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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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W
A
A3mParser (class in conkit.io.a3m)
add_alignment_args() (in module conkit.command_line.conkit_predict)
add_contact_density_args() (in module conkit.command_line.conkit_plot)
add_contact_map_args() (in module conkit.command_line.conkit_plot)
add_contact_map_chord_args() (in module conkit.command_line.conkit_plot)
add_default_args() (in module conkit.command_line.conkit_predict)
add_precision_evaluation_args() (in module conkit.command_line.conkit_plot)
add_sequence_args() (in module conkit.command_line.conkit_predict)
add_sequence_coverage_args() (in module conkit.command_line.conkit_plot)
align_global() (Sequence method)
align_local() (Sequence method)
aligned (SequenceAlignmentState attribute)
AmiseBW (class in conkit.misc.bandwidth)
ascii_matrix (SequenceFile attribute)
assign_sequence_register() (ContactMap method)
ATOM (in module conkit.io.pdb)
author (ContactFile attribute)
B
bandwidth (AmiseBW attribute)
(BandwidthBase attribute)
(BowmanBW attribute)
(LinearBW attribute)
(ScottBW attribute)
(SilvermanBW attribute)
bandwidth_factory() (in module conkit.misc.bandwidth)
BandwidthBase (class in conkit.misc.bandwidth)
BbcontactsCommandline (class in conkit.applications.bbcontacts)
BbcontactsCommandline() (in module conkit.applications)
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[1]
BbcontactsParser (class in conkit.io.bbcontacts)
BCLContactParser (class in conkit.io.bclcontact)
BowmanBW (class in conkit.misc.bandwidth)
bw (BandwidthBase attribute)
bw_method (ContactDensityFigure attribute)
C
calculate_contact_density() (ContactMap method)
calculate_freq() (SequenceFile method)
calculate_jaccard_index() (ContactMap method)
calculate_kernel_density() (ContactMap method)
calculate_meff() (SequenceFile method)
calculate_neff_with_identity() (SequenceFile method)
calculate_scalar_score() (ContactMap method)
calculate_weights() (SequenceFile method)
CaspParser (class in conkit.io.casp)
CCMpredCommandline (class in conkit.applications.ccmpred)
CCMpredCommandline() (in module conkit.applications)
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[1]
CCMpredParser (class in conkit.io.ccmpred)
CdhitCommandline (class in conkit.applications.cdhit)
CdhitCommandline() (in module conkit.applications)
,
[1]
ComsatParser (class in conkit.io.comsat)
conkit (module)
conkit.applications (module)
,
[1]
conkit.applications.bbcontacts (module)
conkit.applications.ccmpred (module)
conkit.applications.cdhit (module)
conkit.applications.hhblits (module)
conkit.applications.hhfilter (module)
conkit.applications.jackhmmer (module)
conkit.applications.psicov (module)
conkit.command_line (module)
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[1]
conkit.command_line.conkit_convert (module)
conkit.command_line.conkit_msatool (module)
conkit.command_line.conkit_plot (module)
conkit.command_line.conkit_precision (module)
conkit.command_line.conkit_predict (module)
conkit.core (module)
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[1]
conkit.core.contact (module)
conkit.core.contactfile (module)
conkit.core.contactmap (module)
conkit.core.sequence (module)
conkit.core.sequencefile (module)
conkit.io (module)
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[1]
conkit.io.a3m (module)
conkit.io.bbcontacts (module)
conkit.io.bclcontact (module)
conkit.io.casp (module)
conkit.io.ccmpred (module)
conkit.io.comsat (module)
conkit.io.epcmap (module)
conkit.io.evfold (module)
conkit.io.fasta (module)
conkit.io.freecontact (module)
conkit.io.gremlin (module)
conkit.io.jones (module)
conkit.io.membrain (module)
conkit.io.ncont (module)
conkit.io.pcons (module)
conkit.io.pdb (module)
conkit.io.plmdca (module)
conkit.io.psicov (module)
conkit.io.stockholm (module)
