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Identifier Index

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P

pA_lower() (in specific_analyses.relax_disp.parameter_object)	pattern_eol_string (in bmrblib.pystarlib.Text)	plotting (in pipe_control)
pack_back_calc_r2eff() (in specific_analyses.relax_disp.data)	pattern_eoline_etcet (in bmrblib.pystarlib.Text)	Polak_ribiere (in minfx.polak_ribiere_cg)
pack_data() (in pipe_control.relax_data)	pattern_nmrView_compress_empty (in bmrblib.pystarlib.Text)	polak_ribiere() (in minfx.polak_ribiere_cg)
pack_structs() (in Internal)	pattern_nmrView_compress_questionmark (in bmrblib.pystarlib.Text)	polak_ribiere_cg (in minfx)
package() (in scons.distrib)	pattern_quoted (in bmrblib.pystarlib.Text)	Polak_ribiere_plus (in minfx.polak_ribiere_plus_cg)
package_checking (in test_suite.unit_tests)	pattern_quoted_2 (in bmrblib.pystarlib.Text)	polak_ribiere_plus() (in minfx.polak_ribiere_plus_cg)
package_info() (in Info_box)	pattern_quotes_needed (in bmrblib.pystarlib.Text)	polak_ribiere_plus_cg (in minfx)
PackageTestCase (in test_suite.unit_tests.package_checking)	pattern_quotes_needed_2 (in bmrblib.pystarlib.Text)	pop_up_menu() (in LogCtrl)
packBytesAsPyFloat() (in lib.float)	pattern_s_quote (in bmrblib.pystarlib.Text)	populate() (in DCObject)
padw2 (in lib.text.gui)	pattern_save_begin (in bmrblib.pystarlib.Text)	populate_self() (in Interpreter)
page_index_from_bundle() (in Analysis_controller)	pattern_save_begin_nws (in bmrblib.pystarlib.Text)	pos_inf (in lib.float)
page_name_from_bundle() (in Analysis_controller)	pattern_save_end (in bmrblib.pystarlib.Text)	PosEpsilonDenorm (in lib.float)
pages (in Clore90)	pattern_save_end_nws (in bmrblib.pystarlib.Text)	PosEpsilonNorm (in lib.float)
pages (in Delaglio95)	pattern_semicolon_block (in bmrblib.pystarlib.Text)	PosInf (in lib.float)
pages (in LipariSzabo82a)	pattern_single_qoute (in bmrblib.pystarlib.Text)	PosMax (in lib.float)
pages (in LipariSzabo82b)	pattern_tag_name (in bmrblib.pystarlib.Text)	PosNaN (in lib.float)
pages (in Ref)	pattern_tag_name_nws (in bmrblib.pystarlib.Text)	PosNaN_A (in lib.float)
pages (in dAuvergneGooley03)	pattern_tagname_2 (in bmrblib.pystarlib.Text)	PosNaN_B (in lib.float)
pages (in dAuvergneGooley06)	pattern_tags_loop (in bmrblib.pystarlib.Text)	PosNaN_C (in lib.float)
pages (in dAuvergneGooley07)	pattern_tags_loop_2 (in bmrblib.pystarlib.Text)	post_input() (in Float_ctrl)
pages (in dAuvergneGooley08a)	pattern_tagtable_loop (in bmrblib.pystarlib.Text)	post_reset() (in Analysis_controller)
pages (in dAuvergneGooley08b)	pattern_tagtable_loop_2 (in bmrblib.pystarlib.Text)	post_run() (in Multi_processor)
palmer (in pipe_control)	pattern_tagtable_loop_nws (in bmrblib.pystarlib.Text)	post_run() (in Processor)
palmer (in test_suite.system_tests)	pattern_tagtable_stop (in bmrblib.pystarlib.Text)	post_run() (in Uni_processor)
Palmer (in test_suite.system_tests.palmer)	pattern_tagtable_stop_2 (in bmrblib.pystarlib.Text)	PosZero (in lib.float)
palmer (in user_functions)	pattern_unquoted_find() (in bmrblib.pystarlib.Text)	potential (in target_functions)
PAM250 (in lib.sequence_alignment.substitution_matrices)	pattern_word (in bmrblib.pystarlib.Text)	pre_input() (in Float_ctrl)
PAM250_SEQ (in lib.sequence_alignment.substitution_matrices)	pca (in lib.structure)	pre_ops() (in BaseSaveframe)
PARAGRAPH (in lib.text.string)	pca() (in pipe_control.structure.main)	pre_ops() (in AutoRelaxationSaveframe)
