nlesc-nano/nano-CAT issues and pull requests

#133 - Bump codecov/codecov-action from 3 to 4

Pull Request - State: open - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#132 - Bump actions/upload-artifact from 3 to 4

Pull Request - State: open - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#131 - Bump actions/setup-python from 4 to 5

Pull Request - State: open - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#130 - Errors with fast_sigma recipes

Issue - State: open - Opened by juliette1996 about 1 year ago

#129 - Bump actions/checkout from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#128 - BLD: Bump QMFlows to >=0.12.0

Pull Request - State: closed - Opened by BvB93 over 2 years ago - 1 comment

#127 - ENH: Add a new ligand branching workflow

Pull Request - State: closed - Opened by BvB93 over 2 years ago - 1 comment
Labels: enhancement

#126 - ENH: Do not abort fast-sigma computations if a crash is encountered for a single property

Pull Request - State: closed - Opened by BvB93 over 2 years ago - 1 comment
Labels: enhancement

#125 - TST: Add more tests for the MD-ASA workflow

Pull Request - State: closed - Opened by BvB93 almost 3 years ago - 1 comment
Labels: Tests

#124 - TST: Add more tests for the MD-ASA workflow

Pull Request - State: closed - Opened by BvB93 almost 3 years ago - 1 comment
Labels: Tests

#123 - BUG: Fix two MD-ASA bugs

Pull Request - State: closed - Opened by BvB93 almost 3 years ago - 1 comment
Labels: bug

#122 - BUG: Do not assume that `Atom.properties.charge_float` is set

Pull Request - State: closed - Opened by BvB93 almost 3 years ago - 1 comment
Labels: bug

#121 - MAINT: Skip the pKa computation instead of raising for non-negative systems

Pull Request - State: closed - Opened by BvB93 almost 3 years ago - 1 comment
Labels: Maintenance

#120 - ENH: Specify bounds for the to-be optimized ligand vector when computing cone angles

Pull Request - State: closed - Opened by BvB93 almost 3 years ago - 1 comment
Labels: enhancement

#119 - TST: Add tests for the cone-angle `remove_anchor_hydrogens` keyword

Pull Request - State: closed - Opened by BvB93 almost 3 years ago - 1 comment
Labels: Tests

#118 - ENH: Add the `remove_anchor_hydrogens` option to the cone-angle workflow

Pull Request - State: closed - Opened by BvB93 almost 3 years ago - 1 comment
Labels: enhancement

#117 - ENH: Add a new workflow for computing ligand cone angles

Pull Request - State: closed - Opened by BvB93 almost 3 years ago - 1 comment
Labels: enhancement

#116 - ENH: Allow computing the bulkiness for multiple lattice spacing values

Pull Request - State: closed - Opened by BvB93 about 3 years ago - 1 comment
Labels: enhancement

#115 - ENH: Allow computing the bulkiness for multiple lattice spacing values

Issue - State: closed - Opened by BvB93 about 3 years ago
Labels: enhancement

#114 - BUG: Fix the frequency analysis component of the BDE being incompatible with custom CP2K settings

Pull Request - State: closed - Opened by BvB93 about 3 years ago - 1 comment
Labels: bug

#113 - ENH: Add the option to optimize QDs and XYn-dissociated QDs in the dissociation workflow

Pull Request - State: closed - Opened by BvB93 about 3 years ago - 1 comment
Labels: enhancement

#112 - TST: Add more tests for the BDE workflow

Pull Request - State: closed - Opened by BvB93 about 3 years ago - 1 comment
Labels: Tests

#111 - BUG: FIxed an issue wherein the `core_index` option was not properly respected

Pull Request - State: closed - Opened by BvB93 about 3 years ago
Labels: bug

#110 - ENH: Apply qmflows templates when using the dissociation workflow

Pull Request - State: closed - Opened by BvB93 about 3 years ago
Labels: enhancement

#109 - REL: Update master branch after release (0.7.1)

Pull Request - State: closed - Opened by BvB93 about 3 years ago - 1 comment
Labels: release

