Versions

Version 1.5.3 [url]

Version 1.5.2 [url]

Fixed bug for using constraints with large molecules in CREST (related to long atom lists in the .xcontrol.sample file that weren't compatible with subprocess.run())
Fixed bug when using squareplanar templates with ligands that bond with the metal centers with the same type of atom (but they are different ligands)
Added the 'Ir_squareplanar' geometry rule
Better print for command lines (more reproducible commands)
QDESCP adds an initial xTB optimization before the single-points (before, the descriptors were obtained from RDKit geometries, and they were pretty bad for metal complexes)
The aqme.py file now takes all the arguments from command lines with vars(args) without specifying the argument names explicitly in the code
Added the chk_path option to add PATH into chk lines
Added the xtb_opt option to optionally disable the initial xTB geometry optimization in QDESCP
Fixed a bug when an xTB calc failed, the whole QDESCP workflow stopped (now the specific conformer just gets ignored)
Fixed bug when GB or MB were not part of the mem argument in QPREP-ORCA
Added the qdescp_opt option for adjusting the convergence criteria of xTB in QDESCP
DBSTEP calcs are deactivated by default in QDESCP (activate them with --dbstep_calc)

Version 1.5.1 [url]

Added the verbose option. When verbose=False, no DAT and CSV files with summaries are printed
Fixed bug for using constraints with SMILES that are not mapped
Changed directory to create AQME-ROBERT databases to working dir (to adapt for full ML workflows in ROBERT)
Added SMARTS pattern recogniton to qdescp_atoms (the option now takes lists of atoms as well as lists of functional groups)
Fix minor bugs in QCORR-ORCA
Added the geometry filter (geom option) to CSEARCH
Added geom and complex_type as options in CSV columns
Fixed QDESCP when using csv_name with columns that are not code_name and SMILES
Added more RDKit descriptors in QDESCP with Descriptors.CalcMolDescriptors() (only for rdkit>=2023)

Version 1.5.0 [url]

A second ConstrainedEmbed() function with a core with no Hs was added to avoid RDKit embedding issues that show up in tricky cases
Fixed the --charge and --mult options when using xyz/sdf/pdf/gjf/com files as inputs in CSEARCH (xyz fixed in QPREP as well)
Options low_check and e_threshold_qprep were added to QPREP (create inputs only for n conformers of below a certain energy threshold)
Option nodup_check was added to QCORR (turns off the duplicate filter)
DBSTEP buried volume added in QDESCP with the qdescp_atoms option
Atomic properties of a single atom type were added in QDESCP with the qdescp_atoms option
Creation of databases for AQME-ROBERT workflows with the --robert option (True by default)

Version 1.4.7 [url]

QCORR is compatible with directories that contain a "." symbol
QCORR is compatible with ORCA calcs (it doesn't detect spin contamination yet)
QCORR includes hessian calculations for calcs with extra imaginary frequencies by default (new option to control this: im_freq_input)
QCORR tries to fix SCF convergence issues in ORCA by adding the SlowConv keyword
qm_end option is added after the genecp section in QPREP
Fixed a bug when using the destination option in CMIN-xTB

Version 1.4.6 [url]

The files and input options are compatible with partial PATHs, full PATHs, and direct names from command lines and Jupyter Notebooks
The SUMM option was fixed in CSEARCH
The files and input options now tolerate PATHs that contain directories with "." characters

Version 1.4.5 [url]

Suffix/prefix options work in CSEARCH, CMIN and QPREP
Automatic recognition of metals with the auto_metal_atom option
In QPREP, if qm_input starts with "p ", the Gaussian inputs starts with "#p"
CSEARCH-CREST updates the CREST outfile as the program calculates (not at the end only)

Version 1.4.4 [url]

When using a CSV as input, the user can specify charge and mult for each species by using the charge/mult columns
QCORR now detects duplicates including the successful calculations from previous runs
Fixed an error in full_check from QCORR when using genecp
Admits lists in command lines specified as ["X"], "[X]" and '["X"]'

Version 1.4.3 [url]

Return metal into RDKit mol object when using the metal_atoms option with CSEARCH-CREST
Doubles bonds do not add extra charges in metal complexes when using the automated charge calculation from SMILES
Deprotonated SiR3 groups add -1 charge to metal complexes when using the automated charge calculation from SMILES

Version 1.4.2 [url]

Fixed an error that raised when using CSEARCH-CREST with organic molecules
Adding more information printed when running CSEARCH
Updated README with citations from external programs
Fixed a bug during filtering of xTB conformers in CMIN (using kcal/mol instead of Hartree in the filters now)
Writing CSEARCH-CREST conformers in kcal/mol instead of Hartrees
Templates are not active when using metals with different number of ligands (i.e. if complex_type='linear' and Cu2+/CuL2 are used simultaneously)
Fixed squarepyramidal templates

Version 1.4.1 [url]

Changed the way xTB works in CMIN. Before, it worked through xtb-python, but in this version xtb is called through the xTB external command. This change speeds up the calculations and avoids problems for people that do not have xtb-python installed.
Fixed some bugs in the PATHs when using AQME through command lines
Updated information printed in QDESCP
Adding more error prints when no program or files are specified

Version 1.4.0 [url]

Fixed a bug in the automated charge and multiplicity detector for metal complexes
Adapted CREST workflows to work with metal templates
Refactored utils and rearrange files to meet code analyzer standards
The mol object that CREST uses as input now comes from the RDKit conformer generator (otherwise, metal templates aren't applied and stereochemistry information might be lost)

Version 1.3.1 [url]

Version 1.3.0 [url]

Version 1.2.0 [url]

This version improves how AQME reads PATHs from arguments to make the program more robust

Version 1.1.0 [url]

Version 1.0.0 [url]