def get_master_phil () : from mmtbx.command_line import generate_master_phil_with_inputs return generate_master_phil_with_inputs( phil_string=""" clash_min = 0.2 .type = float """)
def get_master_phil(): from mmtbx.command_line import generate_master_phil_with_inputs return generate_master_phil_with_inputs( enable_twin_law=True, enable_experimental_phases=True, enable_pdb_interpretation_params=True, enable_stop_for_unknowns=False, enable_full_geometry_params=True, phil_string=""" selection = None .type = atom_selection target_map = 2mFo-DFc .type = str rsr_after_anneal = False .type = bool resolution_factor = 0.25 .type = float reference_sigma = 0.5 .type = float .help = Sigma for harmonic restraints for neighboring atoms not included \ in the selection of interest. output { file_name = annealed.pdb .type = path save_map_coeffs = False .type = path verbose = False .type = bool debug = False .type = bool } simulated_annealing { include scope mmtbx.dynamics.simulated_annealing.master_params } """)
def master_phil () : from mmtbx.command_line import generate_master_phil_with_inputs return generate_master_phil_with_inputs( enable_automatic_twin_detection=True, phil_string=""" hetatms_only = True .type = bool skip_xtal_solution_mols = False .type = bool .help = If True, common crystallization components such as sulfate or \ glycerol will be ignored. skip_single_atoms = True .type = bool skip_alt_confs = True .type = bool min_acceptable_cc = 0.8 .type = float min_acceptable_2fofc = 1.0 .type = float max_frac_atoms_below_min = 0.5 .type = float write_coot_script = True .type = bool write_maps = Auto .type = bool """)
def get_master_phil () : from mmtbx.command_line import generate_master_phil_with_inputs return generate_master_phil_with_inputs( enable_twin_law=True, enable_experimental_phases=True, enable_pdb_interpretation_params=True, enable_stop_for_unknowns=False, enable_full_geometry_params=True, phil_string=""" selection = None .type = atom_selection target_map = 2mFo-DFc .type = str rsr_after_anneal = False .type = bool resolution_factor = 0.25 .type = float reference_sigma = 0.5 .type = float .help = Sigma for harmonic restraints for neighboring atoms not included \ in the selection of interest. output { file_name = annealed.pdb .type = path save_map_coeffs = False .type = path verbose = False .type = bool debug = False .type = bool } simulated_annealing { include scope mmtbx.dynamics.simulated_annealing.master_params } """)
def __init__(self,pdb_file,hklmtz_file, detail,high_resolution=None,mdb_document=None,pdb_code=None, do_flips=False) : assert detail in ['file','residue'],detail assert type(do_flips) == bool self.pdb_file = pdb_file self.hklmtz_file = hklmtz_file self.detail = detail self.pdb_code = pdb_code self.high_resolution = high_resolution self.do_flips = do_flips if not pdb_code : self.pdb_code = 'N/A' pdb_in = file_reader.any_file(pdb_file) self.hierarchy = pdb_in.file_object.hierarchy args = [self.pdb_file] if self.hklmtz_file : args.append(self.hklmtz_file) self.cmdline = load_model_and_data( args=args, master_phil=generate_master_phil_with_inputs(""), require_data=False, create_fmodel=True, process_pdb_file=True, prefer_anomalous=True) # keys are res ids and values are MDBResidue objects. if self.detail == 'residue' : self.initiate_residues() self.set_mdb_document(mdb_document)
def master_phil(): from mmtbx.command_line import generate_master_phil_with_inputs return generate_master_phil_with_inputs( enable_automatic_twin_detection=True, phil_string=""" hetatms_only = True .type = bool skip_xtal_solution_mols = False .type = bool .help = If True, common crystallization components such as sulfate or \ glycerol will be ignored. skip_single_atoms = True .type = bool skip_alt_confs = True .type = bool min_acceptable_cc = 0.8 .type = float min_acceptable_2fofc = 1.0 .type = float max_frac_atoms_below_min = 0.5 .type = float write_coot_script = True .type = bool write_maps = Auto .type = bool """)
def master_phil(): from mmtbx.command_line import generate_master_phil_with_inputs return generate_master_phil_with_inputs( enable_automatic_twin_detection=True, phil_string="""\ output_file = fmodel.pkl .type = path """)
