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CHANGELOG.rst

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2024.11

  • Added generalized interface for LBFGS minimizer
  • Improved adding of hydrogens near links in Reduce2

2024.10

  • Added support for Python 3.13
  • Improved tools for alternate conformations
  • Added option to download maps from the EMDB to iotbx.fetch_pdb
  • Fix random selection of atoms to consistently select the same number of atoms

2024.9

  • Added general minimizer class for LBFGS and LBFGS-B minimizers
  • Enabled linking of modified amino acids for cyclic peptides
  • Added functions for parsing .geo files

2024.8

  • Speed improvements to pdb_interpretation
  • DataManager: add sanity check for specified resolution limits

2024.7

  • Speed improvements in NCS search and process non-bonded links
  • DataManager: add scoring layer to filter arrays for fmodel

2024.6

  • Update pdbtools to use target_output_format
  • Update known residue codes
  • Update CCTBXParser to show diff of DataManager scope with --diff-params

2024.5

  • Added water picking with alternate conformations
  • Removed more unused or not maintained tools in iotbx and mmtbx
  • Added check for NaN in ccp4/mrc maps

2024.4

  • Added mmtbx.holton_geometry_validation tool
  • Removed unused or not maintained tools in mmtbx
  • Fixed bug in PDB remediator for RNA
  • Added ability to add water with alternative conformations

2024.3

  • Fixed loggraph output in xtriage
  • Added initial clashscore2 that uses reduce2 and probe2
  • Clean up MolProbity and clashscore code
  • Clean up Polder maps code
  • Added option to use pyopengl in gltbx if available

2024.2

  • Improved handling of writing models in mmCIF or PDB formats
  • Speedups to reduce2 and probe2

2024.1

  • Added checks to see if a model can be outupt in the PDB format
  • Added custom scattering factors support to fmodel
  • Reogranize fmodel PHIL
  • Fixed boost::timer deprecation

2023.12

  • Fixed bug in model_vs_sequence
  • Updated suitename analysis to ignore DNA
  • Fixed bug where mask parameters were not propagated in f_model

2023.11

  • Initial support for longer alternate locations
  • Added some support functions for quantum refinement
  • Bug fixes and improvements to cctbx.HKLviewer
  • Improved handling of rotable hydrogens

2023.10

  • Improvements to reduce2
  • More improvements for handling long residue names
  • Improvments to mosaic bulk solvent model
  • Fixed bug in CCTBXParser that did not show one label being parsed
  • Added option to customize DataManager PHIL in ProgramTemplate
  • Initial support for Python 3.12

2023.9

  • Added initial support for longer residue names
  • Updated lists of modified amino and nucleic acids
  • Generalized wilson_plot to neutron and elecron scattering tables

2023.8

  • Added JSON output to MolProbity structure validation scripts
  • Added support for segID when converting between PDB and mmCIF formats
  • Fixed bug in CCTBXParser where a file could be processed more than once
  • Reorganized restraints based on quantum mechanics

2023.7

  • Initial support for handling longer residue names in mmCIF
  • Improved handling of real-space maps with unexpected metadata for the origin and cell angles
  • Improvements to reduce2 and probe2
  • Reorganization of quantum mechanical restraints

2023.6

  • Basic space group check when reading mmCIF
  • Fix hybrid36 output in mmCIF
  • Updates to lists of modified amino and nucleic acids
  • DataManager updates for handling multiple uses (types) for generating fmodel

2023.5

  • DataManager updates for handling multiple uses (types) of models and Miller arrays
  • DataManager updates for handling priority of amplitudes and intensities
  • Migration from using any_file when file type is already known
  • Start checking atom names of non-standard amino acids

2023.4

  • Prevent potenially large memory usage when trying to read reflection data
  • CCTBXParser fix to properly re-raise an error when parsing PHIL
  • DataManager fix for handling datatypes with parent classes
  • Improved water picking
  • Improved atom selections to handle more than 10k atoms

2023.3

  • Bug fixes for RNA validation
  • Improved handling of B and pLDDT values in mmtbx.process_predicted_model
  • Bug fixes for validating C-beta deviations for D-amino acids
  • Bug fixes and improvements to cctbx.HKLviewer

2023.2

  • Improved modeling of histidine protonation states
  • Improved tool for merging models
  • Added resolution estimation for map docking (prepare_map_for_docking)
  • Bug fixes and improvements to cctbx.HKLviewer

2023.1

  • Enable rounding of occupancies in the ouput files so that the sum is equal to 1
  • Improved mmCIF support with twinning information and fixes in _pdbx_struct_oper_list handling
  • New tool to validate torsions
  • Bug fixes and improvements to cctbx.HKLviewer

2022.12

  • New code for fitting histidine
  • DataManager can map scattering table types to data types

2022.11

  • Improved occupancy handling of multiple conformations so that the sum does not exceed 1
  • Improvements to reduce2 and probe2 tools for MolProbity

2022.10

  • Added array selection via data labels to CCTBXParser
    • Match partial labels to full labels in data file
    • Combine multiple label selections via the command line
  • Allow mosaic buil solvent model to have initial values
  • Fix bug where atoms may be missing in a super-sphere
  • Bug fixes and improvements to cctbx.HKLviewer
  • Switch to using libsvm-official for Python interface to libsvm