paragraph_atom_id (in user_functions.structure)	pca_analysis() (in lib.structure.pca)	pre_ops() (in HeteronuclNOESaveframe)
paragraph_displace_id (in user_functions.structure)	pcs (in lib.alignment)	pre_ops() (in HeteronuclNOESaveframe_v2_1)
paragraph_multi_struct (in user_functions.structure)	pcs (in pipe_control)	pre_ops() (in HeteronuclT1Saveframe_v2_1)
param_conversion() (in specific_analyses.relax_disp.parameters)	pcs (in test_suite.system_tests)	pre_ops() (in HeteronuclT2Saveframe_v2_1)
param_conversion() (in Test_b14)	Pcs (in test_suite.system_tests.pcs)	pre_run() (in Multi_processor)
param_conversion() (in Test_cr72)	pcs (in user_functions)	pre_run() (in Processor)
param_conversion() (in Test_dpl94)	pcs_constant() (in lib.physical_constants)	pre_run_directory() (in Auto_relax_disp)
param_conversion() (in Test_it99)	pcs_constant_grad() (in lib.alignment.pcs)	pre_run_parameters() (in Relax_disp)
param_conversion() (in Test_lm63)	pcs_numeric_qr_int_double_rotor() (in lib.frame_order.double_rotor)	prepending_string (in bmrblib.pystarlib.Text)
param_conversion() (in Test_m61)	pcs_numeric_qr_int_iso_cone() (in lib.frame_order.iso_cone)	preview_file() (in File_element)
param_conversion() (in Test_m61b)	pcs_numeric_qr_int_iso_cone_torsionless() (in lib.frame_order.iso_cone_torsionless)	preview_file() (in Selector_file)
param_conversion() (in Test_mmq_cr72)	pcs_numeric_qr_int_pseudo_ellipse() (in lib.frame_order.pseudo_ellipse)	preview_file() (in Selector_file_multiple)
param_conversion() (in Test_mp05)	pcs_numeric_qr_int_pseudo_ellipse_torsionless() (in lib.frame_order.pseudo_ellipse_torsionless)	print_data() (in minfx.line_search.more_thuente)
param_conversion() (in Test_ns_cpmg_2site_3d)	pcs_numeric_qr_int_rotor() (in lib.frame_order.rotor)	print_data() (in minfx.line_search.nocedal_wright_interpol)
param_conversion() (in Test_ns_cpmg_2site_expanded)	pcs_numeric_quad_int_double_rotor() (in lib.frame_order.double_rotor)	print_data() (in minfx.line_search.nocedal_wright_wolfe)
param_conversion() (in Test_tap03)	pcs_numeric_quad_int_iso_cone() (in lib.frame_order.iso_cone)	print_elapsed_time() (in lib.timing)
param_conversion() (in Test_tp02)	pcs_numeric_quad_int_iso_cone_torsionless() (in lib.frame_order.iso_cone_torsionless)	print_frame_order_2nd_degree() (in lib.frame_order.format)
param_conversion() (in Test_tsmfk01)	pcs_numeric_quad_int_pseudo_ellipse() (in lib.frame_order.pseudo_ellipse)	print_iter() (in minfx.base_classes)
param_index_to_param_info() (in specific_analyses.relax_disp.parameters)	pcs_numeric_quad_int_pseudo_ellipse_torsionless() (in lib.frame_order.pseudo_ellipse_torsionless)	print_model_title() (in API_base)
Param_list (in specific_analyses.parameter_object)	pcs_numeric_quad_int_rotor() (in lib.frame_order.rotor)	print_model_title() (in Model_free)
param_model_index() (in specific_analyses.n_state_model.parameters)	pcs_pivot_motion_double_rotor_qr_int() (in lib.frame_order.double_rotor)	print_model_title() (in Relax_disp)
param_num() (in specific_analyses.frame_order.parameters)	pcs_pivot_motion_double_rotor_quad_int() (in lib.frame_order.double_rotor)	print_nice() (in Test_kronecker_product)
param_num() (in specific_analyses.n_state_model.parameters)	pcs_pivot_motion_full_qr_int() (in lib.frame_order.matrix_ops)	print_results() (in Frame_order_analysis)
param_num() (in specific_analyses.relax_disp.parameters)	pcs_pivot_motion_full_quad_int() (in lib.frame_order.matrix_ops)	print_sys_info() (in info)
