Releases: jvalegre/aqme
Releases · jvalegre/aqme
v1.6.1
v1.6.0
- 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
v1.5.2
- 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)
v1.5.0
- 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_atom option
- Atomic properties of a single atom type were added in QDESCP with the qdescp_atom option
- Creation of databases for AQME-ROBERT workflows with the --robert option (True by default)
v1.4.7
- 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
v1.4.6
- 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
v1.4.5
- 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)
v1.4.4
- 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"]'
v1.4.3
- 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
v1.4.2
- 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