conkit.misc (module)
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[1]
conkit.misc.bandwidth (module)
conkit.plot (module)
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[1]
conkit.plot.contactdensity (module)
conkit.plot.contactmap (module)
conkit.plot.contactmapchord (module)
conkit.plot.precisionevaluation (module)
conkit.plot.sequencecoverage (module)
conkit.version (module)
Contact (class in conkit.core.contact)
Contact() (in module conkit.core)
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[1]
ContactDensityFigure (class in conkit.plot.contactdensity)
ContactDensityFigure() (in module conkit.plot)
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[1]
ContactFile (class in conkit.core.contactfile)
ContactFile() (in module conkit.core)
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[1]
ContactMap (class in conkit.core.contactmap)
ContactMap() (in module conkit.core)
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[1]
ContactMapChordFigure (class in conkit.plot.contactmapchord)
ContactMapChordFigure() (in module conkit.plot)
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[1]
ContactMapFigure (class in conkit.plot.contactmap)
ContactMapFigure() (in module conkit.plot)
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[1]
ContactMatchState (class in conkit.core.contact)
ContactTemplate (in module conkit.io.casp)
convert() (in module conkit.io)
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[1]
coverage (ContactMap attribute)
curvature() (AmiseBW static method)
cutoff_step (PrecisionEvaluationFigure attribute)
D
define_match() (Contact method)
define_mismatch() (Contact method)
define_unknown() (Contact method)
distance_bound (Contact attribute)
E
empty (ContactMap attribute)
(SequenceFile attribute)
EPCMapParser (class in conkit.io.epcmap)
EVfoldParser (class in conkit.io.evfold)
extended_range() (AmiseBW static method)
F
FastaParser (class in conkit.io.fasta)
filter() (SequenceFile method)
find() (ContactMap method)
FreeContactParser (class in conkit.io.freecontact)
G
GenericStructureParser (class in conkit.io.pdb)
GremlinParser (class in conkit.io.gremlin)
H
HHblitsCommandline (class in conkit.applications.hhblits)
HHblitsCommandline() (in module conkit.applications)
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[1]
HHfilterCommandline (class in conkit.applications.hhfilter)
HHfilterCommandline() (in module conkit.applications)
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[1]
hierarchy (ContactDensityFigure attribute)
(ContactMapChordFigure attribute)
(ContactMapFigure attribute)
(PrecisionEvaluationFigure attribute)
(SequenceCoverageFigure attribute)
I
is_alignment (SequenceFile attribute)
is_match (Contact attribute)
is_mismatch (Contact attribute)
is_unknown (Contact attribute)
J
JackhmmerCommandline (class in conkit.applications.jackhmmer)
JackhmmerCommandline() (in module conkit.applications)
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[1]
JonesParser (class in conkit.io.jones)
L
LinearBW (class in conkit.misc.bandwidth)
long_range_contacts (ContactMap attribute)
lower_bound (Contact attribute)
M
main() (in module conkit.command_line.conkit_convert)
(in module conkit.command_line.conkit_msatool)
(in module conkit.command_line.conkit_plot)
(in module conkit.command_line.conkit_precision)
(in module conkit.command_line.conkit_predict)
match() (ContactMap method)
matched (ContactMatchState attribute)
max_cutoff (PrecisionEvaluationFigure attribute)
medium_range_contacts (ContactMap attribute)
MemBrainParser (class in conkit.io.membrain)
method (ContactFile attribute)
min_cutoff (PrecisionEvaluationFigure attribute)
mismatched (ContactMatchState attribute)
MmCifParser (class in conkit.io.pdb)
ModelTemplate (in module conkit.io.casp)
N
ncontacts (ContactMap attribute)
NcontParser (class in conkit.io.ncont)
neff (SequenceFile attribute)
