Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

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

Open
wants to merge 97 commits into
base: tetr
Choose a base branch
from
Open

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

wants to merge 97 commits into from

Conversation

godenymarta
Copy link
Collaborator

Description

User provides 1 topology for each species, which atoms can be permutated and how many of them should be donors. We automatically create all combinations and the corresponding force field parameters. Keep track of changing donors into acceptors and vice versa to update residues. Maybe switch from distance between O/N to H to checking D to H.

Todos

see TODO and NOTE in testsystems.py

godenymarta and others added 30 commits May 31, 2023 16:20
@godenymarta
donor/acceptor structure for Hs in templates
f769d19
@pre-commit-ci
🛠️ [pre-commit.ci] Auto format from pre-commit.com hooks
1403aed
@florianjoerg
fixed tests
15694db
@pre-commit-ci
🛠️ [pre-commit.ci] Auto format from pre-commit.com hooks
2b30f91
@florianjoerg
Merge pull request #102 from florianjoerg/customnonbondedforce
09f62e1 
CustomNonbondedForce
@godenymarta
Merge branch 'main' into tetr_marta
6512ecd
@godenymarta
Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr…
c74d439 
…_marta
@pre-commit-ci
⬆ [pre-commit.ci] pre-commit autoupdate
4cb0b87 
updates:
- [github.com/asottile/pyupgrade: v3.4.0 → v3.7.0](asottile/pyupgrade@v3.4.0...v3.7.0)
- [github.com/charliermarsh/ruff-pre-commit: v0.0.270 → v0.0.272](astral-sh/ruff-pre-commit@v0.0.270...v0.0.272)
@florianjoerg
Merge pull request #105 from florianjoerg/pre-commit-ci-update-config
9a6e5c7
@pre-commit-ci
⬆ [pre-commit.ci] pre-commit autoupdate
59cd591 
updates:
- [github.com/charliermarsh/ruff-pre-commit: v0.0.272 → v0.0.275](astral-sh/ruff-pre-commit@v0.0.272...v0.0.275)
@florianjoerg
Merge pull request #106 from florianjoerg/pre-commit-ci-update-config
ab09709 
⬆ [pre-commit.ci] pre-commit autoupdate
@godenymarta
deleted unnecessary lines
89a81f6
@pre-commit-ci
🛠️ [pre-commit.ci] Auto format from pre-commit.com hooks
a21ae35
@pre-commit-ci
⬆ [pre-commit.ci] pre-commit autoupdate
f828374 
updates:
- [github.com/asottile/pyupgrade: v3.7.0 → v3.8.0](asottile/pyupgrade@v3.7.0...v3.8.0)
@florianjoerg
Merge pull request #108 from florianjoerg/pre-commit-ci-update-config
14369b0 
⬆ [pre-commit.ci] pre-commit autoupdate
@pre-commit-ci
⬆ [pre-commit.ci] pre-commit autoupdate
fefa5fd 
updates:
- [github.com/asottile/pyupgrade: v3.8.0 → v3.10.1](asottile/pyupgrade@v3.8.0...v3.10.1)
- https://github.com/charliermarsh/ruff-pre-commit → https://github.com/astral-sh/ruff-pre-commit
- [github.com/astral-sh/ruff-pre-commit: v0.0.275 → v0.0.282](astral-sh/ruff-pre-commit@v0.0.275...v0.0.282)
@pre-commit-ci
🛠️ [pre-commit.ci] Auto format from pre-commit.com hooks
36d468e
@florianjoerg
Merge pull request #109 from florianjoerg/pre-commit-ci-update-config
ffad461
@pre-commit-ci
⬆ [pre-commit.ci] pre-commit autoupdate
3818b38 
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.282 → v0.0.284](astral-sh/ruff-pre-commit@v0.0.282...v0.0.284)
@godenymarta
started tests for toh2 system
b924931
@godenymarta
Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr…
f378ba0 
…_marta
@pre-commit-ci
🛠️ [pre-commit.ci] Auto format from pre-commit.com hooks
fba6337
@florianjoerg
Merge pull request #110 from florianjoerg/pre-commit-ci-update-config
