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X
A
a3mToTrimmed() (AlignmentParser method)
ab_initio_cmd() (RosettaModel method)
ab_initio_model() (RosettaModel method)
AbinitioEnsembler (class in ample.ensembler.abinitio)
add_argparse_options() (in module ample.ensembler)
,
[1]
add_cluster_submit_options() (in module ample.util.argparse_util)
add_cmd_options() (in module ample.testing.integration_util)
(in module ample.testing.unittest_util)
add_contact_options() (in module ample.util.argparse_util)
add_core_options() (in module ample.util.argparse_util)
add_general_options() (in module ample.util.argparse_util)
add_mr_options() (in module ample.util.argparse_util)
add_pdb_data() (Sequence method)
add_rfree() (in module ample.util.mtz_util)
add_rosetta_options() (in module ample.util.argparse_util)
add_sidechains() (Scwrl method)
align_clustalw() (in module ample.modelling.rosetta_model)
align_gesamt() (in module ample.ensembler.homologs)
align_mafft() (in module ample.modelling.rosetta_model)
align_mustang() (in module ample.ensembler.homologs)
align_sequences() (AlignmentParser method)
alignment_file() (Theseus method)
AlignmentParser (class in ample.parsers.alignment_parser)
amoptd_fix_path() (in module ample.util.ample_util)
ample (module)
ample.constants (module)
ample.ensembler (module)
,
[1]
ample.ensembler.abinitio (module)
ample.ensembler.cluster_util (module)
ample.ensembler.constants (module)
ample.ensembler.homologs (module)
ample.ensembler.single_model (module)
ample.ensembler.subcluster (module)
ample.ensembler.subcluster_util (module)
ample.ensembler.truncation_util (module)
ample.modelling (module)
,
[1]
ample.modelling.energy_functions (module)
ample.modelling.octopus_predict (module)
ample.modelling.rosetta_model (module)
ample.parsers (module)
ample.parsers.alignment_parser (module)
ample.parsers.dssp_parser (module)
ample.parsers.psipred_parser (module)
ample.parsers.tm_parser (module)
ample.testing (module)
,
[1]
ample.testing.constants (module)
ample.testing.integration_util (module)
ample.testing.run_tests (module)
ample.testing.test_funcs (module)
ample.testing.unittest_util (module)
ample.util (module)
,
[1]
ample.util.ample_util (module)
ample.util.argparse_util (module)
ample.util.benchmark_util (module)
ample.util.cif_parser (module)
ample.util.cluster_entropy (module)
ample.util.clusterize (module)
ample.util.config_util (module)
ample.util.cphasematch (module)
ample.util.csymmatch (module)
ample.util.exit_util (module)
ample.util.fast_protein_cluster (module)
ample.util.logging_util (module)
ample.util.maxcluster (module)
ample.util.mrbump_cmd (module)
ample.util.mrbump_util (module)
ample.util.mtz_util (module)
ample.util.pdb_edit (module)
ample.util.pdb_model (module)
ample.util.phenixer (module)
ample.util.printTable (module)
ample.util.pyrvapi_results (module)
ample.util.reforigin (module)
ample.util.residue_map (module)
ample.util.rio (module)
ample.util.scwrl_util (module)
ample.util.sequence_util (module)
ample.util.shelxe (module)
ample.util.spicker (module)
ample.util.theseus (module)
ample.util.tm_util (module)
ample.util.version (module)
ample.util.worker (module)
ample.util.workers_util (module)
AMPLE_DICT (AMPLEBaseTest attribute)
AMPLEBaseTest (class in ample.testing.integration_util)
AMPLEConfigOptions (class in ample.util.config_util)
AMPLEIntegrationFramework (class in ample.testing.integration_util)
AmpleOutput (class in ample.util.pyrvapi_results)
AMPLEUnittestFramework (class in ample.testing.unittest_util)
analyse() (in module ample.util.benchmark_util)
(MRinfo method)
analyseModels() (in module ample.util.benchmark_util)
analysePdb() (in module ample.util.benchmark_util)
