xTc@ sddlmZddlmZddlZddlmZddlmZddlm Z ddl m Z ddl Zddlm Z dd lmZdd lmZddlZddlZdd lmZdd lmZdd lmZddlZddlZddlmZddlZdZdZdZdZ dZ!dZ"dZ#dZ$dZ%dZ&dZ'dZ(dZ)dZ*dZ+dddZ-dZ.d Z/d!Z0dS("i(tdivision(tflexN(tutils(treflection_file_reader(treflection_file_utils(tStringIO(tcrystal_symmetry_from_any(tadptbx(tSorry(t group_args(tpdb(txray(tmapss pdb_file_name = None .type = str .multiple = False .help = PDB file name (model only). external_da_pdb_file_name = None .type = str .multiple = False .help = PDB file name (dummy atoms only). reflection_file_name = None .type = str .help = File with experimental data (most of formats: CNS, SHELX, MTZ, etc). data_labels = None .type = str .help = Labels for experimental data. refine = *occupancies *adp *sites .type = choice(multi=True) .help = Parameters of DA to refine. stop_reset_occupancies_at_macro_cycle = 5 .type = int .help = Reset occupancies during first stop_reset_occupancies_at_macro_cycle macro-cycles. stop_reset_adp_at_macro_cycle = 5 .type = int .help = Reset ADPs during first stop_reset_adp_at_macro_cycle macro-cycles. start_filtering_at_macro_cycle=10 .type = int .help = Macro-cycle number at which filtering takes off. sphere .multiple=True { center = None .type = floats(size=3) .help = Approximate coordinates of the center of problem density. radius = None .type = float .help = Sphere radius of where the dummy atoms will be placed. } mode = build *build_and_refine .type = choice(multi=False) high_resolution = None .type = float low_resolution = None .type = float output_file_name_prefix = None .type = str initial_occupancy = 0.1 .type = float .help = Starting occupancy value for a newly placed DA initial_b_factor = None .type = float .help = Starting B-factor value for a newly palced DA. Of None, then determined automatically as mean B. atom_gap = 0.7 .type = float .help = Thje gap between the atoms in the grid. .expert_level = 2 overlap_interval = 0.25 .type = float .help = Grid interval size - the gap between two grids. .expert_level = 2 atom_type = H .type = str .help = Atom to use to make grid. Nitrogen is a good choice atom_name = " DA " .type = str residue_name = DUM .type = str .help = Residue name for a DA scattering_table = *n_gaussian wk1995 it1992 neutron .type = choice .help = Scattering table for structure factors calculations number_of_refinement_cycles = 20 .type = int .help = Number of refinement cycles number_of_minimization_iterations = 25 .type = int .help = Number of refinement iterations filter { b_iso_min = 1.0 .type = float .help = Min B-factor value to remove DA. b_iso_max = 100.0 .type = float .help = Max B-factor value to remove DA. occupancy_min = 0.1 .type = float .help = Min occupancy value to remove DA. occupancy_max = 10.0 .type = float .help = Max occupancy value to remove DA. inside_sphere_scale = 1.2 .type = float .help = DA with distance larger than sphere.radius*inside_sphere_scale from sphere.center will be removed. da_model_min_dist = 1. .type = float .help = Max allowable distance between DA and any model atom. } cC stjjtdtS(Ntprocess_includes(tiotbxtphiltparsetmaster_params_strtFalse(((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/grow_density.pyt master_params|scC sd}g}x9|jD].}|j|d|d|jd|jqW|j}|dkrtj|jt j d}ng}d}xrt ||jD]^\}}d}xI|j D]>} x5|j D]*} x!|jD]} |d7}|dkrqn|d7}tj| | | g} td| d |jd|jd |jd |d |jd |jd|j} td| d|j}|jd|jdd}|jdk}||jdkM}|j|}|dkr|j|qqWqWqWqWg}xt|D]\}}xt|D]r\}}||k r2|jd|jdd}|jdk}||j|jkM}|j|||sJ     g  = Y   0