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Prep v1.1 #20

Merged
merged 132 commits into from
Oct 9, 2023
Merged

Prep v1.1 #20

merged 132 commits into from
Oct 9, 2023

Commits on Dec 1, 2022

  1. SMARTS substruct matching with chemicalite

    @diogomart
    diogomart committed Dec 1, 2022
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Commits on Dec 8, 2022

  1. filter substruct within dist from specified xyz 

    did NOT test with multiple --smarts_idxyz queries
    @diogomart
    diogomart committed Dec 8, 2022
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Commits on Dec 14, 2022

  1. Raise error if given smarts pattern with hydrogen

    @althea-hansel
    althea-hansel committed Dec 14, 2022
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  2. fix for smarts search pattern checking

    @althea-hansel
    althea-hansel committed Dec 14, 2022
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  3. fix atomic number comparison for H in SMARTS

    @diogomart
    diogomart committed Dec 14, 2022
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Commits on Dec 15, 2022

  1. Moved substructure search to sqlite query generator function

    @althea-hansel
    althea-hansel committed Dec 15, 2022
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  2. Print number of passing ligands to STDOUT

    @althea-hansel
    althea-hansel committed Dec 15, 2022
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Commits on Dec 16, 2022

  1. Add summary functions

    @althea-hansel
    althea-hansel committed Dec 16, 2022
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  2. Add command-line option for database summary

    @althea-hansel
    althea-hansel committed Dec 16, 2022
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  3. - Bug fix from previous commit 

    - Update README with info about summary option
    @althea-hansel
    althea-hansel committed Dec 16, 2022
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  4. formating changes for summary info

    @althea-hansel
    althea-hansel committed Dec 16, 2022
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  5. more formatting changes to summary

    @althea-hansel
    althea-hansel committed Dec 16, 2022
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Commits on Dec 19, 2022

  1. filter by max_nr_atoms

    @diogomart
    diogomart committed Dec 19, 2022
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  2. removed passed_poses storage table for processing substruct distance … 

    …filter
    @althea-hansel
    althea-hansel committed Dec 19, 2022
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  3. removed passed_poses storage table for processing substruct distance … 

    …filter
    @althea-hansel
    althea-hansel committed Dec 19, 2022
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  4. Merge remote-tracking branch 'origin/develop' into develop

    @althea-hansel
    althea-hansel committed Dec 19, 2022
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Commits on Dec 20, 2022

  1. change to distance sqlite query format

    @althea-hansel
    althea-hansel committed Dec 20, 2022
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Commits on Jan 13, 2023

  1. Add --pymol option for launching molecules to view in pymol

    @althea-hansel
    althea-hansel committed Jan 13, 2023
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  2. Give more helpful info when attempting to run with no options

    @althea-hansel
    althea-hansel committed Jan 13, 2023
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Commits on Jan 18, 2023

  1. Introduced GUI for ringtail

    @nbruciaferri
    nbruciaferri committed Jan 18, 2023
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  2. Added some enable disable handlings on different groupboxes

    @nbruciaferri
    nbruciaferri committed Jan 18, 2023
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  3. Added ringtail logo

    @nbruciaferri
    nbruciaferri committed Jan 18, 2023
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  4. - Change references to 'binding energy' to 'docking score' 

    - Test case updates
- Bug fixes
    @althea-hansel
    althea-hansel committed Jan 18, 2023
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  5. bug fix for parsing atomtypes

    @althea-hansel
    althea-hansel committed Jan 18, 2023
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Commits on Jan 19, 2023

  1. Added double sliders and relative update events.

    @nbruciaferri
    nbruciaferri committed Jan 19, 2023
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  2. Added ligand filter for read tab

    @nbruciaferri
    nbruciaferri committed Jan 19, 2023
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  3. added how to install pyqt5

    @nbruciaferri
    nbruciaferri committed Jan 19, 2023
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  4. typo

    @nbruciaferri
    nbruciaferri committed Jan 19, 2023
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Commits on Jan 20, 2023

  1. adapted spinbox size

    @nbruciaferri
    nbruciaferri committed Jan 20, 2023
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  2. event handling for db lineEdit text changed

    @nbruciaferri
    nbruciaferri committed Jan 20, 2023
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  3. - Remove ligand_smile from Results table (redundant) 

    - Change input_pdbqt to input_model
- Fix bug in dlg atomtype parsing
    @althea-hansel
    althea-hansel committed Jan 20, 2023
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  4. add SMARTS usage to README

    @diogomart
    diogomart committed Jan 20, 2023
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Commits on Jan 23, 2023

