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Added extracting of the atoms positions from sdf string and obtaining centers of the molecule (center of the box circumscribed at the molecule and centroid of the molecule). Started post-processing module 'visual', which works with PyMol and babel.
…le is determined by some point in space. Issues: creation of the molecule is sensitive to the order of applying of degrees of freedom. Need to add more comments for creation of new DOF object for future generetions.
….sdf_string). Added functions for obtainig of coordinates and masses of the molecule.
…tion for the molecule and constrained part in external file /adds/geometry.in.constrained
…ample specifying of the volume). Commit befor splitting of Orientation and self-orientation. Inserted check for clashes between molecule and surroundings and adjusting of the centroid in case of clashes found.
…unding. Separation of the Orientation and Centroid optimizing, now it is possible to optimize one of the DOF, with respect to the ion the result has to be the same
…shes after mutations. Also fix bug with restart scenario.
added 30 commits
June 23, 2018 17:28
…operly (delete this 0001_structure folder)
Pycharm test push
…eaning. Multiple molecules, periodic boundary conditions are impleented. Workflow is valid for random search. Big section regarding single molecules is commented for now since it will be part of the ensemble with case of number of molecules = 1. Random search is really random and very slow for now.
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This is everything Dmitrii has done so far (and really essentially only Dmitrii coded everything and Carsten and I just discussed ideas and the architecture with him).
They include quite substantial changes deep inside FAFOOM. Some of them are the "independence" from RDkit in the code, inclusion of translational and rotational degrees of freedom, protomeric degree of freedom, and many many changes to the routines. Only pieces of the original implementation are still there. Testcases are provided. We suggest that any new developments are branched and based on this new master branch. I will leave the pull request here for a couple of days in case anyone wants to give a look.