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AMSConformers
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Table of contents
1. AMSConformers
2. Components
AMSConformers
Documentation
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AMSConformers
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Index
Index
_
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A
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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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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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W
_
__init__() (ConformerOptimizer method)
(CRESTGenerator method)
(GCExpander method)
(MDExpander method)
(MetadynamicsGenerator method)
(RDKitGenerator method)
(UniqueConformersAMS method)
(UniqueConformersCrest method)
(UniqueConformersRMSD method)
(UniqueConformersTFD method)
_compare_dihedrals_to_conformer_slow() (UniqueConformersAMS method)
_compute_inverse_size() (UniqueConformersCrest method)
_copy_state() (UniqueConformersCrest method)
_estimate_runtime() (CRESTGenerator method)
(GCExpander method)
(MDExpander method)
(MetadynamicsGenerator method)
(RDKitGenerator method)
_finalize_settings() (MDExpander method)
(MetadynamicsGenerator method)
_generate_geometries() (CRESTGenerator method)
(GCExpander method)
(MDExpander method)
(MetadynamicsGenerator method)
_get_dihedral_diffs_slow() (UniqueConformersAMS method)
_get_family() (ConformerOptimizer method)
(CRESTGenerator method)
(GCExpander method)
(MDExpander method)
(MetadynamicsGenerator method)
(RDKitGenerator method)
(UniqueConformersCrest method)
_get_rmsds() (GCExpander method)
_get_rmsds_double_loop() (GCExpander method)
_get_rmsds_parallel() (GCExpander method)
_get_timestep() (MDExpander method)
(MetadynamicsGenerator method)
_get_trimmed_rdmol() (UniqueConformersRMSD method)
_get_trimmed_rdmol_from_conf() (UniqueConformersRMSD method)
_get_value_indices() (UniqueConformersAMS method)
_handle_duplicates() (UniqueConformersCrest method)
_log_all_reading_errors() (UniqueConformersCrest method)
_log_candidate_info() (UniqueConformersCrest method)
_log_energy_filtering() (UniqueConformersCrest method)
_log_reading_errors() (UniqueConformersCrest method)
_md_time_from_flexibility() (MDExpander method)
(MetadynamicsGenerator method)
_rdkit_call_from_thread() (CRESTGenerator static method)
(GCExpander static method)
(MDExpander static method)
(MetadynamicsGenerator static method)
(RDKitGenerator static method)
_rerun_failed_mtdjobs() (MetadynamicsGenerator method)
_run_job() (MDExpander method)
(MetadynamicsGenerator method)
_set_constraints() (MDExpander method)
(MetadynamicsGenerator method)
_set_gotimes() (CRESTGenerator method)
(GCExpander method)
(MDExpander method)
(MetadynamicsGenerator method)
(RDKitGenerator method)
_set_timestep() (MDExpander method)
(MetadynamicsGenerator method)
_write_geometry() (ConformerOptimizer method)
A
add_conformer() (UniqueConformersAMS method)
(UniqueConformersCrest method)
(UniqueConformersRMSD method)
(UniqueConformersTFD method)
add_conformers() (UniqueConformersCrest method)
are_geometries_local_minima() (CRESTGenerator method)
(GCExpander method)
(MDExpander method)
(MetadynamicsGenerator method)
(RDKitGenerator method)
C
clear() (UniqueConformersCrest method)
ConformerOptimizer (class in scm.conformers.pestools.optimizer)
convert_key_to_camelcase() (ConformerOptimizer method)
(CRESTGenerator method)
(GCExpander method)
(MDExpander method)
(MetadynamicsGenerator method)
(RDKitGenerator method)