def master_phil () : from mmtbx.command_line import generate_master_phil_with_inputs return generate_master_phil_with_inputs( enable_automatic_twin_detection=True, phil_string="""\ output_file = fmodel.pkl .type = path """)
def get_master_phil () : from mmtbx.command_line import generate_master_phil_with_inputs return generate_master_phil_with_inputs( enable_automatic_twin_detection=True, phil_string=""" find_peaks .style = auto_align { include scope mmtbx.find_peaks.master_params } map_cutoff = 3.0 .type = float .short_caption = mFo-DFc map cutoff (sigma) anom_map_cutoff = 3.0 .type = float .short_caption = Anomalous map cutoff (sigma) include_peaks_near_model = False .type = bool .short_caption = Don't filter peaks by distance to model .help = By default, the program will only display peaks that map to points \ outside of the current model, ignoring those that overlap with atoms. \ Setting this option to True is equivalent to specifying a distance \ cutoff of zero for the filtering step. .style = OnChange:toggle_min_model_peak_dist wavelength = None .type = float .help = Optional parameter, if defined this will cause all atoms to be \ treated as anomalous scatterers using the standard Sasaki table to \ obtain theoretical fp and fpp values. Only really useful if the Phaser \ LLG map is being used for the anomalous map. filter_peaks_by_2fofc = None .type = float .short_caption = Filter peaks by 2mFo-DFc .help = If this is set, peaks outside 2mFo-DFc density at the \ cutoff will be discarded. (This does not apply to the analysis of \ solvent atoms.) Holes will not be changed. use_phaser_if_available = True .type = bool .short_caption = Use Phaser LLG map .help = If True, and Phaser is installed and configured, an anomalous LLG \ map will be used in place of the simple anomalous difference map. The \ wavelength should be specified for this to be maximally useful. write_pdb = True .type = bool .short_caption = Write peaks to PDB file write_maps = True .type = bool .short_caption = Save map coefficients output_file_prefix = peaks_holes .type = str include scope libtbx.phil.interface.tracking_params """)
def get_master_phil(): from mmtbx.command_line import generate_master_phil_with_inputs return generate_master_phil_with_inputs( enable_automatic_twin_detection=True, phil_string=""" find_peaks .style = auto_align { include scope mmtbx.find_peaks.master_params } map_cutoff = 3.0 .type = float .short_caption = mFo-DFc map cutoff (sigma) anom_map_cutoff = 3.0 .type = float .short_caption = Anomalous map cutoff (sigma) include_peaks_near_model = False .type = bool .short_caption = Don't filter peaks by distance to model .help = By default, the program will only display peaks that map to points \ outside of the current model, ignoring those that overlap with atoms. \ Setting this option to True is equivalent to specifying a distance \ cutoff of zero for the filtering step. .style = OnChange:toggle_min_model_peak_dist wavelength = None .type = float .help = Optional parameter, if defined this will cause all atoms to be \ treated as anomalous scatterers using the standard Sasaki table to \ obtain theoretical fp and fpp values. Only really useful if the Phaser \ LLG map is being used for the anomalous map. filter_peaks_by_2fofc = None .type = float .short_caption = Filter peaks by 2mFo-DFc .help = If this is set, peaks outside 2mFo-DFc density at the \ cutoff will be discarded. (This does not apply to the analysis of \ solvent atoms.) Holes will not be changed. use_phaser_if_available = True .type = bool .short_caption = Use Phaser LLG map .help = If True, and Phaser is installed and configured, an anomalous LLG \ map will be used in place of the simple anomalous difference map. The \ wavelength should be specified for this to be maximally useful. write_pdb = True .type = bool .short_caption = Write peaks to PDB file write_maps = True .type = bool .short_caption = Save map coefficients output_file_prefix = peaks_holes .type = str include scope libtbx.phil.interface.tracking_params """)
