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/* hkl_info.cpp: class file for hkl_info class + children */
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//C Copyright (C) 2000-2006 Kevin Cowtan and University of York
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//L This library is free software and is distributed under the terms
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//L and conditions of version 2.1 of the GNU Lesser General Public
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//L Licence (LGPL) with the following additional clause:
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//L `You may also combine or link a "work that uses the Library" to
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//L produce a work containing portions of the Library, and distribute
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//L that work under terms of your choice, provided that you give
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//L version of the Library is used in it, and that you include or
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//L provide public access to the complete corresponding
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//L machine-readable source code for the Library including whatever
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//L changes were used in the work. (i.e. If you make changes to the
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//L Library you must distribute those, but you do not need to
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//L distribute source or object code to those portions of the work
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//L not covered by this licence.)'
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//L Note that this clause grants an additional right and does not impose
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//L any additional restriction, and so does not affect compatibility
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//L with the GNU General Public Licence (GPL). If you wish to negotiate
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//L other terms, please contact the maintainer.
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//L You can redistribute it and/or modify the library under the terms of
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//L the GNU Lesser General Public License as published by the Free Software
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//L Foundation; either version 2.1 of the License, or (at your option) any
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//L This library is distributed in the hope that it will be useful, but
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//L WITHOUT ANY WARRANTY; without even the implied warranty of
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//L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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//L Lesser General Public License for more details.
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//L You should have received a copy of the CCP4 licence and/or GNU
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//L Lesser General Public License along with this library; if not, write
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//L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK.
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//L The GNU Lesser General Public can also be obtained by writing to the
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//L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
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Message_fatal message_recip_asu_error( "HKL_info: find_sym reciprocal space ASU error" );
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Message_ctor message_ctor_hkl_info( " [HKL_info: constructed]" );
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// methods for 'HKL_info'
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/*! Update all the lookup tables to be consistent with the modified
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void HKL_info::update_hkl_list() {
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hkl_class_lookup.resize( num_reflections() );
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invresolsq_lookup.resize( num_reflections() );
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invresolsq_range_ = Range<ftype>();
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for ( int i = 0; i < num_reflections(); i++ ) {
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hkl_class_lookup[i] = spacegroup_.hkl_class( hkl_of( i ) );
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invresolsq_lookup[i] = hkl_of( i ).invresolsq( cell_ );
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invresolsq_range_.include( invresolsq_lookup[i] );
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// constructors/destructor
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Message::message( message_ctor_hkl_info );
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/*! Construct and initialise HKL_info object. This updates the
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spacegroup and cell and clears the reflection list. The resolution
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is used as a rejection criterion for reflections - no HKL will be
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stored beyond the given limit. Initially there are no reflections in
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the reflection list: see generate_hkl_list().
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If any of the parameters have null values, the existing values will
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be unchanged. The object will only be fully initialised once all
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parameters are available.
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\param spacegroup The spacegroup.
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\param cell The unit cell.
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\param resolution The resolution limit. */
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HKL_info::HKL_info( const Spacegroup& spacegroup, const Cell& cell, const Resolution& resolution, const bool& generate )
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init( spacegroup, cell, resolution, generate );
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Message::message( message_ctor_hkl_info );
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/*! Initialise the HKL_info object. This updates the spacegroup and
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cell and clears the reflection list. The resolution is used as a
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rejection criterion for reflections - no HKL will be stored beyond
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the given limit. Initially there are no reflections in the
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reflection list: see generate_hkl_list().
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If any of the parameters have null values, the existing values will
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be unchanged. The object will only be fully initialised once all
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parameters are available.
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\param spacegroup The spacegroup.
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\param cell The unit cell.
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\param resolution The resolution limit.
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\param generate If true, a reflection list will be generated for an ASU. */
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void HKL_info::init( const Spacegroup& spacegroup, const Cell& cell, const Resolution& resolution, const bool& generate )
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// set spacegroup and cell
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spacegroup_ = spacegroup;
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resolution_ = resolution;
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if ( is_null() ) return;
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// Create the intergised symops (grid irrelevent)
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Grid g( 24, 24, 24 );
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isymop.resize( spacegroup_.num_symops() );
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for ( int sym = 0; sym < spacegroup_.num_symops(); sym++ )
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isymop[sym] = Isymop( spacegroup_.symop(sym), g );
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if ( generate ) generate_hkl_list();
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/*! Initialise the HKL_info object. This updates the spacegroup and
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cell and clears the reflection list. The HKL_sampling determines
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If any of the parameters have null values, the existing values will
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be unchanged. The object will only be fully initialised once all
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parameters are available.
