2009_11_01_0123: Migration to Python 2.6.4. Fixing problem with Visual C++ 8.0 runtime libraries. ------------------------------------------------------------------------------- 2009_09_28_1034: This build was used for Phenix release 1.5-2. Please visit https://lists.sourceforge.net/lists/listinfo/cctbx-cvs to see the full change logs. ------------------------------------------------------------------------------- 2009_02_15_2320: This build was used for CCI Apps release 2009_02_15_2320. Please visit https://lists.sourceforge.net/lists/listinfo/cctbx-cvs to see the full change logs. ------------------------------------------------------------------------------- 2008_09_13_0905: This build was used for CCI Apps release 2008_09_13_0905. Please visit https://lists.sourceforge.net/lists/listinfo/cctbx-cvs to see the full change logs. ------------------------------------------------------------------------------- 2008_08_26_2133: Release for IUCr 2008 Software Fayre. Please visit https://lists.sourceforge.net/lists/listinfo/cctbx-cvs to see the full change logs. ------------------------------------------------------------------------------- 2008_08_16_0004: Release for Kyoto 2008 IUCr Crystallographic Computing School. First release with simplified directory structure. Please visit https://lists.sourceforge.net/lists/listinfo/cctbx-cvs to see the full change logs. ------------------------------------------------------------------------------- 2008_08_09_0053: This build was used for CCI Apps release 2008_08_09_0053 and Phenix release 1.3 final. Please visit https://lists.sourceforge.net/lists/listinfo/cctbx-cvs to see the full change logs. ------------------------------------------------------------------------------- 2008_07_25_1259: This build was used for CCI Apps release 2008_07_25_1259 and Phenix release 1.3 rc4. Please visit https://lists.sourceforge.net/lists/listinfo/cctbx-cvs to see the full change logs. ------------------------------------------------------------------------------- 2008_05_25_1144: This build was used for CCI Apps release 2008_05_25_1144 and Phenix release 1.3 rc2. Please visit https://lists.sourceforge.net/lists/listinfo/cctbx-cvs to see the full change logs. ------------------------------------------------------------------------------- 2008_05_03_2330: Release with SGBgrid 2008 (Quo Vadis) tutorials Please visit https://lists.sourceforge.net/lists/listinfo/cctbx-cvs to see the full change logs. ------------------------------------------------------------------------------- 2008_04_25_1421: This build was used for CCI Apps release 2008_04_25_1421. Please visit https://lists.sourceforge.net/lists/listinfo/cctbx-cvs to see the full change logs. ------------------------------------------------------------------------------- 2008_02_08_1610: This build was used for CCI Apps release 2008_02_08_1610. Please visit https://lists.sourceforge.net/lists/listinfo/cctbx-cvs to see the full change logs. ------------------------------------------------------------------------------- 2008_01_09_2058: This build was used for CCI Apps release 2008_01_09_2058. Please visit https://lists.sourceforge.net/lists/listinfo/cctbx-cvs to see the full change logs. ------------------------------------------------------------------------------- 2007_11_18_2203: This build was used for phenix-1.3b-rc6 and CCI Apps release 2007_11_18_2203. Please visit https://lists.sourceforge.net/lists/listinfo/cctbx-cvs to see the full change logs. ------------------------------------------------------------------------------- 2007_10_29_2045: November 2007 issue of the IUCr Computing Commission Newsletter: http://www.iucr.org/iucr-top/comm/ccom/newsletters/2007nov/ Please visit https://lists.sourceforge.net/lists/listinfo/cctbx-cvs to see the full change logs. ------------------------------------------------------------------------------- 2007_08_18_1856: This build was used for CCI Apps release 2007_08_18_1856. Please visit https://lists.sourceforge.net/lists/listinfo/cctbx-cvs to see the full change logs. ------------------------------------------------------------------------------- 2007_05_29_2026: This build was used for CCI Apps release 2007_05_29_2026. Please visit https://lists.sourceforge.net/lists/listinfo/cctbx-cvs to see the full change logs. ------------------------------------------------------------------------------- 2007_04_26_2350: This build was used for CCI Apps release 2007_04_26_2350. Please visit https://lists.sourceforge.net/lists/listinfo/cctbx-cvs to see the full change logs. ------------------------------------------------------------------------------- 2007_04_06_1210: This build was used for CCI Apps release 2007_04_06_1210. Please visit https://lists.sourceforge.net/lists/listinfo/cctbx-cvs to see the full change logs. ------------------------------------------------------------------------------- 2007_04_04_2342: This build was used for CCI Apps release 2007_04_04_2342. Please visit https://lists.sourceforge.net/lists/listinfo/cctbx-cvs to see the full change logs. ------------------------------------------------------------------------------- 2007_03_26_1903: This build was used for CCI Apps release 2007_03_26_1903. Please visit https://lists.sourceforge.net/lists/listinfo/cctbx-cvs to see the full change logs. ------------------------------------------------------------------------------- 2007_03_13_2155: This build was used for CCI Apps release 2007_03_13_2155. Please visit https://lists.sourceforge.net/lists/listinfo/cctbx-cvs to see the full change logs. ------------------------------------------------------------------------------- 2007_01_24_2154: This build was used for CCI Apps release 2007_01_24_2154. Please visit https://lists.sourceforge.net/lists/listinfo/cctbx-cvs to see the full change logs. ------------------------------------------------------------------------------- 2007_01_11_0918: This build was used for CCI Apps release 2007_01_11_0918. Sorry, we didn't keep track of many changes. Please visit https://lists.sourceforge.net/lists/listinfo/cctbx-cvs to see the full change logs. ------------------------------------------------------------------------------- 2006_11_22_0037: Please visit https://lists.sourceforge.net/lists/listinfo/cctbx-cvs to see all change logs. Transition to Python-2.5 Boost CVS 2006_11_22_0032 SCons CVS 2006_11_19_0205 ------------------------------------------------------------------------------- 2006_07_05_2228: This build was used for phenix release 1.24.1b (2006 Jul 05) Sorry, we didn't keep track of many changes. Please visit https://lists.sourceforge.net/lists/listinfo/cctbx-cvs to see the full change logs. iotbx.mtz: additional in-place manipulations: