v1.4.0 (03/12/2019) - introduced simple semantic versioning according…

Changelog:

v1.4.0 (03/12/2019)

• introduced simple semantic versioning according to https://semver.org

v1.3.8.19 (02/12/2019)

• bug fix: xce to read resolution at Mn(I)/sig(I) of 2.0 (and 1.5 if possible) from aimless log; now only reads either one or the other. D
  atasets table now only shows reso at 2.0 since 1.5 not always shown
• bug fix: read gda barcodes into DB and display in datasets table

v1.3.8.18 (25/11/2019)

• bug fix: added except statement in get_gda_barcodes to catch errors during parsing of multiple visits

v1.3.8.17 (20/11/2019)

• bug fix: refine routine in XChemCootReference.py did not contain argument for covalent bonds

v1.3.8.16 (17/10/2019)

• added CompoundSMILESproduct field in DB to provide SMILES string of product of covalent binders
• new function to use phenix.ligandfit and rhofit to fit ligands into initial maps (all enantiomers are tried and best one is selected)

v1.3.8.15 (15/10/2019)

• new function to define covalent links in XCE COOT interface and to create them with ACEDRG

v1.3.8.14 (14/10/2019)

• new workflow to detect chiral centres in molecules and subsequent enumaration of stereoisomers with phenix.elbow
• selection and modelling of different enantiomers implemented in XCE-COOT interface

v1.3.8.13 (27/09/2019)

• changes to parsing of auto-collected visits ("agamemnon") due to DLS changes to folder structure (now called 'auto' instead of 'agamemno
  n')

v1.3.8.12 (10/09/2019)

• new task for merging CIF file of non-standard ligand with compoound CIF files
• added exception to catch IOError during opening of gzipped gda logfile

v1.3.8.11 (04/09/2019) - added few changes to enable parsing of DLS v…

Changelog:

v1.3.8.11 (04/09/2019)

• added few changes to enable parsing of DLS visit directories transfered to other file system

v1.3.8.10 (14/08/2019)

• bug fix: update DB from file system now looks for refine.split.bound-state.pdb instead of refine.bound.pdb

v1.3.8.9 (07/08/2019)

• added option to parse Agamemnon data structure at DLS
• removed obsolete 'Run DIMPLE on All Autoprocessing MTZ files' option from yellow Datasets action box

v1.3.8.8 (25/06/2019)

• path to selected ground-state MTZ/PDB displayed (deposition tab)
• selected PanDDA directoy for ground-state deposition displayed (deposition tab)
• link to group deposition website added to ligand-bound deposition (deposition tab)
• information about ground-state MTZ file added (deposition tab)

v1.3.8.7 (06/06/2019)

• 'model_building' is now the new default initial_model directory

v1.3.8.6 (31/05/2019)

• XChemCOOT-test: added menu funciton to set occupancy of all protein residues to 1 (IMPORTANT: requires COOT v0.8.9.2 or higher)

v1.3.8.5 (29/05/2019)

• bug fix: selection of ground-state mean-map after pandda pre-run: look for average-map instead of mean-map

v1.3.8.4 (23/05/2019)

• bug fix: new initial refinement mechanism does not use the dimple_rerun_on_selected_file subfolder which meant that the .free.mtz file was not selected after the run
• XChemPanDDA export: changed how models will be selected for refinement
• XChemPanDDA export: removed update of obsolete DimplePANDDAhit field in database
• XChemPanDDA export: removed false alarm during export #217
• XChemDeposit: added check for .free.mtz file
• XChemCOOT: add XCE menu (test version only)
• XChemCOOT: add menue item to set occupancy of all protein residues to 1.0 (test version only)

v1.3.8.3 (22/05/2019)

• XChemCOOT: xce-coot messages are now written to xce.log file (not all, yet)
• XChemCOOT: warning message added in case cootOut/Refine_ folder exists
• bug fix: XChemDB: remove hidden characters like \r and \n when updating depositTable
• XChemDB: changed single to double quotation marks (and vice versa) in update depositTable function to allow for example 5' in structure title

v1.3.8.2 (17/05/2019)

• bug fix: avoid overwriting of ligand confidence when updating DN from file system: removed option to 'Update datasource with results from pandda.inspect' + changed XChemPanDDA that only the panddaTable gets only updated for models that ought to be exportet.
• bug fix (temporary): removed label option because it does not behave as expected
• XChemDB: removed PANDDA_site_ligand_placed constraint from query for pandda models

v1.3.8.1 (17/05/2019)

