Releases | Open Source Science

Changed

Name from MolDrug to moldrug (mainly for documentation).

- Python
Published by ale94mleon over 1 year ago

Fix

It was possible to generate the same children in the same generations. Now there is a filter to avoid repeated evaluations.

- Python
Published by ale94mleon about 2 years ago

Fix

Remove an unnecessary print statement.

- Python
Published by ale94mleon about 2 years ago

Fixed

Calculate SA_score with the molecule without explicit hydrogens for all built-in fitness functions. Based on: https://github.com/rdkit/rdkit/discussions/7047

Added

The moldrug.constraintconf.clashes_present function.

Changed

bio.PDB object is no longer used for filtering of conformations that clash with the protein. Now the coordinates are retrieved from the RDKit molecule object and the distance is calculated with NumPy.

- Python
Published by ale94mleon about 2 years ago

Fix

LICENCE on PyPi.

Add

Extra metadata to the package.

- Python
Published by ale94mleon about 2 years ago

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._getdefault_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:

python 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:

python 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.

- Python
Published by ale94mleon about 2 years ago

moldrug - 3.5.0 - 2023.10.26

Fixed

Refactored changes for for meeko-0.5.0.
Update docs.

Added

An new environmental variable MOLDRUG_VERBOSE can be set to ask for more debug information.

Changed

From csf to toml package configuration.
Structure of the repo. Now src/moldrug.
Improve MolDrug-Dashboard.

- Python
Published by ale94mleon over 2 years ago

moldrug - 3.4.0 - 2023.03.10

Added

Continuation option to the command line.
moldrug.cli.CommandLineHelper class to work with the parameters passed through the command line.
checkpoint option to moldrug.utils.GA.
MolDrug-Dashboard add-on. This is not included on the package itself, but could be used online or locally. In the case of locally you must check Streamlit, the requirements.txt and the app script.
retunr_mol option to utils.to_dataframe

Changed

The warnings are not printed for: moldrug.fitness._vinadock and moldrug.constraintconf.generate_conformers. Now, only at the end of a MolDrug simulation a note will be printed if the error.tar.gz file is created.
moldrug.utils.run does not print extra info if the command fails. It only raises the corresponded RuntimeError.
moldrug.fitness.__vinadock by moldrug.fitness._vinadock.
Remove conformers that clash with the protein in case of scoreonly, for localonly vina will handle the clash.

Fixed

Small bug during initialization of population with multiple seed_mol. Now seed_mol with the same amount of elements as popsize are not submitted to mutations, only evaluation.
Problems with default parameters definition on the command line. Parameters with default values by the type of run defined in the configuration file are not needed to redefined any more; moldrug.cli will guess those.

- Python
Published by ale94mleon almost 3 years ago

moldrug - 3.3.0 - 2022.12.21

Changed

moldrug.utils.__tar_errors__ by moldrug.utils.tar_errors.
Default value of moldrug.utils.tar_errors is error instead of .error.
moldrug.constraintconf.generate_conformers outputs warnings and errors to error instead of .error.
moldrug.fitness.__vinadock by moldrug.fitness._vinadock.
moldrug.fitness._vinadock outputs warnings and errors to error instead of .error.

Fixed

The use of moldrug.utils.tar_errors inside of moldrug.utils.Local and moldrug.utils.GA.
Clean code.

- Python
Published by ale94mleon about 3 years ago

moldrug - 3.2.5 - 2022.12.20

Fixed

Improve docs.
Cleaning of temporal files in /tmp directory. Now it is created temporal directories in the working directory with the pattern: .costfunc_MolDrug_XXXXXXXX.
Cleaning errors. Now all warnings and errors are saved in .error directory and at the end they are compress to error.tar.gz

- Python
Published by ale94mleon about 3 years ago

moldrug - 3.2.2 - 2022.12.12

Fixed

Bug: The initial individual was not printed properly.

