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.

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

New Hybrid Modules #1309

Draft
wants to merge 42 commits into
base: main
Choose a base branch
from
Draft
Changes from 1 commit
Commits
Show all changes
42 commits
Select commit Hold shift + click to select a range
582ffaa
setup hybrid module
jamesmkrieger Feb 16, 2021
830d84e
adaptive ANM hybrid method
jamesmkrieger Feb 16, 2021
21b005e
added filename to writePDBFixed
jamesmkrieger Feb 16, 2021
d925e9b
saveEnsemble works for AdaptiveHybrid
jamesmkrieger Feb 17, 2021
a83133a
setAtoms fixes
jamesmkrieger Feb 17, 2021
fac7df2
added ensemble filtering
jamesmkrieger Feb 17, 2021
c7cab38
import hybrid before ensemble
jamesmkrieger Feb 17, 2021
003d486
tightened imports
jamesmkrieger Feb 17, 2021
d59c9f2
added direction mode
jamesmkrieger Feb 18, 2021
ff2fd5e
aANM convergence docs fix
jamesmkrieger Feb 18, 2021
7ca495d
moved hybrid methods back to dynamics
jamesmkrieger Feb 18, 2021
901e607
clustenm docs fix
jamesmkrieger Feb 19, 2021
9ae1cdf
AdaptiveHybrid_docs_fix
jamesmkrieger Feb 22, 2021
b386c99
AdaptiveHybrid warning fix
jamesmkrieger Feb 22, 2021
593b003
remove changes to clustenm
jamesmkrieger Feb 22, 2021
f5304e7
added comd
jamesmkrieger Feb 24, 2021
e37de5e
comd checks input arguments
jamesmkrieger Feb 24, 2021
43398ed
CoMD as hybrid method
jamesmkrieger Feb 24, 2021
05ef051
comd n_modes
jamesmkrieger Feb 25, 2021
a834ef9
adaptive ANM changes
jamesmkrieger Feb 26, 2021
310b931
comd bug fix
jamesmkrieger Feb 26, 2021
03aad7d
comd convergence parameters
jamesmkrieger Feb 26, 2021
11b40c8
suppressed logs
jamesmkrieger Feb 26, 2021
df83906
save CoMD ensemble
jamesmkrieger Feb 26, 2021
5b02777
added getCoordsB
jamesmkrieger Feb 26, 2021
eed201b
error fix
jamesmkrieger Feb 26, 2021
90dffc6
add calcConvergenceRMSDs
jamesmkrieger Feb 26, 2021
87101ce
init coordsB and indicesB
jamesmkrieger Feb 26, 2021
7afcf7e
ConvergenceRMSDs bug fix
jamesmkrieger Mar 1, 2021
0ad0f0a
comd comment fixes
jamesmkrieger Mar 2, 2021
028bb0f
Merge branch 'master' of github.com:prody/ProDy into hybrid
jamesmkrieger Mar 2, 2021
05c1581
fixed import error
jamesmkrieger Mar 2, 2021
d164095
comment acceptance_ratio is f
jamesmkrieger Mar 2, 2021
9bd1782
added comd to saveEnsemble
jamesmkrieger Mar 3, 2021
fbfe58c
Merge branch 'master' of github.com:prody/ProDy into hybrid
jamesmkrieger Dec 20, 2021
b69bb4e
Merge branch 'master' of https://github.com/prody/ProDy into hybrid
jamesmkrieger Mar 9, 2022
77d2b67
Merge branch 'master' of github.com:prody/ProDy into hybrid
jamesmkrieger Feb 29, 2024
c2e9762
Merge branch 'scipion_minimal' into hybrid
jamesmkrieger Feb 29, 2024
313be4c
Merge branch 'master' of github.com:prody/ProDy into hybrid
jamesmkrieger Mar 28, 2024
8b9a1e7
Merge branch 'main' of github.com:prody/ProDy into hybrid
jamesmkrieger Aug 14, 2024
9316df3
fix bad merge
jamesmkrieger Aug 14, 2024
a422484
Merge branch 'main' of github.com:prody/ProDy into hybrid
jamesmkrieger Dec 1, 2024
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Prev Previous commit
Next Next commit
comd comment fixes
jamesmkrieger committed Mar 2, 2021
commit 0ad0f0ac8b20823f2e4dbbbfb5e3a9555098471f
8 changes: 4 additions & 4 deletions prody/dynamics/comd.py
Original file line number Diff line number Diff line change
@@ -97,10 +97,10 @@ def calcANMMC(initial, final, **kwargs):
else:
accept_para = 0.1

# MC parameter 1 is the acceptance ratio, which should converge on
# MC parameter 1 is the acceptance ratio, f, which should converge on
# the selected value with a tolerance of 0.05 either side
# and accept_para is adjusted to help bring it within these limits.
# This also happens every 5 steps during the run (lines 150 to 156).
# and accept_para, gamma, is adjusted to help bring it within these limits.
# This also happens every 5 steps during the run.

if original_initial_pdb != original_final_pdb:
# difference from the target structure is defined as the energy and the minimum is zero.
@@ -164,7 +164,7 @@ def calcANMMC(initial, final, **kwargs):

if (mod(k,5)==0 and not(k==0)):
# Update of the accept_para to keep the MC para reasonable
# See comment lines 86 to 89.
# See comment lines above.
if f > acceptance_ratio + 0.05:
accept_para /= 1.5
elif f < acceptance_ratio - 0.05: