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basic idea for templates to create permutations of possible donor / acceptor H sites #103

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f769d19
donor/acceptor structure for Hs in templates
godenymarta May 31, 2023
1403aed
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pre-commit-ci[bot] May 31, 2023
15694db
fixed tests
florianjoerg Jun 1, 2023
2b30f91
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pre-commit-ci[bot] Jun 1, 2023
09f62e1
Merge pull request #102 from florianjoerg/customnonbondedforce
florianjoerg Jun 1, 2023
6512ecd
Merge branch 'main' into tetr_marta
godenymarta Jun 5, 2023
c74d439
Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr…
godenymarta Jun 5, 2023
4cb0b87
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pre-commit-ci[bot] Jun 19, 2023
9a6e5c7
Merge pull request #105 from florianjoerg/pre-commit-ci-update-config
florianjoerg Jun 23, 2023
59cd591
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pre-commit-ci[bot] Jun 26, 2023
ab09709
Merge pull request #106 from florianjoerg/pre-commit-ci-update-config
florianjoerg Jun 27, 2023
89a81f6
deleted unnecessary lines
godenymarta Jun 29, 2023
a21ae35
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pre-commit-ci[bot] Jun 29, 2023
f828374
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pre-commit-ci[bot] Jul 3, 2023
14369b0
Merge pull request #108 from florianjoerg/pre-commit-ci-update-config
florianjoerg Jul 3, 2023
fefa5fd
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pre-commit-ci[bot] Aug 7, 2023
36d468e
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pre-commit-ci[bot] Aug 7, 2023
ffad461
Merge pull request #109 from florianjoerg/pre-commit-ci-update-config
florianjoerg Aug 13, 2023
3818b38
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pre-commit-ci[bot] Aug 14, 2023
b924931
started tests for toh2 system
godenymarta Aug 18, 2023
f378ba0
Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr…
godenymarta Aug 18, 2023
fba6337
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pre-commit-ci[bot] Aug 18, 2023
b44cbc1
Merge pull request #110 from florianjoerg/pre-commit-ci-update-config
florianjoerg Aug 21, 2023
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pre-commit-ci[bot] Aug 21, 2023
521092f
Merge pull request #111 from florianjoerg/pre-commit-ci-update-config
florianjoerg Aug 23, 2023
f59a5ec
started on idea for acceptor and donor modes for each residue, settin…
godenymarta Aug 23, 2023
5191426
Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr…
godenymarta Aug 23, 2023
8933e95
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pre-commit-ci[bot] Aug 23, 2023
db83717
started reusing stuff from the h2oac branch for donor/acceptor modes
godenymarta Aug 25, 2023
bb07d58
tests
godenymarta Aug 25, 2023
4dce219
resolved merge conflict
godenymarta Aug 25, 2023
63119f9
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pre-commit-ci[bot] Aug 25, 2023
1be893b
updates mainly to update.py to include donor/acceptor modes
godenymarta Aug 31, 2023
8e719dc
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pre-commit-ci[bot] Aug 31, 2023
33c4a78
small corrections
godenymarta Sep 1, 2023
96632c1
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pre-commit-ci[bot] Sep 4, 2023
8406799
mda reader for openmm rst files
florianjoerg Sep 5, 2023
2051908
Merge pull request #113 from florianjoerg/mda_xml_reader
florianjoerg Sep 5, 2023
a7cf442
Merge branch 'main' into pre-commit-ci-update-config
florianjoerg Sep 5, 2023
9722fb8
Merge pull request #112 from florianjoerg/pre-commit-ci-update-config
florianjoerg Sep 5, 2023
b2f7302
Update helpers.py
florianjoerg Sep 5, 2023
7e91172
Update helpers.py
florianjoerg Sep 5, 2023
44b21c6
Update test_helpers.py
florianjoerg Sep 5, 2023
831f6ff
Update README.md
florianjoerg Sep 6, 2023
f103ccb
first idea to save and load residues and setup donor and acceptor par…
godenymarta Sep 7, 2023
4159b60
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pre-commit-ci[bot] Sep 7, 2023
6a5d566
Merge branch 'main' of github.com:florianjoerg/protex into tetr_marta
godenymarta Sep 22, 2023
fea3977
new force field files for toh2
godenymarta Sep 26, 2023
693b500
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pre-commit-ci[bot] Sep 26, 2023
132cca8
started debugging code with test_h2o.py
godenymarta Sep 26, 2023
536731b
Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr…
godenymarta Sep 26, 2023
1d8f268
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pre-commit-ci[bot] Sep 26, 2023
