Merge FAFOOM v2#5

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mahrossi wants to merge 104 commits intomasterfrom

Commits on Apr 4, 2017

starting to make modifications
Dmitrii Maksimov
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Commits on Apr 12, 2017

vdW radii implementation
maksimovdmitrii
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Commits on Apr 19, 2017

I still not good at commits...(((
maksimovdmitrii
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Added producing of 'valid' and 'invalid' folders for related structures.
maksimovdmitrii
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Merge branch 'dmitrii-mod' of github.com:FHIBioGroup/fafoom-dev into dmitrii-mod
maksimovdmitrii
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Including translation of the atom positions for str3d structure.
maksimovdmitrii
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Commits on Apr 25, 2017

Implementation of Centroid degree of freedom. Centeroid of the molecule is determined by some point in space.
maksimovdmitrii
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Commits on Apr 26, 2017

Operations with lists substituted with operations with np.arrays.
maksimovdmitrii
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Commits on Apr 28, 2017

Centre of mass implemented
maksimovdmitrii
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Commits on May 1, 2017

Tensor of inertia implemented for molecule from sdf_string (for str3d.sdf_string). Added functions for obtainig of coordinates and masses of the molecule.
maksimovdmitrii
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Commits on May 30, 2017

dirty quaternions are in.
maksimovdmitrii
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Commits on Jun 2, 2017

Updated some ongoing chalenges with assinging of centroid and orientation for the molecule and constrained part in external file /adds/geometry.in.constrained
maksimovdmitrii
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Commits on Jun 8, 2017

Degrees of freedom are roughly implemented. Need to be tested and revised changes.
maksimovdmitrii
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adding test_and_examples folder
maksimovdmitrii
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Add files via upload
Dmitrii
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Commits on Jun 14, 2017

Jst fixing a typo
Mariana Rossi
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Typos really
Mariana Rossi
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Commits on Jun 22, 2017

Add preprocessing script
maksimovdmitrii
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Preprocessing folder
maksimovdmitrii
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Merge branch 'dmitrii-mod' of github.com:FHIBioGroup/fafoom-dev into dmitrii-mod
maksimovdmitrii
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Commits on Jul 5, 2017

Preprocessing generator structures, improved centroid setting (for example specifying of the volume). Commit befor splitting of Orientation and self-orientation. Inserted check for clashes between …
maksimovdmitrii
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try to add scripts for generating of valid structures.
maksimovdmitrii
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try
maksimovdmitrii
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Commits on Jul 6, 2017

Adjusting of the generated structures positions with respect to surrounding. Separation of the Orientation and Centroid optimizing, now it is possible to optimize one of the DOF, with respect to th…
maksimovdmitrii
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Commits on Jul 11, 2017

Try to commit from Atom. Pyforcefield added, generating inputs for MD
maksimovdmitrii
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Commits on Jul 20, 2017

ForceField works, generations are produced. Need to fix check for clashes after mutations. Also fix bug with restart scenario.
maksimovdmitrii
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New test files
maksimovdmitrii
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Commits on Jul 27, 2017

Start to replace RDkIT module.
maksimovdmitrii
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update_coords_sdf, quaternion_measure now free of RDkit
maksimovdmitrii
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Commits on Jul 28, 2017

Commits on Aug 17, 2017

Daily update
maksimovdmitrii
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Commits on Aug 28, 2017

Kabsh algorithm works fine without hydrogens, with hydrogens it is for some reason not so accurate in comparison with RDKit
maksimovdmitrii
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Commits on Sep 8, 2017

Seems that it is finally working
maksimovdmitrii
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Also ga.py should be added
maksimovdmitrii
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Add 'ga.py' outside
maksimovdmitrii
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Commits on Sep 12, 2017

Try to clean a little bit first
maksimovdmitrii
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Cleaning up
maksimovdmitrii
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Cleaning up code a little bit. Need to check Reinitialization after restart.
maksimovdmitrii
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Commits on Sep 13, 2017

prepare.py script is added in folder /scripts
maksimovdmitrii
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Preprocessing directory deleted for convinience
maksimovdmitrii
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Restructurization: bin folder should be added to path.
maksimovdmitrii
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Exaple added, Scripts folder deleted. Improved obtaining of the length for connectivity list in measure.py
maksimovdmitrii
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Instructions for centroid optimization example added.
maksimovdmitrii
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bin directory is not a good idea, now it should work.
maksimovdmitrii
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Bug with obtaining of the length of the geometry.in.constrained file is fixed
maksimovdmitrii
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Commits on Sep 14, 2017

Prepare script now more user friendly.
maksimovdmitrii
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Commits on Sep 15, 2017

All RDkit dependencies are disabled in the main developed version (including relaxations with FF)
maksimovdmitrii
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Added flag crossover_method = single_point or random_points. Need to be tested for performance.
maksimovdmitrii
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Commits on Sep 18, 2017