  1. Improve documentation for adding new parser

    @althea-hansel
    althea-hansel committed Jan 23, 2023
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Commits on Jan 24, 2023

  1. Add individual filter columns to Bookmarks table

    @althea-hansel
    althea-hansel committed Jan 24, 2023
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  2. Merge remote-tracking branch 'origin/develop' into develop

    @althea-hansel
    althea-hansel committed Jan 24, 2023
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Commits on Jan 26, 2023

  1. Added new features for the read tab and modified the main window to a… 

    …llow resize
    @nbruciaferri
    nbruciaferri committed Jan 26, 2023
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  2. Added logo

    @nbruciaferri
    nbruciaferri committed Jan 26, 2023
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Commits on Jan 27, 2023

  1. Added new interactions widget to select interactions filter

    @nbruciaferri
    nbruciaferri committed Jan 27, 2023
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  2. started filtering logic on the interaction widget

    @nbruciaferri
    nbruciaferri committed Jan 27, 2023
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  3. Finished filtering logic on interaction widget. Need to add the inter… 

    …action object to the listWidget on mainWindow.
    @nbruciaferri
    nbruciaferri committed Jan 27, 2023
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  4. Added enable and disable functions for interaction filters and delete.

    @nbruciaferri
    nbruciaferri committed Jan 27, 2023
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Commits on Jan 28, 2023

  1. Added edit interaction logic

    @nbruciaferri
    nbruciaferri committed Jan 28, 2023
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  2. some minor refactoring and code cleaning

    @nbruciaferri
    nbruciaferri committed Jan 28, 2023
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  3. Add getters and setters for RTCore options

    @althea-hansel
    althea-hansel committed Jan 28, 2023
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  4. Update README to match last commit

    @althea-hansel
    althea-hansel committed Jan 28, 2023
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Commits on Jan 30, 2023

  1. Modify how filters are stored in bookmark table

    @althea-hansel
    althea-hansel committed Jan 30, 2023
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  2. Bug fix when printing help for command line

    @althea-hansel
    althea-hansel committed Jan 30, 2023
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  3. Fix bug in SDF export

    @althea-hansel
    althea-hansel committed Jan 30, 2023
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Commits on Jan 31, 2023

  1. Added ligand_filter ui

    @nbruciaferri
    nbruciaferri committed Jan 31, 2023
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  2. Bug fix for storing bookmark

    @althea-hansel
    althea-hansel committed Jan 31, 2023
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  3. Update README.md

    @althea-hansel
    althea-hansel authored Jan 31, 2023
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  4. Update README.md

    @althea-hansel
    althea-hansel authored Jan 31, 2023
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Commits on Feb 1, 2023

  1. Added the possibility to call Ligand_Dialog __init__ with an existing… 

    … filter for the edit mode
    @nbruciaferri
    nbruciaferri committed Feb 1, 2023
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  2. Integrated the ligand filter ui with main

    @nbruciaferri
    nbruciaferri committed Feb 1, 2023
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  3. debugging

    @nbruciaferri
    nbruciaferri committed Feb 1, 2023
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Commits on Feb 2, 2023

  1. Some debugging

    @nbruciaferri
    nbruciaferri committed Feb 2, 2023
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Commits on Feb 3, 2023

  1. Integrated ligand filter floating window in the list widget and added… 

    … sanity check on the filter.
    @nbruciaferri
    nbruciaferri committed Feb 3, 2023
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Commits on Feb 4, 2023

  1. corrected some labels

    @nbruciaferri
    nbruciaferri committed Feb 4, 2023
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Commits on Feb 7, 2023

  1. Begfixes in pymol vis

    @althea-hansel
    althea-hansel committed Feb 7, 2023
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  2. Merge remote-tracking branch 'origin/develop' into develop

    @althea-hansel
    althea-hansel committed Feb 7, 2023
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  3. Remove unnecessary exception handling

    @althea-hansel
    althea-hansel committed Feb 7, 2023
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  4. Resolved issue #9

    @nbruciaferri
    nbruciaferri committed Feb 7, 2023
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  5. Added save receptor option in write tab and moved number of poses to … 

    …ligands groupbox
    @nbruciaferri
    nbruciaferri committed Feb 7, 2023
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Commits on Feb 8, 2023

  1. Added borders between elements in ligand filters list

    @nbruciaferri
    nbruciaferri committed Feb 8, 2023
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Commits on Feb 10, 2023

  1. Add timing of filtering query in debug mode

    @althea-hansel
    althea-hansel committed Feb 10, 2023
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  2. Merge remote-tracking branch 'origin/develop' into develop