analyseResult() (ResultsSummary method)
analyseRio() (Rio method)
analyseSolution() (in module ample.util.benchmark_util)
asDict() (DsspParser method)
averageScore() (Csymmatch method)
B
backbone() (in module ample.util.pdb_edit)
binary_avail() (TMapps static method)
BOUNDED_default (RosettaFunctionConstructs attribute)
BOUNDED_gremlin (RosettaFunctionConstructs attribute)
C
calc_map() (residueSequenceMap method)
calc_phase_error_mtz() (in module ample.util.cphasematch)
calc_phase_error_pdb() (in module ample.util.cphasematch)
calc_rmsd() (LsqkabClusterer method)
calcAllAtom() (Rio method)
calcRio() (Rio method)
calculate() (ReforiginRmsd method)
calculate_residues_focussed() (in module ample.ensembler.truncation_util)
calculate_residues_percent() (in module ample.ensembler.truncation_util)
calculate_residues_thresh() (in module ample.ensembler.truncation_util)
calculate_score() (SubClusterer method)
calculate_truncations() (Truncator method)
calpha_only() (in module ample.util.pdb_edit)
canonicalise() (Sequence method)
ccmtzOrigin() (in module ample.util.phenixer)
ccp4_version() (in module ample.util.ample_util)
CctbxClusterer (class in ample.ensembler.subcluster)
check_content() (PsipredSs2Parser method)
check_pdb_directory() (in module ample.util.pdb_edit)
check_pdbs() (in module ample.util.pdb_edit)
checkContent() (PsipredSs2Parser method)
checkSuccess() (in module ample.util.mrbump_util)
CifParser (class in ample.util.cif_parser)
clean() (AMPLEIntegrationFramework method)
cleanUpArrayJob() (ClusterRun method)
cluster() (FPC method)
(Spickerer method)
(in module ample.util.cluster_entropy)
cluster_by_radius() (SubClusterer method)
cluster_models() (AbinitioEnsembler method)
cluster_script() (in module ample.ensembler)
,
[1]
(in module ample.util.benchmark_util)
cluster_table_data() (in module ample.ensembler)
,
[1]
ClusterRun (class in ample.util.clusterize)
cmd_add_restraints() (RosettaModel method)
collate_cluster_data() (in module ample.ensembler)
,
[1]
compare_one_split_folder() (in module ample.util.cluster_entropy)
compare_structures() (TMalign method)
(TMscore method)
compareDirectory() (Maxcluster method)
compareModelList() (Maxcluster method)
compareSingle() (Maxcluster method)
comparison() (TMapps method)
construct_references() (in module ample.util.ample_util)
core (TheseusVariances attribute)
count_files_in_dir() (in module ample.util.cluster_entropy)
create_ensembles() (in module ample.ensembler)
,
[1]
create_input_files() (Spickerer method)
create_log_tab() (AmpleOutput method)
create_results_tab() (AmpleOutput method)
create_summary_tab() (AmpleOutput method)
createDict() (ResultsSummary method)
CrystalInfo (class in ample.util.pdb_model)
Csymmatch (class in ample.util.csymmatch)
cutoff() (ample.modelling.energy_functions.DynamicDistances class method)
D
DebugDict (class in ample.util.config_util)
DEFAULT (Saint2FunctionConstructs attribute)
del_column() (in module ample.util.mtz_util)
display_results() (AmpleOutput method)
DsspParser (class in ample.parsers.dssp_parser)
dump_pdb_matrix() (SubClusterer method)
dump_raw_matrix() (SubClusterer method)
DynamicDistances (class in ample.modelling.energy_functions)
E
emit() (NullHandler method)
ensemble_from_subcluster() (AbinitioEnsembler method)
ensemble_pdb() (AmpleOutput method)
ensemble_summary() (in module ample.ensembler)
,
[1]
ensembler_factory() (in module ample.ensembler)
,
[1]
exit_error() (in module ample.util.exit_util)
extract_chain() (in module ample.util.pdb_edit)
extract_header_pdb_code() (in module ample.util.pdb_edit)
extract_header_title() (in module ample.util.pdb_edit)
extract_model() (in module ample.util.pdb_edit)