(UniqueConformersCrest method)
convert_key_to_underscore_case() (ConformerOptimizer method)
(CRESTGenerator method)
(GCExpander method)
(MDExpander method)
(MetadynamicsGenerator method)
(RDKitGenerator method)
(UniqueConformersCrest method)
convert_keys_to_camelcase() (ConformerOptimizer method)
(CRESTGenerator method)
(GCExpander method)
(MDExpander method)
(MetadynamicsGenerator method)
(RDKitGenerator method)
(UniqueConformersCrest method)
convert_keys_to_underscore_case() (ConformerOptimizer method)
(CRESTGenerator method)
(GCExpander method)
(MDExpander method)
(MetadynamicsGenerator method)
(RDKitGenerator method)
(UniqueConformersCrest method)
copy() (UniqueConformersCrest method)
create_json_entry() (ConformerOptimizer static method)
(CRESTGenerator static method)
(GCExpander static method)
(MDExpander static method)
(MetadynamicsGenerator static method)
(RDKitGenerator static method)
(UniqueConformersCrest static method)
create_tree() (UniqueConformersAMS method)
CRESTGenerator (class in scm.conformers.generators.crest_generators.crest_generator)
D
determine_maxgeoms() (GCExpander method)
E
estimate_gctime() (GCExpander method)
estimate_runtime() (CRESTGenerator method)
(GCExpander method)
(MDExpander method)
(MetadynamicsGenerator method)
(RDKitGenerator method)
F
filter() (UniqueConformersCrest method)
find_clusters() (UniqueConformersCrest method)
find_nth_conformer() (UniqueConformersCrest method)
fit() (UniqueConformersCrest method)
from_rdkitmol() (UniqueConformersCrest class method)
G
GCExpander (class in scm.conformers.generators.crest_generators.gc_generator)
generate() (CRESTGenerator method)
(GCExpander method)
(MDExpander method)
(MetadynamicsGenerator method)
(RDKitGenerator method)
(UniqueConformersCrest method)
geometry_writer() (ConformerOptimizer method)
get_all_energies() (UniqueConformersCrest method)
get_all_geometries() (UniqueConformersCrest method)
get_all_rmsds() (UniqueConformersCrest method)
get_conformers() (UniqueConformersCrest method)
get_cost() (UniqueConformersAMS method)
get_dendrogram() (UniqueConformersCrest method)
get_diffs_for_candidate() (UniqueConformersAMS method)
(UniqueConformersCrest method)
(UniqueConformersRMSD method)
(UniqueConformersTFD method)
get_energies() (UniqueConformersCrest method)
get_group_indices() (UniqueConformersAMS method)
get_json_settings() (ConformerOptimizer method)
(CRESTGenerator method)
(GCExpander method)
(MDExpander method)
(MetadynamicsGenerator method)
(RDKitGenerator method)
(UniqueConformersCrest method)
get_molecule() (UniqueConformersCrest method)
get_partial_cost() (UniqueConformersAMS method)
get_plot_dendrogram() (UniqueConformersCrest method)
get_rdkitmol() (UniqueConformersCrest method)
get_rmsd_time() (GCExpander method)
get_rmsds_from_frame() (UniqueConformersCrest method)
get_torsion_atoms() (UniqueConformersTFD method)
get_torsion_values() (UniqueConformersTFD method)
H
handle_input() (ConformerOptimizer method)
(CRESTGenerator method)
(GCExpander method)
(MDExpander method)
(MetadynamicsGenerator method)
(RDKitGenerator method)
(UniqueConformersCrest method)
I
indices_to_names() (UniqueConformersCrest method)
K
keep_ams_running() (ConformerOptimizer method)
L
last_timings() (ConformerOptimizer property)
M
MDExpander (class in scm.conformers.generators.crest_generators.md_expander)
MetadynamicsGenerator (class in scm.conformers.generators.crest_generators.metadynamics_generator)
molecule() (UniqueConformersCrest property)
O
optimize() (UniqueConformersCrest method)
optimize_and_filter() (CRESTGenerator method)
(GCExpander method)
(MDExpander method)