crystal::set_name(), set_project_name() dataset::set_name(), set_wavelength() column::set_label(), set_type() iotbx: write a test ADSC-format image with arbitrary data iotbx.pdb: - new C++ parser iotbx.reflection_statistics improvements - enumeration of equivalent twin laws, reindexing matrices to find & display the best choice - clear indication of how reindexing matrices are to be used - new --lattice_symmetry_max_delta option iotbx.scalepack: bug fix scalepack no_merge_original_index: the centring type of the space group was not correctly accounted for before cctbx.xray: - new class refinement_flags - new attribute scatterer.refinement_flags cctbx.sgtbx.direct_space_asu: - bug fix: reference_table.asu_096(): Previously the asu was in an incorrect setting. However, the volume was correct anyway, only the sub-conditions for facets, edges and points were incorrect. scitbx.math: - new r3_rotation_axis_and_angle_as_matrix - new r3_rotation_axis_and_angle_from_matrix libtbx: - HP-UX11i support (native aCC compiler) Transition to Python-2.4.3 Boost CVS 2006_06_11_2253 SCons CVS 2006_05_26_2213 ------------------------------------------------------------------------------- 2005_12_29_2029: This build was used for phenix installer 1.22a-d4. Sorry, this time we didn't keep track of many changes. Please visit https://lists.sourceforge.net/lists/listinfo/cctbx-cvs to see the full change logs. basic_map: accessor().all() exposed in the same manner that origin and last are holds a reference to the unit_cell object of the map made all of the ASU mapper-based objects aware of the "minimum distance symmetrically equivalent" whatnots new cctbx.sgtbx.site_constraints adp_constraints reworked site_symmetry_ops cache site_constraints cache adp_constraints new scattering_type_registry old scattering_dict removed libtbx.phil include file include scope Latest Boost CVS (2005_12_28_0908) Latest SCons CVS (2005_12_28_0939) ------------------------------------------------------------------------------- 2005_10_21_1046: Maintenance release to give access to a full set of bundles after recovering from a hard-disk failure. Sorry, this time we didn't keep track of most changes. Please visit https://lists.sourceforge.net/lists/listinfo/cctbx-cvs to see the full change logs. cctbx.sgtbx.lattice_symmetry, iotbx.command_line.lattice_symmetry: - more options to control construction of the supergroup - new code to get rotation matrix for N-fold operator - introspection in group_search to support production of Tables in the Rsymop paper Latest CCP4 I/O CVS (2005_10_21_1039) Latest Boost CVS (2005_10_21_0337) Latest SCons CVS (2005_10_15_1515) ------------------------------------------------------------------------------- 2005_08_18_0201: ************************************************************************ THE RESULTS OF THIS BUILD ARE PARTIALLY LOST DUE TO A HARD-DISK FAILURE. SORRY! ************************************************************************ new mmtbx.xtriage command (Peter Zwart) new mmtbx.scaling module (Peter Zwart) cctbx.maptbx.abstract_interpolator: - new abstract interpolator handling code - get_[cartesian_crystallographic, fractional_crystallographic, non_crystallographic]_interpolator mmtbx.geometry_minimization: - new option: --macro_cycles - new option: --write_pdb_rms_threshold writes PyMOL .pml file for viewing the progress of the minimization iotbx.reflection_statistics: - bug fix: show twin laws with respect to the input unit cell (rather than the minimum cell) cctbx.miller.array: - new map_correlation() method cctbx.maptbx.closest_grid_point(): - interface change: use map.accessor() instead of map to support maps with arbitrary data types cctbx.maptbx: - new average_densities() function, based on code by Pavel Afonine cctbx.sgtbx.space_group_info: - new reflection_intensity_equivalent_groups() method cctbx.sgtbx: - new sgtbx.tensor_rank_2.constraints.independent_curvatures() method cctbx.adptbx: - new debye_waller_factor_u_star_gradient_coefficients - new debye_waller_factor_u_star_gradients - new debye_waller_factor_u_star_curvature_coefficients - new debye_waller_factor_u_star_curvatures new cctbx example: adp_symmetry_constraints.py cctbx.array_family.flex.linear_regression: - new support for weights, based on a Python prototype by Nigel Moriarty obsolete cctbx.mintbx removed scitbx.python_utils.easy_pickle -> libtbx.easy_pickle scitbx.array_family: - new flex.double.add_selected(), flex.vec3_double.add_selected() - new flex.double.matrix_transpose() - new flex.double.matrix_upper_diagonal() - new flex.double.angle() boost_adaptbx: - new boost.optional extension provides boost::optional<> conversions Latest CCP4 I/O CVS (2005_08_10_0129) Latest Clipper (2005_07_15) Latest PyCifRW (PyCifRW-2.0.tar.gz) Latest Boost CVS (2005_08_10_0145) Latest SCons CVS (2005_08_10_0140) ------------------------------------------------------------------------------- 2005_04_29_1615: Sources as included in the Phenix 1.1a release mmtbx: - new scaling procedures (by Peter Zwart) iotbx.mtz.dump: - new --show_column_data option cctbx.xray_structure: - new extract_u_iso_or_u_equiv() - new convert_to_isotropic() - new convert_to_anisotropic() cctbx.miller.array.merge_equivalents(): - new support for complex, Hendrickson-Lattman, bool and int arrays cctbx.miller.array: - new matching_set() - new count_and_fraction_in_bins() - expand_to_p1(): - new support for flex.bool, flex.int - new set() cctbx.miller.array_info: - new systematic_absences_eliminated attribute cctbx.miller.set: - new reflection_intensity_symmetry() - new is_unique_set_under_symmetry() - new unique_under_symmetry_selection() - new unique_under_symmetry() - new generate_r_free_flags() cctbx.maptbx: - new real_space_refinement.lbfgs (by Erik McKee) cctbx.sgtbx: - new tensor_rank_2_constraints - based on space_group.tensor_constraints (removed) - based on adptbx.constraints (removed) - new sym_gradients() - new independent_gradients() cctbx.uctbx.unit_cell: - new box_frac_around_sites() - new buffer_shifts_frac() scitbx.math: - new family of Gamma functions (by Peter Zwart) Latest Clipper release (2005_03_17) Recent CCP4 I/O CVS (2005_04_20_1558) Recent SCons CVS (2005_04_20_1103) Recent Boost CVS (2005_04_20_1126) ------------------------------------------------------------------------------- 2005_03_02_2358: iotbx.reflection_file_reader: - special treatment of SHELX reflection files: =amplitudes =hklf3 =intensities =hklf4 cctbx.sgtbx.space_group: - new average_u_star() - new tensor_constraints() - new adp_constraints() cctbx.xray.minimization: - new u_penalty_exp - new u_penalty_singular_at_zero - new occupancy_penalty - new sqrt_u_iso option cctbx.xray.structure: - new is_positive_definite_u() - new tidy_us() - new shift_us() - show_pairs -> cctbx.crystal.show_distances - new show_distances() method cctbx.xray.scatterer: - new is_positive_definite_u() - new tidy_u() - new shift_u() - apply_symmetry no longer performs eigenvalue filtering for u_star cctbx/xray/fast_gradients.h: - generalized to work for negative u, occupancies, fp cctbx.crystal.pair_asu_table: - new show_distances() method - new pair_counts() method cctbx.crystal.neighbors_simple_pair_generator: cctbx.crystal.neighbors_fast_pair_generator: - new max_distance_sq() method new scitbx.math.basic_statistics new scitbx.math.icosahedron (contributed by Erik McKee) new scitbx.math.lambertw(): Lambert's W function: w(x)*e^(w(x))=x libtbx: - major setpaths overhaul - major config overhaul to introduce --repository support Latest CCP4 I/O CVS (2005_03_02_0129) Latest Clipper (2005_02_25) Recent Boost (2005_02_15_2347) ------------------------------------------------------------------------------- 2005_01_22_0855: mmtbx: - http://iucrcomputing.ccp14.ac.uk/iucr-top/comm/ccom/newsletters/2005jan/ PyCifRW integration: - http://iucrcomputing.ccp14.ac.uk/iucr-top/comm/ccom/newsletters/2005jan/ iotbx.reflection_statistics: - show possible twin laws - show correlations for all possible reindexing choices - show patterson peaks - show perfect merohedral twinning test iotbx.show_distances: - automatic detection and processing of PDB files - new --show_cartesian option iotbx.pdb.interpretation.stage_1.extract_xray_structure(): - label=atom.pdb_format() - new infer_scattering_types_from_names option - new unknown_scattering_type_substitute option iotbx.pdb.atom.selection_cache: - new selection() and iselection() methods operating on expressions such as "rename ala and (name ca or name n)" new iotbx.simple_parser - to support atom selection syntax iotbx.mtz reworked cctbx.xray.structure: - scattering_dict(): optional types_without_a_scattering_contribution parameter - new pair_asu_table() and show_pairs() convenience methods - new set_u_iso_from_u_star() cctbx.miller: - new set.as_non_anomalous_set() - new array.as_non_anomalous_array() - new array.average_bijvoet_mates() - array.change_basis() now supports all array types (phases, complex, hendrickson_lattman) - new set.customized_copy() - new array.customized_copy() - set.common_set() and miller.set.common_sets() changed: a.common_set(b) now returns a set (or array) with the indices ordered as in b, instead of as in a as before; for consistency, a,b = a.common_sets(b) also returns indices ordered as in b. - binner reworked to support nicer output as a side-effect array.show_completeness_in_bins() is obsolete and was removed. cctbx.crystal: - new asu_clusters algorithm - new crystal.reindexing_info class - new crystal.symmetry.reindexing_info() method - new crystal.symmetry.reindexing_matrices() method - new crystal.symmetry.customized_copy() - neighbors_simple, neighbors_fast: new neighbors_of() method cctbx.sgtbx: - new cosets module - new space_group.build_derived_reflection_intensity_group() - new space_group.build_derived_acentric_group() - new rot_mx.transpose() - new rot_mx.as_xyz() - new rot_mx.as_hkl() - new change_of_basis_op.as_xzy() - new change_of_basis_op.as_hkl() - rt_mx and change_of_basis_op constructors accept h,k,l strings cctbx.uctbx.unit_cell: - new similarity_transformations() method - modified constructors: parameters=... metrical_matrix=... orthogonalization_matrix=... new cctbx.crystal.burzlaff_zimmermann_dewolff - demonstration of the practical problems associated with the use of character tables for the determination of the lattice symmetry (by N.K. Sauter) new cctbx.adp_restraints (by P.V. Afonine) scitbx.array_family.flex.double: - new matrix methods: matrix_diagonal matrix_diagonal_sum, matrix_trace matrix_diagonal_product matrix_multiply, dot matrix_lu_decomposition_in_place matrix_lu_back_substitution scitbx.lbfgs: - all parameters for drop_convergence_test included in termination_parameters - objective function value at starting point is now passed to drop_convergence_test ccp4io: - cmtz library is now a shared library on most platforms libtbx: - new libtbx.phil: Python-based hierarchical interchange language http://iucrcomputing.ccp14.ac.uk/iucr-top/comm/ccom/newsletters/2005jan/ - new libtbx.introspection - new support for defining paths to sources via files (instead of softlinks) Transition to Python 2.4 (but Python 2.2 and 2.3 are still supported) Latest Boost CVS (2005_01_21_1616) Latest CCP4 I/O CVS (2004_11_12_0839) Latest SCons CVS (2005_01_21_1609) Latest Clipper (2004_11_01) ------------------------------------------------------------------------------- 2004_09_22_1424: global replacements: - 00000 -> False, 0001 -> True (Python 2.2 compatibility is achieved via the new libtbx.forward_compatibility module) iotbx.pdb.parser: - new columns_73_76_evaluator - decides automatically if columns 73-80 can be ignored because they just contain the PDB ID and the record number new iotbx.pdb.atom new iotbx.pdb.interpretation new mmtbx.geometry_minimization new iotbx.wildcard: - tcsh-like wildcard matching (meta characters: *?[^]) iotbx.crystal_symmetry_from_any: - extract unit cell parameters from xplor maps cctbx.geometry_restraints: - new bond_sorted_asu_proxies.show_sorted_by_residual() - new inverse_power_repulsion_function - repulsion_function renamed -> prolsq_repulsion_function - separate computation of nonbonded_sorted_asu_proxies and bond_sorted_asu_proxies to avoid excessive runtimes caused by very large bond.distance_model - automatic determination of nonbonded_distance_cutoff cctbx.xray.structure: - new selection() method cctbx.miller.array: - apply_selection() -> select() - new phase_integrator() for the conversion of Hendrickson-Lattman coefficients to centroid phases and figures of merit - expand_to_p1() now also works for Hendrickson-Lattman arrays - phase_transfer() now also works with Hendrickson-Lattman array as phase_source cctbx.hendrickson_lattman: - new constructor given centroid phase and figure of merit - new operator+ and operator+= cctbx.array_family.flex.hendrickson_lattman: - new constructor given centroid phases and figures of merit - support for phase combination (via __add__ and __iadd__) cctbx.array_family.xray_scatterer: - new extract_u_cart(), set_u_cart() cctbx.xray.scatterer: - bug fix: u_star eigenvalue filtering was not applied to sites in general positions cctbx.crystal.pair_asu_table: - additional add_pair(pair) overload to facilitate easy combination with the cctbx.crystal.neighbors_fast_pair_generator. cctbx.sgtbx.tr_vec, cctbx.sgtbx.rot_mx: - Python 2.4 compatibility: __float__ removed. Use as_double() instead. scitbx.lbfgs: - new exception_handling_parameters scitbx.math: - new signed_phase_error(), phase_error(), nearest_phase() functions, all in both scalar