#108 - MAINT: Fix a documentation failure and deprecate usage of `Molecule.get_formula`

Pull Request - State: closed - Opened by BvB93 about 3 years ago - 1 comment
Labels: Maintenance

#107 - REL: Release nano-CAT 0.7.0

Pull Request - State: closed - Opened by BvB93 about 3 years ago - 1 comment

#106 - MAINT: Adapt to the new CAT anchor parsing input

Pull Request - State: closed - Opened by BvB93 over 3 years ago - 1 comment

#105 - BLD: Bump the PLAMS minimum version to >= 1.5.1

Pull Request - State: closed - Opened by BvB93 over 3 years ago - 1 comment

#104 - TST: Update the fast-bulkiness tests

Pull Request - State: closed - Opened by BvB93 over 3 years ago - 1 comment
Labels: Tests

#103 - ENH: Do not optimize the geometry for the fast-bulkiness workflow

Pull Request - State: closed - Opened by BvB93 over 3 years ago
Labels: enhancement

#102 - BUG: Fixed an issue wherein the new fast bulkiness workflow could fail for branched systems

Pull Request - State: closed - Opened by BvB93 over 3 years ago - 1 comment
Labels: bug

#101 - ENH: Add the new fast-bulkiness recipe

Pull Request - State: closed - Opened by BvB93 over 3 years ago
Labels: enhancement

#100 - ENH: Add the initial implementation of a new (faster) bulkiness workflow

Pull Request - State: closed - Opened by BvB93 over 3 years ago - 1 comment
Labels: enhancement

#99 - ENH: Add a short recipe for sanitizing dataframes in preparation for fast-sigma merges

Pull Request - State: closed - Opened by BvB93 over 3 years ago - 1 comment
Labels: enhancement

#98 - ENH: Added a new helper function for reading fast_sigma .csv files

Pull Request - State: closed - Opened by BvB93 almost 4 years ago - 1 comment
Labels: enhancement

#97 - MAINT: Check if the pure compound property calculations is succesfull before reading properties

Pull Request - State: closed - Opened by BvB93 almost 4 years ago - 1 comment
Labels: Maintenance

#96 - MAINT: Check for the existence of the `.kf` file before accessing its attributes

Pull Request - State: closed - Opened by BvB93 almost 4 years ago - 1 comment

#94 - MAINT: Remove the (non-van der Waals) area and volume

Pull Request - State: closed - Opened by BvB93 almost 4 years ago - 1 comment

#93 - BUG: Added the previously missing `volumequotient` option to the LogP settings

Pull Request - State: closed - Opened by BvB93 almost 4 years ago - 1 comment
Labels: bug

#92 - MAINT: Check the stdout of `$ASMBIN/prop_prediction` for warnings

Pull Request - State: closed - Opened by BvB93 almost 4 years ago - 1 comment

#91 - ENH: Compute additional fast-sigma-based properties

Pull Request - State: closed - Opened by BvB93 almost 4 years ago - 1 comment
Labels: enhancement

#90 - BUG: Fixed an incorrect return-type when restarting

Pull Request - State: closed - Opened by BvB93 almost 4 years ago - 1 comment
Labels: bug

#89 - ENH: Speed up the fast-sigma workflow

Pull Request - State: closed - Opened by BvB93 almost 4 years ago - 1 comment
Labels: enhancement

#88 - MAINT: Set the number of AMS-spawned processes to 1

Pull Request - State: closed - Opened by BvB93 almost 4 years ago - 1 comment

#87 - BUG: Fix an error pickling the log options

Pull Request - State: closed - Opened by BvB93 almost 4 years ago - 1 comment
Labels: bug

#86 - ENH: Allow for customization of the PLAMS logger

Pull Request - State: closed - Opened by BvB93 almost 4 years ago - 1 comment
Labels: enhancement

#85 - MAINT: Fixed an issue wherein dataframes full `nan`s could not be read

Pull Request - State: closed - Opened by BvB93 almost 4 years ago - 1 comment

#84 - ENH: Preserve the order of elements in the returned dataframe

Pull Request - State: closed - Opened by BvB93 almost 4 years ago - 1 comment
Labels: enhancement

