molssi-seamm/molsystem issues and pull requests

#94 - Bugfix: error reading JSON properties from SDF files

Pull Request - State: closed - Opened by paulsaxe 30 days ago
Labels: bug

#93 - Enhanced coordinate precision in SDF files

Pull Request - State: closed - Opened by paulsaxe about 1 month ago
Labels: enhancement

#92 - Bugfix: yet more issues with property handling

Pull Request - State: closed - Opened by paulsaxe about 2 months ago
Labels: bug

#91 - Bugfix: more issues with property handling.

Pull Request - State: closed - Opened by paulsaxe 2 months ago
Labels: bug

#90 - Bugfix: Properties in SDF files

Pull Request - State: closed - Opened by paulsaxe 2 months ago
Labels: bug

#89 - Significant internal enhancement to property handling.

Pull Request - State: closed - Opened by paulsaxe 2 months ago
Labels: enhancement

#88 - Added support for charge in chemical formulae

Pull Request - State: closed - Opened by paulsaxe 3 months ago
Labels: enhancement

#87 - Bugfix: error with charge and multiplicity

Pull Request - State: closed - Opened by paulsaxe 3 months ago
Labels: bug

#86 - Bugfix: error if OpenEye not available

Pull Request - State: closed - Opened by paulsaxe 3 months ago
Labels: bug

#85 - Versions of openbabel, openeye, and rdkit

Pull Request - State: closed - Opened by paulsaxe 3 months ago
Labels: enhancement

#84 - Added access to OpenEye mols and SMILES

Pull Request - State: closed - Opened by paulsaxe 3 months ago
Labels: enhancement

#83 - Added units to properties in Openbabel molecules

Pull Request - State: closed - Opened by paulsaxe 3 months ago
Labels: enhancement

#82 - Incorrect coordinates from PubChem

Pull Request - State: closed - Opened by paulsaxe 5 months ago
Labels: bug

#81 - Bugfix: current configuration not updated properly

Pull Request - State: closed - Opened by paulsaxe 6 months ago
Labels: bug

#80 - Problem with SMILES containing two or more molecules

Issue - State: open - Opened by paulsaxe 6 months ago

#79 - Bugfix: creating H2 from SMILES failed

Pull Request - State: closed - Opened by paulsaxe 6 months ago
Labels: bug

#78 - Switching SMILES to RDKit

Pull Request - State: closed - Opened by paulsaxe 8 months ago
Labels: enhancement

#77 - Added control to from_RDKMol and from_OBMol

Pull Request - State: closed - Opened by paulsaxe 9 months ago
Labels: enhancement

#76 - Rotated molecule from SMILES, InChI, or InChIKey to standard orientation

Pull Request - State: closed - Opened by paulsaxe 9 months ago
Labels: enhancement

#75 - Bugfix: bonds in RDKit

Pull Request - State: closed - Opened by paulsaxe 9 months ago
Labels: bug

#74 - Adding gradients to atoms

Pull Request - State: closed - Opened by paulsaxe 10 months ago
Labels: enhancement

#73 - Handle uppercase X, Y, Z in strings for symmetry operators

Pull Request - State: closed - Opened by paulsaxe 11 months ago - 1 comment
Labels: enhancement

#72 - Issue with symmetry and 1/3, 2/3

Issue - State: open - Opened by paulsaxe about 1 year ago
Labels: bug

#71 - Bugfixes in symmetry and CIF files

Pull Request - State: closed - Opened by paulsaxe about 1 year ago - 1 comment
Labels: bug

#70 - Bugfix and improvements to symmetry handling.

Pull Request - State: closed - Opened by paulsaxe over 1 year ago - 1 comment
Labels: bug, enhancement

#69 - Updating for changes in configparser.

Pull Request - State: closed - Opened by paulsaxe over 1 year ago - 1 comment

#68 - Support for InChI improved, RMSD and PubChem added...

Pull Request - State: closed - Opened by paulsaxe over 1 year ago - 1 comment
Labels: bug, enhancement

#67 - Support for velocities on atoms

Pull Request - State: closed - Opened by paulsaxe over 1 year ago - 1 comment
Labels: enhancement

#65 - To OpenBabel Mol did not handle charge and spin correctly.

Pull Request - State: closed - Opened by paulsaxe over 1 year ago - 1 comment
Labels: bug

#64 - Improved handling of properties

Pull Request - State: closed - Opened by paulsaxe over 1 year ago - 1 comment
Labels: enhancement

#63 - Bugfix: error in QCSchema bonds; enhancement: RDKit

Pull Request - State: closed - Opened by paulsaxe over 1 year ago - 1 comment
Labels: bug, enhancement

#62 - Added structure creation from InChIKeys using PubChem to dereference.

Pull Request - State: closed - Opened by paulsaxe over 1 year ago - 1 comment
Labels: enhancement

#61 - Added support for InChI and InChIKeys.

Pull Request - State: closed - Opened by paulsaxe over 1 year ago - 1 comment
Labels: enhancement

#60 - Added JSON properties, plus tests for them.

Pull Request - State: closed - Opened by paulsaxe over 1 year ago - 2 comments
Labels: enhancement

#59 - Supporting in-line uncertainties for values in CIF files.

