# -*- coding: utf-8 -*- from __future__ import absolute_import, division, print_function import sys, os from libtbx import adopt_init_args from libtbx.utils import null_out from scitbx.matrix import col # map_symmetry # tool to identify and evaluate reconstruction symmetry in a map class map_symmetry: def __init__(self,params=None, map_data=None, map_coeffs=None, crystal_symmetry=None, ncs_object=None, fourier_filter = None, log=sys.stdout): adopt_init_args(self, locals()) self.cc=None self.score=None self.original_ncs_object=None if ncs_object: self.original_ncs_object=ncs_object.deep_copy() self.ncs_object=ncs_object if self.params and self.params.control.verbose: self.local_log=log else: self.local_log=null_out() if self.params.reconstruction_symmetry.find_ncs_directly and \ not self.map_coeffs: from cctbx.maptbx.segment_and_split_map import get_f_phases_from_map self.map_coeffs,dummy=get_f_phases_from_map(map_data=self.map_data, crystal_symmetry=self.crystal_symmetry, d_min=self.params.crystal_info.resolution, return_as_map_coeffs=True, # required out=self.log) def get_results(self): from libtbx import group_args if not self.ncs_object: from mmtbx.ncs.ncs import ncs self.ncs_object=ncs() self.score=None self.cc=None return group_args( cc = self.cc, ncs_object = self.ncs_object, ncs_name = str(self.ncs_object.get_ncs_name()), ncs_operators = self.ncs_object.max_operators(), score=self.score, ) def clean_up(self): pass def run(self): # Print out values of parameters import iotbx.phil from phenix.programs.map_symmetry import master_phil_str master_phil=iotbx.phil.parse(master_phil_str) print ("\nInput parameters for map_symmetry:\n",file=self.log) master_phil.format(python_object=self.params).show(out=self.log) # Shift the map origin if necessary self.shift_origin() self.get_resolution() print ("Finding symmetry in map",file=self.log) if self.params.reconstruction_symmetry.find_ncs_directly: new_ncs_obj,ncs_cc,ncs_score=self.find_ncs_from_density() else: # usual from cctbx.maptbx.segment_and_split_map import run_get_ncs_from_map new_ncs_obj,ncs_cc,ncs_score=run_get_ncs_from_map(params=self.params, map_data=self.map_data, crystal_symmetry=self.crystal_symmetry, ncs_obj=self.ncs_object, fourier_filter = self.fourier_filter, out=self.log) if not new_ncs_obj: print ("\nNo symmetry found..",file=self.log) return # Now shift back if necessary ncs_object=new_ncs_obj.coordinate_offset( coordinate_offset=col(self.origin_shift_cart)) print ("\nFinal symmetry obtained:",file=self.log) if ncs_object.get_ncs_name(): print ("NCS type: %s" %(ncs_object.get_ncs_name()),file=self.log) print ("Correlation of symmetry-related regions: %.2f Copies: %d " %( ncs_cc,ncs_object.max_operators()), file=self.log) if self.params.control.verbose: ncs_object.display_all(log=self.log) # write to output file if self.params.output_files.symmetry_out: ncs_object.format_all_for_group_specification( file_name=self.params.output_files.symmetry_out) print ("\nWrote operators in .ncs_spec format to %s" %( self.params.output_files.symmetry_out),file=self.log) # Final results self.ncs_object=ncs_object self.cc=ncs_cc self.score=ncs_score def find_ncs_from_density(self): # First test to make sure the function is available try: from phenix.command_line.find_ncs_from_density import \ find_ncs_from_density as find_ncs except Exception as e: ncs_cc=None ncs_object=None ncs_score=None return ncs_object,ncs_cc,ncs_score print ("Finding symmetry in map by search for matching density", file=self.log) # Write out mtz file to search in... temp_dir=self.params.output_files.temp_dir if not os.path.isdir(temp_dir): os.mkdir(temp_dir) map_coeffs_file=os.path.join(temp_dir,"map_coeffs.mtz") self.map_coeffs.as_mtz_dataset( column_root_label='FWT').mtz_object().write(file_name=map_coeffs_file) args=["%s" %(map_coeffs_file),"map_operators_inside_unit_cell=True"] if self.params.crystal_info.resolution: args.append("resolution=%s" %(self.params.crystal_info.resolution)) find_ncs_from_density=find_ncs( args,out=self.log) if hasattr(find_ncs_from_density,'ncs_object') and \ find_ncs_from_density.ncs_object: ncs_object=find_ncs_from_density.ncs_object ncs_cc=ncs_object.overall_cc() ncs_score=ncs_cc*(ncs_object.max_operators())**0.5 else: ncs_cc=None ncs_object=None ncs_score=None return ncs_object,ncs_cc,ncs_score def get_resolution(self): if not self.params.crystal_info.resolution: from cctbx.maptbx import d_min_from_map self.params.crystal_info.resolution=\ d_min_from_map(map_data=self.map_data, unit_cell=self.crystal_symmetry.unit_cell()) print ("\nResolution estimated from map is %.1f A " %( self.params.crystal_info.resolution),file=self.log) def shift_origin(self): origin_shift_grid_units=self.map_data.origin() origin_shift=( self.map_data.origin()[0]/self.map_data.all()[0], self.map_data.origin()[1]/self.map_data.all()[1], self.map_data.origin()[2]/self.map_data.all()[2]) origin_shift_cart=\ self.crystal_symmetry.unit_cell().orthogonalize(origin_shift) acc=self.map_data.accessor() shift_needed = not \ (self.map_data.focus_size_1d() > 0 and self.map_data.nd() == 3 and self.map_data.is_0_based()) if(shift_needed): self.map_data = self.map_data.shift_origin() self.origin_frac=origin_shift self.origin_shift_cart=origin_shift_cart # Adjust likely center position new_location=[] for xx,osc in zip(self.params.reconstruction_symmetry.symmetry_center, origin_shift_cart): new_location.append(xx-osc) self.params.reconstruction_symmetry.symmetry_center=tuple(new_location) print("Shifted guess for symmetry center is at: (%.2f,%.2f,%.2f) A "%( self.params.reconstruction_symmetry.symmetry_center),file=self.log) else: self.origin_frac=(0.,0.,0.) self.origin_shift_cart=(0,0,0) if self.ncs_object: self.ncs_object=self.ncs_object.coordinate_offset( coordinate_offset=-1*col(self.origin_shift_cart))