    @althea-hansel
    althea-hansel committed Feb 10, 2023
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  3. Some improvements in the listwdigetItems graphics

    @nbruciaferri
    nbruciaferri committed Feb 10, 2023
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Commits on Feb 11, 2023

  1. refactor RTCore, make Filters class

    @althea-hansel
    althea-hansel committed Feb 11, 2023
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Commits on Feb 14, 2023

  1. Added logger widget to keep track of what's happening. Still have to … 

    …bind the mode to DEBUG or VERBOSE option.
    @nbruciaferri
    nbruciaferri committed Feb 14, 2023
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  2. Refactor storageman and rtcore to work with new Filters class

    @althea-hansel
    althea-hansel committed Feb 14, 2023
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  3. Initial bug fixes after refactor

    @althea-hansel
    althea-hansel committed Feb 14, 2023
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  4. Bug fix for saving receptor

    @althea-hansel
    althea-hansel committed Feb 14, 2023
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Commits on Feb 15, 2023

  1. Bug fixes and automated test case fixes

    @althea-hansel
    althea-hansel committed Feb 15, 2023
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  2. Additional bugfixes

    @althea-hansel
    althea-hansel committed Feb 15, 2023
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  3. Update setup.py

    @althea-hansel
    althea-hansel authored Feb 15, 2023
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Commits on Feb 16, 2023

  1. modified readLigandsGroupBox rowSpan

    @nbruciaferri
    nbruciaferri committed Feb 16, 2023
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  2. some minor changes

    @nbruciaferri
    nbruciaferri committed Feb 16, 2023
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  3. deleted unnecessary file

    @nbruciaferri
    nbruciaferri committed Feb 16, 2023
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  4. Merge pull request #10 from forlilab/api_refactor 

    Api refactor
    @althea-hansel
    althea-hansel authored Feb 16, 2023
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Commits on Mar 6, 2023

  1. Fix bug in plotting

    Althea Hansel committed Mar 6, 2023
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Commits on Mar 29, 2023

  1. fix smarts searches

    @diogomart
    diogomart committed Mar 29, 2023
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Commits on Apr 20, 2023

  1. Add butina clustering option

    @althea-hansel
    althea-hansel committed Apr 20, 2023
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Commits on Apr 25, 2023

  1. Add handler for keyboard interupt to ensure database closes

    @althea-hansel
    althea-hansel committed Apr 25, 2023
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Commits on Apr 26, 2023

  1. Fixed design flaw causing filtering slowdown

    @althea-hansel
    althea-hansel committed Apr 26, 2023
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  2. Ignore scatter.png

    @althea-hansel
    althea-hansel committed Apr 26, 2023
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  3. Index over possible filter and order by columns at the end of databas… 

    …e writing
    @althea-hansel
    althea-hansel committed Apr 26, 2023
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  4. Create index at end of database writing

    @althea-hansel
    althea-hansel committed Apr 26, 2023
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Commits on Apr 27, 2023

  1. Add framework for receptor export

    @althea-hansel
    althea-hansel committed Apr 27, 2023
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Commits on May 1, 2023

  1. Merge branch 'GUI' into develop

    @althea-hansel
    althea-hansel authored May 1, 2023
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  2. Merge pull request #12 from forlilab/develop 

    Merge develop branch into GUI branch
    @althea-hansel
    althea-hansel authored May 1, 2023
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Commits on May 3, 2023

  1. Bug fix in --name filtering

    @althea-hansel
    althea-hansel committed May 3, 2023
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  2. Fix bug in --max_miss option not working

    @althea-hansel
    althea-hansel committed May 3, 2023
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  3. Merge branch 'GUI' into develop2.0

    @althea-hansel
    althea-hansel authored May 3, 2023
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  4. Merge pull request #13 from forlilab/develop2.0 

    Making one unified development branch (for now)
    @althea-hansel
    althea-hansel authored May 3, 2023
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Commits on May 4, 2023

  1. Improve query structure for filtering by interactions for decreased r… 

    …untime
    @althea-hansel
    althea-hansel committed May 4, 2023
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Commits on May 5, 2023

  1. Always filter over designated window

    @althea-hansel
    althea-hansel committed May 5, 2023
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  2. Get union of interaction_combination filters when using max_miss

    @althea-hansel
    althea-hansel committed May 5, 2023
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Commits on May 8, 2023

  1. - Return only requested outfields with max_miss union 

    - Have export_sdf_path export union when used with max_miss
    @althea-hansel
    althea-hansel committed May 8, 2023
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Commits on May 9, 2023

