Toggle navigation

repository

Index

A

angast (CTF attribute) append_micrograph_id() (MetaDB.Session method) append_twodclasses_id() (MetaDB.Session method)

avgrot (AVGROT attribute) AVGROT (class in pyp.streampyp.metadb_daemon) avgrot_noastig (AVGROT attribute)

B

BOXX (class in pyp.streampyp.metadb_daemon)

C

cat() (in module pyp.utils) (in module pyp.utils.core) cc (CTF attribute) ccc (CTF attribute) cccc (CTF attribute) clear_scratch() (in module pyp.system.utils) cls (BOXX attribute) count() (MetaDB.Micrographs method) (MetaDB.TwoDClassesCollection method)

count_micrographs() (MetaDB.Session method) counts (CTF attribute) create() (MetaDB.Micrograph method) (MetaDB.Session method) (MetaDB.TwoDClasses method) CTF (class in pyp.streampyp.metadb_daemon) ctf_fit (AVGROT attribute) ctime() (in module pyp.system.utils)

D

delete_all() (MetaDB.Micrographs method) (MetaDB.TwoDClassesCollection method)

df1 (CTF attribute) df2 (CTF attribute)

E

eman_load_command() (in module pyp.system.utils) emit() (MongoHandler method)

exists() (MetaDB.Micrograph method) (MetaDB.Session method) (MetaDB.TwoDClasses method)

F

flatten() (in module pyp.utils) (in module pyp.utils.core)

format() (MongoFormatter method) freq (AVGROT attribute)

G

get() (MetaDB.Micrographs method) (MetaDB.Sessions method) (MetaDB.TwoDClassesCollection method) get_avgrot() (MetaDB.Micrograph method) get_bfactor_path() (in module pyp.system.utils) get_bm4d_path() (in module pyp.system.utils) get_boxx() (MetaDB.Micrograph method) get_bsoft_path() (in module pyp.system.utils) get_csp_path() (in module pyp.system.utils) get_ctf() (MetaDB.Micrograph method) get_ctffind4_path() (in module pyp.system.utils) get_ctffind_tilt_path() (in module pyp.system.utils) get_embfactor_path() (in module pyp.system.utils) get_frealign_paths() (in module pyp.system.utils) get_imod_path() (in module pyp.system.utils) get_micrograph_ids() (MetaDB.Session method)

get_multirun_path() (in module pyp.system.utils) get_parameter_files_path() (in module pyp.system.utils) get_project_root() (in module pyp.utils.core) get_pyp_config() (MetaDB.Session method) get_relative_path() (in module pyp.utils.core) get_relion_path() (in module pyp.system.utils) get_shell_multirun_path() (in module pyp.system.utils) get_slurm_path() (in module pyp.system.utils) get_src_path() (in module pyp.utils.core) get_summovie_path() (in module pyp.system.utils) get_tomo_path() (in module pyp.system.utils) get_tomoctf_path() (in module pyp.system.utils) get_twodclasses_ids() (MetaDB.Session method) get_unblur2_path() (in module pyp.system.utils) get_unblur_path() (in module pyp.system.utils) get_updated() (MetaDB.Session method) get_xf() (MetaDB.Micrograph method)

H

h (BOXX attribute)

has_files() (in module pyp.utils.core)

I

imod_load_command() (in module pyp.system.utils) in_bounds (BOXX attribute) is_atrf() (in module pyp.system.utils)

is_atrf_bad() (in module pyp.system.utils) is_biowulf2() (in module pyp.system.utils) is_dcc() (in module pyp.system.utils)

L

logger() (Timer method)

M

magnification (CTF attribute) makedirs_list() (in module pyp.utils.core) mat00 (XF attribute) mat01 (XF attribute) mat10 (XF attribute) mat11 (XF attribute) mean_df (CTF attribute) MetaDB (class in pyp.streampyp.metadb_daemon) MetaDB.Micrograph (class in pyp.streampyp.metadb_daemon) MetaDB.Micrographs (class in pyp.streampyp.metadb_daemon) MetaDB.Session (class in pyp.streampyp.metadb_daemon) MetaDB.Sessions (class in pyp.streampyp.metadb_daemon) MetaDB.TwoDClasses (class in pyp.streampyp.metadb_daemon) MetaDB.TwoDClassesCollection (class in pyp.streampyp.metadb_daemon) micrograph() (MetaDB.Session method) module pyp pyp.analysis pyp.analysis.geometry.transformations pyp.inout pyp.refine pyp.refine.csp pyp.refine.eman pyp.refine.frealign pyp.refine.relion pyp.refine.tomo_avg pyp.stream pyp.streampyp pyp.streampyp.metadb_daemon pyp.system pyp.system.mongo_handler pyp.system.utils pyp.utils pyp.utils.core pyp.utils.timer

MongoFormatter (class in pyp.system.mongo_handler) MongoHandler (class in pyp.system.mongo_handler) movie2regex() (in module pyp.utils.core)

N

name (Timer attribute)

noise (AVGROT attribute)

O

open() (in module pyp.streampyp.metadb_daemon)

P

phenix_load_command() (in module pyp.system.utils) pixel_size (CTF attribute) pyp module pyp.analysis module pyp.analysis.geometry.transformations module pyp.inout module pyp.refine module pyp.refine.csp module pyp.refine.eman module pyp.refine.frealign module pyp.refine.relion module

pyp.refine.tomo_avg module pyp.stream module pyp.streampyp module pyp.streampyp.metadb_daemon module pyp.system module pyp.system.mongo_handler module pyp.system.utils module pyp.utils module pyp.utils.core module pyp.utils.timer module

Q

qos() (in module pyp.system.utils)

quality_fit (AVGROT attribute)

S

session() (MetaDB method) set_avgrot() (MetaDB.Micrograph method) set_boxx() (MetaDB.Micrograph method) set_ctf() (MetaDB.Micrograph method) set_micrograph_ids() (MetaDB.Session method) set_pyp_config() (MetaDB.Session method)

set_twodclasses_ids() (MetaDB.Session method) set_updated_now() (MetaDB.Session method) set_xf() (MetaDB.Micrograph method) start() (Timer method) stop() (Timer method) symlink_force() (in module pyp.utils.core) symlink_relative() (in module pyp.utils.core)

T

text (Timer attribute) timeout_command() (in module pyp.system.utils) Timer (class in pyp.utils.timer)

TimerError timers (Timer attribute) to() (MongoHandler class method) twodclasses() (MetaDB.Session method)

U

update() (MetaDB.Micrographs method) (MetaDB.Sessions method) (MetaDB.TwoDClassesCollection method)

V

voltage (CTF attribute)

W

w (BOXX attribute) write() (MetaDB.Micrographs method) (MetaDB.Sessions method) (MetaDB.TwoDClassesCollection method)

X

x (BOXX attribute) (CTF attribute) (XF attribute)

XF (class in pyp.streampyp.metadb_daemon)

Y

y (BOXX attribute) (CTF attribute) (XF attribute)

Z

z (CTF attribute)