and vector versions scitbx.array_family.flex: - new flex.bool(size, iselection) constructors - new flex.union, flex.intersection functions (returning flex.bool) - items() and indices() member functions removed (use enumerate() and xrange() instead) - new flex.extract_double_attributes() scitbx.matrix: - Python 2.4 compatibility: __float__ -> as_float scitbx.stl.map: - new stl_string_stl_vector_unsigned, int_stl_vector_unsigned libtbx: - new libtbx.forward_compatibility injects False, True and enumerate into the __builtins__ namespace if not already defined libtbx.refresh: - bug fix: use $LIBTBX0... only if defined; this works around problems caused by a blank PYTHONPATH under Mandrake Linux 10.0 libtbx.configure: - save build_options in libtbx_env and restore on warm_start Latest Boost CVS (2004_09_20_1939) Latest SCons CVS (2004_09_20_1712) ------------------------------------------------------------------------------- 2004_08_05_0113: cctbx.geometry_restraints: - Improved and consolidated version of previous cctbx.restraints module which is now removed. - cctbx.crystal.minimization -> cctbx.geometry_restraints.energies, cctbx.geometry_restraints.lbfgs - cctbx.crystal.distance_ls -> cctbx.geometry_restraints.distance_least_squares New cctbx.crystal.coordination_sequences module - based on code from early distance_ls.py iotbx.pdb: - parser: processing of LINK records - New remark_290_interpretation - New format_scale_records() function based on code by Erik McKee iotbx.lattice_symmetry: - reorganized so printout is separate function call ccp4io: - fix for memory leak in cmtz library (fix provided by CCP4) cctbx.xray.structure: - replace_scatterers() preserves existing site_symmetry_table by default New cctbx.xray.minimization_add_restraints_site_gradients New cctbx.crystal.correct_special_position() (fragment from cctbx.restraints.lbfgs.apply_shifts) cctbx.xray.structure: - change_basis(), expand_to_p1() enhanced to also work for anisotropic displacement parameters and moved to C++ Latest Boost CVS (2004_08_03_0137) Latest CCP4 I/O CVS (2004_07_30_0213) Latest SCons CVS (2004_08_03_0130) ------------------------------------------------------------------------------- 2004_07_06_0816: Integration of Kevin Cowtan's Clipper libraries. mmtbx: - Automatic X-ray term weight calculation procedure improved by introducing the model regularization (minimization of geometry term only) prior to the dynamics calculation. - Bulk solvent correction and scaling procedure significantly improved: flat bulk solvent model parameters, ksol and bsol, are now determined via a grid search (minimizing the R-factor) instead of using the minimizer. - Full maximum-likelihood target function with two ways of calculating the distribution parameters (alpha and beta): a) alpha & beta estimated by maximization of the likelihood function given a current model and experimental intensities. b) alpha = 1.0 & beta - calculated by exact formula. - Calculation of a priori probability distribution for ordered solvent. - Presentation of intermediate results during refinement significantly improved. - Python code for restrained Cartesian dynamics moved from Python to C++. - Automatic detection of R-free flags in CNS, SHELX and CCP4 formatted hkl files. cctbx::sgtbx::site_symmetry - derived from new site_symmetry_ops to facilitate tabulation of only the essential data (site_symmetry_ops::special_op, site_symmetry_ops::matrices) - bug fix: uninitialized data member when used in connection with wyckoff::table - Python keyword argument support new cctbx::sgtbx::site_symmetry_table cctbx::crystal::direct_space_asu::asu_mappings: - Integration of cctbx::sgtbx::site_symmetry_table - min_distance_sym_equiv member removed - process variants with site_symmetry_ops/table as parameters cctbx::sgtbx::sym_equiv_sites: - Constructor with site_symmetry_ops parameter Pickle support for cctbx.sgtbx.rt_mx, cctbx.sgtbx.site_symmetry_ops, and cctbx.sgtbx.site_symmetry_table cctbx.crystal.symmetry: - new asu_mappings() - niggli_cell() with relative_epsilon, iteration_limit parameters cctbx.xray.scatterer: - apply_symmetry_site(), apply_symmetry_u_star() with site_symmetry_ops as parameter - Obsolete update_weight() method removed cctbx.xray.structure: - Integration of cctbx.sgtbx.site_symmetry_table - apply_symmetry() overload with site_symmetry_ops as parameter - new apply_symmetry_sites() - new n_undefined_multiplicities() - new set_sites_frac(), set_sites_cart() - rms() -> rms_difference() cctbx.crystal.distance_ls completely overhauled iotbx.kriber.strudat: read_entry.connectivities(self, all_or_nothing=00000) New iotbx.show_distances, iotbx.distance_least_squares New scitbx.stl.map, scitbx.stl.set scitbx.stl.vector modules Python slice wrapper moved to new scitbx.boost_python.slice extension libtbx.configure now adds packages unless the new --only option is used new libtbx.configure --help option Work in progress: geometry restraints reorganized - new bond_sym_table, bond_sym_dict, bond_sym_ops, bond_sym_op - bond_asu_proxy, repulsion_asu_proxy: inherit from asu_mapping_index_pair - new bond_params: base class for bond_simple_proxy, bond_asu_proxy, bond - bond_proxy -> bond_simple_proxy - repulsion_proxy -> repulsion_simple_proxy - sorted_proxies -> sorted_asu_proxies Latest Boost CVS (2004_07_05_2138) Latest CCP4 I/O CVS (2004_07_03_0431) Latest SCons CVS (2004_07_06_0802) ------------------------------------------------------------------------------- 2004_06_14_0239: iotbx.xplor.map: - bug fix in gridding.is_compatible_flex_grid() - second writer for P1 maps - injection of new cctbx.miller.fft_map.as_xplor_map() iotbx.options_parser: - new enable_resolutions() method to define --resolution, --low_resolution cctbx.maptbx.peak_cluster_analysis: - new effective_resolution parameter, _accumulate_significant() function to support work with low-resolution data cctbx.sgtbx.change_of_basis_op: - apply(miller_index): transformation of one Miller index cctbx.sgtbx.search_symmetry: - continuous_shift_flags(assert_principal=True) for safety cctbx/cctbx/examples/map_skewness.py: - reimplementation of randomize_phases() based on flex.random_double() scitbx.array_family: - flex.bool.iselection() for conversion from flex.bool selection to flex.size_t selection - inplace +-*/% for array,array arguments libtbx: - Unix command-line dispatchers: PYTHONPATH and LD_LIBRARY_PATH are restored if necessary - Support for completely self-contained Windows bundle (incl. Python) - new libtbx.path.abs_path_clean to support installation of Windows binary bundles in directories with spaces in the path name The page at http://cci.lbl.gov/cctbx_build/ was redesigned. Latest Boost CVS (2004_06_11_2046) ------------------------------------------------------------------------------- 