Pull Request - State: closed - Opened by paulsaxe almost 2 years ago - 1 comment
Labels: enhancement

#58 - Enhanced handling of QCSchema molecules

Pull Request - State: closed - Opened by paulsaxe almost 2 years ago - 1 comment
Labels: enhancement

#57 - Removing periodicity does not correct coordinates

Issue - State: open - Opened by paulsaxe almost 2 years ago - 1 comment
Labels: bug

#56 - Fixed RDKit issue with valence for e.g. NH4+

Pull Request - State: closed - Opened by paulsaxe almost 2 years ago - 1 comment
Labels: bug, enhancement

#55 - Add CodeQL workflow for GitHub code scanning

Pull Request - State: closed - Opened by lgtm-com[bot] about 2 years ago - 1 comment

#54 - Bugfix: handling of total charge and multiplicity for OBMol

Pull Request - State: closed - Opened by paulsaxe about 2 years ago - 1 comment
Labels: bug

#53 - Added methods for straining the cell

Pull Request - State: closed - Opened by paulsaxe over 2 years ago - 2 comments
Labels: enhancement

#52 - Improved database write performance.

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

#51 - Added access to property metadata

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

#50 - Added transferring properties to/from OpenBabel OBMol

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

#49 - Fixed bug handling symmetry rotations of for x+y.

Pull Request - State: closed - Opened by paulsaxe over 2 years ago - 1 comment
Labels: bug

#48 - Fixed bug getting all properties from a configuration.

Pull Request - State: closed - Opened by paulsaxe over 2 years ago - 1 comment
Labels: bug

#47 - Improved handling of CIF files

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

#46 - Capturing relationship of atoms between conventional and primitive cell.

Pull Request - State: closed - Opened by paulsaxe over 2 years ago
Labels: bug

#45 - Corrected writing systems with no bonds to MMCIF files.

Pull Request - State: closed - Opened by paulsaxe over 2 years ago - 1 comment
Labels: bug

#44 - Generalizing to handle both cif and mmcif files

Pull Request - State: closed - Opened by paulsaxe almost 3 years ago
Labels: enhancement

#43 - Added handling of space group symmetry.

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

#42 - Fixed yet another bug with CIF: atom type symbols may have numbers appended

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

#41 - Fixed bug with CIF file atom labels.

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

#40 - Setting cell from vectors and bug fixes.

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

#39 - Fixed bug reading CIF files due to atom types & labels

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

#38 - Fixing issue#37: ignoring charge when using SMILES

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

#37 - fromSMILES ignores charges

Issue - State: closed - Opened by paulsaxe about 3 years ago
Labels: bug

#36 - Fixed typo in test for 'formal_charge' column in atoms.

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

#35 - Crash due to formal_charge already defined

Issue - State: closed - Opened by paulsaxe about 3 years ago
Labels: bug

#34 - Correcting PDB output to remove CONECT lines for atoms.

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

#33 - Incorrect PDB file written for atoms.

Issue - State: closed - Opened by paulsaxe about 3 years ago
Labels: bug

#32 - Corrected initial errors in to_RDKMol

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

#31 - Added handling of the k-mesh for periodic systems

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

#30 - Added charge, spin multiplicity and active orbitals to configurations

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

#29 - Add the star schema for properties to the database.

Pull Request - State: closed - Opened by paulsaxe over 3 years ago - 2 comments

#28 - implements rdkit_.py w/ tests

Pull Request - State: closed - Opened by SinaMostafanejad over 3 years ago - 3 comments

#27 - Enhancements to support ReaxFF

Pull Request - State: closed - Opened by paulsaxe over 3 years ago - 2 comments
Labels: enhancement

#26 - Bugfixes in support of PyXtal

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

#25 - Alternate symmetry information in a CIF file causes problems.

Issue - State: closed - Opened by paulsaxe over 3 years ago
Labels: bug

#24 - Reading an XYZ file results in Y coordinate == Z coordinate

Issue - State: closed - Opened by paulsaxe over 3 years ago
Labels: bug

#23 - Writing XYZ file gives all coordinates as zero.

Issue - State: closed - Opened by paulsaxe over 3 years ago
Labels: bug

#22 - System handling

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

#21 - Switched from yap to black in CI

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

#20 - A quite substantial rewrite mainly of the templates & subsets.

Pull Request - State: closed - Opened by seamm about 4 years ago - 4 comments
Labels: enhancement

#19 - Bugfix: system was not properly cleared before reading in data.

Pull Request - State: closed - Opened by seamm about 4 years ago - 1 comment
Labels: bug

#18 - Adding ability to set coordinates and remove atoms and bonds.

Pull Request - State: closed - Opened by seamm about 4 years ago - 10 comments
Labels: enhancement

#17 - Issue#16 Problem setting the cell in periodic systems.

Pull Request - State: closed - Opened by seamm over 4 years ago

#16 - Crash setting cell in Packmol step (Eliseo's bug)

Issue - State: closed - Opened by paulsaxe over 4 years ago - 1 comment

#15 - Hotfix for missed code with hydrogen atoms needed for atom typing.

Pull Request - State: closed - Opened by seamm over 4 years ago - 1 comment

#14 - Changes for the new system classes.

Pull Request - State: closed - Opened by paulsaxe over 4 years ago - 3 comments