Versions

Version 1.6.0 [url]

  • CSEARCH uses multithreading to accelerate jobs

  • QDESP uses multithreading to accelerate jobs

  • QDESCP now accepts multi-SMILES columns in CSV files

  • CSEARCH now handles multiple metals without program interruption

  • Check for N@@ or N@ in SMILES to avoid RDKit issues

  • CSEARCH now performs conformational search only for unique SMILES to avoid redundant calculations

  • QDESCP now automatically obtains SMARTS patterns from input files if no patterns are provided

  • QDESCP now uses a single processor for xtb calculations to ensure reproducibility

  • Fixed bug in QCORR when analyzing TD-DFT, ONIOM and G4 calculations in Gaussian

  • CSEARCH is now compatible with mapped atoms

  • QPREP now warns if the level of theory is not defined in ORCA

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]

  • Workflows were updated

  • Small fixes in CREST when using constraints

  • Readme was updated

  • GoodVibes added in installation requirements

Version 1.3.0 [url]

  • Publication version

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]

  • Fixes pip install issue coming from older versions

Version 1.0.0 [url]

  • First official version of AQME ready to generate publication-quality results