EVcouplings
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Alignment
Couplings Analysis
Folding Analysis
Visualization
Utilities
EVcouplings
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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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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
A
AClusterSubmitter (class in evcouplings.utils.batch)
add_distances() (in module evcouplings.compare.ecs)
add_precision() (in module evcouplings.compare.ecs)
aggregate() (evcouplings.compare.distances.DistanceMap class method)
alignment (evcouplings.align.tools.HmmsearchResult attribute)
(evcouplings.align.tools.JackhmmerResult attribute)
alignment_index_mapping() (in module evcouplings.compare.mapping)
apc() (evcouplings.couplings.model.CouplingsModel class method)
APluginRegister (class in evcouplings.utils.batch)
ASubmitter (class in evcouplings.utils.batch)
B
best_hit() (in module evcouplings.complex.protocol)
by_alignment() (evcouplings.compare.sifts.SIFTS method)
by_pdb_id() (evcouplings.compare.sifts.SIFTS method)
by_uniprot_id() (evcouplings.compare.sifts.SIFTS method)
C
CANCEL (evcouplings.utils.batch.EJob attribute)
cancel() (evcouplings.utils.batch.AClusterSubmitter method)
(evcouplings.utils.batch.ASubmitter method)
(evcouplings.utils.batch.LocalSubmitter method)
cancel_command (evcouplings.utils.batch.AClusterSubmitter attribute)
(evcouplings.utils.batch.LSFSubmitter attribute)
(evcouplings.utils.batch.SGESubmitter attribute)
(evcouplings.utils.batch.SlurmSubmitter attribute)
Chain (class in evcouplings.compare.pdb)
check_required() (in module evcouplings.utils.config)
ClassicPDB (class in evcouplings.compare.pdb)
close() (evcouplings.utils.helpers.PersistentDict method)
cn() (evcouplings.couplings.model.CouplingsModel method)
cn_scores (evcouplings.couplings.model.CouplingsModel attribute)
Command (class in evcouplings.utils.batch)
complex() (in module evcouplings.align.protocol)
(in module evcouplings.mutate.protocol)
contacts() (evcouplings.compare.distances.DistanceMap method)
convert_sequences() (evcouplings.couplings.model.CouplingsModel method)
coupling_scores_compared() (in module evcouplings.compare.ecs)
CouplingsModel (class in evcouplings.couplings.model)
create_family_size_table() (in module evcouplings.align.pfam)
create_prefix_folders() (in module evcouplings.utils.system)
create_sequence_file() (evcouplings.compare.sifts.SIFTS method)
cut_sequence() (in module evcouplings.align.protocol)
D
db (evcouplings.utils.batch.AClusterSubmitter attribute)
(evcouplings.utils.batch.LSFSubmitter attribute)
(evcouplings.utils.batch.SGESubmitter attribute)
(evcouplings.utils.batch.SlurmSubmitter attribute)
default_chain_name() (evcouplings.couplings.mapping.Segment method)
DefaultOrderedDict (class in evcouplings.utils.helpers)
delta_hamiltonian() (evcouplings.couplings.model.CouplingsModel method)
describe_concatenation() (in module evcouplings.complex.protocol)
describe_coverage() (in module evcouplings.align.protocol)
describe_frequencies() (in module evcouplings.align.protocol)
describe_seq_identities() (in module evcouplings.align.protocol)
detect_secstruct_clash() (in module evcouplings.fold.filter)
dihedral_angle() (in module evcouplings.utils.calculations)
dist() (evcouplings.compare.distances.DistanceMap method)
DistanceMap (class in evcouplings.compare.distances)
disulfide_clashes() (in module evcouplings.fold.filter)
dmm() (evcouplings.couplings.model.CouplingsModel method)
docking_restraints() (in module evcouplings.fold.restraints)
domtblout (evcouplings.align.tools.HmmscanResult attribute)
(evcouplings.align.tools.HmmsearchResult attribute)
(evcouplings.align.tools.JackhmmerResult attribute)
double_mut_mat (evcouplings.couplings.model.CouplingsModel attribute)
download_ftp_file() (in module evcouplings.utils.update_database)
dump() (evcouplings.utils.helpers.PersistentDict method)
E
