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CHANGELOG.rst

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Changelog

0.2.8

  • Fixed issue with gemmi missing entities
  • Fixed issue with using enantiomorphs in phaser

0.2.7

Changed

  • Fixed bug in windows bat files

0.2.6

Changed

  • Lots of minor bug fixes including issue with amore rotation search
  • Added back in user defined MTZ column labels after changes to the MTZ parser meant this was lost

Changelog

0.2.3

Changed

  • Lots of changes to the code to improve python3 compatibility
  • Updated tests
  • Replaced RCSB REST API which has been deprecated

Added

  • Logging util and logging.json to set default logging behaviour and fix logging in py2/3

0.2.1

Changed

  • Fixed issues with simbad-database code
  • Changed how the tests are called to allow automatic testing in ccp4

0.2.0

Added

  • Added MTZ parser which uses GEMMI to get information about the input MTZ
  • Added nmol flag to MR submit options [default 1] (0 for automatic selection)
  • Added run.bat files to examples for testing on windows
  • Added bibliography file for CCP4i2 interface

Changed

  • Set Phaser as default rotation and MR program
  • Altered Phaser to allow it to search for more than 1 search model in MR mode
  • Removed GetLabels function from mtz_util and replaced with MTZ parser
  • Removed CCTBX for calculating the Matthews coefficient
  • Improved the efficiency of the Matthews coefficient calculation
  • Removed CCTBX for PDB manipulations
  • Updated PDB tests to accomodate subtle changes in output
  • Replaced deprecated PyJob imports
  • Altered how MR search deals with low solvent content predictions
  • Modified anomalous util to work with new MTZ parser
  • Altered parent class for parsers
  • Made a parent class for Matthews probability
  • Made a parent class for Rotation functions
  • Fixed issues preventing contaminant search from working on windows
  • Fixed Windows tests
  • Fixed CCP4i2 interface issues
  • Added rot_program and nmol options to ccp4i2 interface
  • Updated pyrapi output to plot graphs for the phaser rotation search

0.1.20

Added

  • Support for Windows
  • Updated all code to be python 3 ready

Changed

  • Fixed a test cases
  • Removed generation of map files following Uglymol update
  • database updates

0.1.19

Changed

  • Fixed documentation errors
  • Formatted code with Black
  • Let tests be run without patching CCP4 for local SIMBAD installation
  • Used named tuples instead of custom scores
  • Fixed PdbStruct Save command
  • Fix to get labels
  • Numerous database updates

0.1.18

Changed

  • Updated stats script
  • Changed code to use the modular version of MrBUMP

0.1.17

Added

  • When using phaser, a LLG/TFZ > 120/8 was added as an additional criteria for early termination
  • Added a process all flag to amore/phaser rotation functions so that they skip the early termination funciton
  • Added option to run ANODE code directly from the command line

Changed

  • Default sequence identity changed from 30 percent to 70
  • Fixed a test case that was broken
  • Fixed several bugs when running jobs as multiple chunks
  • Changed process to skip successive chunks if a solution is found
  • Fixed path in pyvapi

0.1.16

Added

  • Added link to CCP4 SW 2019 presentation

Changed

  • Changed Phaser settings so it doesn't check ensemble deviation. We want to run all the ensembles even if they're poor.
  • Fixed bugs with how ctruncate was being called in mrbump
  • Refactored the code to assign mtz labels and fixed a bug caused by changes to the latest CCTBX version

0.1.15

Added

  • Added code to Pyrvapi to return metadata when performing a lattice search with a space group and unit cell

Changed

  • Changed phaser to just look for 1 molecule in the ASU in full MR search due to time constraints.
  • Fixed a bug that was providing the wrong number of processors to PyJob
  • Fixed bug in the simbad-database code

0.1.14

Added

  • Added code to Pyrvapi to allow SIMBAD to work on CCP4online
  • Added reference manager code
  • Added bibtex file containing SIMBAD references
  • Added citation tab to pyvapi

Changed

  • Changed -morda_db argument in simbad.command_line.simbad-database and simbad.command_line so that it now has a default location and so that after generating the database the -morda_db flag doesn't need to be called every time.
  • Fixed a bug in how pointless was called that was changing the a,b,c,alpha,beta,gamma order.
  • tidied up clean up function

0.1.13

Added

  • Added in code that uses pointless to reindex mtz files
  • EXE_EXT calls to all executable commands to allow for windows compatibility
  • Completely reformatted all pyjob calls to use version 0.2.0 and updated dependencies list.
  • Function to get the sequence from a pdb file
  • Function to generate ensemble database

Changed

  • Replaced CCTBX code that checked the columns in the input MTZ with MrBump code as CCTBX was giving errors for certain input MTZs.
  • Replaced simbad.util.mtz_util.get_labels with a class called simbad.util.mtz_util.GetLabels. This returns more types of input labels and simplifies how the labels are passed into other functions.
  • Updated test cases affected by changes
  • simbad.util.mtz_util.GetLabels was changed to use miller arrays and is therefore more robust when handling columns with non-standard names
  • simbad.rotsearch.phaser_search changed to rank models by RFZ rather than LLG.