extract_models() (in module ample.util.ample_util)
extract_tar() (in module ample.util.ample_util)
extract_zip() (in module ample.util.ample_util)
extractResults() (ResultsSummary method)
F
FADE (RosettaFunctionConstructs attribute)
FADE_default (RosettaFunctionConstructs attribute)
fasta_str() (Sequence method)
filename_append() (in module ample.util.ample_util)
FileNotFoundError
fill_table() (AmpleOutput method)
finalSummary() (in module ample.util.mrbump_util)
find_binary() (RosettaModel method)
find_exe() (in module ample.util.ample_util)
find_maxcluster() (in module ample.util.maxcluster)
findChunks() (Rio method)
findOrigin() (Rio method)
fix_path() (AmpleOutput method)
fixpath() (in module ample.util.benchmark_util)
format_num() (Table method)
found_exe() (in module ample.testing.test_funcs)
FPC (class in ample.util.fast_protein_cluster)
FpcClusterer (class in ample.ensembler.subcluster)
fragment_cmd() (RosettaModel method)
from_fasta() (Sequence method)
from_pdb() (Sequence method)
fromHetatm() (PdbAtom method)
fromInfo() (residueSequenceMap method)
fromLine() (CrystalInfo method)
(PdbAtom method)
(PdbModres method)
G
gdtha (ModelData attribute)
gdtts (ModelData attribute)
generate_distance_matrix() (CctbxClusterer method)
(FpcClusterer method)
(GesamtClusterer method)
(LsqkabClusterer method)
(MaxClusterer method)
(SubClusterer method)
generate_ensembles() (AbinitioEnsembler method)
(HomologEnsembler method)
(SingleModelEnsembler method)
generate_ensembles_from_amoptd() (AbinitioEnsembler method)
(HomologEnsembler method)
(SingleModelEnsembler method)
generate_fragments() (RosettaModel method)
generate_seeds() (RosettaModel method)
generate_thresholds() (in module ample.ensembler.truncation_util)
generateMap() (in module ample.util.phenixer)
GesamtClusterer (class in ample.ensembler.subcluster)
get_bin_dir() (RosettaModel method)
get_info() (in module ample.util.pdb_edit)
get_labels() (in module ample.util.mtz_util)
get_length() (Spickerer method)
get_max_width() (Table method)
get_rfree() (in module ample.util.mtz_util)
get_run_dir() (AMPLEIntegrationFramework method)
get_version() (RosettaModel method)
getAssignment() (DsspParser method)
getFasta() (OctopusPredict method)
getPredict() (OctopusPredict method)
getResName() (DsspParser method)
getRmsd() (ReforiginRmsd method)
getRunningJobList() (ClusterRun method)
getSecondaryStructure() (PsipredSs2Parser method)
getSequence() (PdbInfo method)
H
handle_starttag() (ParseFileUrl method)
helixFromContacts() (Rio method)
helixFromPdbs() (Rio method)
HomologEnsembler (class in ample.ensembler.homologs)
I
ideal_helices() (in module ample.util.ample_util)
idealize_cmd() (RosettaModel method)
idealize_models() (RosettaModel method)
idealize_pdbout() (RosettaModel method)
idx (ScoreVariances attribute)
(TheseusVariances attribute)
import_cluster() (in module ample.ensembler.cluster_util)
import_ensembles() (in module ample.ensembler)
,
[1]
internet_on() (in module ample.testing.test_funcs)
is_exe() (in module ample.util.ample_util)
is_file() (in module ample.util.ample_util)
isFloating() (OriginInfo method)
J
job_unfinished() (in module ample.util.mrbump_util)
JobServer (class in ample.util.workers_util)
jobSucceeded() (in module ample.util.mrbump_util)
K
keep_matching() (in module ample.util.pdb_edit)
keyword_dict() (in module ample.util.mrbump_cmd)
L
length() (Sequence method)
load_cases() (SuiteLoader method)
load_module() (SuiteLoader method)
load_suite() (SuiteLoader method)
log_fname (ModelData attribute)
LsqkabClusterer (class in ample.ensembler.subcluster)
M
main() (in module ample.testing.run_tests)
(in module ample.util.tm_util)
make_workdir() (in module ample.util.ample_util)
