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A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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X
A
add() (worms.database.SpliceDB method)
alignment() (worms.criteria.base.NullCriteria method)
(worms.criteria.bounded.AxesIntersect method)
(worms.criteria.cyclic.Cyclic method)
(worms.criteria.unbounded.AxesAngle method)
allowed_attributes (worms.criteria.base.WormCriteria attribute)
,
[1]
allowed_pairs (worms.segments.Spliceable attribute)
angle (worms.criteria.bounded.AxesIntersect attribute)
AnnoPose (class in worms.pose_contortions)
AxesAngle (class in worms.criteria.unbounded)
AxesIntersect (class in worms.criteria.bounded)
B
BBlock() (in module worms.bblock)
bblock() (worms.database.BBlockDB method)
bblock_components() (in module worms.bblock)
bblock_dump_pdb() (in module worms.bblock)
bblock_str() (in module worms.bblock)
BBlockDB (class in worms.database)
bblockfile() (worms.database.BBlockDB method)
bigprod() (in module worms.util)
body (worms.segments.Spliceable attribute)
bodyid (worms.segments.Segment attribute)
(worms.segments.Spliceable attribute)
build_pdb_data() (worms.database.BBlockDB method)
C
cachepath() (worms.database.SpliceDB method)
cgo_cyl() (in module worms.vis)
cgo_lineabs() (in module worms.vis)
cgo_segment() (in module worms.vis)
cgo_sphere() (in module worms.vis)
chain (worms.segments.SpliceSite attribute)
chain_of_ires (in module worms.bblock)
chains (worms.segments.Spliceable attribute)
check_lock_cachedir() (worms.database.BBlockDB method)
children (worms.criteria.base.CriteriaList attribute)
clear_caches() (worms.segments.Worms method)
contig_idx_breaks (in module worms.util)
contort_pose_chains() (in module worms.pose_contortions)
cpu_count() (in module worms.util)
criteria (worms.segments.Worms attribute)
CriteriaList (class in worms.criteria.base)
Crystal_F432_C3_C4() (in module worms.criteria.unbounded)
Crystal_I213_C2_C3() (in module worms.criteria.unbounded)
Crystal_I432_C2_C4() (in module worms.criteria.unbounded)
Crystal_P213_C3_C3() (in module worms.criteria.unbounded)
Crystal_P4132_C2_C3() (in module worms.criteria.unbounded)
Crystal_P432_C4_C4() (in module worms.criteria.unbounded)
crystinfo() (worms.criteria.unbounded.AxesAngle method)
Cyclic (class in worms.criteria.cyclic)
cyclic_entry (worms.pose_contortions.AnnoPose attribute)
CyclicTrim (class in worms.pose_contortions)
D
D2() (in module worms.criteria.bounded)
D3() (in module worms.criteria.bounded)
D4() (in module worms.criteria.bounded)
D5() (in module worms.criteria.bounded)
D6() (in module worms.criteria.bounded)
detail (worms.segments.Worms attribute)
dicts_to_items() (in module worms.util)
distinct_axes (worms.criteria.bounded.AxesIntersect attribute)
E
Edge() (in module worms.edge)
end_of_chain (worms.segments.Spliceable attribute)
entrypol (worms.segments.Segment attribute)
entryresid (worms.segments.Segment attribute)
entrysiteid (worms.segments.Segment attribute)
exitpol (worms.segments.Segment attribute)
exitresid (worms.segments.Segment attribute)
exitsiteid (worms.segments.Segment attribute)
expand_array_if_needed (in module worms.util)
expert (worms.segments.Segment attribute)
F
first_duplicate() (in module worms.util)
flatten_path() (in module worms.database)
format_atom() (in module worms.vis)
from_seg (worms.criteria.base.NullCriteria attribute)
(worms.criteria.bounded.AxesIntersect attribute)
G
get (worms.data.PoseLib attribute)
get_allowed_splices() (in module worms.edge)
get_bb_coords() (in module worms.util)
get_bb_stubs() (in module worms.util)
get_chain_bounds() (in module worms.util)
get_symdata (in module worms.util)
