Aqme

- 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

- Hotfix of v1.6.0 (moved dbstep import in QDESCP)

- 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

- 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)

- 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)

- 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