Removed

Redundant code in moldrug.utils.GA

- Python
Published by ale94mleon about 3 years ago

moldrug - 3.2.0 - 2022.11.28

Fix

Bug: The output error name when constraint fails has a idx prefix. E.g. 33_conf_27_error.pbz2 now is: idx_33_conf_27_error.pbz2. Now it is easy to delete all of this files at the end of the simulation if they are not needed. (on the last version the naming was not changing)

Removed

moldrug.fitness.is_inside_box
Bug: constraint_check_inside_box option for the cost functions of moldrug.fitness

- Python
Published by ale94mleon about 3 years ago

moldrug - 3.1.0 - 2022.11.28

Added

moldrug.constraintconf.gen_aligned_conf
In case that moldrug.constraintconf.generate_conformers fails with rdkit.Chem.AllChem.ConstrainedEmbed it will try with moldrug.constraintconf.gen_aligned_conf.
moldrug.fitness.is_inside_box
constraint_check_inside_box arguments to the cost functions of moldrug.fitness. If the coordinates of the constraint conformation are outside the box; use always local_only, by default False

Changed

The output error name when constraint fails has a idx prefix. E.g. 33conf27error.pbz2 now is: idx33conf27_error.pbz2. Now it is easy to delete all of this files at the end of the simulation if they are not needed.

Fix

Clean code.
Improve docs.

- Python
Published by ale94mleon about 3 years ago

moldrug - 3.0.3 - 2022.11.26

Added

Warning in case moldrug.utils.Local or moldrug.utils.GA are called with a different MolDrug as they were initialized.

Changed

Convert to absolute path receptor_pdbqt_path and vina_executable (in case that it points to a file) inside of moldruf.fitness.__vinadock.

Fixed

Bug for hydrogens coordinates when constrain docking was used.
Improve docs.

- Python
Published by ale94mleon about 3 years ago

moldrug - 3.0.1 - 2022.11.24

Fixed

Cleaning code.
Sort the initial population based on the cost attribute when it is saved on disk.
Improve docs.

- Python
Published by ale94mleon about 3 years ago

moldrug - 3.0.0 - 2022.11.23

Changed

Name of moldrug.fitness.get_mol_cost to moldrug.fitness.__get_mol_cost function.
The class moldrug.utils.GA does not have any more the method roulette_wheel_selection; now is part a function that could be called from moldrug.utils
max for max_conf in moldrug.constraintconf.constraintconf() function.
Entrance point constraintconf was changed to constraintconfmoldrug and now it is link to `moldrug.cli.constraintconfcmdinsteadmoldrug.constrainconf.constraintconf_cmd`.
Name of the function moldrug.fitness.vinadock now is moldrug.fitness.__vinadock.
Name of the function moldrug.cli.moldrug_cmd now is moldrug.cli.__moldrug_cmd.

Fixed

Cleaning the code
If vina_executable is provided (to any cost function) and it represents a path. It will be try to convert to absolute path. Previously relative path to the executable were not understood properly.
Improve docs.

Added

ad4map in all the cost functions of the moldrug.fitness module. This parameters specify the path where the ad4 map files are. To use this feature you must have the AutoDcok Vina v1.2.3 of above. Now you can use the force fields of AD4 inside of Vina. Future release will extend the integration with this versions.
moldrug.utils.to_dataframe. THis function was previously isolated as a method of the class moldrug.utils.GA; now it could also be called as a function.
kept_gens attribute to the Individuals inside of moldrug.utils.GA. This is a set that contains the generations for which the Individual was conserved.
acceptance attribute to moldrug.utils.GA. This is a dictionary that has as keyword the generation ID, and as values a dictionary with keywords: accepted (number of generated molecules accepted on the current generation) and generated (number of total molecules generated)
Print Accepted rate= accepted / generated during running.
Add hydrogens before create pdbt file with meeko when constrain docking i used.
seed_mol of moldrug.utils.GA now could be a list (or iterable in a general way) of RDKit molecules. This feature could be used to combine several MolDrug runs and create a final runs with this combined population.
seed_mol from the command line could be: a valid SMILES, a list of valid SMILES or a list of path to the _pop.pbz2 binary files. In the last case all the populations will be combined and sorted based on the cost attribute. If the result population is less that popsize new structures will be generated to complete the initial population. The individuals of this initial population will be reinitialized and the cost function will be calculated.