def master_phil () : from mmtbx.command_line import generate_master_phil_with_inputs return generate_master_phil_with_inputs( enable_automatic_twin_detection=True, enable_pdb_interpretation_params=True, enable_stop_for_unknowns=False, phil_string=""" include scope mmtbx.ions.identify.ion_master_phil debug = True .type = bool nproc = Auto .type = int """)
def get_master_phil () : from mmtbx.command_line import generate_master_phil_with_inputs return generate_master_phil_with_inputs( enable_automatic_twin_detection=True, phil_string=""" prune { %s } output { file_name = None .type = path } """ % model_prune_master_phil)
def master_phil(): from mmtbx.command_line import generate_master_phil_with_inputs return generate_master_phil_with_inputs( enable_automatic_twin_detection=True, enable_pdb_interpretation_params=True, enable_stop_for_unknowns=False, phil_string=""" include scope mmtbx.ions.identify.ion_master_phil debug = True .type = bool nproc = Auto .type = int """)
def get_master_phil(): from mmtbx.command_line import generate_master_phil_with_inputs return generate_master_phil_with_inputs( enable_automatic_twin_detection=True, phil_string=""" prune { %s } output { file_name = None .type = path } """ % model_prune_master_phil)
def master_phil () : from mmtbx.command_line import generate_master_phil_with_inputs return generate_master_phil_with_inputs( enable_stop_for_unknowns=False, enable_pdb_interpretation_params=True, phil_string=""" ignore_inconsistent_occupancy = True .type = bool pickle = False .type = bool verbose = False .type = bool """)
def master_phil(): from mmtbx.command_line import generate_master_phil_with_inputs return generate_master_phil_with_inputs( enable_stop_for_unknowns=False, enable_pdb_interpretation_params=True, phil_string=""" ignore_inconsistent_occupancy = True .type = bool pickle = False .type = bool verbose = False .type = bool """)
def master_phil () : from mmtbx.command_line import generate_master_phil_with_inputs return generate_master_phil_with_inputs( enable_automatic_twin_detection=True, phil_string=""" ligand_code = None .type = str .multiple = True reference_structure = None .type = path only_segid = None .type = str verbose = False .type = bool """)
def master_phil(): from mmtbx.command_line import generate_master_phil_with_inputs return generate_master_phil_with_inputs( enable_automatic_twin_detection=True, phil_string=""" ligand_code = None .type = str .multiple = True reference_structure = None .type = path only_segid = None .type = str verbose = False .type = bool """)
def master_phil(): from mmtbx.command_line import generate_master_phil_with_inputs return generate_master_phil_with_inputs(phil_string=""" selection = None .type = atom_selection nproc = Auto .type = int output { file_name = alternates.pdb .type = path verbose = False .type = bool debug = False .type = bool } include scope mmtbx.building.alternate_conformations.single_residue.master_phil_str """)
def master_phil () : from mmtbx.command_line import generate_master_phil_with_inputs return generate_master_phil_with_inputs( phil_string=""" selection = None .type = atom_selection nproc = Auto .type = int output { file_name = alternates.pdb .type = path verbose = False .type = bool debug = False .type = bool } include scope mmtbx.building.alternate_conformations.single_residue.master_phil_str """)
def master_phil () : from mmtbx.command_line import generate_master_phil_with_inputs return generate_master_phil_with_inputs( phil_string=""" alt_confs { selection = None .type = atom_selection macro_cycles = 1 .type = int(value_min=1) .optional = False include scope libtbx.easy_mp.parallel_phil_str_no_threading include scope mmtbx.building.alternate_conformations.single_residue.master_phil_str # sliding_window { # include scope mmtbx.building.alternate_conformations.sliding_window.master_params_str # } refinement { include scope phenix.automation.refinement.refine_hires_phil_str constrain_correlated_occupancies = True .type = bool } merging { include scope mmtbx.building.alternate_conformations.rejoin_phil } } output { prefix = alternates .type = str output_dir = None .type = path create_dir = True .type = bool directory_number = None .type = int debug = 0 .type = int verbose = True .type = bool remove_hydrogens = False .type = bool } """)