2004_06_04_1825: mmtbx: - new dynamics module (simple Cartesian dynamics) iotbx: - new support for reading Mar345 image plate images. - requires a third party module, cbflib, and an adaptor module, cbflib_adaptbx, available from the cctbx authors. - new command iotbx.emma - automatically detects PDB, SDB, SOLVE, SHELX and strudat files - new reflection_file_converter - obsolete reflection_file_writer removed iotbx.mtz: - bug fix: long titles (>70 characters) have to be truncated in order to avoid memory access errors - mtz reader automatically combines delta-anomalous arrays - mtz writer produces column order f+,sig+,f-,sig- instead of f+,f-,sig+,sig- iotbx.lattice_symmetry & cctbx/examples/lattice_symmetry.cpp: - use identity change-of-basis operator if possible cctbx.restraints: - code moved from mmtbx.stereochemistry to cctbx.restraints - new bond_sorted_proxies cctbx.crystal.direct_space_asu.asu_mappings: - is_symmetry_interaction() replaced by is_direct_interaction() (different semantics) - new interaction_type_id() - new asu_mappings.find_i_sym() - special_ops, special_op_indices data members cctbx.web.emma: - automatic detection of PDB and SDB files; symmetry information is reused as much as possible if necessary cctbx.miller.match_bijvoet_mates: - bug fix: pairs_hemisphere_selection bool selection was useless, replaced by std::size_t selection - singles_hemisphere_selection also converted to std::size_t selection for consistency cctbx.miller.array: - apply_scaling() - show_comprehensive_summary() - completeness in resolution range, with d_max=infinity libtbx: - support for optional_packages - correct merging of dependency chains - new libtbx.assert_stdin command-line utility to support regression tests Latest Boost CVS (2004_06_04_1823) Latest SCons CVS (2004_06_04_1817) Most builds switched to Python 2.3.4 ------------------------------------------------------------------------------- 2004_05_17_0534: new top-level mmtbx (macromolecular toolbox) - experimental, interfaces expected to change substantially - automatic mask determination - bulk solvent correction - simple maximum likelihood target - stereochemistry restraints: - bond, angle, dihedral, chirality, planarity, repulsion cctbx.miller: - new array.common_sets() - new array.as_anomalous() - new array.correlation() - array.anomalous_signal() with binning cctbx.crystal.symmetry: - new is_similar_symmetry() cctbx.crystal.neighbors_simple_pair_generator, cctbx.crystal.neighbors_fast_pair_generator: - changed to support a simple scheme for adding up gradients of bonded and nonbonded interactions that also works for atoms on special positions cctbx.crystal.distance_ls: - prototype distance-least-squares - at this point mainly a regression test for bond residual and gradient calculations iotbx: - new command iotbx.reflection_statistics - computation of reflection file statistics: completeness correlation anomalous signal overall and in bins, for each array and for all pairs of arrays - iotbx.xplor map reading and writing completely reorganized and generalized - new option.parser.show_help() scitbx.math: - new matrix_inversion_in_place for N*N matrices scitbx.array_family: - new flex.random_permutation() - flex..count() for numeric types and flex.std_string - new scitbx.math.bessel.ln_of_i0() Adjustments for Mac OS 10.3 Xcode tools v1.2 Latest Boost CVS (2004_05_13_0200) Latest CCP4 I/O CVS (2004_05_10_0840) Latest SCons CVS (2004_05_13_0152) ------------------------------------------------------------------------------- 2004_04_22_2215: cctbx.crystal: - new close_packing.hexagonal_sampling - based on new crystal::close_packing::hexagonal_sampling_generator cctbx.euclidean_model_matching.transform_model(): - bug fix: wrong space group if model1 and model2 have enantiomorphic space groups cctbx.sgtbx: - new search_symmetry, search_symmetry_flags - direct_space_asu.volume_vertices() implementation replaced with a simpler, faster and more general algorithm - min_sym_equiv_distance_info: - additional constructor with array of others - Python keyword argument support - structure_seminvariant renamed as structure_seminvariants cctbx.maptbx, translation_search, euclidean_model_matching: - new sgtbx.search_symmetry used instead of custom code scitbx.array_family.flex: - append(array) renamed as flex.extend(array) (to be compatible with the standard Python list interface) - additional operator overloads: - scalar + array, scalar * array (via __radd__ and __rmul__) - real_array * complex_array, complex_array * real_array (via __mul__ and __rmul__) - Python keyword argument support for nested_loop Latest Boost CVS (2004_04_22_2025) Latest CCP4 I/O CVS (2004_04_22_2142) Latest SCons CVS (2004_04_22_2017) ------------------------------------------------------------------------------- 2004_04_16_0829: cctbx.xray.structure_factors: - fix for SEVERE bug in FFT gradient calculation (permuted values) scitbx.array_family: - new flex.mersenne_twister + convenience functions: flex.random_generator() flex.set_random_seed() flex.random_size_t() flex.random_double() - additional flex.vec3_double arithmetic operators and dot product ccp4io: - avoid hang while reading garbled MTZ files iotbx.pdb.parser: - bug fix: reading of PDB files with lines that have less than 80 characters - new-line characters are now removed correctly iotbx.pdb.residue_info: - bug fix: spaces removed from atom names before lookup - scattering type "H'" -> "H" to adjust to changes in handling of scattering types introduced a few months ago (cctbx.eltbx) iotbx.scalepack: - merge.reader: ignore empty lines Latest Boost CVS (2004_04_15_1122) Latest SCons CVS (2004_04_15_0506) ------------------------------------------------------------------------------- 2004_04_12_1055: iotbx.scalepack: - new merge.write() function cctbx: - new examples/lattice_symmetry.cpp - pure C++ implementation of iotbx.lattice_symmetry script - new C++ crystal::symmetry class - crystal.find_best_cell.cmp_orthorhombic_cell_parameters moved to uctbx::unit_cell::compare_orthorhombic - crystal.find_best_cell.cmp_monoclinic_cell_parameters moved to uctbx::unit_cell::compare_monoclinic scitbx: - new set_policy in boost_python/container_conversions.h - new array_family.shared.std_set_size_t Latest Boost CVS (2004_04_10_1636) Latest SCons CVS (2004_04_10_1630) ------------------------------------------------------------------------------- 2004_04_07_1428: cctbx.adptbx: - analytic computation of eigenvalues removed - wrong results for certain tensors - eigensystem is now a thin wrapper around scitbx::math::eigensystem::real_symmetric - the latter is much faster than the old adptbx::eigensystem implementation cctbx.crystal: - new direct_space_asu.asu_mappings.is_symmetry_interaction() - new