#83 - REV: Use the hashed SMILES as jobnames

Pull Request - State: closed - Opened by BvB93 almost 4 years ago - 1 comment

#82 - ENH: Validate that the passed solvents exist in the fast-sigma workflow

Pull Request - State: closed - Opened by BvB93 almost 4 years ago - 1 comment
Labels: enhancement

#81 - BUG: Use regex for identifying the to-be concatenated .csv files

Pull Request - State: closed - Opened by BvB93 almost 4 years ago - 1 comment
Labels: bug

#80 - BUG: Fixed an incorrect number of returned values whenever .compkf generation fails

Pull Request - State: closed - Opened by BvB93 almost 4 years ago - 1 comment
Labels: bug

#79 - BUG: Fixed an issue wherein certain properties were incorrectly ordered in the fast-sigma recipe

Pull Request - State: closed - Opened by BvB93 almost 4 years ago - 1 comment
Labels: bug

#78 - ENH: Add a new recipe for perforiming fast-sigma COSMO-RS calculations

Pull Request - State: closed - Opened by BvB93 almost 4 years ago - 1 comment
Labels: enhancement

#77 - BUG: Fixed an issue where the `core_atom` key was not properly passed on

Pull Request - State: closed - Opened by BvB93 almost 4 years ago - 1 comment
Labels: bug

#76 - BUG: Fixed an issue where the `core_atom` key was not properly parsed

Pull Request - State: closed - Opened by BvB93 almost 4 years ago - 1 comment
Labels: bug

#75 - ENH: Made the `symbol_y` parameter optional

Pull Request - State: closed - Opened by BvB93 almost 4 years ago - 1 comment
Labels: enhancement

#74 - ENH: Add the `r_max` parameter to the `dissociate_bulk` recipe

Pull Request - State: closed - Opened by BvB93 almost 4 years ago - 1 comment
Labels: enhancement

#73 - ENH: Add a recipe for removing `XY` fragments from the bulk of a molecule

Pull Request - State: closed - Opened by BvB93 almost 4 years ago - 1 comment
Labels: enhancement

#72 - ENH: Add a recipe for dissociating from the bulk

Issue - State: closed - Opened by BvB93 about 4 years ago - 1 comment
Labels: enhancement

#71 - ENH: Update the default CDFT settings

Pull Request - State: closed - Opened by BvB93 about 4 years ago - 1 comment
Labels: enhancement

#70 - MAINT: Raise a `NotImplementedError` when calculating the bulkiness with <2 anchor atoms

Pull Request - State: closed - Opened by BvB93 about 4 years ago - 1 comment

#69 - ENH: Allow access to the `h_lim` and `d` parameters in the bulkiness workflow

Pull Request - State: closed - Opened by BvB93 about 4 years ago - 1 comment
Labels: enhancement

#68 - MAINT: Relax the PLAMS version requirement

Pull Request - State: closed - Opened by BvB93 about 4 years ago - 1 comment

#67 - ENH: Added a recipe for calculating rotational and translational entropies

Pull Request - State: closed - Opened by BvB93 about 4 years ago - 1 comment
Labels: enhancement

#66 - Explicitly disable the frozen core approximation when running CDFT

Pull Request - State: closed - Opened by BvB93 over 4 years ago - 2 comments

#65 - MAINT: Fix a capitalization issue

Pull Request - State: closed - Opened by BvB93 over 4 years ago - 1 comment
Labels: bug

#64 - Error computing Pka

Issue - State: closed - Opened by felipeZ over 4 years ago - 1 comment
Labels: bug

#63 - Calculate the pKa when running the COSMO-RS workflow

Pull Request - State: closed - Opened by BvB93 over 4 years ago - 1 comment
Labels: enhancement

#62 - TST: Switch from travis to github actions

Pull Request - State: closed - Opened by BvB93 over 4 years ago - 1 comment
Labels: Tests

#61 - ENH: Extract and report the octanol/water partition coefficient (LogP)

Pull Request - State: closed - Opened by BvB93 over 4 years ago
Labels: enhancement