0.1.12

Added

  • Check for SSL_CERT_FILE environmental variable in all command line scripts
  • eRMSD calculation added into the phaser rotation search, default set to 70% ID for now but this may change
  • Added SIMBAD paper to docs
  • Added output_files directory to store all output files

Changed

  • Fixed bug in phaser that fixed a problem in check all/enant spacegroups
  • Changed molrep/phaser to output an hkl, this is needed for changes of basis as a result of all/enant searches
  • Altered the cleanup algorithm to completely remove the mr_search directory and instead rely on the newly created output_files directory
  • Altered logging to use enum, closes #81
  • Removed eRMSD calculation and changed to use the seqenence identity directly through phaser, therefore using their equation directly.
  • Altered phaser so that it outputs the input MTZ with a basis change instead of the phaser output mtz, due to missing r-free columns
  • Fixed bug in rotation search solution check due to missing argument

0.1.11

Added

  • CCP4 container for related information
  • standardize function in simbad.util.pdb_util to remove hydrogen and hetatm atoms from downloaded PDB. This resolves a bug in refmac5 where unknown ligands are bound to a pdb.
  • Test cases for simbad.mr.molrep_mr added
  • .bat files so that simbad can be run in windows
  • Fix for bug calling multiple programs from a single script in Windows.
  • mtz_util.change_space_group function to change the space group of an mtz.
  • Test case for simbad.util.pdb_util added
  • Added in a function to check if there is a solution in the rotation search given a sufficiently high peak height
  • Perform a cell content analysis prior to the AMORE search in order to rank search models by molecular weight
  • Phaser rotation search module
  • parsers.anode_parser added

Changed

  • ccp4_root function changed to CCP4RootDirectory class
  • ccp4_version function changed to CCP4Version class and version extracted from official CCP4 release file
  • -enant flag replaced by sga
  • simbad.mr.molrep_mr and simbad.mr.phaser_mr altered to check all space groups
  • simbad.mr.molrep_mr modified so that if an alternative space group is found the input mtz space group will be changed accordingly.
  • simbad.mr.anomalous DANO map calculation modified and the scores reported have been changed
  • simbad.util.mtz_util Altered how converted miller arrays are handled and how the R-free column label is identified
  • simbad.lattice.latticesearch modified to use standardise function
  • i2 code updated to use sga
  • Updated lattice and mtz_util test cases
  • Altered default MR program used in i2 to molrep
  • simbad.mr.phaser_mr altered to use phaser python interface
  • Reduced the number of refinement cycles for the lattice search
  • Reduced the max penalty score in the lattice search from 12 to 7 to speed up the search
  • Reduce the max lattice results from 50 to 20 to speed up the search
  • Fixed bug when standardising files in the lattice search
  • Updated ccp4i2 files to reflect recent changes made to ccp4i2
  • simbad.rotsearch.amore_search moved to simbad.rotsearch.__init__.py in addition to phaser module
  • Fixed test cases and parsers affected by change to rotation search code
  • Altered anomalous fourier calulcation to use ANODE
  • Refactored the rotsearch module and the scoring classes

0.1.10

Added

  • run_tests.py script to execute all unittests
  • PDB-redo download for structures
  • Test cases for pyrvapi metadata object added
  • Test case for latticesearch.pdb_in_results added
  • -tab_prefix option added for JScoFe

Changed

  • Removed reference to deprecated module iotbx.pdb.mining
  • Bug fix in simbad.lattice.latticescore string representation
  • Bug fixes to all unittests
  • Bug fix plus added test cases for simbad.parsers.molrep_parser
  • Standardised parsers internal structure
  • Bug fix in simbad.command_line.simbad_morda and simbad.command_line.simbad_full to fix missing ccp4i2 argument
  • Bug fix in simbad.lattice.latticesearch for duplicate entries from alternative unit cells
  • Bug fix for logging and error message handling prior to logger initialisation
  • Bug fix in simbad.util.pdb_util variable name

0.1.0

  • Initial release