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__init__(self,
ct,
interactive=False,
do_flips=True,
asl='',
noprot_asl='',
atoms=[],
use_xtal=False,
torsion_penalty=False,
sample_waters=True,
sample_acids=True,
freeze_existing=False,
include_initial=False,
max_comb=10000,
logging_level=1,
quiet_flag=False,
debug_flag=False,
add_labels=True,
label_pkas=False,
pH='neutral',
use_propka=True,
propka_pH=7.0,
user_states=[],
minimize=False) |
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| apply_pkas(self,
changeables,
changes,
propka_pH) |
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| assign_best_combinations(self,
ct) |
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| assign_cluster_combination(self,
ct,
icluster,
icombination) |
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| assign_state_of_changeable(self,
ct,
ichangeable,
istate) |
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| decrement_state_of_changeable(self,
ct,
ichangeable) |
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| delete_atoms(self,
ct,
atoms) |
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| enumerate_changeable_states(self,
ct) |
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| extend_targeted_to_hyds(self,
ct) |
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find_protonation_state_changes(self,
ct,
clusters='all') |
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| freeze_existing_hydrogens(self,
ct) |
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| identify_all_hbonders(self,
ct) |
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| identify_species(self,
ct) |
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| increment_state_of_changeable(self,
ct,
ichangeable) |
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| lock_protonation_states(self,
ct) |
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| minimize_hydrogens(self,
ct) |
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| optimize_cluster(self,
ct,
icluster,
assign=True) |
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| record_current_indices(self,
ct) |
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| remove_changeables_from_hbonders(self) |
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| remove_zero_order_bonds(self,
ct) |
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| run_propka(self,
changeables,
ct,
use_xtal=False) |
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| set_user_states(self,
ct) |
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| single_point_cluster(self,
ct,
icluster) |
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