#60 - ENH: Extract more properties from the COSMO-RS workflow

Issue - State: closed - Opened by BvB93 over 4 years ago - 2 comments
Labels: enhancement

#59 - Databasing update: Remove all .csv-related functionality

Pull Request - State: open - Opened by BvB93 over 4 years ago
Labels: enhancement

#58 - Move from travis to GitHub Actions

Issue - State: closed - Opened by BvB93 over 4 years ago
Labels: Tests

#57 - Nano-CAT 0.6.1

Pull Request - State: closed - Opened by BvB93 over 4 years ago
Labels: enhancement

#56 - Nano-CAT 0.6.0

Pull Request - State: closed - Opened by BvB93 over 4 years ago
Labels: enhancement

#55 - Add the CDFT recipe to the main CAT workflows

Issue - State: closed - Opened by BvB93 over 4 years ago
Labels: enhancement

#54 - Nano-CAT 0.5.4

Pull Request - State: closed - Opened by BvB93 over 4 years ago
Labels: enhancement

#53 - Create a function for identifying sub-surface shells

Issue - State: closed - Opened by BvB93 over 4 years ago
Labels: enhancement

#52 - Nano-CAT 0.5.3

Pull Request - State: closed - Opened by BvB93 over 4 years ago
Labels: enhancement

#51 - Nano-CAT 0.5.2

Pull Request - State: closed - Opened by BvB93 over 4 years ago
Labels: enhancement

#50 - Create a recipe for calculating conceptual DFT functions

Issue - State: closed - Opened by BvB93 over 4 years ago - 1 comment
Labels: enhancement

#49 - Expand the bulkiness recipe

Issue - State: closed - Opened by BvB93 over 4 years ago
Labels: enhancement

#48 - Nano-CAT 0.5.1

Pull Request - State: closed - Opened by BvB93 almost 5 years ago
Labels: enhancement

#47 - Added the invert_idx parameter

Pull Request - State: closed - Opened by BvB93 almost 5 years ago
Labels: enhancement

#46 - Updated the get_lig_charge() recipe

Pull Request - State: closed - Opened by BvB93 almost 5 years ago
Labels: enhancement

#45 - Coordination number workflow

Pull Request - State: closed - Opened by BvB93 almost 5 years ago - 1 comment
Labels: enhancement

#44 - Added a short recipe for calculating and rescaling ligand charges

Pull Request - State: closed - Opened by BvB93 almost 5 years ago
Labels: enhancement

#43 - Create a recipe for scaling charges

Issue - State: closed - Opened by BvB93 almost 5 years ago
Labels: enhancement

#42 - Changed the default surface identification function to a convex-hull based approach

Pull Request - State: closed - Opened by BvB93 almost 5 years ago
Labels: enhancement

#41 - Cleaned up MatchJob

Pull Request - State: closed - Opened by BvB93 almost 5 years ago
Labels: bug, enhancement

#40 - Add forcefield guessing options

Issue - State: open - Opened by BvB93 almost 5 years ago
Labels: enhancement

#39 - Changed the default match forcefield-type to `top_all36_cgenff_new`

Pull Request - State: closed - Opened by BvB93 almost 5 years ago
Labels: enhancement

#38 - Devel

Pull Request - State: closed - Opened by BvB93 almost 5 years ago

#37 - Devel

Pull Request - State: closed - Opened by BvB93 almost 5 years ago

#36 - Added a function for identifying surfaces using a convex hull-based approach

Pull Request - State: closed - Opened by BvB93 almost 5 years ago
Labels: enhancement

#35 - Exposed the max_dist and tolerance keywords

Pull Request - State: closed - Opened by BvB93 almost 5 years ago
Labels: enhancement

#34 - Documentation updates and fixes

Pull Request - State: closed - Opened by BvB93 almost 5 years ago
Labels: documentation

#33 - Nano-CAT 0.5.0

Pull Request - State: closed - Opened by BvB93 almost 5 years ago
Labels: enhancement

GitHub / nlesc-nano/nano-CAT issues and pull requests