  1. - fix bug in SDF writing from max_miss union 

    - Speed-up SDF writing
- Add citation to epilog
    Althea Hansel committed May 9, 2023
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  2. Merge pull request #14 from forlilab/develop2.0 

    - fix bug in SDF writing from max_miss union
    @althea-hansel
    althea-hansel authored May 9, 2023
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  3. Finish export_receptor functionality

    @althea-hansel
    althea-hansel committed May 9, 2023
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Commits on May 19, 2023

  1. - Make max_miss only return union by default 

    - Make option for enumerating interaction combinations with max_miss
    @althea-hansel
    althea-hansel committed May 19, 2023
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Commits on May 22, 2023

  1. Change name of ligand fingerprint clustering option

    @althea-hansel
    althea-hansel committed May 22, 2023
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  2. Add interaction fingerprint clustering filter

    @althea-hansel
    althea-hansel committed May 22, 2023
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Commits on Jun 1, 2023

  1. Add option for returning rdkit mols with export_sdf python interface

    @althea-hansel
    althea-hansel committed Jun 1, 2023
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Commits on Jun 13, 2023

  1. Add table containing information on fingerprint clusters

    @althea-hansel
    althea-hansel committed Jun 13, 2023
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  2. Add option for exporting receptor

    @althea-hansel
    althea-hansel committed Jun 13, 2023
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  3. Merge remote-tracking branch 'origin/GUI' into GUI

    @althea-hansel
    althea-hansel committed Jun 13, 2023
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Commits on Jun 14, 2023

  1. Add option for finding similar ligands by ligand name from previous c… 

    …lustering
    @althea-hansel
    althea-hansel committed Jun 14, 2023
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  2. Update README for v1.1 release

    @althea-hansel
    althea-hansel committed Jun 14, 2023
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  3. Removed GUI directory for v1.1

    @althea-hansel
    althea-hansel committed Jun 14, 2023
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  4. Syntax fix

    @althea-hansel
    althea-hansel committed Jun 14, 2023
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  5. Update readme with filtering timings

    @althea-hansel
    althea-hansel committed Jun 14, 2023
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  6. Add link for timings

    @althea-hansel
    althea-hansel committed Jun 14, 2023
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  7. Update README.md

    @althea-hansel
    althea-hansel authored Jun 14, 2023
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  8. Update README.md

    @althea-hansel
    althea-hansel authored Jun 14, 2023
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  9. Update README.md

    @althea-hansel
    althea-hansel authored Jun 14, 2023
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  10. Update README.md

    @althea-hansel
    althea-hansel authored Jun 14, 2023
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  11. Update README.md

    @althea-hansel
    althea-hansel authored Jun 14, 2023
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Commits on Jun 15, 2023

  1. Add functions and script to update database(s) to v1.1.0

    @althea-hansel
    althea-hansel committed Jun 15, 2023
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  2. cosmetic changes to README.md

    @sforli
    sforli authored Jun 15, 2023
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  3. Update readme; add test case for sdf writing

    @althea-hansel
    althea-hansel committed Jun 15, 2023
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Commits on Jun 16, 2023

  1. Fix for sdf writing testcase

    @althea-hansel
    althea-hansel committed Jun 16, 2023
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Commits on Jul 11, 2023

  1. Add option to return iterable from rtcore filter method

    @althea-hansel
    althea-hansel committed Jul 11, 2023
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  2. Merge remote-tracking branch 'origin/prep-v1.1' into prep-v1.1

    @althea-hansel
    althea-hansel committed Jul 11, 2023
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Commits on Jul 26, 2023

  1. Write error log for unparsable files instead of exiting

    @althea-hansel
    althea-hansel committed Jul 26, 2023
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Commits on Jul 27, 2023

  1. Fixed bug where wasn't writing database version to pragma user_version

    @althea-hansel
    althea-hansel committed Jul 27, 2023
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Commits on Aug 10, 2023

  1. Add debug traceback for multiprocessing parsing errors

    @althea-hansel
    althea-hansel committed Aug 10, 2023
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  2. bug fix for parsing with no interactions found

    @althea-hansel
    althea-hansel committed Aug 10, 2023
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Commits on Aug 11, 2023

  1. Fix bug introduced in previous commit

    @althea-hansel
    althea-hansel committed Aug 11, 2023
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  2. Fix bug in kill_all_workers with source error

    @althea-hansel
    althea-hansel committed Aug 11, 2023
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Commits on Aug 21, 2023

  1. Added check for bookmark names starting with digit

    @althea-hansel
    althea-hansel committed Aug 21, 2023
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