(MetadynamicsGenerator method)
(RDKitGenerator method)
optimize_conformers() (CRESTGenerator method)
(GCExpander method)
(MDExpander method)
(MetadynamicsGenerator method)
(RDKitGenerator method)
optimize_geometries() (ConformerOptimizer method)
optimize_molecules() (ConformerOptimizer method)
P
pass_settings() (ConformerOptimizer method)
(CRESTGenerator method)
(GCExpander method)
(MDExpander method)
(MetadynamicsGenerator method)
(RDKitGenerator method)
(UniqueConformersCrest method)
prepare_state() (UniqueConformersAMS method)
(UniqueConformersCrest method)
(UniqueConformersRMSD method)
(UniqueConformersTFD method)
R
RDKitGenerator (class in scm.conformers.generators.simple_generators.rdkit_generator)
rdmol() (UniqueConformersTFD property)
read() (UniqueConformersCrest method)
read_settings() (ConformerOptimizer method)
(CRESTGenerator method)
(GCExpander method)
(MDExpander method)
(MetadynamicsGenerator method)
(RDKitGenerator method)
(UniqueConformersCrest method)
remove_conformer() (UniqueConformersCrest method)
remove_high_energy() (UniqueConformersCrest method)
remove_non_minima() (UniqueConformersCrest method)
reorder() (UniqueConformersCrest method)
rmsds() (UniqueConformersCrest property)
S
score() (UniqueConformersCrest method)
set_atom_types() (ConformerOptimizer method)
set_blocknames() (ConformerOptimizer method)
(CRESTGenerator method)
(GCExpander method)
(MDExpander method)
(MetadynamicsGenerator method)
(RDKitGenerator method)
(UniqueConformersCrest method)
set_cleaning_preference() (ConformerOptimizer method)
set_convergence_quality() (CRESTGenerator method)
(GCExpander method)
(MDExpander method)
(MetadynamicsGenerator method)
(RDKitGenerator method)
set_energies() (UniqueConformersCrest method)
set_generator() (UniqueConformersCrest method)
set_max_energy() (CRESTGenerator method)
(GCExpander method)
(MDExpander method)
(MetadynamicsGenerator method)
(RDKitGenerator method)
set_maxgeoms() (GCExpander method)
set_number_initial_conformers() (RDKitGenerator method)
set_number_of_identical_mdruns() (MDExpander method)
set_number_of_starting_geometries() (MDExpander method)
set_optimizer() (CRESTGenerator method)
(GCExpander method)
(MDExpander method)
(MetadynamicsGenerator method)
(RDKitGenerator method)
set_partial_permutator_checks() (UniqueConformersAMS method)
set_preoptimizer() (CRESTGenerator method)
(GCExpander method)
(MDExpander method)
(MetadynamicsGenerator method)
(RDKitGenerator method)
set_printing_level() (CRESTGenerator method)
(GCExpander method)
(MDExpander method)
(MetadynamicsGenerator method)
(RDKitGenerator method)
set_rngseed() (CRESTGenerator method)
(GCExpander method)
(MDExpander method)
(MetadynamicsGenerator method)
(RDKitGenerator method)
set_shake() (CRESTGenerator method)
(MDExpander method)
(MetadynamicsGenerator method)
subset_indices() (UniqueConformersCrest property)
T
time_to_timestring() (CRESTGenerator static method)
(GCExpander static method)
(MDExpander static method)
(MetadynamicsGenerator static method)
(RDKitGenerator static method)
to_json() (ConformerOptimizer method)
(CRESTGenerator method)
(GCExpander method)
(MDExpander method)
(MetadynamicsGenerator method)
(RDKitGenerator method)
(UniqueConformersCrest method)
U
UniqueConformersAMS (class in scm.conformers.conformers.conformers_ams)
UniqueConformersCrest (class in scm.conformers.conformers.conformers_crest)
UniqueConformersRMSD (class in scm.conformers.conformers.conformers_rmsd)
UniqueConformersTFD (class in scm.conformers.conformers.conformers_tfd)
W
write() (UniqueConformersCrest method)
write_geometries() (RDKitGenerator method)