match_resseq() (in module ample.util.pdb_edit)
max_min_resolution() (in module ample.util.mtz_util)
Maxcluster (class in ample.util.maxcluster)
MaxClusterer (class in ample.ensembler.subcluster)
maxsub (ModelData attribute)
maxsub() (RosettaScoreParser method)
maxsubSorted() (Maxcluster method)
(RosettaScoreParser method)
merge() (in module ample.util.pdb_edit)
merge_mtz() (in module ample.util.cphasematch)
merge_mtz_cctbx() (in module ample.util.cphasematch)
mk_native_files() (MRinfo method)
model_fname (ModelData attribute)
model_name (ModelData attribute)
ModelData (class in ample.util.tm_util)
molecular_weight() (in module ample.util.pdb_edit)
monitorQueue() (ClusterRun method)
mr_cmd() (RosettaModel method)
mrbump_cmd() (in module ample.util.mrbump_cmd)
mrbump_keyword_file() (in module ample.util.mrbump_cmd)
MRinfo (class in ample.util.shelxe)
mutate_residue() (Sequence method)
N
nmr_remodel() (RosettaModel method)
nonRedundantAlternateOrigins() (OriginInfo method)
nr_residues_common (ModelData attribute)
NullHandler (class in ample.util.mrbump_util)
num_atoms_and_residues() (in module ample.util.pdb_edit)
num_residues (Truncation attribute)
numAtoms() (PdbInfo method)
numCalpha() (PdbInfo method)
numChains() (PdbInfo method)
numSequences() (Sequence method)
O
octopusFileUrls() (OctopusPredict method)
OctopusPredict (class in ample.modelling.octopus_predict)
origin() (Csymmatch method)
OriginInfo (class in ample.util.pdb_model)
P
parse() (DsspParser method)
(PsipredSs2Parser method)
(TMalignLogParser method)
(TMscoreLogParser method)
parse_args() (in module ample.testing.test_funcs)
parse_cluster_method() (AbinitioEnsembler method)
parse_cphasematch_log() (in module ample.util.cphasematch)
parse_lsqkab_output() (LsqkabClusterer method)
parse_variances() (Theseus method)
parseFile() (RosettaScoreParser method)
ParseFileUrl (class in ample.modelling.octopus_predict)
parseLog() (Csymmatch method)
parseLogDirectory() (Maxcluster method)
parseLogSingleRmsd() (Maxcluster method)
parseLogSingleTm() (Maxcluster method)
parseNcontLog() (Rio method)
parseTableDat() (ResultsSummary method)
PdbAtom (class in ample.util.pdb_model)
PdbHetatm (class in ample.util.pdb_model)
PdbInfo (class in ample.util.pdb_model)
PdbModel (class in ample.util.pdb_model)
PdbModres (class in ample.util.pdb_model)
percentile() (ample.modelling.energy_functions.DynamicDistances class method)
pick_nmodels() (in module ample.ensembler.subcluster_util)
pirStr() (Sequence method)
place_native_pdb() (in module ample.util.cphasematch)
populate() (AMPLEConfigOptions method)
pprint_table() (Table method)
prepareNative() (Maxcluster method)
preparePlacedPdb() (ReforiginRmsd method)
prettify_parameters() (AMPLEConfigOptions method)
process_directory() (Scwrl method)
process_fasta() (in module ample.util.sequence_util)
process_log() (Spickerer method)
process_models() (Scwrl method)
processMrbumpPkl() (ResultsSummary method)
processReflectionFile() (in module ample.util.mtz_util)
prune_residues() (in module ample.ensembler.truncation_util)
PsipredSs2Parser (class in ample.parsers.psipred_parser)
Q
queueDirectives() (ClusterRun method)
R
random_cluster() (in module ample.ensembler.cluster_util)
read() (AlignmentParser method)
read_amoptd() (in module ample.util.ample_util)
read_pdb() (residueSequenceMap method)
redundantAlternateOrigins() (OriginInfo method)
ref2target() (residueSequenceMap method)
refIncomparable() (residueSequenceMap method)
ReforiginRmsd (class in ample.util.reforigin)
reliable_sidechains() (in module ample.util.pdb_edit)
reliable_sidechains_cctbx() (in module ample.util.pdb_edit)
remodel() (RosettaModel method)
remodel_proc_map() (RosettaModel method)