ec_dist_restraints() (in module evcouplings.fold.restraints)
ecs (evcouplings.couplings.model.CouplingsModel attribute)
EJob (class in evcouplings.utils.batch)
entropy() (in module evcouplings.utils.calculations)
entropy_map() (in module evcouplings.utils.calculations)
entropy_vector() (in module evcouplings.utils.calculations)
EResource (in module evcouplings.utils.batch)
EStatus (in module evcouplings.utils.batch)
evcouplings.align.pfam (module)
evcouplings.align.protocol (module)
evcouplings.align.tools (module)
evcouplings.compare.distances (module)
evcouplings.compare.ecs (module)
evcouplings.compare.mapping (module)
evcouplings.compare.pdb (module)
evcouplings.compare.sifts (module)
evcouplings.complex.protocol (module)
evcouplings.couplings.mapping (module)
evcouplings.couplings.model (module)
evcouplings.fold.filter (module)
evcouplings.fold.restraints (module)
evcouplings.fold.tools (module)
evcouplings.mutate.calculations (module)
evcouplings.mutate.protocol (module)
evcouplings.utils.batch (module)
evcouplings.utils.calculations (module)
evcouplings.utils.config (module)
evcouplings.utils.constants (module)
evcouplings.utils.helpers (module)
evcouplings.utils.system (module)
evcouplings.utils.update_database (module)
existing() (in module evcouplings.align.protocol)
ExternalToolError
extract_header_annotation() (in module evcouplings.align.protocol)
extract_mutations() (in module evcouplings.mutate.calculations)
F
fetch_sequence() (in module evcouplings.align.protocol)
fetch_uniprot_mapping() (in module evcouplings.compare.sifts)
fi() (evcouplings.couplings.model.CouplingsModel method)
fij() (evcouplings.couplings.model.CouplingsModel method)
filter_atoms() (evcouplings.compare.pdb.Chain method)
filter_positions() (evcouplings.compare.pdb.Chain method)
find_homologs() (in module evcouplings.compare.sifts)
find_segments() (in module evcouplings.utils.helpers)
fn() (evcouplings.couplings.model.CouplingsModel method)
fn_scores (evcouplings.couplings.model.CouplingsModel attribute)
from_coords() (evcouplings.compare.distances.DistanceMap class method)
from_file() (evcouplings.compare.distances.DistanceMap class method)
(evcouplings.compare.pdb.ClassicPDB class method)
(evcouplings.compare.pdb.PDB class method)
from_files() (evcouplings.compare.distances.DistanceMap class method)
from_id() (evcouplings.compare.pdb.ClassicPDB class method)
(evcouplings.compare.pdb.PDB class method)
from_list() (evcouplings.couplings.mapping.Segment class method)
G
genome_distance() (in module evcouplings.complex.protocol)
get() (in module evcouplings.utils.system)
get_chain() (evcouplings.compare.pdb.ClassicPDB method)
(evcouplings.compare.pdb.PDB method)
get_urllib() (in module evcouplings.utils.system)
H
hamiltonians() (evcouplings.couplings.model.CouplingsModel method)
hi() (evcouplings.couplings.model.CouplingsModel method)
hmmbuild_and_search() (in module evcouplings.align.protocol)
HmmbuildResult (class in evcouplings.align.tools)
hmmfile (evcouplings.align.tools.HmmbuildResult attribute)
HmmscanResult (class in evcouplings.align.tools)
HmmsearchResult (class in evcouplings.align.tools)
I
index_list (evcouplings.couplings.model.CouplingsModel attribute)
insert_dir() (in module evcouplings.utils.system)
inter_dists() (in module evcouplings.compare.distances)
intra_dists() (in module evcouplings.compare.distances)
InvalidParameterError
isBlocking (evcouplings.utils.batch.ASubmitter attribute)
(evcouplings.utils.batch.LSFSubmitter attribute)
(evcouplings.utils.batch.LocalSubmitter attribute)
(evcouplings.utils.batch.SGESubmitter attribute)
(evcouplings.utils.batch.SlurmSubmitter attribute)
iterate_files() (in module evcouplings.utils.config)
itu() (evcouplings.couplings.model.CouplingsModel method)
J
jackhmmer_search() (in module evcouplings.align.protocol)
JackhmmerResult (class in evcouplings.align.tools)
Jij() (evcouplings.couplings.model.CouplingsModel method)
job_id_pattern (evcouplings.utils.batch.AClusterSubmitter attribute)
