slurm_subs module feature_scale (class in fast.sampling.scalings)

G

generate_aij() (in module fast.sampling.rankings) get_running_jobs() (in module fast.submissions.lsf_subs) (in module fast.submissions.slurm_subs) get_submission_names() (fast.submissions.lsf_subs.LSFWrap method) (fast.submissions.os_sub.OSWrap method) (fast.submissions.slurm_subs.SlurmWrap method)

get_unique_states() (in module fast.sampling.rankings) Gromax (class in fast.md_gen.gromax) GromaxProcessing (class in fast.md_gen.gromax)

L

load_domain_indices() (in module fast.analysis.distances) load_trjs() (in module fast.msm_gen.clustering)

LSFSub (class in fast.submissions.lsf_subs) LSFWrap (class in fast.submissions.lsf_subs)

M

minimize_energies() (in module fast.analysis.minimize) MinimizeWrap (class in fast.analysis.minimize) module fast.analysis.contacts fast.analysis.distances fast.analysis.minimize fast.analysis.pockets fast.analysis.rmsd fast.md_gen.gromax fast.msm_gen.clustering fast.msm_gen.save_states fast.sampling.core fast.sampling.rankings fast.sampling.scalings fast.submissions.lsf_subs fast.submissions.os_sub fast.submissions.slurm_subs

O

OSWrap (class in fast.submissions.os_sub)

P

page_ranking (class in fast.sampling.rankings) parse_logs_for_energies() (in module fast.analysis.minimize) parse_pockets() (fast.analysis.pockets.ResiduePockets method) (fast.analysis.pockets.TopPockets method)

PocketWrap (class in fast.analysis.pockets) print_parameters() (fast.sampling.core.AdaptiveSampling method) push_forward() (in module fast.sampling.core)

R

rank() (fast.sampling.rankings.counts method) (fast.sampling.rankings.evens method) (fast.sampling.rankings.FAST method) (fast.sampling.rankings.page_ranking method) (fast.sampling.rankings.string method) rank_aij() (in module fast.sampling.rankings) ResiduePockets (class in fast.analysis.pockets) RMSDWrap (class in fast.analysis.rmsd) run() (fast.analysis.contacts.ContactsWrap method) (fast.analysis.distances.DistWrap method) (fast.analysis.minimize.MinimizeWrap method) (fast.analysis.pockets.PocketWrap method) (fast.analysis.rmsd.RMSDWrap method) (fast.md_gen.gromax.Gromax method) (fast.md_gen.gromax.GromaxProcessing method) (fast.msm_gen.clustering.ClusterWrap method) (fast.msm_gen.save_states.SaveWrap method) (fast.sampling.core.AdaptiveSampling method) (fast.submissions.lsf_subs.LSFSub method) (fast.submissions.os_sub.SPSub method) (fast.submissions.slurm_subs.SlurmSub method)

S

save_pocket_elements() (in module fast.analysis.pockets) save_states() (in module fast.msm_gen.save_states) SaveWrap (class in fast.msm_gen.save_states) scale() (fast.sampling.scalings.feature_scale method) (fast.sampling.scalings.sigmoid_scale method) select_states() (fast.sampling.rankings.base_ranking method) (fast.sampling.rankings.evens method)

set_filenames() (fast.msm_gen.clustering.ClusterWrap method) setup_run() (fast.md_gen.gromax.Gromax method) sigmoid_scale (class in fast.sampling.scalings) SlurmSub (class in fast.submissions.slurm_subs) SlurmWrap (class in fast.submissions.slurm_subs) SPSub (class in fast.submissions.os_sub) string (class in fast.sampling.rankings)

T

TopPockets (class in fast.analysis.pockets)

W

wait_for_pids() (fast.submissions.lsf_subs.LSFWrap method) (fast.submissions.os_sub.OSWrap method) (fast.submissions.slurm_subs.SlurmWrap method)