Index

_

__init__() (Align method) (Aligned method) (AminoAcid method) (DSSP method) (GOR3 method) (PSSM method) (ScoreMatrix method) (Sequence method)

A

add() (PSSM method) Align (class in pyprot.align.align)

Aligned (class in pyprot.align.align) AminoAcid (class in pyprot.base.aminoacid)

B

belongs() (in module pyprot.align.blosum) blosumFromFasta() (in module pyprot.align.blosum)

blosumFromProbabilities() (in module pyprot.align.blosum)

D

DSSP (class in pyprot.data.dssp)

E

extend() (Sequence method)

G

getAllNames() (AminoAcid static method) getBottomSequence() (Aligned method) getDescription() (PSSM method) (Sequence method) getFrequencies() (in module pyprot.align.blosum) getGapPenalty() (PSSM method) getName() (AminoAcid method) getNames() (AminoAcid static method) getNamesInRange() (AminoAcid static method)

getQuality() (GOR3 method) getScore() (PSSM method) (ScoreMatrix method) getSequencesFromFasta() (in module pyprot.data.fasta) getSequenceStructure() (DSSP method) getStructures() (GOR3 method) globalAlign() (Align method) GOR3 (class in pyprot.structure.gor)

I

insert() (Sequence method) isGap() (AminoAcid method)

isTermination() (AminoAcid method)

L

localAlign() (Align method)

M

makeGroupsFromFasta() (in module pyprot.align.blosum)

multiAlign() (Align method)

N

neighbourOffsets() (GOR3 method)

neighbourValues() (GOR3 method)

P

plotROC() (GOR3 method) predict() (GOR3 method) PSSM (class in pyprot.align.score) pyprot (module) pyprot.align (module) pyprot.align.align (module) pyprot.align.blosum (module) pyprot.align.score (module)

pyprot.base (module) pyprot.base.aminoacid (module) pyprot.base.sequence (module) pyprot.data (module) pyprot.data.dssp (module) pyprot.data.fasta (module) pyprot.structure (module) pyprot.structure.gor (module)

S

ScoreMatrix (class in pyprot.align.score) Sequence (class in pyprot.base.sequence) setDescription() (Sequence method) setGapPenalty() (PSSM method)

setNameMode() (Sequence method) setScore() (ScoreMatrix method) setSeparator() (Sequence method) sumFrequenciesToProb() (in module pyprot.align.blosum)

T

train() (GOR3 method)

V

valueDictsFromGroups() (in module pyprot.align.blosum)