direct_space_asu.asu_mappings.map_moved_site_to_asu() - neighbors_simple_pair_generator, neighbors_fast_pair_generator: - new full_matrix option - new prototype: close_packing.py cctbx::sgtbx: - C++ reference documentation for tr_vec, rot_mx scitbx.math: - new principal_axes_of_inertia scitbx.array_family: - new method: flex.size_t.next_permutation() libtbx.itertbx: - new class step (like count but with user-defined step size) libtbx, boost_adaptbx: - support for FSF gcc 3.5 (FSF gcc 3.4 is no longer supported) libtbx: - unset PYTHONHOME in all dispatchers Latest ccp4/lib/src (ccp4io) Latest Boost CVS (2004_04_06_1818) Latest SCons CVS (2004_04_06_1813) ------------------------------------------------------------------------------- 2004_04_06_2355: This build removed because of problems under Red Hat 9. Please use the most recent build. ------------------------------------------------------------------------------- 2004_03_30_2144: This build removed because of problems under Red Hat 9. Please use the most recent build. ------------------------------------------------------------------------------- 2004_03_15_1222: iotbx: - Support for MarCCD detector images. - ImageFactory function takes a file name and returns an image object of type ADSCImage or MarImage, whichever is appropriate. Unsupported formats raise an exception. libtbx: - Support for Python installations without Python's include directory (Mac OS X 10.3 without Xcode). - unsetenv PYTHONHOME (conflict with MGL Tools setup) Latest Boost CVS (2004_03_15_1147) Latest SCons CVS (2004_03_12_1148) ------------------------------------------------------------------------------- 2004_02_26_2127: global cleanup: - sys.stdout removed from all function signatures libtbx: - minor fixes (some SConscripts called twice) Latest Boost CVS (2004_02_26_1222) Latest SCons CVS (2004_02_26_1158) ------------------------------------------------------------------------------- 2004_02_17_1720: cctbx.xray: - new xray.structure.asu_mappings() method - sampled_model_density, fast_gradients: - speed improvements: - more sophisticated determination of sampling box - loop over points in sampling box optimized by pre-computing some intermediates - manually inlined code - distinction between wing_cutoff and rho_cutoff - rho_cutoff is determined as the average Gaussian Fourier transform at zero * wing_cutoff and the same rho_cutoff is used for all scatterers - default wing_cutoff=1.e-3 - distinction of u_base and u_extra: - u_extra determined as u_base - u_radius_min - sampling of negative density is now supported cctbx.crystal: - find_best_cell: faster algorithm for monoclinic space groups - new crystal.direct_space_asu (floating-point parameterization) - new crystal.direct_space_asu.asu_mappings - new crystal.neighbors_simple_pair_generator - new crystal.neighbors_fast_pair_generator cctbx.miller: - binner.bin_legend(): support formatting of binned data - class binned_data, grouping the binner and binned data - set.completeness(use_binning=True) - set.use_binning_of(): same binning for different array of miller indices cctbx.euclidean_model_matching: - new model_matches.transform_model() cctbx.uctbx: - new unit_cell::shortest_vector_sq() scitbx.math: - new scitbx.math.minimum_covering_sphere (Python N-dimensional, C++ 3-dimensional) - new scitbx::math::bessel::i1_over_i0() Moved from cctbx to scitbx: - array_family.flex.vec3_double - cctbx.matrix -> scitbx.matrix libtbx: - warn if scons is in source directory but packages required for build are missing - libtbx.itertbx: wrapper/emulator for Python 2.3 itertools - use -ffast-math (gcc) and -fast (Tru64 cxx) Latest Boost CVS (2004_02_17_1555) Latest SCons CVS (2004_02_17_1546) ------------------------------------------------------------------------------- 2004_01_20_2338: cctbx.maptbx additions: - eight_point_interpolation (flex.double.eight_point_interpolation) - closest_grid_point (flex.double.closest_grid_point) - value_at_closest_grid_point (flex.double.value_at_closest_grid_point) cctbx.crystal.find_best_cell improvement: - Search for best monoclinic cell enhanced. scitbx.flex.nested_loop: - Python wrapper for scitbx::af::nested_loop Latest Boost 1.31 release candidate CVS (2004_01_20_2319) Latest SCons CVS (2004_01_20_1227) ------------------------------------------------------------------------------- 2004_01_16_1718: scitbx.math.gaussian_fit: cctbx.eltbx.gaussian_fit: - new zig-zag fit strategy New: cctbx::eltbx::xray_scattering::n_gaussian - builtin table of N-Gaussian fits Latest Boost 1.31 release candidate CVS (2004_01_16_1712) Latest SCons CVS (2004_01_16_1711) ------------------------------------------------------------------------------- 2004_01_10_0130: scitbx::lbfgsb improvements: - complete C++ interface, Python bindings, tests and documentation - to make C++ interface safe all variables are initialized - workaround for rounding error problems introduced by the gcc 2.96 and Intel C++ 7.1 optimizers - fix for division by zero bug in dcstep scitbx.math.gaussian_fit, cctbx.eltbx.gaussian_fit: - Integration of lbfgsb minimizer cctbx.crystal.find_best_cell: - keep list of all transformed cells (all_cells() method) Latest Boost 1.31 release candidate CVS (2004_01_09_2254) Latest SCons CVS (2004_01_08_0958) ------------------------------------------------------------------------------- 2004_01_07_0245: new flex.linear_interpolation() new scitbx.math.golay_24_12_generator new scitbx::math::floating_point_epsilon template (from L-BFGS-B 2.1) new scitbx::lbfgsb (based on L-BFGS-B Version 2.1) ------------------------------------------------------------------------------- 2003_12_19_1245: cctbx.eltbx & scitbx.math.gaussian: N-Gaussian fits against tabulated data or reference approximations libtbx: support "packages_required_for_use": ["boost_adaptbx"] boost_adaptbx: boost.python.injector boost.python.import_ext (removed from libtbx) scitbx.rational -> to boost.rational scitbx.test_utils -> libtbx.test_utils scitbx.array_family.flex: select(sequence, permutation) export_to(target_module) ------------------------------------------------------------------------------- 2003_12_11_1020: cctbx.eltbx.xray_scattering: - 2-Gaussian and 1-Gaussian approximations of Agarwal (1978). - gaussian.gradient_at_d_star() - gaussian.integral_at_d_star() - IT1992 H' and H swapped to make the labelling of H compatible with that of WK1995 and Agarwal & Isaacs. The new IT1992 H' copied to WK1995 instead of the old IT1992 H'. cctbx.eltbx.gaussian_fit: - Fitting of N-Gaussian approximations (N=1,2,3,4,5) to Waasmaier & Kirfel (1995) approximations. cctbx.web.emma: - Fix for stupid bug: the tolerence and diffraction_index_equivalent parameters were not passed to