2022.9

  • Improvements to cctbx.HKLviewer for viewing output from xtriage or xtricorder
  • Improve stability of prepare_map_for_docking
  • DataManager models can now have multiple types (e.g. x-ray, neutron, etc.)
  • Fix any_reflection_file_reader when reading "hklf+ins/res" (#787)
  • Fix binary and source installers when /usr/bin/python is not available (#788)

2022.8

  • Update to handle new PAE format from AlphaFold
  • CCTBXParser can parse DataManager PHIL parameters and provide more information about ambiguous parameters
  • Initial support for density dependent restraints
  • Bug fixes and updates for cctbx.HKLviewer

2022.7

  • Clean up multiple mmtbx tests
  • Updated to RCSB API v2 for accessing data

2022.6

  • Added --dry-run flag to CCTBXParser to validate inputs
  • Bug fixes for cctbx.HKLviewer
  • Updates to reduce2 and probe2
  • Updates to restraints based on quantum mechanics

2022.5

  • Added function to return fmodel object in DataManager
  • Added options for cubic box and soft masking to resolve_cryo_em
  • Updates to tool for preparing maps for docking
  • More improvements to cctbx.HKLviewer

2022.4

  • Added option to keep unmerged data in DataManager
  • Bug fixes for cctbx.HKLviewer
  • Improvements to finding water in maps

2022.3

  • Added mmtbx.process_predicted_model command
  • Updates and bug fixes to cctbx.HKLviewer
  • Added methods for improved handling of heavy hydrogens in model

2022.2

  • Added --quiet flag to CCTBXParser to suppress output
  • Updates to restraints based on quantum mechanics
  • Updates and bug fixes to cctbx.HKLviewer

2022.1

  • Added option to use legacy bulk solvent mask
  • Added option to any_reflection_file_reader to control averaging of anomalous data columns in MTZ files
  • Fix SHELXF formatting where integer values may be interpreted as decimal

2021.12

  • Initial support for Python 3.10
  • Added support for outputting multi-model mmCIF files
  • Adjusted mask gridding for bulk solvent

2021.11

  • Added right-handed nucleic acids for DNA
  • Improved handling of different unit cells in MTZ file
  • Avoid division by zero when rotating 0 degrees
  • Added option to ignore secondary strucure annotations when reading models through the DataManager
  • Initial support for restraints based on quantum mechanics
  • Improved consistency of binning by d_star_sq

2021.10

  • Initial migration of MolProbity functionality (probe and reduce) to mmtbx
  • Initial tool for likelihood-based map preparation for docking
  • Improvements to ADP refinement for real-space

2021.9

  • Improved structure factor calculation at ultra-low resolution
  • Improved processing of prediced models
  • Added diffBragg to simtbx for modeling pixels in stills to improve structure factors
  • Added suitename to mmtbx for classifying RNA

2021.8

  • Added tools for processing predicted models based on the error estimate
  • Updated list of modified amino and nucleic acids
  • Better handling of sequence files with empty sequences

2021.7

  • Fix pickling error with anomalous_probability_plot
  • Fix bug in reading data CIF file with paired data and sigma arrays of different sizes
  • Added functions for retrieving H-bond types and Van der Waals radii to the model manager class
  • Sequence validation will only use protein or nucleic acid residues for alignment

2021.6

  • More improvements to bulk solvent masking for multiple regions
  • Updates to ensemble refinement
  • Enable conversion of some numpy types into flex types instead of requiring that the types match (e.g. int to float is now supported)

2021.5

  • Improved bulk solvent masking with support for multiple regions

2021.4

  • Improved parsing of reciprocal space data in CIF
  • CCTBXParser can handle intermixed arguments for Python >= 3.7
  • Consolidate management of conda depenencies with conda-devenv

2021.3

  • Initial support for native compilation on Apple Silicon
  • Real-space refinement of occupancies and isotropic ADP
  • Improvements in map_model_manager
    • Split up map and model by NCS groups
    • Create new map_model_manager with resampled maps

2021.2

  • Improved remediator code for converting PDB version 2 format to version 3
  • Add compilation support for Boost 1.72 and 1.74

2021.1

  • Improvements to cctbx.HKLviewer for displaying reciprocal space data

2020.12

  • BIOMT/MTRIX matrices in model reading
    • Added option to loosen handling of improper matrices in DataManager
    • Make behavior conistent between mmCIF and PDB formats
  • Improvements to map_model_manager
    • Better handling of cases when information is missing
    • Calculate the RMSD of matching residues between models

2020.11

  • Updated API for fetching data from RCSB

2020.10

  • Added basic flex arrays for fixed width integer types (#533)
    • Signed types (int8, int16, int32, int64)
    • Unsigned types (uint8, uint16, uint32, uint64)
    • Additional functions may be wrapped in the future to support these types
  • Improved building of downstream software with cctbx conda package
    • In some cases, the location of annlib is not found properly

2020.8

  • First release on GitHub and conda-forge