- Python
Published by ale94mleon about 3 years ago

moldrug - 2.1.12 - 2022.09.29

Added

score_only bool parameter to moldrug.fitness.get_mol_cost.
Print starting date when MolDrug is called from the command line.

Removed

Type Hints int for attribute idx onmoldrug.utils.Individual.

Changed

If vina fails inside moldrug.fitness.vinadock; give as pdbqt the string "VinaFailed".
If the molecule has a molecular weight highest than wt_cutoff when moldrug.fitness.CostOnlyVina (or moldrug.fitness.CostMultiReceptorsOnlyVina) is called; the pdbqt attribute of the returned Individual will be the string "TooHeavy" (or the list of strings List["TooHeavy"])

- Python
Published by ale94mleon over 3 years ago

moldrug - 2.1.7 - 2022.09.02

Fixed

Bug on moldrug.fitness.vinadock during searching of MCS between Individual.mol and constraint_ref. Before was needed to manually specified the atom ids of the seed_mol that match constraint_ref, now it is not needed any more.
Bug during handling exception in moldrug.constraintconf.generate_conformers.
Bug during handling exception moldrug.constraintconf.generate_conformers in moldrug.fitness.vinadock.
Bug(s) when constraint docking is used on different vina versions. The output of vina is not the same and therefore moldrug.fitness.vinadock failed.

Changed

In case constraint = True in moldrug.fitness.vinadock, ref_smi will be the the MCF between individual.mol amd constraint_ref instead the SMILES string of constraint_ref when moldrug.constrainconf.generate_conformers is internally called.

Added

moldrug.fitness.get_mol_cost function.
Attribute genID to the generated individuals during a moldrug.utils.GA run.

- Python
Published by ale94mleon over 3 years ago

moldrug - 2.1.0 - 2022.08.30

Fixed

Bug during the calculation of probabilities when costs are larger numbers.
Expose hidden error if some Exception ocurred during parallel run.

Added

moldrug.constrainconf module.
Raise ValueError if ref_smi is invalid in moldrug.utils.constrainconf.generate_conformers.

Changed

In case constraint = True in moldrug.fitness.vinadock, ref_smi will be the SMILES string of constraint_ref when moldrug.constrainconf.generate_conformers is internally called. This is in order to avoid error when moldrug.utils.constrainconf.generate_conformers tries to guess ref_smi based on MCS and fails, see this RDKit bug. The work around for constraint docking is explained here: Constraint Docking.
moldrug.fitness.generate_conformers does not fail. In case of Exception it returns the same mol without conformers and write the error in a log file into the working directory.
The attribute name bestcost by best_cost of moldrug.utils.GA.
The functions duplicate_conformers, get_mcs, generate_conformers, constraintconf and constraintconf_cmd and the class ProteinLigandClashFilter were moved from moldrug.fitness module to moldrug.constrainconf module.
Entrance point constraintconf now it is link to moldrug.constrainconf.constraintconf_cmd instead moldrug.fitness.constraintconf_cmd.

