Index

A

add_sequence() (modpipe.filesystem.FileSystem method) (modpipe.sequence.UniqueFile method)

C

calculate_superpositions() (modpipe.ce.CE method) (modpipe.tmalign.TMAlign method) CDHit (class in modpipe.cdhit) CE (class in modpipe.ce)

clean() (modpipe.sequence.Sequence method) cluster() (modpipe.cdhit.CDHit method) CLUSTERALI Config (class in modpipe.config)

D

DATDIR

DEMO digest() (in module modpipe.crc64)

E

environment variable CLUSTERALI DATDIR DEMO NCBISEQDB NRDBTAG NRSEQDB NUMMODELS PDB_REPOSITORY PRFUPDATE, [1] TEMPLATESEQDB, [1] TMPDIR XPRF_LIST XPRF_PSSMDB

Error, [1]

F

FASTAFile (class in modpipe.sequence) file_name_from_seqfile() (modpipe.sequence.UniqueFile method) FileFormatError

FileSystem (class in modpipe.filesystem) fix_alignment() (modpipe.ce.CE method) (modpipe.tmalign.TMAlign method)

G

get() (in module modpipe.version) get_alignment() (modpipe.ce.CE method) (modpipe.tmalign.TMAlign method) get_alignment_dir() (modpipe.filesystem.FileSystem method) get_blast() (in module modpipe.binaries) get_cd_hit() (in module modpipe.binaries) get_ce() (in module modpipe.binaries) get_ce_mkdb() (in module modpipe.binaries) get_hhsuite() (in module modpipe.binaries) get_id() (modpipe.sequence.Sequence method) get_jess() (in module modpipe.binaries)

get_model_dir() (modpipe.filesystem.FileSystem method) get_modeling_alignment() (modpipe.fold_assignment.Hit method) get_modpipe_binary_path() (modpipe.test.TestCase method) get_modpipe_script() (in module modpipe.binaries) get_seg() (in module modpipe.binaries) get_selected_file() (modpipe.filesystem.FileSystem method) get_sequence_dir() (modpipe.filesystem.FileSystem method) get_sequence_file() (modpipe.filesystem.FileSystem method) get_spasm() (in module modpipe.binaries) get_tess2jess() (in module modpipe.binaries) get_tmalign() (in module modpipe.binaries)

H

Hit (class in modpipe.fold_assignment) (class in modpipe.serialize)

M

Matrix2D (class in modpipe.matrix2d) message() (in module modpipe.version) MissingBinaryError Model (class in modpipe.serialize) modpipe.binaries module modpipe.cdhit module modpipe.ce module modpipe.config module modpipe.crc64 module modpipe.filesystem module modpipe.fold_assignment module modpipe.matrix2d module modpipe.sequence module

modpipe.serialize module modpipe.test module modpipe.tmalign module modpipe.version module module modpipe.binaries modpipe.cdhit modpipe.ce modpipe.config modpipe.crc64 modpipe.filesystem modpipe.fold_assignment modpipe.matrix2d modpipe.sequence modpipe.serialize modpipe.test modpipe.tmalign modpipe.version

N

NCBISEQDB NRDBTAG

NRSEQDB NUMMODELS

P

parse_clusters() (modpipe.cdhit.CDHit method) parse_file() (modpipe.config.Config method) parse_output() (modpipe.ce.CE method) (modpipe.tmalign.TMAlign method) PDB_REPOSITORY

PIRFile (class in modpipe.sequence) PRFUPDATE, [1] ProfileSequence (class in modpipe.fold_assignment) Python Enhancement Proposals PEP 8

R

read() (modpipe.sequence.FASTAFile method) (modpipe.sequence.PIRFile method) (modpipe.sequence.SPTRFile method) read_file() (in module modpipe.config) read_hits_file() (in module modpipe.serialize) read_models_file() (in module modpipe.serialize)

read_program_output() (modpipe.ce.CE method) (modpipe.tmalign.TMAlign method) require_clean_exit() (modpipe.test.TestCase method) run_binary() (modpipe.test.TestCase method) run_perl_code() (modpipe.test.TestCase method) run_script() (modpipe.test.TestCase method)

S

search() (modpipe.fold_assignment.ProfileSequence method) (modpipe.fold_assignment.SequenceSequence method)

Sequence (class in modpipe.sequence) SequenceSequence (class in modpipe.fold_assignment) SPTRFile (class in modpipe.sequence)

T

TEMPLATESEQDB, [1] TestCase (class in modpipe.test)

TMAlign (class in modpipe.tmalign) TMPDIR

U

UniqueFile (class in modpipe.sequence)

W

write() (modpipe.matrix2d.Matrix2D method) (modpipe.sequence.FASTAFile method) (modpipe.sequence.PIRFile method) (modpipe.sequence.UniqueFile method) write_alignment() (modpipe.ce.CE method) (modpipe.tmalign.TMAlign method)

write_hits_file() (in module modpipe.serialize) write_models_file() (in module modpipe.serialize) write_program_output() (modpipe.ce.CE method) (modpipe.tmalign.TMAlign method)

X

XPRF_LIST

XPRF_PSSMDB