(evcouplings.utils.batch.LSFSubmitter attribute)
(evcouplings.utils.batch.SGESubmitter attribute)
(evcouplings.utils.batch.SlurmSubmitter attribute)
join() (evcouplings.utils.batch.AClusterSubmitter method)
(evcouplings.utils.batch.ASubmitter method)
(evcouplings.utils.batch.LocalSubmitter method)
L
load() (evcouplings.utils.helpers.PersistentDict method)
load_structures() (in module evcouplings.compare.pdb)
LocalSubmitter (class in evcouplings.utils.batch)
LSFSubmitter (class in evcouplings.utils.batch)
M
makedirs() (in module evcouplings.utils.system)
map_indices() (in module evcouplings.compare.mapping)
median_absolute_deviation() (in module evcouplings.utils.calculations)
mi_apc() (evcouplings.couplings.model.CouplingsModel method)
mi_raw() (evcouplings.couplings.model.CouplingsModel method)
mi_scores_apc (evcouplings.couplings.model.CouplingsModel attribute)
mi_scores_raw (evcouplings.couplings.model.CouplingsModel attribute)
MissingParameterError
mn() (evcouplings.couplings.model.CouplingsModel method)
modify_alignment() (in module evcouplings.align.protocol)
modify_complex_segments() (in module evcouplings.complex.protocol)
MONITOR (evcouplings.utils.batch.EJob attribute)
monitor() (evcouplings.utils.batch.AClusterSubmitter method)
(evcouplings.utils.batch.ASubmitter method)
(evcouplings.utils.batch.LocalSubmitter method)
monitor_command (evcouplings.utils.batch.AClusterSubmitter attribute)
(evcouplings.utils.batch.LSFSubmitter attribute)
(evcouplings.utils.batch.SGESubmitter attribute)
(evcouplings.utils.batch.SlurmSubmitter attribute)
mui() (evcouplings.couplings.model.CouplingsModel method)
multimer_dists() (in module evcouplings.compare.distances)
MultiSegmentCouplingsModel (class in evcouplings.couplings.mapping)
N
name (evcouplings.utils.batch.ASubmitter attribute)
(evcouplings.utils.batch.LSFSubmitter attribute)
(evcouplings.utils.batch.LocalSubmitter attribute)
(evcouplings.utils.batch.SGESubmitter attribute)
(evcouplings.utils.batch.SlurmSubmitter attribute)
O
output (evcouplings.align.tools.HmmbuildResult attribute)
(evcouplings.align.tools.HmmscanResult attribute)
(evcouplings.align.tools.HmmsearchResult attribute)
(evcouplings.align.tools.JackhmmerResult attribute)
P
parse_config() (in module evcouplings.utils.config)
parse_maxcluster_clustering() (in module evcouplings.fold.tools)
parse_maxcluster_comparison() (in module evcouplings.fold.tools)
patch_model() (evcouplings.couplings.mapping.SegmentIndexMapper method)
PDB (class in evcouplings.compare.pdb)
PersistentDict (class in evcouplings.utils.helpers)
pfam_hits() (in module evcouplings.align.pfam)
pfamtblout (evcouplings.align.tools.HmmscanResult attribute)
PID (evcouplings.utils.batch.EJob attribute)
predict_mutation_table() (in module evcouplings.mutate.calculations)
prefix (evcouplings.align.tools.HmmbuildResult attribute)
(evcouplings.align.tools.HmmscanResult attribute)
(evcouplings.align.tools.HmmsearchResult attribute)
(evcouplings.align.tools.JackhmmerResult attribute)
Progressbar (class in evcouplings.utils.helpers)
R
range_overlap() (in module evcouplings.utils.helpers)
read_config_file() (in module evcouplings.utils.config)
read_hmmer_domtbl() (in module evcouplings.align.tools)
read_hmmer_tbl() (in module evcouplings.align.tools)
read_psipred_prediction() (in module evcouplings.fold.tools)
registry (evcouplings.utils.batch.ASubmitter attribute)
remap() (evcouplings.compare.pdb.Chain method)
remap_chains() (in module evcouplings.compare.distances)
remap_complex_chains() (in module evcouplings.compare.distances)
remove_clan_overlaps() (in module evcouplings.align.pfam)
render_template() (in module evcouplings.utils.helpers)
resource_flags (evcouplings.utils.batch.AClusterSubmitter attribute)
(evcouplings.utils.batch.LSFSubmitter attribute)
(evcouplings.utils.batch.SGESubmitter attribute)
(evcouplings.utils.batch.SlurmSubmitter attribute)
ResourceError