nseq (SequenceFile attribute)
O
optimal_bandwidth_equation() (AmiseBW static method)
other (ContactMapFigure attribute)
P
PconsParser (class in conkit.io.pcons)
PdbParser (class in conkit.io.pdb)
PlmDCAParser (class in conkit.io.plmdca)
precision (ContactMap attribute)
PrecisionEvaluationFigure (class in conkit.plot.precisionevaluation)
PrecisionEvaluationFigure() (in module conkit.plot)
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[1]
PsicovCommandline (class in conkit.applications.psicov)
PsicovCommandline() (in module conkit.applications)
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[1]
PsicovParser (class in conkit.io.psicov)
R
raw_score (Contact attribute)
read() (A3mParser method)
(BCLContactParser method)
(BbcontactsParser method)
(CCMpredParser method)
(CaspParser method)
(ComsatParser method)
(EPCMapParser method)
(EVfoldParser method)
(FastaParser method)
(FreeContactParser method)
(GremlinParser method)
(JonesParser method)
(MemBrainParser method)
(MmCifParser method)
(NcontParser method)
(PconsParser method)
(PdbParser method)
(PlmDCAParser method)
(PsicovParser method)
(StockholmParser method)
(in module conkit.io)
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[1]
redraw() (ContactDensityFigure method)
(ContactMapChordFigure method)
(ContactMapFigure method)
(PrecisionEvaluationFigure method)
(SequenceCoverageFigure method)
reference (ContactMapFigure attribute)
remark (ContactFile attribute)
(Sequence attribute)
(SequenceFile attribute)
remove_neighbors() (ContactMap method)
repr_sequence (ContactMap attribute)
repr_sequence_altloc (ContactMap attribute)
res1 (Contact attribute)
res1_altseq (Contact attribute)
res1_chain (Contact attribute)
res1_seq (Contact attribute)
res2 (Contact attribute)
res2_altseq (Contact attribute)
res2_chain (Contact attribute)
res2_seq (Contact attribute)
rescale() (ContactMap method)
S
scalar_score (Contact attribute)
ScottBW (class in conkit.misc.bandwidth)
seq (Sequence attribute)
seq_ascii (Sequence attribute)
seq_len (Sequence attribute)
Sequence (class in conkit.core.sequence)
sequence (ContactMap attribute)
Sequence() (in module conkit.core)
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[1]
SequenceAlignmentState (class in conkit.core.sequencefile)
SequenceCoverageFigure (class in conkit.plot.sequencecoverage)
SequenceCoverageFigure() (in module conkit.plot)
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[1]
SequenceFile (class in conkit.core.sequencefile)
SequenceFile() (in module conkit.core)
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[1]
setup_logging() (in module conkit.command_line)
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[1]
short_range_contacts (ContactMap attribute)
SilvermanBW (class in conkit.misc.bandwidth)
sort() (ContactFile method)
(ContactMap method)
(SequenceFile method)
status (Contact attribute)
(SequenceFile attribute)
stiffness_integral() (AmiseBW static method)
StockholmParser (class in conkit.io.stockholm)
T
target (ContactFile attribute)
top_contact (ContactMap attribute)
top_map (ContactFile attribute)
top_sequence (SequenceFile attribute)
trim() (SequenceFile method)
U
unaligned (SequenceAlignmentState attribute)
unknown (ContactMatchState attribute)
(SequenceAlignmentState attribute)
upper_bound (Contact attribute)
W
weight (Contact attribute)
write() (A3mParser method)
(BCLContactParser method)
(BbcontactsParser method)
(CCMpredParser method)
(CaspParser method)
(ComsatParser method)
(EPCMapParser method)
(EVfoldParser method)
(FastaParser method)
(FreeContactParser method)
(GremlinParser method)
(JonesParser method)
(MemBrainParser method)
(MmCifParser method)
(NcontParser method)
(PconsParser method)
(PdbParser method)
(PlmDCAParser method)
(PsicovParser method)
(StockholmParser method)
(in module conkit.io)
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[1]