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X
A
a3mToTrimmed() (AlignmentParser method)
ab_initio_cmd() (RosettaModel method)
ab_initio_model() (RosettaModel method)
add_cluster_submit_options() (in module ample.util.argparse_util)
add_cmd_options() (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_ensembler_options() (in module ample.util.argparse_util)
add_general_options() (in module ample.util.argparse_util)
add_missing_single_chain_ids() (in module ample.util.pdb_edit)
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_mafft() (in module ample.modelling.rosetta_model)
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.modelling (module)
,
[1]
ample.modelling.energy_functions (module)
ample.modelling.multimer_definitions (module)
ample.modelling.octopus_predict (module)
ample.modelling.rosetta_model (module)
ample.modelling.rosetta_scorer (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.unittest_util (module)
ample.util (module)
,
[1]
ample.util.ample_util (module)
ample.util.argparse_util (module)
ample.util.benchmark_util (module)
ample.util.ccp4 (module)
ample.util.cif_parser (module)
ample.util.clusterize (module)
ample.util.cphasematch (module)
ample.util.csymmatch (module)
ample.util.exit_util (module)
ample.util.logging_util (module)
ample.util.mrbump_cmd (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.process_models (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.theseus (module)
ample.util.tm_util (module)
ample.util.version (module)
ample.util.worker (module)
ample.util.workers_util (module)
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)
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)
BoolAction (class in ample.util.argparse_util)
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)
calcAllAtom() (Rio method)
calcRio() (Rio method)
calculate() (ReforiginRmsd method)
calpha_only() (in module ample.util.pdb_edit)
canonicalise() (Sequence method)
ccmtzOrigin() (in module ample.util.phenixer)
CCP4 (class in ample.util.ccp4)
CCP4RootDirectory (class in ample.util.ccp4)
CCP4Version (class in ample.util.ccp4)
chain_data() (in module ample.util.sequence_util)
chain_id_is_blank() (in module ample.util.pdb_edit)
chain_sequence() (in module ample.util.sequence_util)
check_content() (PsipredSs2Parser method)
check_models() (in module ample.util.process_models)
check_models_dir() (in module ample.util.process_models)
check_sequences_match() (in module ample.util.process_models)
checkContent() (PsipredSs2Parser method)
CheckModelsResult (class in ample.util.process_models)
CifParser (class in ample.util.cif_parser)
cleanUpArrayJob() (ClusterRun method)
cluster_script() (in module ample.util.benchmark_util)
ClusterRun (class in ample.util.clusterize)
cmd_add_restraints() (RosettaModel method)
compare_structures() (TMalign method)
(TMscore method)
comparison() (TMapps method)
core (TheseusVariances attribute)
create_broker_definition_file() (RosettaModel method)
create_multimer_constraints_file() (RosettaModel method)
create_multimer_flagsfile() (RosettaModel method)
create_multimer_symmetry_file() (RosettaModel method)
CRITICAL (LogColors attribute)
CrystalInfo (class in ample.util.pdb_model)
Csymmatch (class in ample.util.csymmatch)
cutoff() (ample.modelling.energy_functions.DynamicDistances class method)
D
DEBUG (LogColors attribute)
DEFAULT (LogColors attribute)
(Saint2FunctionConstructs attribute)
del_column() (in module ample.util.mtz_util)
disable_logging() (in module ample.util.ample_util)
do_multimer_modelling() (RosettaModel method)
do_nmr_remodel() (RosettaModel method)
DsspParser (class in ample.parsers.dssp_parser)
DynamicDistances (class in ample.modelling.energy_functions)
E
empty_job_queue() (JobServer method)
entries (TMapps attribute)
ERROR (LogColors attribute)
executable (TMapps attribute)
exit_error() (in module ample.util.exit_util)
extract_and_validate_models() (in module ample.util.process_models)