removeGaps() (AlignmentParser method)
rename_chains() (in module ample.util.pdb_edit)
renumber_residues() (in module ample.util.pdb_edit)
renumber_residues_gaps() (in module ample.util.pdb_edit)
reorder_models() (in module ample.ensembler)
,
[1]
reset() (TMalignLogParser method)
(TMscoreLogParser method)
resetA3M() (AlignmentParser method)
residueSequenceMap (class in ample.util.residue_map)
resName (TheseusVariances attribute)
resSeq (ScoreVariances attribute)
(TheseusVariances attribute)
resseq() (in module ample.util.pdb_edit)
resSeqMatch() (residueSequenceMap method)
RESULTS_PKL (AMPLEBaseTest attribute)
results_section() (AmpleOutput method)
results_summary() (Spickerer method)
results_table() (ResultsSummary method)
ResultsSummary (class in ample.util.mrbump_util)
Rio (class in ample.util.rio)
RioData (class in ample.util.rio)
rm_pending_section() (AmpleOutput method)
rms() (RosettaScoreParser method)
rmsd (ModelData attribute)
(TheseusVariances attribute)
rmsd() (Maxcluster method)
rmsSorted() (RosettaScoreParser method)
RosettaFunctionConstructs (class in ample.modelling.energy_functions)
RosettaModel (class in ample.modelling.rosetta_model)
RosettaScoreData (class in ample.modelling.rosetta_model)
RosettaScoreParser (class in ample.modelling.rosetta_model)
run() (AMPLEIntegrationFramework method)
(AMPLEUnittestFramework method)
(Csymmatch method)
RUN_CLUSTER() (in module ample.util.cluster_entropy)
run_command() (in module ample.util.ample_util)
run_compare_model_list() (Maxcluster method)
run_cphasematch() (in module ample.util.cphasematch)
run_integration() (in module ample.testing.run_tests)
run_scripts() (in module ample.util.workers_util)
(RosettaModel method)
run_scripts_cluster() (in module ample.util.workers_util)
run_scripts_serial() (in module ample.util.workers_util)
run_unittest() (in module ample.testing.run_tests)
run_unittest_suite() (AMPLEIntegrationFramework method)
runCompareDirectory() (Maxcluster method)
runNcont() (Rio method)
rvapi_shutdown() (AmpleOutput method)
S
Saint2FunctionConstructs (class in ample.modelling.energy_functions)
save_amoptd() (in module ample.util.ample_util)
saveAmoptd() (in module ample.util.ample_util)
scoreOrigin() (Rio method)
ScoreVariances (class in ample.ensembler.truncation_util)
Scwrl (class in ample.util.scwrl_util)
scwrl_models() (AbinitioEnsembler method)
secondary_structure (PsipredSs2Parser attribute)
select_residues() (in module ample.util.pdb_edit)
seq_id (ModelData attribute)
Sequence (class in ample.util.sequence_util)
sequence() (in module ample.util.pdb_edit)
(Sequence method)
sequence_data() (in module ample.util.pdb_edit)
set() (TMalignLogParser method)
(TMscoreLogParser method)
set_from_dict() (RosettaModel method)
set_paths() (RosettaModel method)
set_phaser_rms_from_subcluster_score() (in module ample.ensembler)
,
[1]
setJobs() (JobServer method)
setUp() (AMPLEBaseTest method)
setup() (AmpleOutput method)
setup_console_logging() (in module ample.util.logging_util)
setup_domain_restraints() (RosettaModel method)
setup_file_logging() (in module ample.util.logging_util)
setUpClass() (ample.util.pdb_edit.Test class method)
sfcif2mtz() (CifParser method)
SIGMOID_default (RosettaFunctionConstructs attribute)
SIGMOID_gremlin (RosettaFunctionConstructs attribute)
SingleModelEnsembler (class in ample.ensembler.single_model)
slice_subcluster() (in module ample.ensembler.subcluster_util)
SORT_clusters() (in module ample.util.cluster_entropy)
sort_ensembles() (in module ample.ensembler)
,
[1]
sortResults() (ResultsSummary method)
sortResultsStatic() (ResultsSummary static method)
spaceGroup() (OriginInfo method)
Spickerer (class in ample.util.spicker)