paramag (in pipe_control)	pcs_pivot_motion_rotor_qr_int() (in lib.frame_order.rotor)	print_time() (in lib.timing)
paramag (in user_functions)	pcs_pivot_motion_rotor_quad_int() (in lib.frame_order.rotor)	printout() (in Method_of_multipliers)
paramag_centre (in lib.alignment)	pcs_pivot_motion_torsionless_qr_int() (in lib.frame_order.matrix_ops)	PROC (in test_suite.system_tests.frame_order)
paramag_info() (in N_state_opt)	pcs_pivot_motion_torsionless_quad_int() (in lib.frame_order.matrix_ops)	PROC (in test_suite.system_tests.model_free)
parameter_object (in specific_analyses.consistency_tests)	pcs_tensor() (in lib.alignment.pcs)	process() (in DCDetails)
parameter_object (in specific_analyses.frame_order)	pdb_model() (in specific_analyses.frame_order.uf)	process() (in DCIntegrals)
parameter_object (in specific_analyses.jw_mapping)	pdb_read (in lib.structure)	process() (in DCObject)
parameter_object (in specific_analyses.model_free)	pdb_write (in lib.structure)	process() (in DCParams)
parameter_object (in specific_analyses.n_state_model)	peak_intensity (in gui.wizards)	process() (in DCResults)
parameter_object (in specific_analyses.noe)	peak_intensity_type() (in pipe_control.relax_data)	process() (in DCSampleInfo)
parameter_object (in specific_analyses)	Peak_intensity_wizard (in gui.wizards.peak_intensity)	process_click() (in About_base)
parameter_object (in specific_analyses.relax_disp)	Peak_list (in lib.spectrum.objects)	process_mass() (in lib.periodic_table)
parameter_object (in specific_analyses.relax_fit)	peak_list (in lib.spectrum)	process_result() (in Multi_processor)
parameters (in specific_analyses.frame_order)	peak_lists (in test_suite.system_tests)	process_symbol() (in lib.periodic_table)
parameters (in specific_analyses.model_free)	Peak_lists (in test_suite.system_tests.peak_lists)	processor (in multi)
parameters (in specific_analyses.n_state_model)	peak_wizard_launch() (in Auto_noe)	Processor (in multi.processor)
parameters (in specific_analyses.relax_disp)	peak_wizard_launch() (in Auto_relax_disp)	Processor_box (in multi)
parameters (in specific_analyses.relax_fit)	peak_wizard_launch() (in Auto_rx)	processor_io (in multi)
params (in Local_tm_list)	pec (in lib.geometry)	processor_name() (in Info_box)
params (in Mf_list)	pec() (in lib.geometry.pec)	processor_size() (in Processor)
params (in Disp_model_list)	per_atom_rmsd() (in lib.structure.statistics)	processor_size() (in Uni_processor)
params (in Model_list)	periodic_table (in lib)	profile_module (in dep_check)
PARAMS_CHEM_SHIFT_DIFF (in lib.dispersion.variables)	Periodic_table (in lib.periodic_table)	progress (in lib.text)
PARAMS_CHEM_SHIFT_DIFF_MMQ (in lib.dispersion.variables)	periodic_table (in lib.periodic_table)	progress_meter() (in lib.text.progress)
PARAMS_GLOBAL (in lib.dispersion.variables)	permute_axes() (in specific_analyses.frame_order.uf)	Prompt (in gui.relax_prompt)
PARAMS_R1 (in lib.dispersion.variables)	phi_ex (in lib.text.gui)	prompt
PARAMS_R20 (in lib.dispersion.variables)	phi_exB (in lib.text.gui)	prompt() (in prompt.interpreter)
PARAMS_SPIN (in lib.dispersion.variables)	phi_exC (in lib.text.gui)	prompt_colour_off() (in Interpreter)
parse() (in File)	phi_max() (in Cosine)	prompt_colour_on() (in Interpreter)
parse() (in TagTable)	phi_max() (in Elliptic)	protected_exec() (in gui.misc)
parse_noe_restraints() (in lib.software.xplor)	phi_max() (in Iso_cone)	Protocol_mode_sel_window (in gui.analyses.auto_model_free)
