Index

A | B | C | D | E | F | G | H | I | J | L | M | N | P | R | S | T | U | W

A

A3mIO (class in conkit.io.A3mIO)
add() (Entity method)
align_global() (Sequence method), [1], [2]

align_local() (Sequence method), [1], [2]
assign_sequence_register() (ContactMap method), [1], [2]
author (ContactFile attribute), [1], [2]

B

BbcontactsCommandLine (class in conkit.applications.Bbcontacts)
BbcontactsParser (class in conkit.io.BbcontactsIO)

BCLContactParser (class in conkit.io.BCLContactIO)

C

calculate_freq() (SequenceFile method), [1], [2]
calculate_jaccard_index() (ContactMap method), [1], [2]
calculate_meff() (SequenceFile method), [1], [2]
calculate_scalar_score() (ContactMap method), [1], [2]
CaspParser (class in conkit.io.CaspIO)
CCMpredCommandLine (class in conkit.applications.CCMpred)
CCMpredParser (class in conkit.io.CCMpredIO)
CdhitCommandLine (class in conkit.applications.Cdhit)
child_dict (Entity attribute)
child_list (Entity attribute)
ComsatParser (class in conkit.io.ComsatIO)
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.constants (module)
conkit.core (module), [1]
conkit.core.Contact (module)
conkit.core.ContactFile (module)
conkit.core.ContactMap (module)
conkit.core.Entity (module)
conkit.core.Sequence (module)

conkit.core.SequenceFile (module)

conkit.io (module), [1]

conkit.io.A3mIO (module)

conkit.io.BbcontactsIO (module)

conkit.io.BCLContactIO (module)

conkit.io.CaspIO (module)

conkit.io.CCMpredIO (module)

conkit.io.ComsatIO (module)

conkit.io.EPCMapIO (module)

conkit.io.EVfoldIO (module)

conkit.io.FastaIO (module)

conkit.io.FreeContactIO (module)

conkit.io.GremlinIO (module)

conkit.io.JonesIO (module)

conkit.io.MemBrainIO (module)

conkit.io.PconsIO (module)

conkit.io.PdbIO (module)

conkit.io.PlmDCAIO (module)

conkit.io.PsicovIO (module)

conkit.io.StockholmIO (module)

Contact (class in conkit.core), [1]

(class in conkit.core.Contact)

ContactFile (class in conkit.core), [1]

(class in conkit.core.ContactFile)

ContactMap (class in conkit.core), [1]

(class in conkit.core.ContactMap)

ContactTemplate (in module conkit.io.CaspIO)

convert() (in module conkit.io), [1]

copy() (Entity method)

coverage (ContactMap attribute), [1], [2]

D

deepcopy() (Entity method)
define_false_positive() (Contact method), [1], [2]

define_true_positive() (Contact method), [1], [2]
distance_bound (Contact attribute), [1], [2]

E

Entity (class in conkit.core.Entity)
EPCMapParser (class in conkit.io.EPCMapIO)

EVfoldParser (class in conkit.io.EVfoldIO)

F

FastaIO (class in conkit.io.FastaIO)
find() (ContactMap method), [1], [2]

FreeContactParser (class in conkit.io.FreeContactIO)
full_id (Entity attribute)

G

GremlinParser (class in conkit.io.GremlinIO)

H

HHblitsCommandLine (class in conkit.applications.HHblits)

HHfilterCommandLine (class in conkit.applications.HHfilter)

I

id (Entity attribute)
is_alignment (SequenceFile attribute), [1], [2]

is_false_positive (Contact attribute), [1], [2]
is_true_positive (Contact attribute), [1], [2]

J

JackhmmerCommandLine (class in conkit.applications.Jackhmmer)

JonesIO (class in conkit.io.JonesIO)

L

lower_bound (Contact attribute), [1], [2]

M

match() (ContactMap method), [1], [2]
MemBrainParser (class in conkit.io.MemBrainIO)

method (ContactFile attribute), [1], [2]
ModelTemplate (in module conkit.io.CaspIO)

N

ncontacts (ContactMap attribute), [1], [2]

nseqs (SequenceFile attribute), [1], [2]

P

parent (Entity attribute)
PconsParser (class in conkit.io.PconsIO)
PdbParser (class in conkit.io.PdbIO)
PlmDCAParser (class in conkit.io.PlmDCAIO)

plot_map() (ContactMap method), [1], [2]
precision (ContactMap attribute), [1], [2]
PsicovCommandLine (class in conkit.applications.Psicov)
PsicovParser (class in conkit.io.PsicovIO)

R

raw_score (Contact attribute), [1], [2]

read() (A3mIO method)

(BCLContactParser method)
(BbcontactsParser method)
(CCMpredParser method)
(CaspParser method)
(ComsatParser method)
(EPCMapParser method)
(EVfoldParser method)
(FastaIO method)
(FreeContactParser method)
(GremlinParser method)
(JonesIO method)
(MemBrainParser method)
(PconsParser method)
(PdbParser method)
(PlmDCAParser method)
(PsicovParser method)
(StockholmIO method)
(in module conkit.io), [1]

remark (ContactFile attribute), [1], [2]

(Sequence attribute), [1], [2]
(SequenceFile attribute), [1], [2]

remove() (Entity method)

remove_neighbors() (ContactMap method), [1], [2]

repr_sequence (ContactMap attribute), [1], [2]

repr_sequence_altloc (ContactMap attribute), [1], [2]

res1 (Contact attribute), [1], [2]

res1_altseq (Contact attribute), [1], [2]
res1_chain (Contact attribute), [1], [2]
res1_seq (Contact attribute), [1], [2]
res2 (Contact attribute), [1], [2]
res2_altseq (Contact attribute), [1], [2]
res2_chain (Contact attribute), [1], [2]
res2_seq (Contact attribute), [1], [2]
rescale() (ContactMap method), [1], [2]

S

T

target (ContactFile attribute), [1], [2]
top_contact (ContactMap attribute), [1], [2]

top_map (ContactFile attribute), [1], [2]
top_sequence (SequenceFile attribute), [1], [2]

U

upper_bound (Contact attribute), [1], [2]

W