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D
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W
A
accession_and_seginfo (cathpy.align.Sequence attribute)
add_groupsim() (cathpy.align.Align method)
add_scorecons() (cathpy.align.Align method)
add_sequence() (cathpy.align.Align method)
Align (class in cathpy.align)
AlignmentSummary (class in cathpy.util)
AlignmentSummaryRunner (class in cathpy.util)
aln_positions (cathpy.align.Align attribute)
AminoAcid (class in cathpy.models)
AminoAcids (class in cathpy.models)
ApiClientBase (class in cathpy.funfhmmer)
apply_seqres_segments() (cathpy.align.Correspondence method)
as_csv() (cathpy.funfhmmer.ResultResponse method)
as_json() (cathpy.funfhmmer.ResultResponse method)
atom_length (cathpy.align.Correspondence attribute)
atom_sequence (cathpy.align.Correspondence attribute)
AtomFastaFileType (class in cathpy.datafiles)
C
cath_id (cathpy.models.CathID attribute)
cath_id_to_depth() (cathpy.models.CathID method)
CathID (class in cathpy.models)
cathpy.align (module)
cathpy.datafiles (module)
cathpy.error (module)
cathpy.funfhmmer (module)
cathpy.models (module)
cathpy.tests (module)
cathpy.util (module)
cathpy.version (module)
CathVersion (class in cathpy.version)
check() (cathpy.funfhmmer.Client method)
CheckResponse (class in cathpy.funfhmmer)
Client (class in cathpy.funfhmmer)
cluster_id (cathpy.align.Sequence attribute)
ClusterFile (class in cathpy.models)
ClusterID (class in cathpy.models)
CombsFastaFileType (class in cathpy.datafiles)
copy() (cathpy.align.Align method)
(cathpy.align.Sequence method)
Correspondence (class in cathpy.align)
count_positions (cathpy.util.GroupsimResult attribute)
count_sequences (cathpy.align.Align attribute)
D
depth (cathpy.models.CathID attribute)
dirname (cathpy.version.CathVersion attribute)
DuplicateSequenceError
F
FileEmptyError
FileNotFoundError
find_first_seq_by_accession() (cathpy.align.Align method)
find_seq_by_accession() (cathpy.align.Align method)
find_seq_by_id() (cathpy.align.Align method)
first_residue (cathpy.align.Correspondence attribute)
funfam_id_from_file() (cathpy.util.FunfamFileFinder method)
FunfamFileFinder (class in cathpy.util)
FunfamID (class in cathpy.models)
G
GapError
GcfFileType (class in cathpy.datafiles)
GeneralError
GenericFileType (class in cathpy.datafiles)
get() (cathpy.funfhmmer.ApiClientBase method)
get_by_id() (cathpy.models.AminoAcids class method)
get_file() (cathpy.datafiles.ReleaseDir method)
get_offset_at_seq_position() (cathpy.align.Sequence method)
get_res_at_offset() (cathpy.align.Correspondence method)
(cathpy.align.Sequence method)
get_res_at_seq_position() (cathpy.align.Sequence method)
get_res_by_atom_pos() (cathpy.align.Correspondence method)
get_res_by_pdb_label() (cathpy.align.Correspondence method)
get_res_by_seq_num() (cathpy.align.Correspondence method)
get_res_offset_by_atom_pos() (cathpy.align.Correspondence method)
get_residues() (cathpy.align.Sequence method)
get_seq_at_offset() (cathpy.align.Align method)
get_seq_position_at_offset() (cathpy.align.Sequence method)
GroupsimResult (class in cathpy.util)
GroupsimRunner (class in cathpy.util)
H
HttpError
I
id (cathpy.align.Align attribute)
(cathpy.align.Sequence attribute)
insert_gap_at_offset() (cathpy.align.Align method)
(cathpy.align.Sequence method)
InvalidInputError
is_cath_domain (cathpy.align.Sequence attribute)
is_current (cathpy.version.CathVersion attribute)
is_gap() (cathpy.align.Sequence static method)
is_valid_aa() (cathpy.models.AminoAcids class method)
is_valid_domain_id() (in module cathpy.tests)
J
join() (cathpy.version.CathVersion method)
JsonError