- Python
Published by ale94mleon over 3 years ago

moldrug - 2.0.0 - 2022.08.25

Added

The functions duplicate_conformers, get_mcs, generate_conformers, constraintconf and constraintconf_cmd and the class ProteinLigandClashFilter. The code was borrowed from Pat Walters. It is used if constraint docking is needed.
constraintconf can be called from the command line.
moldrug.fitness.vinadock() a simple wrapper around vina. This function will be used for all the implemented cost functions inside of the module moldrug.fitness. It could be used for constraint docking.
moldrug.data.constraintref. This module is used for testing in case constraint docking is needed. It has two MolBlock strings: r_6lu7 and r_x0161. That could be easily converted in RDKit molecules..

python from rdkit import Chem from moldrug.data import constraintref mol = Chem.MolFromMolBlock(constraintref.r_x0161)

This molecule is needed for the keyword argument constraint_ref of the functions of the moldrug.fitness module in case of constraint docking is used.
Constraint docking capability in all implemented cost functions of the module moldrug.fitness.
moldrug.data.receptor_pdb. This module is similar to moldrug.data.receptor_pdbqt but in pdb format.
Documentation and tutorials.

Changed

moldrug.utils.make_sdf only will create the sdf file based on the pdbqt attribute. If pdbqt is a list, it will work as previous version works with pdbqts attribute.
Name of the module moldrug.data.receptors to moldrug.data.receptor_pdbqt.
Name of keyword argument receptor_path to receptor_pdbqt_path on the cost functions: moldrug.fitness.Cost and moldrug.fitness.CostOnlyVina.
Name of keyword arguments receptor_path, vina_score_types, boxcenters and boxsizes to receptor_pdbqt_path, vina_score_type, boxcenter and boxsize respectively on the cost functions: moldrug.fitness.CostMultiReceptors and moldrug.fitness.CostMultiReceptorsOnlyVina.
smiles attribute in moldrug.utils.Individual now it is always without explicit Hs, despite if the mol attribute has them.

- Python
Published by ale94mleon over 3 years ago

moldrug - 1.1.0 - 2022.08.23

Changed

moldrug.utils.Individual now is a hashable object.
moldrug.utils.GA.SawIndividuals now is a set instead of a list
moldrug.utils.update_reactant_zone sets the keywords matchValences and ringMatchesRingOnly to True on rdFMCS.FindMCS. This prevent undesired effects. E.g:

python from moldrug.utils import update_reactant_zone from rdkit import Chem mol1 = Chem.MolFromSmiles('c1ccccc1') mol2 = Chem.MolFromSmiles('CCCN') update_reactant_zone(parent=mol1,offspring=mol2 parent_replace_ids = [0,2])

Before the results was: ([0, 2, 3], []). Now it is: ([0, 1, 2, 3], []). The behavior was because the ringMatchesRingOnly is set to False by default inside RDKit.

Removed

moldrug.utils.timeit. No longer needed.

Added

Documentation.

- Python
Published by ale94mleon over 3 years ago

moldrug - 1.0.2 - 2022.08.08

Removed

Popen option in moldrug.utils.run.

Changed

RuntimeError by warnings.warn when vina run fails and save every error as idx_error.pbz2. Where idx is the index of the failed individual.
Print format when mutate fails inside of moldrug.utils.GA

Added

Print MolDrug's version when the command line is used.

- Python
Published by ale94mleon over 3 years ago

moldrug - 1.0.0 - 2022.07.30

Fixed

Hidden RuntimeError in moldrug.fitness module.
Bug printing number of generations in final info.

Removed

Unused code in moldrug.home module.
3D conformation in the mol attribute of the Individual during initialization.
The use of grow_mol in the initialization of the populating when get_similar = True. Now the population is initialized with mutate_mol and the same set of crem parameters used during the searching.
The automatic addition of Hs in the case where min_size and/or max_size were equal to zero. Now if your intention is work with the hydrogens, you must provided a SMILES with the explicit Hs. In the future the input could be just a RDKit mol. Now you must specify if you would like to add explicit Hs to the molecule withe keyword AddHs; default is False and is used for both moldrug.utils.GA and moldrug.utils.Local.

Added

Handling vina RuntimeError and keeping track for debug. This feature is used to identify what is the error. In the future will be removed.
Two new fitness functions: moldrug.fitness.CostOnlyVina and moldrug.fitness.CostMultiReceptorsOnlyVina. They only use the information of vina scoring function. See the docs for more info about it.
Tracking of atom indexes during generations in order to use protected_ids and replace_ids options of mutate_mol function of CReM. Before it was not possible; the use of these features generate undesired solutions because the indexes are not static over generations. Even so, there are still some problems for symmetric molecules. We are working on it.