parse_noe_restraints() (in pipe_control.noesy)	phi_max() (in Pseudo_elliptic)	prototype (in data_store)
parse_token() (in lib.selection)	phi_max() (in Pseudo_elliptic2)	Prototype (in data_store.prototype)
parse_version() (in Star_version)	phi_max() (in Square)	prune_mol() (in Mol_res_spin_tree)
part_int_daeg1_pseudo_ellipse_00() (in lib.frame_order.pseudo_ellipse)	phi_max() (in Zig_zag)	prune_res() (in Mol_res_spin_tree)
part_int_daeg1_pseudo_ellipse_00() (in lib.frame_order.pseudo_ellipse_torsionless)	physical_constants (in lib)	prune_spin() (in Mol_res_spin_tree)
part_int_daeg1_pseudo_ellipse_11() (in lib.frame_order.pseudo_ellipse)	pipe (in user_functions)	PS1_COLOUR (in prompt.interpreter)
part_int_daeg1_pseudo_ellipse_11() (in lib.frame_order.pseudo_ellipse_torsionless)	pipe_bundle() (in Pipe_editor)	PS1_ORIG (in prompt.interpreter)
part_int_daeg1_pseudo_ellipse_22() (in lib.frame_order.pseudo_ellipse)	pipe_centre_of_mass() (in pipe_control.structure.mass)	PS2_COLOUR (in prompt.interpreter)
part_int_daeg1_pseudo_ellipse_22() (in lib.frame_order.pseudo_ellipse_torsionless)	pipe_container (in data_store)	PS2_ORIG (in prompt.interpreter)
part_int_daeg1_pseudo_ellipse_free_rotor_22() (in lib.frame_order.pseudo_ellipse_free_rotor)	pipe_control	PS3_COLOUR (in prompt.interpreter)
part_int_daeg2_pseudo_ellipse_00() (in lib.frame_order.pseudo_ellipse)	pipe_delete() (in Pipe_editor)	PS3_ORIG (in prompt.interpreter)
part_int_daeg2_pseudo_ellipse_04() (in lib.frame_order.pseudo_ellipse)	pipe_deletion() (in Analysis_controller)	pseudo_ellipse (in lib.frame_order)
part_int_daeg2_pseudo_ellipse_08() (in lib.frame_order.pseudo_ellipse)	PIPE_DESC (in pipe_control.pipes)	pseudo_ellipse_free_rotor (in lib.frame_order)
part_int_daeg2_pseudo_ellipse_11() (in lib.frame_order.pseudo_ellipse)	PIPE_DESC_LIST (in pipe_control.pipes)	pseudo_ellipse_torsionless (in lib.frame_order)
part_int_daeg2_pseudo_ellipse_13() (in lib.frame_order.pseudo_ellipse)	pipe_editor (in gui)	Pseudo_elliptic (in lib.structure.cones)
part_int_daeg2_pseudo_ellipse_22() (in lib.frame_order.pseudo_ellipse)	Pipe_editor (in gui.pipe_editor)	Pseudo_elliptic2 (in lib.structure.cones)
part_int_daeg2_pseudo_ellipse_26() (in lib.frame_order.pseudo_ellipse)	pipe_loop() (in pipe_control.pipes)	pseudoatom_loop() (in pipe_control.mol_res_spin)
part_int_daeg2_pseudo_ellipse_40() (in lib.frame_order.pseudo_ellipse)	pipe_names() (in pipe_control.pipes)	pubmed_id (in Bieri11)
part_int_daeg2_pseudo_ellipse_44() (in lib.frame_order.pseudo_ellipse)	pipe_switch() (in Analysis_controller)	pubmed_id (in Delaglio95)
part_int_daeg2_pseudo_ellipse_48() (in lib.frame_order.pseudo_ellipse)	pipe_switch() (in Pipe_editor)	pubmed_id (in Ref)
part_int_daeg2_pseudo_ellipse_55() (in lib.frame_order.pseudo_ellipse)	PipeContainer (in data_store.pipe_container)	pubmed_id (in dAuvergneGooley03)
part_int_daeg2_pseudo_ellipse_57() (in lib.frame_order.pseudo_ellipse)	pipes (in pipe_control)	pubmed_id (in dAuvergneGooley06)
part_int_daeg2_pseudo_ellipse_80() (in lib.frame_order.pseudo_ellipse)	pipes (in test_suite.gui_tests)	pubmed_id (in dAuvergneGooley07)
part_int_daeg2_pseudo_ellipse_84() (in lib.frame_order.pseudo_ellipse)	Pipes (in test_suite.gui_tests.pipes)	pubmed_id (in dAuvergneGooley08a)
part_int_daeg2_pseudo_ellipse_88() (in lib.frame_order.pseudo_ellipse)	pipes (in test_suite.system_tests)	pubmed_id (in dAuvergneGooley08b)
