Removed redundant UFF optimization, corrected type on conformer index in the writing of XYZ file and added debugging functionality for clustering.
Changed import statements and added shebang to increase portability
Extended documentation of run_isolated and prep_run
Implemented function to prepare the runs and reorganized the checks for using or not energy minima as conformers
Implemented clustering for Affinity matrices
Downgraded numpy to 1.16 for problems with libraries using it.
Moved adapt_format to be available in all module and catching an error on get_rmsd when its argument is not valid.
Retrieve relevant magnitudes for clustering by calling the relative functions
mmff_opt_confs function allows to carry out single point energy calculations if max_iters is set to 0.
Implemented tests for the new functions
Split the generation of conformers and computation of their rmsd in two different functions. Added new functions to obtain the conformers moment of inertia and to optimize them using MMFF force field.
Changes rms to rmsd of new files
Revert "Changed rmsd for rms"
This reverts commit 5571316d
Added molec_file to wrong.inp
Extended gen_confs documentation and incorporated the possibility to choose whether molecule conformers should be minimum energy conformers or not.
Added tests for functions in isolated.py
Changed the way RMS between two conformers gets calculated. Now the RMS is performed by not considering hydrogens bonded to carbons but it does consider hydrogens bonded to all other atoms or not bonded at all.
Disabled the removal of hydrogens when using rdkit sdl mol file reader. Now, rdkit mol object contain hydrogens explicitly.
Moved logger to a global variable
Changed rmsd for rms
Created a module for each stage of DockOnSurf and started developing the isolated one
Improved the documentation of the consequent docstrings
Included, the necessity to specify the molecule file to be adsorbed, in the input.
Changed the read_coords.py module name to formats.py which states more clearly the purpose of the module.
Moved the printing of input variables from dockonsurf.py to dos_input.py
« Précédent 1 ... 9 10 11 12 13 14 Suivant » (251-275/338) | Par page : 25, 50, 100
Formats disponibles : Atom