Changed

The whole MolDrug works base on the RDKit mol instead of the SMILES string:
1. moldrug.utils.Individual is now initialized mol instead smiles. Now the SMILES string is generated internally, it still used as identifying for the instance.
2. moldrug.utils.GA changed smiles for seed_mol and it is not needed the mol variable any more.
3. moldrug.utils.Local changed mol for seed_mol in the initialization variables..
4. moldrug.utils.confgen changed smiles for mol variable.

- Python
Published by ale94mleon over 3 years ago

moldrug - 0.1.0 - 2022.07.25

Fixed

Minor cleaning code.
Bug during the import of user custom cost function.

Added

outdir option for the command line.
User custom desirability.

- Python
Published by ale94mleon over 3 years ago

moldrug - 0.0.4

Fix minor compatibility issue with Python 3.8 (issue #4).
Add Local class to the command line.
Fix supplied custom fitness function from the command line.
Better code covering during testing.
Cleaning code.

- Python
Published by ale94mleon over 3 years ago

moldrug - 0.0.3

Fix issue with molecules that does not produce a correct pdbqt file

- Python
Published by ale94mleon over 3 years ago

moldrug - 0.0.2

Follow jobs on the command line
Fixing make_sdf for multiple receptors
Much better documentation

- Python
Published by ale94mleon over 3 years ago

moldrug - 0.0.1.beta.9

Comand line available
Adding sdf export
Eliminate OpenBabel dependency
Adding meeko for working with pdbqt

- Python
Published by ale94mleon over 3 years ago

moldrug - 0.0.1.beta7

Here we add the automatic detection based on mutate_crem_kwargs on GA of the need of add explicit hydrogens inside of the mutate function

- Python
Published by ale94mleon over 3 years ago

moldrug - 0.0.1.beta6

- Python
Published by ale94mleon over 3 years ago

Recent Releases of moldrug

moldrug - 3.7.3 - 2024.07.05

Changed

moldrug - 3.7.2 - 2024.01.22

Fix

moldrug - 3.7.1 - 2024.01.14

Fix

moldrug - 3.7.0 - 2024.01.14

Fixed

Added

Changed

moldrug - 3.6.1 - 2023.12.11

Fix

Add

moldrug - 3.6.0 - 2023.12.07

Added

Removed

Changed

Fixed

moldrug - 3.5.0 - 2023.10.26

Fixed

Added

Changed

moldrug - 3.4.0 - 2023.03.10

Added

Changed

Fixed

moldrug - 3.3.0 - 2022.12.21

Changed

Fixed

moldrug - 3.2.5 - 2022.12.20

Fixed

moldrug - 3.2.2 - 2022.12.12

Fixed

Removed

moldrug - 3.2.0 - 2022.11.28

Fix

Removed

moldrug - 3.1.0 - 2022.11.28

Added

Changed

Fix

moldrug - 3.0.3 - 2022.11.26

Added

Changed

Fixed

moldrug - 3.0.1 - 2022.11.24

Fixed

moldrug - 3.0.0 - 2022.11.23

Changed

Fixed

Added

moldrug - 2.1.12 - 2022.09.29

Added

Removed

Changed

moldrug - 2.1.7 - 2022.09.02

Fixed

Changed

Added

moldrug - 2.1.0 - 2022.08.30

Fixed

Added

Changed

moldrug - 2.0.0 - 2022.08.25

Added

Changed

moldrug - 1.1.0 - 2022.08.23

Changed

Removed

Added

moldrug - 1.0.2 - 2022.08.08

Removed

Changed

Added

moldrug - 1.0.0 - 2022.07.30

Fixed

Removed

Added

Changed