get_symdata_modified() (in module worms.util)
get_symfile_contents (in module worms.util)
H
hash_str_to_int() (in module worms.util)
I
Icosahedral() (in module worms.criteria.bounded)
index() (worms.segments.Segments method)
indices (worms.segments.Worms attribute)
infer_cyclic_symmetry() (in module worms.util)
init_segment_data() (worms.segments.Segment method)
InProcessExecutor (class in worms.util)
is_compatible() (worms.segments.Spliceable method)
is_rosetta_pose() (in module worms.vis)
iseg (worms.pose_contortions.AnnoPose attribute)
islocked_cachedir() (worms.database.BBlockDB method)
items_to_dicts() (in module worms.util)
J
jit_lossfunc() (worms.criteria.base.NullCriteria method)
(worms.criteria.cyclic.Cyclic method)
L
len (worms.util.MultiRange attribute)
lever (worms.criteria.bounded.AxesIntersect attribute)
lineno() (in module worms.segments)
load_cached_bblock_into_memory() (worms.database.BBlockDB method)
load_cached_pose_into_memory() (worms.database.BBlockDB method)
load_from_pdbs() (worms.database.BBlockDB method)
load_from_pdbs_inner() (worms.database.BBlockDB method)
lock_cachedir() (worms.database.BBlockDB method)
M
make_contorted_pose() (in module worms.pose_contortions)
make_head() (worms.segments.Segment method)
make_pose_chains() (worms.segments.Segment method)
make_tail() (worms.segments.Segment method)
map() (worms.util.InProcessExecutor method)
max_sites (worms.segments.Segment attribute)
merge_idx() (worms.segments.Segment method)
merge_idx_slow() (worms.segments.Segment method)
min_seg_len (worms.segments.Spliceable attribute)
min_sites (worms.segments.Segment attribute)
MultiRange (class in worms.util)
N
nchains (worms.segments.Segment attribute)
no_overlapping_adjacent_residues() (in module worms.util)
no_overlapping_residues() (in module worms.util)
NonFuture (class in worms.util)
nside (worms.util.MultiRange attribute)
nsite (worms.segments.Spliceable attribute)
NullCriteria (class in worms.criteria.base)
numcom (in module worms.vis)
numline (in module worms.vis)
numpy_stub_from_rosetta_stub() (in module worms.util)
numray (in module worms.vis)
numseg (in module worms.vis)
numvec (in module worms.vis)
O
Octahedral() (in module worms.criteria.bounded)
P
parallel_batch_map() (in module worms.util)
parallel_nobatch_map() (in module worms.util)
partial() (worms.database.SpliceDB method)
polarity (worms.segments.SpliceSite attribute)
pose (worms.pose_contortions.AnnoPose attribute)
pose() (worms.database.BBlockDB method)
(worms.segments.Worms method)
pose_bounds() (in module worms.util)
posefile() (worms.database.BBlockDB method)
PoseLib (class in worms.data)
positions (worms.segments.Worms attribute)
psum (worms.util.MultiRange attribute)
pymol_load() (in module worms.vis)
pymol_load_pose() (in module worms.vis)
pymol_xform() (in module worms.vis)
Q
query() (worms.database.BBlockDB method)
query_names() (worms.database.BBlockDB method)
R
random() (in module worms.search)
reorder_spliced_as_N_to_C() (in module worms.pose_contortions)
resid() (worms.segments.SpliceSite method)
resids() (worms.segments.Spliceable method)
residue_coords() (in module worms.util)
residue_sym_err() (in module worms.util)
result() (worms.util.NonFuture method)
rosetta_stub_from_numpy_stub() (in module worms.util)
rot_tol (worms.criteria.bounded.AxesIntersect attribute)
S
same_bodies_as() (worms.segments.Segment method)
score() (worms.criteria.base.CriteriaList method)
(worms.criteria.base.NullCriteria method)
(worms.criteria.base.WormCriteria method)
(worms.criteria.bounded.AxesIntersect method)
(worms.criteria.cyclic.Cyclic method)
(worms.criteria.unbounded.AxesAngle method)
score0 (worms.segments.Worms attribute)