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_tar() (in module ample.util.ample_util)
extract_zip() (in module ample.util.ample_util)
F
FADE (RosettaFunctionConstructs attribute)
FADE_default (RosettaFunctionConstructs attribute)
fasta_str() (Sequence method)
filename_append() (in module ample.util.ample_util)
FileNotFoundError
FilePathAction (class in ample.util.argparse_util)
find_binary() (RosettaModel method)
find_exe() (in module ample.util.ample_util)
findChunks() (Rio method)
findOrigin() (Rio method)
fixpath() (in module ample.util.benchmark_util)
FLAT_HARMONIC (RosettaFunctionConstructs attribute)
format() (LogColorFormatter method)
format_num() (Table method)
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
GAUSSIAN (RosettaFunctionConstructs attribute)
gdtha (ModelData attribute)
(TMscoreLogParser attribute)
gdtts (ModelData attribute)
(TMscoreLogParser attribute)
generate_fragments() (RosettaModel method)
generate_seeds() (RosettaModel method)
generateMap() (in module ample.util.phenixer)
get_bin_dir() (RosettaModel method)
get_info() (in module ample.util.pdb_edit)
get_labels() (in module ample.util.mtz_util)
get_max_width() (Table method)
get_rfree() (in module ample.util.mtz_util)
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_model_import() (in module ample.util.process_models)
handle_starttag() (ParseFileUrl method)
helixFromContacts() (Rio method)
helixFromPdbs() (Rio method)
I
ideal_helices() (in module ample.util.ample_util)
idealize_cmd() (RosettaModel method)
idealize_models() (RosettaModel method)
idealize_pdbout() (RosettaModel method)
idx (TheseusVariances attribute)
is_exe() (in module ample.util.ample_util)
is_file() (in module ample.util.ample_util)
isFloating() (OriginInfo method)
J
JobServer (class in ample.util.workers_util)
K
keep_matching() (in module ample.util.pdb_edit)
keyword_dict() (in module ample.util.mrbump_cmd)
L
length() (Sequence method)
load_suite() (SuiteLoader method)
log_fname (ModelData attribute)
LogColorFormatter (class in ample.util.logging_util)
LogColors (class in ample.util.logging_util)
M
main() (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)
maxsub (ModelData attribute)
(TMscoreLogParser attribute)
maxsub() (RosettaScoreParser method)
maxsub_sorted() (RosettaScoreParser method)
merge() (in module ample.util.pdb_edit)
merge_chains() (in module ample.util.pdb_edit)
merge_mtz() (in module ample.util.cphasematch)
merge_mtz_cctbx() (in module ample.util.cphasematch)
method (TMapps attribute)
mk_native_files() (MRinfo method)
model_fname (ModelData attribute)
model_from_flagsfile() (RosettaModel method)
model_name (ModelData attribute)
ModelData (class in ample.util.tm_util)
molecular_weight() (in module ample.util.pdb_edit)
monitorQueue() (ClusterRun method)
MPE (MRinfo attribute)
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
nonRedundantAlternateOrigins() (OriginInfo method)
nr_residues_common (ModelData attribute)
(TMalignLogParser attribute)
(TMscoreLogParser attribute)
num_atoms_and_residues() (in module ample.util.pdb_edit)
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)
originShift (MRinfo attribute)
P
parse() (DsspParser method)
(PsipredSs2Parser method)
(TMalignLogParser method)
(TMscoreLogParser method)
parse_cphasematch_log() (in module ample.util.cphasematch)
parse_file() (RosettaScoreParser method)
parse_variances() (Theseus method)
ParseFileUrl (class in ample.modelling.octopus_predict)
parseLog() (Csymmatch method)
parseNcontLog() (Rio 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)
pirStr() (Sequence method)
place_native_pdb() (in module ample.util.cphasematch)
pprint_table() (Table method)
preparePlacedPdb() (ReforiginRmsd method)
process_cmd_list() (RosettaModel static method)
process_command_line() (in module ample.util.argparse_util)
process_directory() (Scwrl method)
process_fasta() (in module ample.util.sequence_util)
