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Sang nanoparticle #286

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Sang nanoparticle #286

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acf0495
added PCBM-fullerene generation code with the polyply branch
Shtkddud123 Nov 29, 2022
cfff153
added PCBM-fullerene generation code with the polyply branch
Shtkddud123 Nov 29, 2022
2ad2fdf
updated much of the functions as required - further changes to be made
Shtkddud123 Jan 5, 2023
1fb9868
added new functionalities to ensure gro files are correctly generated
Shtkddud123 Jan 5, 2023
c6bfecc
removed some datetime libraries not being utilized
Shtkddud123 Jan 5, 2023
3ce1d3a
removed . files that are too large!
Shtkddud123 Jan 14, 2023
949fbe1
removed notebook
Shtkddud123 Jan 15, 2023
47cc745
rebased and forced push
Shtkddud123 Jan 28, 2023
1dfa72d
rebased and forced push
Shtkddud123 Jan 28, 2023
6e4ed35
added basic lattice generator
Shtkddud123 Jan 28, 2023
2d8804e
very basic gold lattice generation now works - but need to add in the…
Shtkddud123 Jan 29, 2023
04305f9
removed build
Shtkddud123 Feb 2, 2023
67b8afd
added new nanoparticle part
Shtkddud123 Mar 3, 2023
b5a2e50
added additional ligand compatibility
Shtkddud123 Mar 30, 2023
8f78896
removed some extraeous files
Shtkddud123 Mar 30, 2023
dab2e43
new
Shtkddud123 Mar 30, 2023
f42c1be
nearly fixed force field issue..
Shtkddud123 Mar 30, 2023
9bdc2c6
modified the bond adder to make it work
Shtkddud123 Mar 31, 2023
cd6dd70
modified the bond adder to make it work
Shtkddud123 Mar 31, 2023
ae6620c
more progress - need to fix key issues
Shtkddud123 Mar 31, 2023
523d299
fixed more code
Shtkddud123 Apr 2, 2023
b8aee50
Added working model - checked that opls works
Shtkddud123 Apr 5, 2023
a992d02
finally resolve some longstanding index issues. Also cleaned some code
Shtkddud123 Apr 9, 2023
447599f
new features added - but need to delete others!
Shtkddud123 May 8, 2023
b562afe
making PCBM NP
Shtkddud123 Jun 6, 2023
be460b0
added PCBM model
Shtkddud123 Jun 17, 2023
7a97aec
A version of PCBM model working..
Shtkddud123 Jun 19, 2023
65a7572
fixed the rotation matrix - should work now for both gold nanoparticl…
Shtkddud123 Jun 20, 2023
76de52b
still need to fix smaller points, but overall in good shape. Now to w…
Shtkddud123 Jun 22, 2023
1f7925f
fixed weird issue with the PCBM ligand
Shtkddud123 Jun 22, 2023
fea287f
changed some docstrings for the nps
Shtkddud123 Jun 22, 2023
fc03adb
removed code that were not required anymore
Shtkddud123 Jun 22, 2023
ab9b8ff
shorted some of the pattern recognition to a single function
Shtkddud123 Jun 22, 2023
c69a902
Adding some new generic nanoparticle creation functions
Shtkddud123 Jul 2, 2023
28d3a90
fixing some inner ligands placement inside core
Shtkddud123 Jul 3, 2023
12df3d1
still not perfect but updated
Shtkddud123 Jul 4, 2023
bb6d5fd
progress on generic NP object
Shtkddud123 Jul 4, 2023
a78504a
moved generic gold nanoparticle class to nanoparticle_generic
Shtkddud123 Jul 6, 2023
23f79f5
new
Shtkddud123 Aug 4, 2023
9dfc31d
new
Shtkddud123 Aug 15, 2023
2952955
new
Shtkddud123 Sep 4, 2023
1a49794
updated nanoparticle generic
Shtkddud123 Oct 13, 2023
7c6e79a
made more modifications
Shtkddud123 Oct 14, 2023
864305b
updated
Shtkddud123 Oct 14, 2023
5c9e8c5
added python 2 function
Shtkddud123 Oct 15, 2023
b1c2552
fixed more parts
Shtkddud123 Oct 15, 2023
0859812
fixed itp issue again
Shtkddud123 Oct 16, 2023
4702bc4
modified the artificial core generation code
Shtkddud123 Oct 21, 2023
5ac47e6
fix: more changes
Shtkddud123 Oct 29, 2023
dd23bd5
added martini3 small molecules to work with articifical NPs
Shtkddud123 Nov 6, 2023
eb5b00e
new: added new modules
Shtkddud123 Dec 5, 2023
07aeadb
fixed weird issue
Shtkddud123 Jan 8, 2024
2829c37
corrected bond generator
Shtkddud123 Jan 8, 2024
bb4bc6e
new
Shtkddud123 Jan 10, 2024
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4 changes: 0 additions & 4 deletions .coveragerc
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3 changes: 3 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -22,3 +22,6 @@ tests/test_data/gen_seq/output/*.itp
doc/build
doc/source/api
doc/source/.doctrees

.ipynb_checkpoints/**
.pylintrc
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