def get_master_phil () : from mmtbx.command_line import generate_master_phil_with_inputs return generate_master_phil_with_inputs( enable_automatic_twin_detection=True, enable_pdb_interpretation_params=True, enable_stop_for_unknowns=False, enable_unmerged_data=True, enable_cdl=Auto, phil_string=""" molprobity { outliers_only = True .type = bool keep_hydrogens = Auto .type = bool .help = Keep hydrogens in input file (instead of re-generating them with \ Reduce). If set to Auto, the behavior will depend on whether the \ neutron scattering table is used (regardless of whether we actually \ have experimental data). # nuclear = False # redundant parameter, same as # .type = bool # pdb_interpretation.use_neutron_distances # .short_caption = "Use nuclear hydrogen positions" min_cc_two_fofc = 0.8 .type = float .short_caption = "CC threshold" .help = Values for real-space correlations below the CC threshold are \ considered outliers n_bins = 10 .type = int .short_caption = Number of resolution bins use_pdb_header_resolution_cutoffs = False .type = bool .short_caption = Use resolution cutoffs in PDB header count_anomalous_pairs_separately = False .type = bool .expert_level = 2 rotamer_library = 500 *8000 .type = choice .help = Library of rotamer probabilities (Top500 or Top8000) .expert_level = 2 flags .expert_level = 3 { include scope mmtbx.validation.molprobity.master_phil_str } ligand_selection = None .type = atom_selection .expert_level = 3 } polygon { include scope mmtbx.polygon.polygon_params_str } output { quiet = False .type = bool probe_dots = True .type = bool .short_caption = Save Probe dots for Coot kinemage = False .type = bool .short_caption = Save Kinemage file for KiNG percentiles = False .type = bool .help = Show percentile rankings for summary statistics coot = True .type = bool .help = Write Coot script maps = Auto .type = bool .short_caption = Save map coefficients .help = Write map coefficients (if experimental data supplied) map_options .short_caption = Advanced options for map coefficients { fill_missing_f_obs = True .type = bool exclude_free_r_reflections = False .type = bool } prefix = None .type = str .style = hidden pickle = False .type = bool .style = hidden wxplots = False .type = bool .help = Display plots in wxPython .style = hidden gui_dir = None .type = path .short_caption = Output directory .help = Output directory (Phenix GUI only). .style = output_dir include scope libtbx.phil.interface.tracking_params } """)
def master_phil () : from mmtbx.command_line import generate_master_phil_with_inputs return generate_master_phil_with_inputs( phil_string=master_phil_str, enable_automatic_twin_detection=True)
def get_master_phil(): from mmtbx.command_line import generate_master_phil_with_inputs return generate_master_phil_with_inputs( enable_twin_law=True, enable_experimental_phases=True, enable_pdb_interpretation_params=True, enable_stop_for_unknowns=False, enable_full_geometry_params=True, phil_string=""" selection = None .type = atom_selection whole_residues = False .type = bool .help = If the initial selection includes partial residues, expand it to \ include each residue in its entirety. selection_delete = None .type = atom_selection .help = Designates atoms to be removed from the structure before \ calculating the target map. target_map = *mFo-DFc 2mFo-DFc .type = choice occ = 0.5 .type = float .help = Partial occupancy for selected atoms for map calculation. rsr_after_anneal = False .type = bool resolution_factor = 0.25 .type = float negate_surrounding_sites = False .type = bool .help = Set map values to negative around atoms outside of the target \ selection. reference_sigma = 0.5 .type = float .help = Sigma for harmonic restraints for neighboring atoms not included \ in the selection of interest. wc = 1 .type = float .help = Geometry restraints weight n_confs = 1 .type = int nproc = Auto .type = int random_seed = None .type = int output { file_name = disordered.pdb .type = path include_starting_model = True .type = bool map_file_name = None .type = path verbose = False .type = bool debug = False .type = bool } simulated_annealing { include scope mmtbx.dynamics.simulated_annealing.master_params } """)