split() (in module ample.util.cluster_entropy)
split_into_chains() (in module ample.util.pdb_edit)
split_jobs() (RosettaModel method)
split_models() (in module ample.util.ample_util)
split_pdb() (in module ample.util.pdb_edit)
split_quark() (in module ample.util.ample_util)
ssIsOK() (Rio method)
standardise() (in module ample.util.pdb_edit)
start() (JobServer method)
std_residues_cctbx() (in module ample.util.pdb_edit)
stdDev (TheseusVariances attribute)
strip() (in module ample.util.pdb_edit)
structure_fname (ModelData attribute)
structure_name (ModelData attribute)
subcluster_models() (AbinitioEnsembler method)
subcluster_models_fixed_radii() (AbinitioEnsembler method)
subcluster_models_floating_radii() (AbinitioEnsembler method)
subcluster_nmodels() (in module ample.ensembler.subcluster_util)
SubClusterer (class in ample.ensembler.subcluster)
subclusterer_factory() (AbinitioEnsembler method)
submitArrayJob() (ClusterRun method)
submitJob() (ClusterRun method)
SuiteLoader (class in ample.testing.integration_util)
(class in ample.testing.unittest_util)
summariseResults() (ResultsSummary method)
summaryString() (ResultsSummary method)
superpose_models() (Theseus method)
T
Table (class in ample.util.printTable)
target2ref() (residueSequenceMap method)
targetIncomparable() (residueSequenceMap method)
Test (class in ample.util.pdb_edit)
test_2_files() (in module ample.util.cluster_entropy)
testCheckPdbs() (Test method)
testGetInfo1() (Test method)
testGetInfo2() (Test method)
testReliableSidechains() (Test method)
testSelectResidues() (Test method)
testSelectResiduesKeepIdxs() (Test method)
testSequence1() (Test method)
testStdResidues() (Test method)
testStdResiduesCctbx() (Test method)
testStripAtomTypes() (Test method)
testStripHetatm() (Test method)
testStripHydrogen() (Test method)
testXyzCbCoordinates() (Test method)
testXyzCoordinates() (Test method)
Theseus (class in ample.util.theseus)
TheseusVariances (class in ample.util.theseus)
tm() (Maxcluster method)
tm2_make_patch() (RosettaModel method)
tm_make_files() (RosettaModel method)
tm_set_paths() (RosettaModel method)
TMalign (class in ample.util.tm_util)
TMalignLogParser (class in ample.parsers.tm_parser)
TMapps (class in ample.util.tm_util)
tmp_file_name() (in module ample.util.ample_util)
tmpFileName() (in module ample.util.ample_util)
TMscore (class in ample.util.tm_util)
tmscore (ModelData attribute)
TMscoreLogParser (class in ample.parsers.tm_parser)
tmSorted() (Maxcluster method)
to_hkl() (in module ample.util.mtz_util)
to_single_chain() (in module ample.util.pdb_edit)
toLine() (PdbAtom method)
(PdbModres method)
topFiles() (ResultsSummary method)
toPir() (Sequence method)
translate() (in module ample.util.pdb_edit)
truncate_models() (Truncator method)
Truncation (class in ample.ensembler.truncation_util)
Truncator (class in ample.ensembler.truncation_util)
U
unfinished_scripts() (in module ample.util.mrbump_util)
V
variance (ScoreVariances attribute)
(TheseusVariances attribute)
W
worker() (in module ample.util.worker)
wrapModelToNative() (Csymmatch method)
write() (AlignmentParser method)
write_config_file() (AMPLEConfigOptions method)
write_fasta() (Sequence method)
write_jobscript() (in module ample.util.mrbump_util)
write_mrbump_files() (in module ample.util.mrbump_util)
write_script() (AMPLEIntegrationFramework method)
writeFiles() (OctopusPredict method)
X
XgetJobStatus() (ClusterRun method)
Xselect_residues() (in module ample.util.pdb_edit)
Xsplit() (in module ample.util.pdb_edit)
Xstd_residues() (in module ample.util.pdb_edit)
XtestSplit() (Test method)
xyz_cb_coordinates() (in module ample.util.pdb_edit)
xyz_coordinates() (in module ample.util.pdb_edit)