ale94mleon/MolDrug: 3.6.0 - 2023.12.07

Added

• vina_seed argument for:
  • all the cost functions of moldrug.fitness,
  • moldrug.fitness._vinadock.
• randomseed:
  • moldrug.utils.confgen,
  • moldrug.utils.Individual,
  • moldrug.utils.Local,
  • moldrug.utils.GA,
  • moldrug.constraintconf.constraintconf as well its CLI with the flag --seed.
• -V and --verbose flag in the CLI of moldrug.
• moldrug.utils.softmax function.
• moldrug.utils.deep_update function.
• moldrug.utils.__get_default_desirability` to store the default desirability values.
• vina_score_type = 'ensemble', this is used by CostMultiReceptors* functions. It is meant to be used to account for flexibility in the receptor. This is equivalent to performing ensemble docking.

Removed

• outdir flag in moldrug CLI.

Changed

• Use random.random instead numpy.random.rand function for some small cases.

• AllChem.MMFFOptimizeMolecule is only used internally for moldrug.utils.confgen and moldrug.constraintconf.gen_aligned_conf if randomseed is not set and with maxIters = 500.

• pickle module is replaced by dill. It is better to handle users' custom fitness functions.

• Data now is retrieved with moldrug``.data.get_data function.

• Is not needed to input the whole desirability definition if only is intended to change one part of the default desirability used internally by the cost functions of moldrug.fitness. For example, if you would like to change the Target value of vina_score from its default value.

  Before:

  ga = GA(
    ...
    costfunc = moldrug.fitness.Cost
    costfunc_kwargs = {
      ...
      "desirability": {
        "qed": {
            "w": 1,
            "LargerTheBest": {
              "LowerLimit": 0.1,
              "Target": 0.75,
              "r": 1
            }
        },
        "sa_score": {
            "w": 1,
            "SmallerTheBest": {
              "Target": 3,
              "UpperLimit": 7,
              "r": 1
            }
        },
        "vina_score": {
            "w": 1,
            "SmallerTheBest": {
              "Target": -12,
              "UpperLimit": -6,
              "r": 1
            }
        }
      },
      ...
    }
    ...
  )
  

  Now:

  ga = GA(
    ...
    costfunc = moldrug.fitness.Cost
    costfunc_kwargs = {
      ...
      "desirability": {
        "vina_score": {
            "SmallerTheBest": {
              "Target": -12,
            }
        }
      },
      ...
    }
    ...
  )
  

  The same from the CLI.

Fixed

• Small bug when the population has Individuals with the same cost. Better reproducibility.
• Refactored changes.
• Handled properly in case receptor_pdbqt_path = None.
• Convert self.crem_db_path to absolute path in moldrug.utils.Local and moldrug.utils.GA.