retry() (in module evcouplings.utils.helpers)
run() (in module evcouplings.align.protocol)
(in module evcouplings.complex.protocol)
(in module evcouplings.mutate.protocol)
(in module evcouplings.utils.system)
(in module evcouplings.utils.update_database)
run_cns() (in module evcouplings.fold.tools)
run_cns_13() (in module evcouplings.fold.tools)
run_hhfilter() (in module evcouplings.align.tools)
run_hmmbuild() (in module evcouplings.align.tools)
run_hmmscan() (in module evcouplings.align.tools)
run_hmmsearch() (in module evcouplings.align.tools)
run_jackhmmer() (in module evcouplings.align.tools)
run_maxcluster_cluster() (in module evcouplings.fold.tools)
run_maxcluster_compare() (in module evcouplings.fold.tools)
run_psipred() (in module evcouplings.fold.tools)
S
search_thresholds() (in module evcouplings.align.protocol)
secstruct_angle_restraints() (in module evcouplings.fold.restraints)
secstruct_clashes() (in module evcouplings.fold.filter)
secstruct_dist_restraints() (in module evcouplings.fold.restraints)
Segment (class in evcouplings.couplings.mapping)
segment_map_ecs() (in module evcouplings.couplings.mapping)
SegmentIndexMapper (class in evcouplings.couplings.mapping)
seq() (evcouplings.couplings.model.CouplingsModel method)
SGESubmitter (class in evcouplings.utils.batch)
SIFTS (class in evcouplings.compare.sifts)
SIFTSResult (class in evcouplings.compare.sifts)
single_mut_mat (evcouplings.couplings.model.CouplingsModel attribute)
single_mut_mat_full (evcouplings.couplings.model.CouplingsModel attribute)
single_mutant_matrix() (in module evcouplings.mutate.calculations)
SlurmSubmitter (class in evcouplings.utils.batch)
smm() (evcouplings.couplings.model.CouplingsModel method)
sn() (evcouplings.couplings.model.CouplingsModel method)
split_mutants() (in module evcouplings.mutate.calculations)
standard() (in module evcouplings.align.protocol)
(in module evcouplings.mutate.protocol)
STOP (evcouplings.utils.batch.EJob attribute)
structure_coverage() (evcouplings.compare.distances.DistanceMap method)
SUBMIT (evcouplings.utils.batch.EJob attribute)
submit() (evcouplings.utils.batch.AClusterSubmitter method)
(evcouplings.utils.batch.ASubmitter method)
(evcouplings.utils.batch.LocalSubmitter method)
submit_command (evcouplings.utils.batch.LSFSubmitter attribute)
(evcouplings.utils.batch.SGESubmitter attribute)
(evcouplings.utils.batch.SlurmSubmitter attribute)
submit_command() (evcouplings.utils.batch.AClusterSubmitter method)
symlink_force() (in module evcouplings.utils.update_database)
sync() (evcouplings.utils.helpers.PersistentDict method)
T
target_seq (evcouplings.couplings.model.CouplingsModel attribute)
tblout (evcouplings.align.tools.HmmscanResult attribute)
(evcouplings.align.tools.HmmsearchResult attribute)
(evcouplings.align.tools.JackhmmerResult attribute)
temp() (in module evcouplings.utils.system)
tempdir() (in module evcouplings.utils.system)
to_file() (evcouplings.compare.distances.DistanceMap method)
(evcouplings.compare.pdb.Chain method)
(evcouplings.couplings.model.CouplingsModel method)
to_independent_model() (evcouplings.couplings.model.CouplingsModel method)
to_inter_segment_model() (evcouplings.couplings.mapping.MultiSegmentCouplingsModel method)
to_list() (evcouplings.couplings.mapping.Segment method)
to_model() (evcouplings.couplings.mapping.SegmentIndexMapper method)
to_seqres() (evcouplings.compare.pdb.Chain method)
to_target() (evcouplings.couplings.mapping.SegmentIndexMapper method)
transpose() (evcouplings.compare.distances.DistanceMap method)
U
UPDATE (evcouplings.utils.batch.EJob attribute)
update() (evcouplings.utils.helpers.Progressbar method)
V
valid_file() (in module evcouplings.utils.system)
verify_resources() (in module evcouplings.utils.system)
W
wrap() (in module evcouplings.utils.helpers)
write_config_file() (in module evcouplings.utils.config)
write_file() (in module evcouplings.utils.system)
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