part_int_daeg2_pseudo_ellipse_free_rotor_00() (in lib.frame_order.pseudo_ellipse_free_rotor)	Pipes (in test_suite.system_tests.pipes)	put() (in Immediate_result_queue)
part_int_daeg2_pseudo_ellipse_free_rotor_08() (in lib.frame_order.pseudo_ellipse_free_rotor)	pivot() (in specific_analyses.frame_order.uf)	put() (in Result_queue)
part_int_daeg2_pseudo_ellipse_free_rotor_11() (in lib.frame_order.pseudo_ellipse_free_rotor)	Pivot_finder (in target_functions.ens_pivot_finder)	put() (in Threaded_result_queue)
part_int_daeg2_pseudo_ellipse_free_rotor_44() (in lib.frame_order.pseudo_ellipse_free_rotor)	pivot_fixed() (in specific_analyses.frame_order.data)	pwd() (in pipe_control.system)
part_int_daeg2_pseudo_ellipse_free_rotor_48() (in lib.frame_order.pseudo_ellipse_free_rotor)	pivot_grid_bound() (in specific_analyses.frame_order.parameter_object)	PY_FILE_EXTENSION (in test_suite.unit_tests.unit_test_runner)
part_int_daeg2_pseudo_ellipse_free_rotor_80() (in lib.frame_order.pseudo_ellipse_free_rotor)	pivot_x_lower() (in specific_analyses.frame_order.parameter_object)	py_to_gui() (in gui.string_conv)
part_int_daeg2_pseudo_ellipse_free_rotor_88() (in lib.frame_order.pseudo_ellipse_free_rotor)	pivot_x_upper() (in specific_analyses.frame_order.parameter_object)	PY_VER (in test_suite.system_tests.frame_order)
part_int_daeg2_pseudo_ellipse_torsionless_00() (in lib.frame_order.pseudo_ellipse_torsionless)	pivot_y_lower() (in specific_analyses.frame_order.parameter_object)	PY_VER (in test_suite.system_tests.model_free)
part_int_daeg2_pseudo_ellipse_torsionless_04() (in lib.frame_order.pseudo_ellipse_torsionless)	pivot_y_upper() (in specific_analyses.frame_order.parameter_object)	PY_VERSION (in lib.compat)
part_int_daeg2_pseudo_ellipse_torsionless_08() (in lib.frame_order.pseudo_ellipse_torsionless)	pivot_z_lower() (in specific_analyses.frame_order.parameter_object)	Pymol (in pipe_control.pymol_control)
part_int_daeg2_pseudo_ellipse_torsionless_11() (in lib.frame_order.pseudo_ellipse_torsionless)	pivot_z_upper() (in specific_analyses.frame_order.parameter_object)	pymol (in specific_analyses.model_free)
part_int_daeg2_pseudo_ellipse_torsionless_22() (in lib.frame_order.pseudo_ellipse_torsionless)	plot_disp_curves() (in specific_analyses.relax_disp.data)	Pymol (in specific_analyses.model_free.pymol)
part_int_daeg2_pseudo_ellipse_torsionless_44() (in lib.frame_order.pseudo_ellipse_torsionless)	plot_disp_curves_to_file() (in specific_analyses.relax_disp.data)	pymol_control (in pipe_control)
part_int_daeg2_pseudo_ellipse_torsionless_48() (in lib.frame_order.pseudo_ellipse_torsionless)	plot_exp_curves() (in specific_analyses.relax_disp.data)	pymol_control (in user_functions)
part_int_daeg2_pseudo_ellipse_torsionless_55() (in lib.frame_order.pseudo_ellipse_torsionless)	plot_int_corr() (in Relax_disp_rep)	pymol_macro() (in API_base)
part_int_daeg2_pseudo_ellipse_torsionless_88() (in lib.frame_order.pseudo_ellipse_torsionless)	plot_int_stat() (in Relax_disp_rep)	pymol_macro() (in Pymol)
partition_params() (in pipe_control.value)	plot_min_corr() (in Relax_disp_rep)	pymol_module (in dep_check)
paths_from_test_module() (in Unit_test_runner)	plot_min_stat() (in Relax_disp_rep)	pymol_obj (in pipe_control.pymol_control)
pattern_d_quote (in bmrblib.pystarlib.Text)	plot_r2eff_corr() (in Relax_disp_rep)	pystarlib (in bmrblib)
pattern_double_qoute (in bmrblib.pystarlib.Text)	plot_r2eff_stat() (in Relax_disp_rep)
pattern_e_semicolon (in bmrblib.pystarlib.Text)	plotting (in lib)