v1.7.0

• 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

v1.6.1

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

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