process_models() (Scwrl method)
process_multimer_models() (RosettaModel method)
processReflectionFile() (in module ample.util.mtz_util)
PsipredSs2Parser (class in ample.parsers.psipred_parser)
Q
queueDirectives() (ClusterRun method)
R
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)
reset() (TMalignLogParser method)
(TMscoreLogParser method)
resetA3M() (AlignmentParser method)
residueSequenceMap (class in ample.util.residue_map)
resName (TheseusVariances attribute)
resSeq (TheseusVariances attribute)
resseq() (in module ample.util.pdb_edit)
resSeqMatch() (residueSequenceMap method)
Rio (class in ample.util.rio)
RioData (class in ample.util.rio)
rms() (RosettaScoreParser method)
rms_sorted() (RosettaScoreParser method)
rmsd (ModelData attribute)
(TMalignLogParser attribute)
(TMscoreLogParser attribute)
(TheseusVariances attribute)
RosettaFunctionConstructs (class in ample.modelling.energy_functions)
RosettaModel (class in ample.modelling.rosetta_model)
RosettaScoreData (class in ample.modelling.rosetta_scorer)
RosettaScoreParser (class in ample.modelling.rosetta_scorer)
run() (AMPLEUnittestFramework method)
(Csymmatch method)
run_command() (in module ample.util.ample_util)
run_cphasematch() (in module ample.util.cphasematch)
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)
runNcont() (Rio 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)
Scwrl (class in ample.util.scwrl_util)
secondary_structure (PsipredSs2Parser attribute)
select_residues() (in module ample.util.pdb_edit)
seq_id (ModelData attribute)
(TMalignLogParser attribute)
Sequence (class in ample.util.sequence_util)
sequence() (in module ample.util.sequence_util)
(Sequence method)
sequence_data() (in module ample.util.sequence_util)
set() (TMalignLogParser method)
(TMscoreLogParser method)
set_from_dict() (RosettaModel method)
set_paths() (RosettaModel method)
setJobs() (JobServer method)
setup_console_logging() (in module ample.util.logging_util)
setup_domain_restraints() (RosettaModel method)
setup_file_logging() (in module ample.util.logging_util)
setup_logging() (in module ample.util.logging_util)
sfcif2mtz() (CifParser method)
shelxe_exe (MRinfo attribute)
SIGMOID_default (RosettaFunctionConstructs attribute)
SIGMOID_gremlin (RosettaFunctionConstructs attribute)
single_chain_models_with_same_sequence() (in module ample.util.process_models)
single_ensemble (CheckModelsResult attribute)
spaceGroup() (OriginInfo method)
split_into_chains() (in module ample.util.pdb_edit)
split_jobs() (RosettaModel method)
split_pdb() (in module ample.util.pdb_edit)
split_quark_alldecoy() (in module ample.util.process_models)
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)
stem (MRinfo attribute)
strip() (in module ample.util.pdb_edit)
structure (TMapps attribute)
structure_fname (ModelData attribute)
structure_name (ModelData attribute)
submitArrayJob() (ClusterRun method)
submitJob() (ClusterRun method)
SuiteLoader (class in ample.testing.unittest_util)
superpose_models() (Theseus method)
T
Table (class in ample.util.printTable)
target2ref() (residueSequenceMap method)
targetIncomparable() (residueSequenceMap method)
Theseus (class in ample.util.theseus)
TheseusVariances (class in ample.util.theseus)
tm (TMalignLogParser attribute)
(TMscoreLogParser attribute)
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)
to_hkl() (in module ample.util.mtz_util)
toLine() (PdbAtom method)
(PdbModres method)
toPir() (Sequence method)
translate() (in module ample.util.pdb_edit)
V
variance (TheseusVariances attribute)
W
WARNING (LogColors attribute)
wMPE (MRinfo attribute)
work_dir (MRinfo attribute)
(TMapps attribute)
worker() (in module ample.util.worker)
wrapModelToNative() (Csymmatch method)
write() (AlignmentParser method)
write_fasta() (Sequence method)
writeFiles() (OctopusPredict method)
X
xyz_cb_coordinates() (in module ample.util.pdb_edit)
xyz_coordinates() (in module ample.util.pdb_edit)