--- clipper/contrib/edcalc.cpp.orig Thu Jul 31 18:11:30 2003 +++ clipper/contrib/edcalc.cpp Wed Jun 15 18:29:29 2005 @@ -1,19 +1,44 @@ /* edcalc.cpp: Electron density calculation implementation */ -//C Copyright (C) 2000-2003 Kevin Cowtan and University of York -//L This library is free software; you can redistribute it and/or modify -//L it under the terms the CCP4 licence agreement as `Part 0' software, -//L which is defined as version 2.1 of the GNU Lesser General Public -//L License (LGPL). See the file 'license.txt' in the top CCP4 directory, -//L or the file 'COPYING' in this directory or its parent directory. -//L -//L This library is distributed in the hope that it will be useful, but -//L WITHOUT ANY WARRANTY; without even the implied warranty of -//L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -//L Lesser General Public License for more details. -//L -//L You should have received a copy of the CCP4 license and/or GNU Lesser -//L General Public License along with this library; if not, write to the -//L CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. +//C Copyright (C) 2000-2004 Kevin Cowtan and University of York +//L +//L This library is free software and is distributed under the terms and +//L conditions of the CCP4 licence agreement as `Part 0' (Annex 2) +//L software, which is version 2.1 of the GNU Lesser General Public +//L Licence (LGPL) with the following additional clause: +//L +//L `You may also combine or link a "work that uses the Library" to +//L produce a work containing portions of the Library, and distribute +//L that work under terms of your choice, provided that you give +//L prominent notice with each copy of the work that the specified +//L version of the Library is used in it, and that you include or +//L provide public access to the complete corresponding +//L machine-readable source code for the Library including whatever +//L changes were used in the work. (i.e. If you make changes to the +//L Library you must distribute those, but you do not need to +//L distribute source or object code to those portions of the work +//L not covered by this licence.)' +//L +//L Note that this clause grants an additional right and does not impose +//L any additional restriction, and so does not affect compatibility +//L with the GNU General Public Licence (GPL). If you wish to negotiate +//L other terms, please contact the maintainer. +//L +//L You can redistribute it and/or modify the library under the terms of +//L the GNU Lesser General Public License as published by the Free Software +//L Foundation; either version 2.1 of the License, or (at your option) any +//L later version. +//L +//L This library is distributed in the hope that it will be useful, but +//L WITHOUT ANY WARRANTY; without even the implied warranty of +//L MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +//L Lesser General Public License for more details. +//L +//L You should have received a copy of the CCP4 licence and/or GNU +//L Lesser General Public License along with this library; if not, write +//L to the CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. +//L The GNU Lesser General Public can also be obtained by writing to the +//L Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, +//L MA 02111-1307 USA #include "edcalc.h" @@ -38,7 +63,7 @@ xyz = atoms[i].coord_orth(); g0 = xmap.coord_map( xyz ).coord_grid() + gd.min(); g1 = xmap.coord_map( xyz ).coord_grid() + gd.max(); - i0 = Xmap::Map_reference_coord( xmap, g0 ); + i0 = typename Xmap::Map_reference_coord( xmap, g0 ); for ( iu = i0; iu.coord().u() <= g1.u(); iu.next_u() ) for ( iv = iu; iv.coord().v() <= g1.v(); iv.next_v() ) for ( iw = iv; iw.coord().w() <= g1.w(); iw.next_w() ) @@ -64,7 +89,7 @@ xyz = atoms[i].coord_orth(); g0 = nxmap.coord_map( xyz ).coord_grid() + gd.min(); g1 = nxmap.coord_map( xyz ).coord_grid() + gd.max(); - i0 = NXmap::Map_reference_coord( nxmap, g0 ); + i0 = typename NXmap::Map_reference_coord( nxmap, g0 ); for ( iu = i0; iu.coord().u() <= g1.u(); iu.next_u() ) for ( iv = iu; iv.coord().v() <= g1.v(); iv.next_v() ) for ( iw = iv; iw.coord().w() <= g1.w(); iw.next_w() ) @@ -92,15 +117,15 @@ atoms[i].u_iso(), atoms[i].occupancy() ); g0 = xmap.coord_map( atoms[i].coord_orth() ).coord_grid() + gd.min(); g1 = xmap.coord_map( atoms[i].coord_orth() ).coord_grid() + gd.max(); - i0 = Xmap::Map_reference_coord( xmap, g0 ); + i0 = typename Xmap::Map_reference_coord( xmap, g0 ); for ( iu = i0; iu.coord().u() <= g1.u(); iu.next_u() ) for ( iv = iu; iv.coord().v() <= g1.v(); iv.next_v() ) for ( iw = iv; iw.coord().w() <= g1.w(); iw.next_w() ) xmap[iw] += sf.rho( iw.coord_orth() ); } - typename Xmap::Map_reference_index ix; - for ( ix = xmap.first(); !ix.last(); ix.next() ) + for ( typename Xmap::Map_reference_index ix = xmap.first(); + !ix.last(); ix.next() ) xmap[ix] *= xmap.multiplicity( ix.coord() ); return true; @@ -122,7 +147,7 @@ atoms[i].u_iso(), atoms[i].occupancy() ); g0 = nxmap.coord_map( atoms[i].coord_orth() ).coord_grid() + gd.min(); g1 = nxmap.coord_map( atoms[i].coord_orth() ).coord_grid() + gd.max(); - i0 = NXmap::Map_reference_coord( nxmap, g0 ); + i0 = typename NXmap::Map_reference_coord( nxmap, g0 ); for ( iu = i0; iu.coord().u() <= g1.u(); iu.next_u() ) for ( iv = iu; iv.coord().v() <= g1.v(); iv.next_v() ) for ( iw = iv; iw.coord().w() <= g1.w(); iw.next_w() ) @@ -151,15 +176,15 @@ u, atoms[i].occupancy() ); g0 = xmap.coord_map( atoms[i].coord_orth() ).coord_grid() + gd.min(); g1 = xmap.coord_map( atoms[i].coord_orth() ).coord_grid() + gd.max(); - i0 = Xmap::Map_reference_coord( xmap, g0 ); + i0 = typename Xmap::Map_reference_coord( xmap, g0 ); for ( iu = i0; iu.coord().u() <= g1.u(); iu.next_u() ) for ( iv = iu; iv.coord().v() <= g1.v(); iv.next_v() ) for ( iw = iv; iw.coord().w() <= g1.w(); iw.next_w() ) xmap[iw] += sf.rho( iw.coord_orth() ); } - typename Xmap::Map_reference_index ix; - for ( ix = xmap.first(); !ix.last(); ix.next() ) + for ( typename Xmap::Map_reference_index ix = xmap.first(); + !ix.last(); ix.next() ) xmap[ix] *= xmap.multiplicity( ix.coord() ); return true; @@ -183,7 +208,7 @@ u, atoms[i].occupancy() ); g0 = nxmap.coord_map( atoms[i].coord_orth() ).coord_grid() + gd.min(); g1 = nxmap.coord_map( atoms[i].coord_orth() ).coord_grid() + gd.max(); - i0 = NXmap::Map_reference_coord( nxmap, g0 ); + i0 = typename NXmap::Map_reference_coord( nxmap, g0 ); for ( iu = i0; iu.coord().u() <= g1.u(); iu.next_u() ) for ( iv = iu; iv.coord().v() <= g1.v(); iv.next_v() ) for ( iw = iv; iw.coord().w() <= g1.w(); iw.next_w() )