Merge FAFOOM v2 - #5

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mahrossi wants to merge 104 commits into

Commits on Apr 4, 2017

starting to make modifications
Dmitrii Maksimov
committed
f3c6417

Commits on Apr 12, 2017

vdW radii implementation
maksimovdmitrii
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4197ea8

Commits on Apr 19, 2017

I still not good at commits...(((
maksimovdmitrii
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84613e7
Added producing of 'valid' and 'invalid' folders for related structures.
maksimovdmitrii
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101cbcc
Merge branch 'dmitrii-mod' of github.com:FHIBioGroup/fafoom-dev into dmitrii-mod
maksimovdmitrii
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d3502fc
Including translation of the atom positions for str3d structure.
maksimovdmitrii
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76c485e

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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7159723

Commits on Apr 26, 2017

Operations with lists substituted with operations with np.arrays.
maksimovdmitrii
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192cea4

Commits on Apr 28, 2017

Centre of mass implemented
maksimovdmitrii
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57baf87

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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b05fb10

Commits on May 30, 2017

dirty quaternions are in.
maksimovdmitrii
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40e0d11

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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21f3a93

Commits on Jun 8, 2017

Degrees of freedom are roughly implemented. Need to be tested and revised changes.
maksimovdmitrii
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a9ca446
adding test_and_examples folder
maksimovdmitrii
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14398ea
Add files via upload
Dmitrii
authored
35b7333

Commits on Jun 14, 2017

Jst fixing a typo
Mariana Rossi
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5427aa2
Typos really
Mariana Rossi
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de23227

Commits on Jun 22, 2017

Add preprocessing script
maksimovdmitrii
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9aff8ec
Preprocessing folder
maksimovdmitrii
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a6ebd5a
Merge branch 'dmitrii-mod' of github.com:FHIBioGroup/fafoom-dev into dmitrii-mod
maksimovdmitrii
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10a2733

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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d7c4b03
try to add scripts for generating of valid structures.
maksimovdmitrii
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2def24a
try
maksimovdmitrii
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a020e3f

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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e53d75f

Commits on Jul 11, 2017

Try to commit from Atom. Pyforcefield added, generating inputs for MD
maksimovdmitrii
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871e5b5

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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9638d72
New test files
maksimovdmitrii
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2dc361e

Commits on Jul 27, 2017

Start to replace RDkIT module.
maksimovdmitrii
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a08e82f
update_coords_sdf, quaternion_measure now free of RDkit
maksimovdmitrii
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ba071d1

Commits on Jul 28, 2017

Ready to test dihedral test, seems to be okay
maksimovdmitrii
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adb8ab7
Seems that measure.py is free of RDKit, but need to check closely pyranosing rings mutations. Test, test, test.
maksimovdmitrii
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0c6e77a
Utilities module is free from RDKit. Need to check Kabsh algorithm vs RDKit rmsd algorithm. Kabsh was brought from https://github.com/charnley/rmsd/blob/master/rmsd/calculate_rmsd.py
maksimovdmitrii
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77f78ad
Good Bye RDKit, now testing time!!! (pyff.py uses RDKit naturally, need also to disable)
maksimovdmitrii
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ba7be7a

Commits on Aug 17, 2017

Daily update
maksimovdmitrii
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4990095

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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084856e

Commits on Sep 8, 2017

Seems that it is finally working
maksimovdmitrii
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ec0b540
Also ga.py should be added
maksimovdmitrii
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977373d
Add 'ga.py' outside
maksimovdmitrii
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d917062

Commits on Sep 12, 2017

Try to clean a little bit first
maksimovdmitrii
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2390683
Cleaning up
maksimovdmitrii
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8295a3e
Cleaning up code a little bit. Need to check Reinitialization after restart.
maksimovdmitrii
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069319e

Commits on Sep 13, 2017

prepare.py script is added in folder /scripts
maksimovdmitrii
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d48249c
Preprocessing directory deleted for convinience
maksimovdmitrii
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41844e0
Restructurization: bin folder should be added to path.
maksimovdmitrii
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88cb989
Exaple added, Scripts folder deleted. Improved obtaining of the length for connectivity list in measure.py
maksimovdmitrii
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d732e2d
Instructions for centroid optimization example added.
maksimovdmitrii
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605e59b
bin directory is not a good idea, now it should work.
maksimovdmitrii
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bdd9112
Bug with obtaining of the length of the geometry.in.constrained file is fixed
maksimovdmitrii
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f34c45f

Commits on Sep 14, 2017

Prepare script now more user friendly.
maksimovdmitrii
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b112410