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\param spacegroup The spacegroup.
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\param cell The unit cell.
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\param hkl_sampling The resolution limit.
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\param generate If true, a reflection list will be generated for an ASU. */
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void HKL_info::init( const Spacegroup& spacegroup, const Cell& cell, const HKL_sampling& hkl_sampling, const bool& generate )
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// set spacegroup and cell
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spacegroup_ = spacegroup;
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hkl_sampling_ = hkl_sampling;
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if ( spacegroup_.is_null() || cell_.is_null() || hkl_sampling_.is_null() ) return;
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// estimate resolution
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resolution_ = hkl_sampling.resolution( cell );
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// Create the intergised symops (grid irrelevent)
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Grid g( 24, 24, 24 );
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isymop.resize( spacegroup_.num_symops() );
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for ( int sym = 0; sym < spacegroup_.num_symops(); sym++ )
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isymop[sym] = Isymop( spacegroup_.symop(sym), g );
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std::vector<HKL> add;
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// make a reflection list for the given refln sampling
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HKL lim = hkl_sampling.hkl_limit();
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// make a list of valid reflections
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for (rfl.h()=-lim.h(); rfl.h()<=lim.h(); rfl.h()++)
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for (rfl.k()=-lim.k(); rfl.k()<=lim.k(); rfl.k()++)
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for (rfl.l()=-lim.l(); rfl.l()<=lim.l(); rfl.l()++)
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if ( spacegroup_.recip_asu(rfl) &&
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hkl_sampling.in_resolution( rfl ) &&
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!( spacegroup_.hkl_class(rfl).sys_abs() ) ) add.push_back(rfl);
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// update the reflection data lists
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/*! \return true if the object has not been initalised. */
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bool HKL_info::is_null() const
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{ return ( spacegroup_.is_null() || cell_.is_null() || resolution_.is_null() ); }
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/*! Using current cell, spacegroup, resolution. */
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void HKL_info::generate_hkl_list()
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std::vector<HKL> add;
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// make a reflection list for the given cell, symm and resolution
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/* TO MAKE A BOX TO HOLD A SPHERE IN REAL OR RECIPROCAL SPACE
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In reciprocal space, use the real space cell dimension / resolution
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In real space, use the recip space dimension * radius */
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int hmax = int(cell_.descr().a()/resolution_.limit());
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int kmax = int(cell_.descr().b()/resolution_.limit());
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int lmax = int(cell_.descr().c()/resolution_.limit());
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ftype s_lim = resolution_.invresolsq_limit();
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// make a list of valid reflections
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for (rfl.h()=-hmax; rfl.h()<=hmax; rfl.h()++)
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for (rfl.k()=-kmax; rfl.k()<=kmax; rfl.k()++)
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for (rfl.l()=-lmax; rfl.l()<=lmax; rfl.l()++)
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if ( spacegroup_.recip_asu(rfl) && rfl.invresolsq(cell_) < s_lim &&
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!( spacegroup_.hkl_class(rfl).sys_abs() ) ) add.push_back(rfl);
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// update the reflection data lists
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/*! The new HKLs are transformed to the default reciprocal ASU, and
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added to the reflection list. Duplicates and reflections outside the
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resoluution limit are ignored. Then the fast lookup tables for HKL,
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invresolsq, and reflection class are rebuilt.
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\param add The list of new reflections to add. */
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void HKL_info::add_hkl_list( const std::vector<HKL>& add ) {
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HKL equiv; int sym; bool friedel;
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for ( int i = 0; i < add.size(); i++ ) {
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if ( add[i].invresolsq( cell_ ) <= resolution_.invresolsq_limit() ) {
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equiv = find_sym( add[i], sym, friedel );
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if ( lookup.index_of( equiv ) < 0 ) hkl.push_back( equiv );
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/*! Returns the index of the reflection, the sym no. and Friedel flag.
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HKL HKL_info::find_sym( const HKL& rfl, int& sym, bool& friedel ) const
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// find the symmetry operator mapping hkl into the reflection
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// list and determine the friedel flag
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// now find the symop which gives a reflection from the list
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for (sym = 0; sym < spacegroup_.num_primops(); sym++) {
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equiv = rfl.transform(isymop[sym]);
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if ( spacegroup_.recip_asu(equiv) ) { friedel = false; return equiv; }
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if ( spacegroup_.recip_asu(equiv) ) { friedel = true ; return equiv; }
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Message::message( message_recip_asu_error );
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void HKL_info::debug() const
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std::cout << "Num reflns " << hkl.size() << "\n";
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} // namespace clipper
added
removed
clipper/core/hkl_info.cpp