score0sym (worms.segments.Worms attribute)
scores (worms.segments.Worms attribute)
Segment (class in worms.segments)
Segments (class in worms.segments)
segments (worms.segments.Segments attribute)
(worms.segments.Worms attribute)
selections (worms.segments.SpliceSite attribute)
seq() (worms.pose_contortions.AnnoPose method)
Sheet_P321() (in module worms.criteria.unbounded)
Sheet_P4212() (in module worms.criteria.unbounded)
Sheet_P6() (in module worms.criteria.unbounded)
show_with_axis() (in module worms.vis)
show_with_z_axes() (in module worms.vis)
showcom() (in module worms.vis)
showcyl() (in module worms.vis)
showline() (in module worms.vis)
showlineabs() (in module worms.vis)
showme() (in module worms.vis)
showme_pymol() (in module worms.vis)
showme_state (in module worms.vis)
showsegment() (in module worms.vis)
showsphere() (in module worms.vis)
showvecfrompoint() (in module worms.vis)
sitepair_allowed() (worms.segments.Spliceable method)
sites (worms.segments.Spliceable attribute)
splice_metrics_pair() (in module worms.edge)
Spliceable (class in worms.segments)
spliceable_positions() (worms.segments.Spliceable method)
spliceables (worms.segments.Segment attribute)
SpliceDB (class in worms.database)
splicepoint_cache (worms.segments.Worms attribute)
splicepoints() (worms.segments.Worms method)
splices() (worms.segments.Worms method)
SpliceSite (class in worms.segments)
split_at() (worms.segments.Segments method)
split_idx() (worms.segments.Segment method)
src_lb (worms.pose_contortions.AnnoPose attribute)
src_ub (worms.pose_contortions.AnnoPose attribute)
srcpose (worms.pose_contortions.AnnoPose attribute)
srcseq() (worms.pose_contortions.AnnoPose method)
start_of_chain (worms.segments.Spliceable attribute)
submit() (worms.util.InProcessExecutor method)
subpose() (in module worms.util)
sym_axes (worms.criteria.bounded.AxesIntersect attribute)
sym_seg_from (worms.pose_contortions.CyclicTrim attribute)
sym_seg_to (worms.pose_contortions.CyclicTrim attribute)
symfile_modifiers() (worms.criteria.unbounded.AxesAngle method)
symfile_path() (in module worms.util)
symname (worms.criteria.bounded.AxesIntersect attribute)
sympose() (worms.segments.Worms method)
sync_to_disk() (worms.database.SpliceDB method)
T
Tetrahedral() (in module worms.criteria.bounded)
tgtaxis1 (worms.criteria.bounded.AxesIntersect attribute)
tgtaxis2 (worms.criteria.bounded.AxesIntersect attribute)
to_seg (worms.criteria.base.NullCriteria attribute)
(worms.criteria.bounded.AxesIntersect attribute)
tol (worms.criteria.bounded.AxesIntersect attribute)
tqdm_parallel_map() (in module worms.util)
trim_pose() (in module worms.util)
U
unique_key() (in module worms.util)
unique_key_int32s() (in module worms.util)
unlock_cachedir() (worms.database.BBlockDB method)
Ux (in module worms.criteria.base)
Uy (in module worms.criteria.base)
Uz (in module worms.criteria.base)
V
Vertex() (in module worms.vertex)
vertex_single() (in module worms.vertex)
W
WormCriteria (class in worms.criteria.base)
Worms (class in worms.segments)
worms (module)
worms.bblock (module)
worms.criteria (module)
worms.criteria.base (module)
worms.criteria.bounded (module)
worms.criteria.cyclic (module)
worms.criteria.unbounded (module)
worms.data (module)
worms.database (module)
worms.edge (module)
worms.khash (module)
worms.khash.khash_cffi (module)
worms.pose_contortions (module)
worms.search (module)
worms.segments (module)
worms.util (module)
worms.vertex (module)
worms.vis (module)
worst_CN_connect() (in module worms.util)
X
x2exit (worms.segments.Segment attribute)
x2orgn (worms.segments.Segment attribute)
xform_pose() (in module worms.util)
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