Package AutoDockTools :: Module DockingParameters

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Module DockingParameters

source code

Classes

[hide private]

DockingParameters

DockingParameterFileMaker
Accept a <ligand>.pdbq and <receptor>.pdbqs and create <ligand>_<receptor>.dpf

DockingParameter4FileMaker
Accept a <ligand>.pdbqt and <receptor>.pdbqt and create <ligand>_<receptor>4.dpf

Variables

[hide private]

cluster_list = ['types', 'rmstol', 'cluster', 'analysis']

genetic_algorithm_list = ['outlev', 'seed', 'types', 'fld', 'map', 'move', 'a...

genetic_algorithm_local_search_list = ['outlev', 'seed', 'types', 'fld', 'map', 'move', 'a...

local_search_list = ['outlev', 'seed', 'types', 'fld', 'map', 'move', 'a...

simulated_annealing_list = ['outlev', 'seed', 'types', 'fld', 'map', 'move', 'a...

docking_parameter_list = ['about', 'accs', 'analysis', 'cluster', 'cycles', '...

genetic_algorithm_list4 = ['outlev', 'custom_parameter_file', 'include_1_4_int...

genetic_algorithm_local_search_list4 = ['outlev', 'custom_parameter_file', 'include_1_4_int...

genetic_algorithm_local_search_list4_with_parameter_file = ['outlev', 'parameter_file', 'include_1_4_interactio...

local_search_list4 = ['outlev', 'custom_parameter_file', 'include_1_4_int...

simulated_annealing_list4 = ['outlev', 'custom_parameter_file', 'include_1_4_int...

docking_parameter_list4 = ['about', 'accs', 'analysis', 'cluster', 'compute_un...

cluster_list4 = ['custom_parameter_file', 'ligand_types', 'rmstol', ...

genetic_algorithm_list4_1 = ['outlev', 'custom_parameter_file', 'parameter_file'...

genetic_algorithm_local_search_list4_1 = ['outlev', 'custom_parameter_file', 'parameter_file'...

genetic_algorithm_local_search_list4_1_with_parameter_file = ['outlev', 'parameter_file', 'include_1_4_interactio...

local_search_list4_1 = ['outlev', 'custom_parameter_file', 'parameter_file'...

simulated_annealing_list4_1 = ['outlev', 'custom_parameter_file', 'parameter_file'...

docking_parameter_list4_1 = ['about', 'accs', 'analysis', 'cluster', 'compute_un...

implemented = ['accs', 'about', 'analysis', 'cluster', 'compute_un...

dpo = DockingParameters('receptor.test.pdbqs', 'ligand.pdbq')

tmp_filename = '/tmp/%d.dpf' %(os.getpid())

new_dpo = DockingParameters()

Variables Details

[hide private]

cluster_list

None

Value:

['types', 'rmstol', 'cluster', 'analysis']

genetic_algorithm_list

None

Value:

['outlev', 'seed', 'types', 'fld', 'map', 'move', 'about', 'tran0', 'q
uat0']

genetic_algorithm_local_search_list

None

Value:

['outlev', 'seed', 'types', 'fld', 'map', 'move', 'about', 'tran0', 'q
uat0']

local_search_list

None

Value:

['outlev', 'seed', 'types', 'fld', 'map', 'move', 'about', 'tran0', 'q
uat0']

simulated_annealing_list

None

Value:

['outlev', 'seed', 'types', 'fld', 'map', 'move', 'about', 'tran0', 'q
uat0']

docking_parameter_list

None

Value:

['about',
 'accs',
 'analysis',
 'cluster',
 'cycles',
 'dihe0',
 'dihrf',
 'do_global_only',
...

genetic_algorithm_list4

None

Value:

['outlev',
 'custom_parameter_file',
 'include_1_4_interactions',
 'include_1_4_interactions_flag',
 'intelec',
 'seed',
 'unbound_intnbp_coeffs',
 'unbound_intnbp_coeffs_flag',
...

genetic_algorithm_local_search_list4

None

Value:

['outlev',
 'custom_parameter_file',
 'include_1_4_interactions',
 'include_1_4_interactions_flag',
 'intelec',
 'seed',
 'unbound_intnbp_coeffs',
 'unbound_intnbp_coeffs_flag',
...

genetic_algorithm_local_search_list4_with_parameter_file

None

Value:

['outlev',
 'parameter_file',
 'include_1_4_interactions',
 'include_1_4_interactions_flag',
 'intelec',
 'seed',
 'unbound_intnbp_coeffs',
 'unbound_intnbp_coeffs_flag',
...

local_search_list4

None

Value:

['outlev',
 'custom_parameter_file',
 'include_1_4_interactions',
 'include_1_4_interactions_flag',
 'intelec',
 'seed',
 'unbound_intnbp_coeffs',
 'unbound_intnbp_coeffs_flag',
...

simulated_annealing_list4

None

Value:

['outlev',
 'custom_parameter_file',
 'include_1_4_interactions',
 'include_1_4_interactions_flag',
 'intelec',
 'seed',
 'unbound_intnbp_coeffs',
 'unbound_intnbp_coeffs_flag',
...

docking_parameter_list4

None

Value:

['about',
 'accs',
 'analysis',
 'cluster',
 'compute_unbound_extended',
 'compute_unbound_extended_flag',
 'cycles',
 'dihe0',
...

cluster_list4

None

Value:

['custom_parameter_file', 'ligand_types', 'rmstol', 'cluster', 'analys
is']

genetic_algorithm_list4_1

None

Value:

['outlev',
 'custom_parameter_file',
 'parameter_file',
 'include_1_4_interactions',
 'include_1_4_interactions_flag',
 'intelec',
 'seed',
 'unbound_intnbp_coeffs',
...

genetic_algorithm_local_search_list4_1

None

Value:

['outlev',
 'custom_parameter_file',
 'parameter_file',
 'include_1_4_interactions',
 'include_1_4_interactions_flag',
 'intelec',
 'seed',
 'unbound_intnbp_coeffs',
...

genetic_algorithm_local_search_list4_1_with_parameter_file

None

Value:

['outlev',
 'parameter_file',
 'include_1_4_interactions',
 'include_1_4_interactions_flag',
 'intelec',
 'seed',
 'unbound_intnbp_coeffs',
 'unbound_intnbp_coeffs_flag',
...

local_search_list4_1

None

Value:

['outlev',
 'custom_parameter_file',
 'parameter_file',
 'include_1_4_interactions',
 'include_1_4_interactions_flag',
 'intelec',
 'seed',
 'unbound_intnbp_coeffs',
...

simulated_annealing_list4_1

None

Value:

['outlev',
 'custom_parameter_file',
 'parameter_file',
 'include_1_4_interactions',
 'include_1_4_interactions_flag',
 'intelec',
 'seed',
 'unbound_intnbp_coeffs',
...

docking_parameter_list4_1

None

Value:

['about',
 'accs',
 'analysis',
 'cluster',
 'compute_unbound_extended',
 'compute_unbound_extended_flag',
 'cycles',
 'dihe0',
...

implemented

None

Value:

['accs',
 'about',
 'analysis',
 'cluster',
 'compute_unbound_extended',
 'compute_unbound_extended_flag',
 'cycles',
 'dihe0',
...

dpo

None

Value:

DockingParameters('receptor.test.pdbqs', 'ligand.pdbq')

tmp_filename

None

Value:

'/tmp/%d.dpf' %(os.getpid())

new_dpo

None

Value:

DockingParameters()