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A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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X
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Y
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Z
A
add() (RvapiMetadata method)
adjust_paths_of_files() (SimbadOutput method)
ALPHA (AmoreRotationScore attribute)
alt (LatticeSearchResult attribute)
AmoreRotationScore (class in simbad.core.amore_score)
AmoreRotsearchParser (class in simbad.parsers.rotsearch_parser)
angle_penalty (LatticeSearchResult attribute)
AnodeParser (class in simbad.parsers.anode_parser)
AnomScore (class in simbad.core.anode_score)
assert_hierarchy() (PdbStructure method)
B
BETA (AmoreRotationScore attribute)
C
calculate_content_ncopies_from_file() (MatthewsProbability method)
calculate_content_ncopies_from_struct() (MatthewsProbability method)
calculate_from_file() (SolventContent method)
calculate_from_struct() (SolventContent method)
calculate_niggli_cell() (LatticeSearch static method)
calculate_penalty() (simbad.lattice.lattice_search.LatticeSearch class method)
calculate_probability() (simbad.lattice.lattice_search.LatticeSearch class method)
calculate_volume_difference() (simbad.lattice.lattice_search.LatticeSearch class method)
CC_F (AmoreRotationScore attribute)
CC_F_Z_score (AmoreRotationScore attribute)
CC_I (AmoreRotationScore attribute)
CC_P (AmoreRotationScore attribute)
CC_P_Z_score (AmoreRotationScore attribute)
cell_within_tolerance() (simbad.lattice.lattice_search.LatticeSearch class method)
check_sg() (LatticeSearch static method)
citation_list_as_text (ReferenceManager attribute)
citations_as_html (ReferenceManager attribute)
citations_as_text (ReferenceManager attribute)
convert_dat_to_pdb() (in module simbad.db)
convert_pdb_to_dat() (in module simbad.db)
copy_results() (LatticeSearch method)
create_contaminant_results_tab() (SimbadOutput method)
create_graphs() (SimbadOutput static method)
create_lattice_results_tab() (SimbadOutput method)
create_log_tab() (SimbadOutput method)
create_morda_db_results_tab() (SimbadOutput method)
create_table() (SimbadOutput method)
D
dano_peak_height (AnomScore attribute)
(MrScore attribute)
dat_path (AmoreRotationScore attribute)
(DatModelScore attribute)
(PhaserRotationScore attribute)
DatModelScore (class in simbad.core.dat_score)
display_citation_tab() (SimbadOutput method)
display_gui (SimbadOutput attribute)
display_results() (SimbadOutput method)
display_summary_tab() (SimbadOutput method)
download_results() (LatticeSearch method)
E
exit_error() (in module simbad.exit)
F
f (Phaser attribute)
,
[1]
FileCollection (class in simbad.util.simbad_results)
final_r_fact (MrScore attribute)
final_r_free (MrScore attribute)
find_simbad_dat_files() (in module simbad.db)
fix_path() (SimbadOutput method)
from_file() (PdbStructure method)
from_pdb_code() (PdbStructure method)
G
GAMMA (AmoreRotationScore attribute)
GENERAL (ReferenceManager.SECTIONS attribute)
get_arguments_from_log() (SimbadOutput static method)
get_chunk_size() (in module simbad.rotsearch)
,
[1]
get_files() (SimbadResults method)
get_mrbump_ensemble() (in module simbad.util)
,
[1]
get_pdb_content() (PdbStructure static method)
get_sequence() (in module simbad.util)
,
[1]
get_sequence_info (PdbStructure attribute)
get_total_chunk_cycles() (in module simbad.rotsearch)
,
[1]
H
hires (Phaser attribute)
,
[1]
hklin (Phaser attribute)
,
[1]
I
i (Phaser attribute)
,
[1]
Icp (AmoreRotationScore attribute)
init_from_ccp4i2_xml() (SimbadOutput method)
integration_box (PdbStructure attribute)
intrad (DatModelScore attribute)
is_valid_dat() (in module simbad.db)
K
keep_first_chain_only() (PdbStructure method)
L
lattice_db_fname (LatticeSearch attribute)
lattice_mr_results (SimbadResults attribute)
lattice_results (SimbadResults attribute)
LatticeSearch (class in simbad.lattice.lattice_search)
LatticeSearchResult (class in simbad.core.lattice_score)
length_penalty (LatticeSearchResult attribute)
llg (PhaserRotationScore attribute)
logfile (Phaser attribute)
(SimbadOutput attribute)
M
MatthewsProbability (class in simbad.util.matthews_prob)
methods_as_html (ReferenceManager attribute)
model_dir (LatticeSearch attribute)
molecular_weight (PdbStructure attribute)
molrep_score (MrScore attribute)
molrep_tfscore (MrScore attribute)
MolrepParser (class in simbad.parsers.molrep_parser)
