Skip to content

Releases: molssi-seamm/molsystem

Bugfix: Incorrect coordinates from PubChem

01 Oct 15:11
48e3573
Compare
Choose a tag to compare
  • Fixed bug where the coordinates from PubChem were accidentally the 2-D rather than 3-D coordinates.

Bugfix: current configuration not updated properly

17 Aug 21:27
985d037
Compare
Choose a tag to compare
  • Existing instances of systems did not correctly update when the default configuration was changed. This is release fixes the problem.

Bugfix: creating H2 from SMILES failed

05 Aug 19:30
8a53509
Compare
Choose a tag to compare
  • Fixed bug where creating molecules consisting of just hydrogen failed because RDKit by default ignores all hydrogens when reorienting the molecule.

Switching default for SMILES to RDKit rather than OpenBabel

21 Jun 14:39
9c5a57e
Compare
Choose a tag to compare
  • RDKit seems more robust, and also the atom typing uses RDkit, so compatibility is important.

Added more control over RDKit and OpenBabel creating systems

08 May 16:41
a03f639
Compare
Choose a tag to compare
  • Added control to from_RDKMol and from_OBMol to allow selectively updating the atoms, coordinates, and bonds

Rotated molecule from SMILES, InChI, or InChIKey to standard orientation

05 May 22:11
10ce340
Compare
Choose a tag to compare
  • Molecules created from line notation are created in an random orientation. This enhancement rotates them to the standard orientation, which will look nice for small, symmetric molecules.

Bugfix: bonds in RDKit

05 May 21:21
c6b5bcf
Compare
Choose a tag to compare
  • There was an indexing bug translating bonds back from RDKit to SEAMM. The famous 0/1 problem!

Added gradients to atoms

06 Apr 01:32
c784b53
Compare
Choose a tag to compare
  • Added gradient on atoms as a separate table alongside atoms, so they take no space unless actually used.

Handle uppercase X, Y, Z in strings for symmetry operators

13 Mar 19:18
af9b00b
Compare
Choose a tag to compare
  • the Crystallographic Open Database CIF files seems to use upper case X, Y, Z in explicit symmetry operators. These need to be lowercased in the code.

Bugfixes in symmetry and CIF files

19 Nov 14:42
2e28abb
Compare
Choose a tag to compare
  • Reading CIF files could fail if the symmetry operators were given
  • The symmetry handling did not recognize hexagonal spacegroups without :H. Changed so if the hexagonal group name has neither :H or :R, the hexagonal setting is assumed.
  • When finding the spacegroup from the symmetry operators, hard-coded to the P1 case to avoid what seems like a bug in spglib.
  • Enhanced to use the full International Tables HM name for spacegroups, translating the input to that standard name.