Commits on Sep 15, 2017

All RDkit dependencies are disabled in the main developed version (including relaxations with FF)
maksimovdmitrii
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1d49143
Added flag crossover_method = single_point or random_points. Need to be tested for performance.
maksimovdmitrii
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b0514c1

Commits on Sep 18, 2017

Improved reinitialization after backup. Improved mutattions for centroid and orientation.
maksimovdmitrii
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06a804b

Commits on Sep 26, 2017

Quick and dirty omplementation for adjusting too large distances
maksimovdmitrii
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2a3cd1c

Commits on Sep 28, 2017

Structures_gen.py Script is improved and ready to use.
maksimovdmitrii
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151fa09
Improved the behavior after not converged SCF cycle: folder is deleted and GA continued. Need to check indexes that are assigned during this improved process.
maksimovdmitrii
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4bfabab

Commits on Sep 29, 2017

Start experimental GA with more than one molecule.
maksimovdmitrii
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1570722

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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1048917

Commits on Oct 12, 2017

Now Population is not decreasing after failed relaxations.
maksimovdmitrii
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1501cdc

Commits on Oct 24, 2017

Preparing for documentation and general update.
maksimovdmitrii
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81653fe

Commits on Oct 25, 2017

Daily update
maksimovdmitrii
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b62f400

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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d61d009

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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9b85419

Commits on Nov 7, 2017

WhatsNew in Fafoom folder added for tracking
maksimovdmitrii
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9d84033

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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40ad59a

Commits on Nov 28, 2017

Protomeric Degree of freedom is now available: Generation of random structures is perfect.
maksimovdmitrii
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7e6b110

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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d3b4d2c

Commits on Feb 27, 2018

Lot's of updates.
maksimovdmitrii
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86012b1
Correect naming of folders after restart
maksimovdmitrii
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f63fe28

Commits on Mar 22, 2018

Fixing Adjustment of the molecule with respect to Ion in the origin
Dmitrii Maksimov
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a040e6d
Untrack *.pyc files
Dmitrii Maksimov
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eb568a8
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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88ff458

Commits on Mar 28, 2018

Typos corrected
Dmitrii Maksimov
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250a4d3

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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b898f1f

Commits on Jun 23, 2018

Small change test pycharm
Dmitrii Maksimov
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cd2e8f3
Test commit after a while
damaksimovda
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3aec21c

Commits on Jul 23, 2018

Commented unfinished TESTOBject. Now should not raise an errorwqX
damaksimovda
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d3e1238

Commits on Jul 25, 2018

Small changes to output
damaksimovda
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ed0abb1
If there is no backup files produced - fafoom will clean directory properly (delete this 0001_structure folder)
damaksimovda
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8932ec0
After restart fafoom the correct unfinished directory will be removed
damaksimovda
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72433ed
Another restart options correction
damaksimovda
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489223a

Commits on Jul 26, 2018

Fixed bug of sorting of structures after restar
damaksimovda
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b770ad8

Commits on Jul 27, 2018

Automated production of final xyz file is added
damaksimovda
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c0c271f
Fix of the last commit
damaksimovda
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0111e18
Another fix
damaksimovda
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e9a1375
Make it nice and finally work
damaksimovda
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e23e0a2
Added script collect_strucutres.py, Minor changes in output
damaksimovda
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293092e

Commits on Jul 29, 2018

Change prepare.py scipt a little bit
damaksimovda
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e5426a3
Blacklist update after GA part is corrected
damaksimovda
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4ae26b0
Clean and store at correct moment for Aims
damaksimovda
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7499bb2
Small bug in restart fixed
damaksimovda
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29b55b0
Python environment for workshop is changed
damaksimovda
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600257d
Typo
damaksimovda
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bafdfd7
Inconsistent spaces in prepare.py fixed
damaksimovda
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d0adcfb
IDENTANTION NIGHTMARE
damaksimovda
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6dcba8f
One more
damaksimovda
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e65f075
Molecule adjustment
damaksimovda
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03178fe

Commits on Aug 1, 2018

Prepare.py changed
damaksimovda
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644c740

Commits on Aug 29, 2018

Routines for connectivity identifying
damaksimovda
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55d8b62

Commits on Oct 17, 2018

Scripts folder with additional scripts for postprocessing is added.
maksimovdmitrii
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bad6b6b

Commits on Sep 2, 2019

typo fixed.
maksimovdmitrii
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ca14481
Cleaning up of the directory flag is added for faster testing.
maksimovdmitrii
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be31b32

Commits on Sep 10, 2019

Multiple molecule generator first commit
maksimovdmitrii
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ae71d3e

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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67ac5cf
typo
maksimovdmitrii
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b8aac08