History#

2024.11.21.1 – Versions of openbabel, openeye, and rdkit

  • Added functions to get the versions of openbabel, openeye, and rdkit that are installed.

2024.11.21 – Added access to OpenEye mols and SMILES

  • Added the ability to create a system from an OpenEye molecule and vice versa. This gives access to the OpenEye toolkit for generating conformers, etc.

  • Added the ability to create a system from a SMILES string and create the SMILES string from a system using OpenEye.

2024.11.12 – Added units to properties in Openbabel molecules

  • Any properties on the system and configuration are optionally added to the Openbabel Molecule object for e.g. writing to an SDF file. This adds the units of the properties explicitly

2024.10.1 – Bugfix: Incorrect coordinates from PubChem

  • Fixed bug where the coordinates from PubChem were accidentally the 2-D rather than 3-D coordinates.

2024.8.17 – Bugfix: current configuration not updated properly

  • Existing instances of systems did not correctly update when the default configuration was changed. This is release fixes the problem.

2024.8.5 – Bugfix: creating H2 from SMILES failed

  • Fixed bug where creating molecules consisting of just hydrogen failed because RDKit by default ignores all hydrogens when reorienting the molecule.

2024.6.21 – Switching default for SMILES to RDKit rather than OpenBabel

  • RDKit seems more robust, and also the atom typing uses RDkit, so compatibility is important.

2024.5.8 – Added more control over RDKit and OpenBabel creating systems

  • Added control to from_RDKMol and from_OBMol to allow selectively updating the atoms, coordinates, and bonds

2024.5.6 – Rotated molecule from SMILES, InChI, or InChIKey to standard orientation

  • 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.

2024.5.5 – Bugfix: bonds in RDKit

  • There was an indexing bug translating bonds back from RDKit to SEAMM. The famous 0/1 problem!

2024.4.6 – Added gradients

  • Added gradient on atoms as a separate table alongside atoms, so they take no space unless actually used.

2024.3.13 – Handle uppercase X, Y, Z in strings for symmetry operators

  • 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.

2023.12.5 – Bugfixes for symmetry

  • Fixed issue #72, where symmetry was not correctly handled for trigonal and hexagonal cells where atoms had coordinates of 1/3 or 2/3.

2023.11.19 – Bugfixes in symmetry and CIF files

  • 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.

2023.11.5 – Bugfix and improved symmetry handling

  • Fixed bug with symmetry operators containing blanks, e.g. ‘x, y, z’ rather than ‘x,y,z’

  • Added handling of symmetry when get properties of atoms

  • Added method to lower symmetry to P1/C1

2023.10.30 – Support for InChI improved, RMSD and PubChem added…

  • Adds support for aligning structures and calculating RMSD

  • Adds support for working directly with PubChem to get structures, IUPAC names, etc.

  • Improves support for InChI, working around issues in both OpenBabel and RDKit.

  • Added substantial new functionality for spacegroups and primitive cell handling, but still not complete.

2023.9.20 – Better support for primitive cells and spacegroups

  • Added getting the spacegroup from the symmetry operators

  • Fixed updating the coordinates from the primitive cell

2023.9.5 – Support for velocities of atoms.

2023.8.30 – Support for spacegroup symmetry.

2023.8.27 – Bugfix: writing SDF did not handle charge and multiplicity.

2023.7.30 – Improved handling of properties

  • Added ability to get lists of systems or configurations filtered by name

  • Improved handling of properties on just a system, not configuration

  • Added ability to filter properties retrieved

  • Improved handling of properties when creating OpenBabel OB_MOL object

2023.7.26 – Bugfix: error in QCSchema bonds; enhancement: RDKit

  • Fixed bug in the bond indices in QCSchema

  • Added ability to use RDKit for SMILES and InChI

2023.7.18.1 – Added support for creating structures from InChIKeys

  • Uses PubChem to translate the InChiKey to InChI.

2023.7.18 – Added support for InChI and InChIKeys

2023.7.9 – Added JSON properties

  • Added properties stored as JSON, which allows, vectors, tensors, etc.

2023.4.6 – Enhancements for CIF files

  • Handle uncertainties in CIF files expressed as ‘(x)’ at end of value.

2023.3.30 – Enhancements to QCSchema support

  • Improved naming of molecule in QCSchema

  • Added creation of configurations from QCSchema objects.

2023.2.13 – Fixed issue with valence in RDkit for cations like NH4+

2022.11.20 – Added a method to copy a configuration.

Added a new method to the system class, copy_configuration, that creates a copy of the configuration using the same atomset and bonset, but new coordinates and cell so that any changes to coordinates and cell are not shared between the configurations. By default it copies the current configuration.

2022.11.18 – Fixed bug with handling for Open Babel

The total charge and multiplicity were not correctly set when creating an Open Babel molecule.

2022.11.3 – Add handling of strain and improved handling of properties

Added methods for straining the unit cell, and also straining a configuration, correctly handling the coordinates for an affine transformation. In the future will add e.g. affine transformation of the centers of molecules, which is useful for molecular fluids.

Added the system for properties, in addition to the configuration. This allows system properties that are not associated with a particular configuration, which is often appropriate for experimental results. It also makes it much easier to search for systems where any configuration has a particular property.

2022.10.26 – Improved database write performance.

Switched to write-ahead mode and tweaked memory settings. This gives a large performance improvement (10x or more) for large database (~1 GB).