def master_phil(): from mmtbx.command_line import generate_master_phil_with_inputs return generate_master_phil_with_inputs( phil_string=master_phil_str, enable_automatic_twin_detection=True)
def get_master_phil () : from mmtbx.command_line import generate_master_phil_with_inputs return generate_master_phil_with_inputs( enable_automatic_twin_detection=True, enable_pdb_interpretation_params=True, enable_stop_for_unknowns=False, enable_unmerged_data=True, enable_cdl=Auto, phil_string=""" molprobity { outliers_only = True .type = bool keep_hydrogens = Auto .type = bool .help = Keep hydrogens in input file (instead of re-generating them with \ Reduce). If set to Auto, the behavior will depend on whether the \ neutron scattering table is used (regardless of whether we actually \ have experimental data). nuclear = False .type = bool .short_caption = "Use nuclear hydrogen positions" min_cc_two_fofc = 0.8 .type = float .short_caption = "CC threshold" .help = Values for real-space correlations below the CC threshold are \ considered outliers n_bins = 10 .type = int .short_caption = Number of resolution bins use_pdb_header_resolution_cutoffs = False .type = bool .short_caption = Use resolution cutoffs in PDB header count_anomalous_pairs_separately = False .type = bool .expert_level = 2 rotamer_library = 500 *8000 .type = choice .help = Library of rotamer probabilities (Top500 or Top8000) .expert_level = 2 flags .expert_level = 3 { include scope mmtbx.validation.molprobity.master_phil_str } ligand_selection = None .type = atom_selection .expert_level = 3 } output { quiet = False .type = bool probe_dots = True .type = bool .short_caption = Save Probe dots for Coot kinemage = False .type = bool .short_caption = Save Kinemage file for KiNG percentiles = False .type = bool .help = Show percentile rankings for summary statistics coot = True .type = bool .help = Write Coot script maps = Auto .type = bool .short_caption = Save map coefficients .help = Write map coefficients (if experimental data supplied) map_options .short_caption = Advanced options for map coefficients { fill_missing_f_obs = True .type = bool exclude_free_r_reflections = False .type = bool } prefix = None .type = str .style = hidden pickle = False .type = bool .style = hidden wxplots = False .type = bool .help = Display plots in wxPython .style = hidden gui_dir = None .type = path .short_caption = Output directory .help = Output directory (Phenix GUI only). .style = output_dir include scope libtbx.phil.interface.tracking_params } """)
def get_master_phil () : from mmtbx.command_line import generate_master_phil_with_inputs return generate_master_phil_with_inputs( enable_twin_law=True, enable_experimental_phases=True, enable_pdb_interpretation_params=True, enable_stop_for_unknowns=False, enable_full_geometry_params=True, phil_string=""" selection = None .type = atom_selection whole_residues = False .type = bool .help = If the initial selection includes partial residues, expand it to \ include each residue in its entirety. selection_delete = None .type = atom_selection .help = Designates atoms to be removed from the structure before \ calculating the target map. target_map = *mFo-DFc 2mFo-DFc .type = choice occ = 0.5 .type = float .help = Partial occupancy for selected atoms for map calculation. rsr_after_anneal = False .type = bool resolution_factor = 0.25 .type = float negate_surrounding_sites = False .type = bool .help = Set map values to negative around atoms outside of the target \ selection. reference_sigma = 0.5 .type = float .help = Sigma for harmonic restraints for neighboring atoms not included \ in the selection of interest. wc = 1 .type = float .help = Geometry restraints weight n_confs = 1 .type = int nproc = Auto .type = int random_seed = None .type = int output { file_name = disordered.pdb .type = path include_starting_model = True .type = bool map_file_name = None .type = path verbose = False .type = bool debug = False .type = bool } simulated_annealing { include scope mmtbx.dynamics.simulated_annealing.master_params } """)