emma.model_matches() ------------------------------------------------------------------------------- 2003_12_04_0625: libtbx: - new command: libtbx.any2unix - converts DOS or MAC text files to Unix text files scitbx: - new functions: scitbx::math::erf, erfc, erfcx cctbx: - 2-Gaussian approximations for H,C,N,O,S (from CCP4): eltbx.xray_scattering.two_gaussian_agarwal_isaacs - new command: cctbx.structure_factor_timings ------------------------------------------------------------------------------- 2003_12_03_0321: Interface changes: - cctbx::xray::scatterer - fp_fdp split into fp, fdp - caasf member (pointer to static Gaussian approximation) replaced by scattering_type (a string) - cctbx::eltbx::caasf renamed to cctbx::eltbx::xray_scattering New features: - new cctbx::eltbx::xray_scattering::gaussian - variable number of terms (max. 10 + constant) - new cctbx::xray::scattering_dictionary - cctbx.xray.structure.scattering_dict() - automatic or custom assignment of Gaussian approximations to the scattering factor - cctbx.xray.structure.structure_factors() - automatic determination of anomalous_flag - cctbx.xray.structure.show_scatterers() - show scattering type, u_cart_as_u_iso, u_cart on separate line - iotbx.pdb.xray_structure - write element symbol (columns 77-78) - optional res_name argument Current Boost CVS (2003_12_02_1339) Current SCons CVS (2003_12_02_1337) ------------------------------------------------------------------------------- 2003_11_24_1254: New commands: libtbx.create_unzipsfx libtbx.bundle_as_exe Renamed command: libtbx.bundle_as_selfx (was bundle_up) ------------------------------------------------------------------------------- 2003_11_23_1030: scitbx.lbfgs (interface change): - use traditional convergence test by default - lbfgs.termination_parameters, lbfgs.core_parameters objects cctbx.xray.structure_factors (interface change): - direct=, fft= -> algorithm="direct" or algorithm="fft" cctbx.miller: - new binner::interpolate() - used by miller.quasi_normalize_structure_factors New commands: - libtbx.find_clutter - libtbx.clean_clutter - libtbx.start_binary_bundle - libtbx.bundle_up - libtbx.create_selfx - libtbx.py_compile_all ------------------------------------------------------------------------------- 2003_11_14_0949: Fix for unnecessary rebuild problem: - do not use __file__ in source code generators (variable extension: .py, .pyc) Latest Boost CVS (2003_11_14_0928) ------------------------------------------------------------------------------- 2003_11_13_1228: libtbx: - In the absence of special rules use unix_gcc (enables SunOS gcc build) - MIPSpro 7.41 support - New libtbx.dblite to manage .sconsign on all platforms Latest SCons CVS (2003_11_12_1218) Latest Boost CVS (2003_11_12_1217) - boost/mpl/aux_/preprocessed/plain/full_lambda.hpp patched for MIPSpro 7.41 cctbx_install_script.csh: - re-use cctbx_build/python/bin/python if available ccp4io/lib/src/ccp4_sysdep.h: - Patched to support AMD Opteron build ------------------------------------------------------------------------------- 2003_11_09_0049: New implementation of cctbx.xray.minimization: - pass shifts to minimizer - when applying shifts allow only physically meaningful parameters: - treatment of special positions - u_iso >= 0 - eigenvalue filtering on u_cart - occupancy >= 0 - fp >= -f0(d_min) ------------------------------------------------------------------------------- 2003_11_05_1217: Additional maptbx::structure_factors::from_map constructor: Symmetry sum of data for given Miller indices. cctbx::xray::sampled_model_density::apply_symmetry removed using cctbx::maptbx::structure_factors::from_map with symmetry sum instead structure_factors_direct.h optimizations: special case for "const" scatterers scatterer.weight() and scatterer.fp_fdp moved up one loop level special treatment of centric and origin-centric space groups special processing of lattice translations structure_factors_simple.h: simple reference implementation for regression tests Red Hat 9 with Python 2.2: LD_ASSUME_KERNEL=2.4.1 Support for native Apple compiler (gcc 3.3 build 1493). This comiler is now used by default under OS 10. Latest SCons CVS (2003_11_04_1701) Latest Boost CVS (2003_11_05_1154) ------------------------------------------------------------------------------- 2003_10_21_0128: libtbx: Under Windows use new assoc_ftype.py script to suppress output from assoc and ftype commands. Latest SCons CVS (2003_10_21_0111, no patches) ------------------------------------------------------------------------------- 2003_10_20_1528: Interface changes: - major reorganization of cctbx.xray subpackage - integration of fast_gradients in high-level xray.structure_factors interfaces - reorganization of direct summation code: xray/structure_factor.h split into structure_factors_direct.h, gradients_direct.h - eliminate_u_extra -> apply_u_extra - xray density sampling: wing_cutoff default 1.e-6 instead of 1.e-3 New: - direct summation optionally with cos_sin_table - apply_u_extra with multiplier array - fast xray gradient calculation for non-anomalous data sets - adptbx.grad_u_star_as_u_cart,grad_u_cart_as_u_star vector versions - flex_sym_mat3_double.as_double,from_double libtbx: Under Windows use the ASSOC and FTYPE commands to enable wrappers in libtbx/bin. The wrappers have now the extension .px . ------------------------------------------------------------------------------- 2003_10_16_1610: Interface changes: cctbx::maptbx::determine_gridding(): additional mandatory_factors parameter. cctbx::xray::direct_with_first_derivatives uses new gradient_flags type. cctbx::xray::fast_gradients also uses new gradient_flags type. cctbx/cctbx/development/fast_gradients.py -> cctbx/cctbx/regression/tst_xray_fast_gradients.py ------------------------------------------------------------------------------- 2003_10_16_0708: libtbx: configure.py asserts at start that Python 2.2 or higher is used. Under Unix use /bin/sh wrappers instead of softlinks. Under Windows copy python.exe only, otherwise use python execfile wrappers. More support for Linux Intel C++: generate LD_PRELOAD Python 2.2 support: replace all False, True by 00000, 0001 patch scons to avoid False, True problem ------------------------------------------------------------------------------- 2003_10_15_1156: New examples: - Generation of random f_calc (based on a random structure). - View an FFT map in PyMOL. The map is computed using the cctbx from within PyMOL. Also includes peak search and display. Bug fixes: - Computation of gradient w.r.t. site for scatterer with anisotropic displacement parameters (direct summation). - Fast gradient calculation: d_target_d_f_calc must be multiplied with epsilon before computing the FFT. - Latest CVS version of scons (2003_10_15_1118; fixed: