Versions

Version 1.7.1 [url]

• Fixed bug from QCORR when using gen(ECP)

• CSEARCH uses multithreading to ensure reproducbility acorss runs

• Added T1-S0 gap (not only S0-T1)

• PTB is now used to calculate HOMO-LUMO gaps, charges, dipole moments, and other descriptors

• Using xTB v6.7.1 and CREST v2.12

• Fixed bug from MORFEUS descriptors in QDESCP

• Improved SDF reader compatible with SDF files from GaussView

• Refactoring of the QDESCP module and its utils (faster code execution)

Version 1.7.0 [url]

• Fixed bug from CSEARCH when using CSV inputs with metal atoms (removed SELF variables in multithreading)

• Added --sample to CSEARCH-CREST through RMS-based Butina sampling

• Changing to pip install by default in Read the Docs installation instructions

• CMIN and QDESCP don't stop if an xTB calculation fails, instead they keep running the remaining calculations

• CSEARCH doesn't stop if a conformer search fails, instead it keeps running the remaining searches

• Adding many new descriptors in QDESCP within three levels of human interpretation (denovo, interpret and full)

• Empty generated SDF files are removed

• Prints of missing dependencies are also added when using Jupyter Notebooks (not only in the command line)

• DBSTEP functions were removed

• MORFEUS functions were added to include steric descriptors

• Number of initial samples generated by RDKit was limited to 500

• Selection of conformers from RDKit through the sample option is now controlled by a combination of stable RDKit conformers and Butina sampling

• Add solvent descriptors in QDESCP

• Lists with atom descriptors are not shown in the main descriptor CSV in QDESCP (but they are still stored in the raw_csv_databases folder)

• Great acceleration of QDESCP using multithreading across molecules (instead of conformers)

• QDESCP generates only 2 raw xTB files (instead of 11), and performs a clean-up before each calculation to avoid reading from previous restart points

• qdescp_atoms works from SDF with no property SMILES

• Automatic pattern recognition for qdescp_atoms now works for all types of atoms and multiple instances (not only metals)

• QDESCP refactoring to make the workflows easier to follow

• Add automated workflow from SMILES to descriptors using --input FILENAME.csv in QDESCP

• QDESCP calculates charges from SDF that doesn't come from CSEARCH

Version 1.6.1 [url]

• Hotfix of v1.6.0 (just moving the import of dbstep in QDESCP)

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)

• --auto_sample now modulates the amount of initial RDKit conformers generated with three options: low, mid and high

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