Improved reinitialization after backup. Improved mutattions for centroid and orientation.
maksimovdmitrii
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Commits on Sep 26, 2017

Quick and dirty omplementation for adjusting too large distances
maksimovdmitrii
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Commits on Sep 28, 2017

Commits on Sep 29, 2017

Start experimental GA with more than one molecule.
maksimovdmitrii
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Commits on Oct 11, 2017

Minor changes related to execution and storage of results and to sendind to blacklist of the structures.
maksimovdmitrii
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Commits on Oct 12, 2017

Now Population is not decreasing after failed relaxations.
maksimovdmitrii
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Commits on Oct 24, 2017

Preparing for documentation and general update.
maksimovdmitrii
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Commits on Oct 25, 2017

Daily update
maksimovdmitrii
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Commits on Oct 26, 2017

Restart remastered. Backup file now can be used as starting point with use of another calculations (for example from aminoaciddb)
maksimovdmitrii
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Commits on Nov 1, 2017

Adjustment of the flag, that reduces criteria for vdW radii is added, now it is done automatically with minimum value for the flag = 0.8
maksimovdmitrii
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Commits on Nov 7, 2017

WhatsNew in Fafoom folder added for tracking
maksimovdmitrii
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Commits on Nov 17, 2017

Lots of changes: Iterations counting are corrected, Output file made nicer, Restart routines are adjusted.
maksimovdmitrii
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Commits on Nov 28, 2017

Protomeric Degree of freedom is now available: Generation of random structures is perfect.
maksimovdmitrii
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Commits on Nov 30, 2017

Protomeric state is ready. Need to chack 'right_order_to_assign' flag and try different ordering.
maksimovdmitrii
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Commits on Feb 27, 2018

Lot's of updates.
maksimovdmitrii
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Correect naming of folders after restart
maksimovdmitrii
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Commits on Mar 22, 2018

Fixing Adjustment of the molecule with respect to Ion in the origin
Dmitrii Maksimov
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Untrack *.pyc files
Dmitrii Maksimov
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Delted unused fucnctions, stylistic errors improved, typos, just to make code more cleaner and readable, will do it again for sure.
Dmitrii Maksimov
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Commits on Mar 28, 2018

Typos corrected
Dmitrii Maksimov
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Commits on May 3, 2018

Shared blacklist is implemented. Now only unique structures across directories named 'GARUN_$NUMBER' are in the blacklists of the folder, where GA is running.
Dmitrii Maksimov
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Commits on Jun 23, 2018

Small change test pycharm
Dmitrii Maksimov
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Test commit after a while
damaksimovda
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Commits on Jul 23, 2018

Commented unfinished TESTOBject. Now should not raise an errorwqX
damaksimovda
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Commits on Jul 25, 2018

Small changes to output
damaksimovda
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If there is no backup files produced - fafoom will clean directory properly (delete this 0001_structure folder)
damaksimovda
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After restart fafoom the correct unfinished directory will be removed
damaksimovda
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Another restart options correction
damaksimovda
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Commits on Jul 26, 2018

Fixed bug of sorting of structures after restar
damaksimovda
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Commits on Jul 27, 2018

Automated production of final xyz file is added
damaksimovda
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Fix of the last commit
damaksimovda
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Another fix
damaksimovda
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Make it nice and finally work
damaksimovda
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Added script collect_strucutres.py, Minor changes in output
damaksimovda
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Commits on Jul 29, 2018

Change prepare.py scipt a little bit
damaksimovda
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Blacklist update after GA part is corrected
damaksimovda
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Clean and store at correct moment for Aims
damaksimovda
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Small bug in restart fixed
damaksimovda
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Python environment for workshop is changed
damaksimovda
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Typo
damaksimovda
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Inconsistent spaces in prepare.py fixed
damaksimovda
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IDENTANTION NIGHTMARE
damaksimovda
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One more
damaksimovda
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Molecule adjustment
damaksimovda
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Commits on Aug 1, 2018

Prepare.py changed
damaksimovda
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Commits on Aug 29, 2018

Routines for connectivity identifying
damaksimovda
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Commits on Oct 17, 2018

Scripts folder with additional scripts for postprocessing is added.
maksimovdmitrii
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Commits on Sep 2, 2019

typo fixed.
maksimovdmitrii
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Cleaning up of the directory flag is added for faster testing.
maksimovdmitrii
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Commits on Sep 10, 2019

Multiple molecule generator first commit
maksimovdmitrii
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Commits on Sep 30, 2019

Multiple molecule generator intermediate commit before testing and cleaning. Multiple molecules, periodic boundary conditions are impleented. Workflow is valid for random search. Big section regard…
maksimovdmitrii
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typo
maksimovdmitrii
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