parallel build hangs after printing error messages). ------------------------------------------------------------------------------- 2003_10_06_1749: Latest SCons CVS (2003_10_06_1739) with patch libtbx: new include_registry (affects all SConscript files) CScanSetFlags, CScanRegisterFlags removed ------------------------------------------------------------------------------- 2003_10_02_1153: scitbx::lbfgs::minimizer: Avoid use of user-supplied array (diagonal elements of inverse Hessian) as scratch array for line search. cctbx::translation_search: fast_nv1995 refactored to enable use of individual terms for other purposes. cctbx::miller: miller::hash_compare renamed to fast_less_than; now actually used when matching lists of miller indices. ------------------------------------------------------------------------------- 2003_09_30_0603: tst_krivy_gruber.py --Forever option ------------------------------------------------------------------------------- 2003_09_25_1908: uctbx.fast_minimum_reduction: Detection of A4-A8 cycles replaced by test for significant changes of unit cell lengths. New example: map_skewness.py Latest Boost CVS (2003_09_23_2324) ------------------------------------------------------------------------------- 2003_09_23_2250: Pickle incompatibility: Pickling of flex.xray_scatterer arrays has changed. Before the weight() was in the pickle, new weight_without_occupancy(). MTZ reader: Turn non-anomalous arrays into anomalous arrays if more than 2/3 of the reflections are in Bijvoet pairs. Equivalent reflections are merged by default when converted to a miller.array. First version (without full Python interface): FFT x-ray structure factor gradient calculation ------------------------------------------------------------------------------- 2003_09_09_1700: New command-line options: libtbx/configure.py --compiler --static_libraries --static_exe xray.targets_least_squares_residual: optional fixed scale_factor ------------------------------------------------------------------------------- 2003_09_08_1449: Bug fix: cctbx/sgtbx/lattice_symmetry.cpp: sort permutation was not used New: xray.structure atomic_weights, center_of_mass Changed: iotbx.lattice_symmetry: show centro-symmetric subgroups libtbx/configure.py: emit setpaths.sh safety check at top of setpaths.csh, unsetpaths.csh refresh checks both isfile and islink use SconsignFile() Latest SCons CVS (2003_09_06_2114) with patch (anydbm, dumbdbm) Latest Boost CVS (2003_09_08_0332) ------------------------------------------------------------------------------- 2003_09_03_1905: Change: uctbx::unit_cell::is_degenerated() -> is_degenerate() Latest version of Boost CVS (2003_09_03_0916) ------------------------------------------------------------------------------- 2003_09_02_0256: New: uctbx::unit_cell::is_degenerated() ------------------------------------------------------------------------------- 2003_09_01_0052: change of terminology: minimal cell -> minimum cell sgtbx.lattice_symmetry uses minimum cell instead of Niggli cell Assertions in fast_minimum_reduction.h replaced by throw error_degenerated_unit_cell_parameters(); ------------------------------------------------------------------------------- 2003_08_31_1957: New cctbx/uctbx/fast_minimal_reduction.h ------------------------------------------------------------------------------- 2003_08_30_0218: uctbx.cpp: sin_eps and cos_eps removed krivy_gruber_1976: avoid use of multiplication in evaluation of conditions and in actions sign function eliminated assert that a,b,c>0 at all times count each action as one iteration assert that change-of-basis is correct extreme cell test eliminated New: cctbx/web/lattice_symmetry.html cctbx/web/lattice_symmetry.py iotbx/solve/fpfm_reader.py ------------------------------------------------------------------------------- 2003_08_27_1802: Latest SCons CVS snapshot ------------------------------------------------------------------------------- 2003_08_26_0958: Latest boost CVS snapshot ------------------------------------------------------------------------------- 2003_08_25_1708: cctbx.sgtbx.lattice_symmetry: new function find_max_delta() entire submodule reimplemented in C++ iotbx.lattice_symmetry: report lattice_symmetry.find_max_delta() diffraction_angle_comparison removed sort subgroups by order_z() and space group number show only subgroups corresponding to Bravais types ------------------------------------------------------------------------------- 2003_08_24_0142: libtbx/bin dispatchers are now softlinks or copies ------------------------------------------------------------------------------- 2003_08_21_1457: - Using latest boost cvs snapshot. - miller/sym_equiv.cpp: fix for processing hkl=000 - xray/boost_python/scatterer.cpp: more elegant make_setter MIPSpro workaround - New: iotbx/cns/index_fobs_sigma_reader.py ------------------------------------------------------------------------------- 2003_08_19_0643: New: cctbx/crystal/find_best_cell.py cctbx/sgtbx/lattice_symmetry.py cctbx/sgtbx/subgroups.py iotbx/command_line/lattice_symmetry.py ------------------------------------------------------------------------------- 2003_08_10_1037: New: - The Mac OS X binaries are now compiled with full optimization. - cctbx::adptbx::eigenvalue_filtering() Default arguments changed: - cctbx::xray::scatterer::apply_symmetry() u_star_tolerance=0 assert_is_positive_definite=false I.e. by default any anisotropic displacement parameters are accepted, but Eigenvalue filtering and symmetry averaging is used to correct non-sensical parameters. ------------------------------------------------------------------------------- 2003_08_09_0503: Removed: - cctbx::sgtbx::space_group::is_compatible_metrical_matrix() New: - cctbx::sgtbx::space_group::average_metrical_matrix() - cctbx::sgtbx::space_group::average_unit_cell() Changed interface and implementation: - cctbx::sgtbx::space_group::is_compatible_unit_cell() is_compatible_unit_cell() is less strict than before. Use average_unit_cell() to ensure that a unit cell is compatible with the space group symmetry within floating point precision. This is done automatically by the Python class cctbx.crystal.symmetry. ------------------------------------------------------------------------------- 2003_07_18_1638: New features: - cctbx.maptbx.peak_list with interpolation. Interpolation is used by default. Interface changes: - cctbx::maptbx::peak_list Before: peak_list.entries()[i].index peak_list.entries()[i].value New: peak_list.grid_indices()[i] // replaces .index peak_list.grid_heights()[i] // replaces .value peak_list.sites()[i] // interpolated fractional coordinates peak_list.heights()[i] // interpolated peak heights -------------------------------------------------------------------------------