cdf9207
debugging
godenymarta Oct 2, 2023
94f0c47
Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr…
godenymarta Oct 2, 2023
f2db5d7
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pre-commit-ci[bot] Oct 2, 2023
5b0ff4f
debugging (ordered names, H_D parms)
godenymarta Oct 11, 2023
5c6c878
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pre-commit-ci[bot] Oct 11, 2023
af67d68
debugging
godenymarta Oct 17, 2023
df859f6
Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr…
godenymarta Oct 17, 2023
64ac762
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pre-commit-ci[bot] Oct 17, 2023
b884d80
CustomNonBondedForce works only with fast
godenymarta Oct 18, 2023
37d22e5
Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr…
godenymarta Oct 18, 2023
e9833ea
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pre-commit-ci[bot] Oct 18, 2023
f06af2e
changes to donor/acceptor modes, still need to think about when to up…
godenymarta Oct 20, 2023
0a67828
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pre-commit-ci[bot] Oct 20, 2023
f51f539
debugging
godenymarta Nov 2, 2023
e8f12cb
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pre-commit-ci[bot] Nov 2, 2023
3a31bc0
saving and loading whole protex system
godenymarta Nov 14, 2023
0d7398d
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pre-commit-ci[bot] Nov 14, 2023
0ff1a0c
fixed parameters not being saved and loaded
godenymarta Nov 16, 2023
2863015
Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr…
godenymarta Nov 16, 2023
75fc214
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pre-commit-ci[bot] Nov 16, 2023
2e07bc5
use HBonds per default for water systems, cleanup of notes and todos
godenymarta Nov 17, 2023
9cd458d
Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr…
godenymarta Nov 17, 2023
acad25e
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pre-commit-ci[bot] Nov 17, 2023
8cc8877
removed unused pair_13_list
godenymarta Nov 20, 2023
8bfea5a
Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr…
godenymarta Nov 20, 2023
5717ef6
fixing bug with DrudeForceThole (not present in water)
godenymarta Dec 4, 2023
40b2739
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pre-commit-ci[bot] Dec 4, 2023
7a6540e
larger changes to check is force is present for each residue before t…
godenymarta Dec 6, 2023
2434950
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pre-commit-ci[bot] Dec 6, 2023
ca4819a
fixing drude vs drudethole problem
godenymarta Dec 13, 2023
0a18009
Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr…
godenymarta Dec 13, 2023
09ac68c
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pre-commit-ci[bot] Dec 13, 2023
c274ddd
fixing detect_forces
godenymarta Dec 14, 2023
8ca220e
Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr…
godenymarta Dec 14, 2023
ebad8fd
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pre-commit-ci[bot] Dec 14, 2023
e221950
changed extract_templates to account for residues being bound togethe…
godenymarta Jan 4, 2024
e511d35
Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr…
godenymarta Jan 4, 2024
156ecfd
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pre-commit-ci[bot] Jan 4, 2024
87a9c4b
fixing CustomNonbondedForce, now updating NBF and CNBF for each H and D
godenymarta Jan 5, 2024
90f616d
Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr…
godenymarta Jan 5, 2024
1bae514
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pre-commit-ci[bot] Jan 5, 2024
f610e78
trying to find a way to update nonbonded exclusions for H/D, needs a …
godenymarta Jan 12, 2024
d96852d
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pre-commit-ci[bot] Jan 12, 2024
8736194
working on customnonbondedforce
godenymarta Aug 21, 2024
ea5259e
Merge branch 'tetr_marta' of github.com:cbc-univie/protex into tetr_m…
godenymarta Aug 21, 2024
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pre-commit-ci[bot] committed Dec 14, 2023
commit ebad8fd758f4dfe32e1cf7385eab0cbf00a400c6
4 changes: 2 additions & 2 deletions protex/system.py
Original file line number Diff line number Diff line change
@@ -600,9 +600,9 @@ def _is_populated_in_residue(force, residue):
detected_forces[residue.name] = []
for force in self.system.getForces():
if _is_populated_in_residue(force, residue):
detected_forces[residue.name].append(type(force).__name__)
detected_forces[residue.name].append(type(force).__name__)
detected_forces[residue.name] = set(detected_forces[residue.name]) # remove duplicates

# logger.debug(detected_forces)
print(detected_forces)
return detected_forces