• XCE now ignores empty directories when updating DB from file system

v1.3.8 (25/04/2019)

• added possibility to deposit protein-protein complex structure
• XChemDeposit - create table_1 from final mmcif file
• XChemDeposit - add option to not include event maps in SF mmcif file
• bug fix: XChemDeposit - use beamline information from mainTable

v1.3.7 (18/03/2019)

• implemented pop-up window to remind users where they started xce - minor change

v1.3.6 (14/03/2019)

• new deposition tab with step-by-step instructions regarding PanDDA group depositions
• some obsolete commands were removed from menu and action boxes
• added instructions about how to update DB with PDB codes after group deposition of ligand bound structures
• bug fix: add only structures which are '5-ready for deposition' to tar archive for PDB upload
• increment existing .tar.bz2 files in group_deposition folder before creating a new one
• bug fix: '5-ready for deposition' models can now be added and removed if respective field in COOT interface is triggered

v1.3.5 (07/03/2019)

• added option to use pipedream or phenix.ligand_pipeline for initial refinement (see preferences)

v1.3.4 (01/03/2019)

• bug fix: remove sourcing of pandda setup script in panddaRefine module in case of non-DLS refinement

v1.3.3 (19/02/2019)

• bug fix: wavelength information for apo mmcif file data_template is now also taken from ground-state mtz file
• added additional instructions to deposition tab about ground-state aimless LOG file
• bug fix: removed not supported 'group leader' and 'investigator' option from edit deposition data menu

v1.3.2 (12/02/2019)

• bug fix: removed reference to non-existent labels (prevented opening of pandda models/ maps)

v1.3.1 (25/01/2019)

• bug fix: support of new autoProc directory structure at DLS
• bug fix: removal of non-existent DataProcessingProgram entries at DLS from collectionTable
• bug fix: xce coot plugin: changed layout so that full window can be displayed on any screen

v1.3 (16/01/2019)

• bug fix: get space group from aimless log file if file contains output from other programs like unique
• bug fix: change qsub command for dimple and restraints generation so that it works outside DLS
• new feature: assign labels to datasets in xce-coot interface
• bug fix: accomodate None value when querying DB for event map information
• new feature: preparation of apo mmcif files containing SF's all all datasets used for pandda.analyse
• improvement: refinement of pandda models enabled where ligand binding did not lead to any differences between bound-state and ground-state
• bug fix: update data_rxxxxsf field in apo mmcif file
• fix pandda button in settings tab
• add XCE manual to help menu

xce-dev-tk

• bug fix: parsing and display of transferred processed directory enabled
• new deposition tab with step-by-step instructions regarding PanDDA group depositions
• some obsolete commands were removed from menu and action boxes
• enable initial refinement with pipedream and phenix.ligand_pipeline (v1.3.5)

test release

v1.3.4 (01/03/2019): for non-dls refinement; remove sourcing of pandd…

…a setup script in panddaRefine module

v1.3 tk-dev

new features:

changed version to v1.3
inclusion of all apo SF files in one mmcif file
deposition of apo structures as one entry
users can define up to 5 labels in XCE and use buttons in the COOT interface to assign a label to the current crystals; the information is currently recorded in the DB, but not used in any other context; in the future it may be used for sorting in pandda or maps tab.

bug fixes:

XCE now allows refinement of pandda models where ligand binding did not lead to any differences between bound-state and ground-state; refinement failed in the past since in such cases it is not possible to split the model prior to refinement
allow None value when querying DB for event map information
change qsub command for dimple and restraints generation so that it works outside DLS
XChemUtils -> parse: get space group from aimless log file if file contains output from other programs like unique

current stable pre-release

bug fix: dimple failed to run on local macine in tcsh shell
bug fix: : pandda.analyse failed to run on local macine in tcsh shell ( *** not tested ***)

current stable pre-release

• new mechanism for preparation of files for group deposition
• new mechanism for preparation of HTML summary documents
• HTML documents now use NGLviewer for 3D visualization
• parsing of reprocessed datasets is enabled
• event map assignment by CC calculation of ligand in event map
• bug fix: H3 accepted as space group during file preparation for dimple
• bug fix: counterions in smiles string are removed before passing it to restraints generation program

Current stable pre-release

Merge pull request #125 from reskyner/master

better dimple messages on error, clear broken links