L
last_residue (cathpy.align.Correspondence attribute)
length() (cathpy.align.Sequence method)
lower_case_at_offset() (cathpy.align.Align method)
(cathpy.align.Sequence method)
M
merge_alignment() (cathpy.align.Align method)
MergeCheckError
MergeCorrespondenceError
MissingExecutableError
MissingGroupsimError
MissingScoreconsError
MissingSegmentsError
N
new_from_fasta() (cathpy.align.Align class method)
new_from_file() (cathpy.models.ClusterID class method)
(cathpy.util.GroupsimResult class method)
new_from_gcf() (cathpy.align.Correspondence class method)
new_from_io() (cathpy.util.GroupsimResult class method)
new_from_pir() (cathpy.align.Align class method)
new_from_stockholm() (cathpy.align.Align class method)
new_from_string() (cathpy.version.CathVersion class method)
NoMatchesError
O
OutOfBoundsError
P
ParamError
ParseError
pg_dbname (cathpy.version.CathVersion attribute)
post() (cathpy.funfhmmer.ApiClientBase method)
R
read_sequences_from_fasta() (cathpy.align.Align method)
read_sequences_from_pir() (cathpy.align.Align method)
ReleaseDir (class in cathpy.datafiles)
remove_alignment_gaps() (cathpy.align.Align method)
remove_sequence_by_id() (cathpy.align.Align method)
Residue (class in cathpy.models)
ResponseBase (class in cathpy.funfhmmer)
ResultResponse (class in cathpy.funfhmmer)
results() (cathpy.funfhmmer.Client method)
run_alignment() (cathpy.util.GroupsimRunner method)
(cathpy.util.ScoreconsRunner method)
run_fasta() (cathpy.util.ScoreconsRunner method)
run_stockholm() (cathpy.util.ScoreconsRunner method)
S
Scan (class in cathpy.models)
ScanHit (class in cathpy.models)
ScanHsp (class in cathpy.models)
ScanResult (class in cathpy.models)
ScoreconsResult (class in cathpy.util)
ScoreconsRunner (class in cathpy.util)
search_by_domain_id() (cathpy.util.FunfamFileFinder method)
search_fasta() (cathpy.funfhmmer.Client method)
Segment (class in cathpy.models)
seq (cathpy.align.Sequence attribute)
seq_no_gaps (cathpy.align.Sequence attribute)
SeqIOError
seqres_length (cathpy.align.Correspondence attribute)
seqres_sequence (cathpy.align.Correspondence attribute)
Sequence (class in cathpy.align)
sequences (cathpy.align.Align attribute)
set_all_gap_chars() (cathpy.align.Sequence method)
set_cluster_id() (cathpy.align.Sequence method)
set_gap_char_at_offset() (cathpy.align.Align method)
(cathpy.align.Sequence method)
set_id() (cathpy.align.Align method)
(cathpy.align.Correspondence method)
(cathpy.align.Sequence method)
set_lower_case_to_gap() (cathpy.align.Sequence method)
sfam_id (cathpy.models.CathID attribute)
slice_seq() (cathpy.align.Sequence method)
slice_seqs() (cathpy.align.Align method)
split_hdr() (cathpy.align.Sequence class method)
split_path() (cathpy.models.ClusterFile class method)
StructuralClusterMerger (class in cathpy.util)
submit() (cathpy.funfhmmer.Client method)
SubmitResponse (class in cathpy.funfhmmer)
T
to_aln() (cathpy.align.Correspondence method)
to_fasta() (cathpy.align.Align method)
(cathpy.align.Correspondence method)
(cathpy.align.Sequence method)
to_gcf() (cathpy.align.Correspondence method)
to_pir() (cathpy.align.Align method)
(cathpy.align.Sequence method)
to_sequences() (cathpy.align.Correspondence method)
to_string (cathpy.util.ScoreconsResult attribute)
to_string() (cathpy.models.ClusterFile method)
(cathpy.version.CathVersion method)
TooManyMatchesError
total_gap_positions (cathpy.align.Align attribute)
total_positions (cathpy.align.Align attribute)
W
write_fasta() (cathpy.align.Align method)
write_pir() (cathpy.align.Align method)
write_sto() (cathpy.align.Align method)
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