MR (ReferenceManager.SECTIONS attribute)
mr_job_succeeded() (in module simbad.rotsearch)
,
[1]
MrScore (class in simbad.core.mr_score)
mw_diff (DatModelScore attribute)
N
n_results (RvapiMetadata attribute)
nchains (PdbStructure attribute)
nearest_atom (AnomScore attribute)
(MrScore attribute)
nmol (DatModelScore attribute)
(Phaser attribute)
no_stdout() (in module simbad.util.matthews_prob)
nres (PdbStructure attribute)
Number_of_rotation_searches_producing_peak (AmoreRotationScore attribute)
O
output_files() (in module simbad.util)
,
[1]
output_log_files() (SimbadOutput method)
output_result_files() (SimbadOutput method)
P
pdb_code (AmoreRotationScore attribute)
(DatModelScore attribute)
(LatticeSearchResult attribute)
(MrScore attribute)
(PhaserRotationScore attribute)
pdb_in_results() (LatticeSearch static method)
pdb_path (LatticeSearchResult attribute)
pdbin (Phaser attribute)
,
[1]
pdbout (Phaser attribute)
PdbStructure (class in simbad.util.pdb_util)
Phaser (class in simbad.rotsearch.phaser_rotation_search)
phaser_llg (MrScore attribute)
phaser_rfz (MrScore attribute)
phaser_tfz (MrScore attribute)
PhaserParser (class in simbad.parsers.phaser_parser)
PhaserRotationScore (class in simbad.core.phaser_score)
PhaserRotsearchParser (class in simbad.parsers.rotsearch_parser)
probability_score (LatticeSearchResult attribute)
R
read_dat() (in module simbad.db)
ReferenceManager (class in simbad.util.reference_manager)
ReferenceManager.SECTIONS (class in simbad.util.reference_manager)
REFINEMENT (ReferenceManager.SECTIONS attribute)
RefmacParser (class in simbad.parsers.refmac_parser)
rel_path_for_ccp4online() (SimbadOutput method)
rel_path_for_jscofe() (SimbadOutput method)
result_by_score_from_csv() (in module simbad.util)
,
[1]
RF_F (AmoreRotationScore attribute)
rfz (PhaserRotationScore attribute)
ROTATION (ReferenceManager.SECTIONS attribute)
rotation_search_factory() (in module simbad.rotsearch)
,
[1]
run() (Phaser method)
RvapiMetadata (class in simbad.util.pyrvapi_results)
S
save() (PdbStructure method)
save_citations_to_file() (ReferenceManager method)
save_document() (SimbadOutput method)
ScoreBase (class in simbad.core)
,
[1]
search() (LatticeSearch method)
SEC_TAG (ReferenceManager attribute)
select_chain_by_id() (PdbStructure method)
select_chain_by_idx() (PdbStructure method)
set_crystal_symmetry() (PdbStructure method)
setup_references() (ReferenceManager method)
setup_sections() (ReferenceManager method)
sigf (Phaser attribute)
,
[1]
sigi (Phaser attribute)
,
[1]
simbad (module)
simbad.chemistry (module)
simbad.core (module)
,
[1]
simbad.core.amore_score (module)
simbad.core.anode_score (module)
simbad.core.dat_score (module)
simbad.core.lattice_score (module)
simbad.core.mr_score (module)
simbad.core.phaser_score (module)
simbad.db (module)
simbad.exit (module)
simbad.lattice (module)
,
[1]
simbad.lattice.lattice_search (module)
simbad.parsers (module)
simbad.parsers.anode_parser (module)
simbad.parsers.molrep_parser (module)
simbad.parsers.phaser_parser (module)
simbad.parsers.refmac_parser (module)
simbad.parsers.rotsearch_parser (module)
simbad.rotsearch (module)
,
[1]
simbad.rotsearch.phaser_rotation_search (module)
simbad.util (module)
,
[1]
simbad.util.matthews_prob (module)
simbad.util.pdb_util (module)
simbad.util.pyrvapi_results (module)
simbad.util.reference_manager (module)
simbad.util.simbad_results (module)
simbad.version (module)
SimbadOutput (class in simbad.util.pyrvapi_results)
SimbadResults (class in simbad.util.simbad_results)
solvent (DatModelScore attribute)
(Phaser attribute)
,
[1]
SolventContent (class in simbad.util.matthews_prob)
standardize() (PdbStructure method)
store_entry_in_rvapi_meta() (SimbadOutput method)
submit_chunk() (in module simbad.util)
,
[1]
summarize() (LatticeSearch method)
summarize_result() (in module simbad.util)
,
[1]
summary (SimbadOutput attribute)
T
timeout (Phaser attribute)
tmp_dir() (in module simbad.util)
,
[1]
tmp_file() (in module simbad.util)
,
[1]
to_json() (RvapiMetadata method)
top_files() (SimbadResults method)
total_penalty (LatticeSearchResult attribute)
U
unit_cell (LatticeSearchResult attribute)
V
volume_difference (LatticeSearchResult attribute)
W
webserver_uri (SimbadOutput attribute)
work_dir (Phaser attribute)
(SimbadOutput attribute)
(SimbadResults attribute)
X
x (DatModelScore attribute)
Y
y (DatModelScore attribute)
Z
z (DatModelScore attribute)