b44cbc1 
⬆ [pre-commit.ci] pre-commit autoupdate
@pre-commit-ci
⬆ [pre-commit.ci] pre-commit autoupdate
941fe35 
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.284 → v0.0.285](astral-sh/ruff-pre-commit@v0.0.284...v0.0.285)
@florianjoerg
Merge pull request #111 from florianjoerg/pre-commit-ci-update-config
521092f 
⬆ [pre-commit.ci] pre-commit autoupdate
@godenymarta
started on idea for acceptor and donor modes for each residue, settin…
f59a5ec 
…g H and D nonbonded parameters extra after transfer
@godenymarta
Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr…
5191426 
…_marta
@pre-commit-ci
🛠️ [pre-commit.ci] Auto format from pre-commit.com hooks
8933e95
@godenymarta
started reusing stuff from the h2oac branch for donor/acceptor modes
db83717
@godenymarta
tests
bb07d58
godenymarta and others added 30 commits November 14, 2023 13:04
@godenymarta
saving and loading whole protex system
3a31bc0
@pre-commit-ci
🛠️ [pre-commit.ci] Auto format from pre-commit.com hooks
0d7398d
@godenymarta
fixed parameters not being saved and loaded
0ff1a0c
@godenymarta
Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr…
2863015 
…_marta
@pre-commit-ci
🛠️ [pre-commit.ci] Auto format from pre-commit.com hooks
75fc214
@godenymarta
use HBonds per default for water systems, cleanup of notes and todos
2e07bc5
@godenymarta
Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr…
9cd458d 
…_marta
@pre-commit-ci
🛠️ [pre-commit.ci] Auto format from pre-commit.com hooks
acad25e
@godenymarta
removed unused pair_13_list
8cc8877
@godenymarta
Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr…
8bfea5a 
…_marta
@godenymarta
fixing bug with DrudeForceThole (not present in water)
5717ef6
@pre-commit-ci
🛠️ [pre-commit.ci] Auto format from pre-commit.com hooks
40b2739
@godenymarta
larger changes to check is force is present for each residue before t…
7a6540e 
…rying to update
@pre-commit-ci
🛠️ [pre-commit.ci] Auto format from pre-commit.com hooks
2434950
@godenymarta
fixing drude vs drudethole problem
ca4819a
@godenymarta
Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr…
0a18009 
…_marta
@pre-commit-ci
🛠️ [pre-commit.ci] Auto format from pre-commit.com hooks
09ac68c
@godenymarta
fixing detect_forces
c274ddd
@godenymarta
Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr…
8ca220e 
…_marta
@pre-commit-ci
🛠️ [pre-commit.ci] Auto format from pre-commit.com hooks
ebad8fd
@godenymarta
changed extract_templates to account for residues being bound togethe…
e221950 
…r in proteins
@godenymarta
Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr…
e511d35 
…_marta
@pre-commit-ci
🛠️ [pre-commit.ci] Auto format from pre-commit.com hooks
156ecfd
@godenymarta
fixing CustomNonbondedForce, now updating NBF and CNBF for each H and D
87a9c4b
@godenymarta
Merge branch 'tetr_marta' of github.com:florianjoerg/protex into tetr…
90f616d 
…_marta
@pre-commit-ci
🛠️ [pre-commit.ci] Auto format from pre-commit.com hooks
1bae514
@godenymarta
trying to find a way to update nonbonded exclusions for H/D, needs a …
f610e78 
…lot of refining
@pre-commit-ci
🛠️ [pre-commit.ci] Auto format from pre-commit.com hooks
d96852d
@godenymarta
working on customnonbondedforce
8736194
@godenymarta
Merge branch 'tetr_marta' of github.com:cbc-univie/protex into tetr_m…
ea5259e 
…arta
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@godenymarta @florianjoerg