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Add constraints #84

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merged 1 commit into from
May 16, 2024
Merged

Add constraints #84

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28 changes: 17 additions & 11 deletions package/ClayCode/builder/assembly.py
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Original file line number Diff line number Diff line change
Expand Up @@ -410,7 +410,7 @@ def run_em(
ndx_list.append(
self.stack.with_suffix(".ndx")
) # .insert(0, self.stack.with_suffix(".ndx"))

topfile = self.stack.top
while len(freeze_grps_list) < n_runs:
freeze_grps_list.append(None)
freeze_dims_list.append(None)
Expand Down Expand Up @@ -443,7 +443,7 @@ def run_em(
):
result = run_em(
crdin=self.stack,
topin=self.stack.top,
topin=topfile,
odir=self.args.outpath,
topout=self.args.outpath / f"{outname}.top",
outname=outname,
Expand All @@ -459,9 +459,7 @@ def run_em(
else:
logger.ferror(f"Energy minimisation failed.")
outgro = None
break
# freeze_grps = None
# freeze_dims = None
break # freeze_grps = None # freeze_dims = None
# if outgro is not False:
# result = run_em(
# crdin=self.stack,
Expand All @@ -481,10 +479,10 @@ def run_em(
# logger.ferror(f"Energy minimisation failed.")
if outgro is not None:
outpath = Dir(self.args.outpath)
top_files = outpath._get_filelist(ext=".top")
crd_top_files = [
*outpath.gro_filelist,
*outpath.itp_filelist,
*outpath._get_filelist(ext=".top"),
*outpath.itp_filelist, # *outpath._get_filelist(ext=".top"),
*outpath._get_filelist(ext=".csv"),
*outpath._get_filelist(ext=".mdp"),
*outpath._get_filelist(ext=".edr"),
Expand All @@ -493,10 +491,16 @@ def run_em(
]
em_files = []
backups = []
for file in sorted(
outpath.iterdir(), key=lambda f: f.suffix, reverse=True
):
if file not in crd_top_files and not file.is_dir():
for file in [
*sorted(
outpath.iterdir(), key=lambda f: f.suffix, reverse=True
),
*top_files,
]:
if (
file not in [*crd_top_files, *top_files]
and not file.is_dir()
):
file.unlink(missing_ok=True)
else:
if file.stem.split("_")[-1] == "em":
Expand Down Expand Up @@ -527,6 +531,8 @@ def run_em(
shutil.copy2(file, new_file)
except shutil.SameFileError:
pass
except FileNotFoundError:
pass
else:
if (
file.suffix == ".gro"
Expand Down
132 changes: 132 additions & 0 deletions package/ClayCode/data/data/UCS/CD11/constraints/C1000_distconstr.itp
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Original file line number Diff line number Diff line change
@@ -0,0 +1,132 @@
#ifdef TSheets
[ distance_restraints ]
; i j ? label funct lo up1 up2 weight
5 14 1 8 1 0.164367 0.364367 1.36437 1
6 7 1 9 1 0.164127 0.364127 1.36413 1
6 9 1 11 1 0.16889 0.36889 1.36889 1
6 13 1 15 1 0.166874 0.366874 1.36687 1
7 9 1 18 1 0.157101 0.357101 1.3571 1
7 13 1 22 1 0.158884 0.358884 1.35888 1
8 11 1 26 1 0.164571 0.364571 1.36457 1
8 12 1 27 1 0.158884 0.358884 1.35888 1
8 14 1 29 1 0.162724 0.362724 1.36272 1
9 10 1 30 1 0.163911 0.363911 1.36391 1
9 13 1 33 1 0.162724 0.362724 1.36272 1
11 12 1 39 1 0.164203 0.364203 1.3642 1
12 13 1 42 1 0.162857 0.362857 1.36286 1
12 14 1 43 1 0.157101 0.357101 1.3571 1
#endif
#ifdef ClaySheets
[ distance_restraints ]
; i j ? label funct lo up1 up2 weight
1 5 1 3 1 0.061459 0.261459 1.26146 1
1 14 1 12 1 0.0616818 0.261682 1.26168 1
2 8 1 38 1 0.0588899 0.25889 1.25889 1
2 11 1 41 1 0.0607607 0.260761 1.26076 1
2 12 1 42 1 0.0624407 0.262441 1.26244 1
2 14 1 44 1 0.0625977 0.262598 1.2626 1
3 12 1 73 1 0.0616075 0.261608 1.26161 1
3 13 1 74 1 0.0619537 0.261954 1.26195 1
4 6 1 97 1 0.060826 0.260826 1.26083 1
4 7 1 98 1 0.0621542 0.262154 1.26215 1
4 9 1 100 1 0.0604151 0.260415 1.26042 1
4 13 1 104 1 0.061558 0.261558 1.26156 1
5 14 1 134 1 0.164367 0.364367 1.36437 1
5 17 1 137 1 0.0920989 0.292099 1.2921 1
5 18 1 138 1 0.093902 0.293902 1.2939 1
5 21 1 141 1 0.137828 0.337828 1.33783 1
5 31 1 151 1 0.158407 0.358407 1.35841 1
6 7 1 155 1 0.164127 0.364127 1.36413 1
6 9 1 157 1 0.16889 0.36889 1.36889 1
6 13 1 161 1 0.166874 0.366874 1.36687 1
6 16 1 164 1 0.0930932 0.293093 1.29309 1
6 24 1 172 1 0.140443 0.340443 1.34044 1
7 9 1 184 1 0.157101 0.357101 1.3571 1
7 13 1 188 1 0.158884 0.358884 1.35888 1
8 11 1 212 1 0.164571 0.364571 1.36457 1
8 12 1 213 1 0.158884 0.358884 1.35888 1
8 14 1 215 1 0.162724 0.362724 1.36272 1
9 10 1 236 1 0.163911 0.363911 1.36391 1
9 13 1 239 1 0.162724 0.362724 1.36272 1
10 16 1 266 1 0.0922446 0.292245 1.29224 1
10 25 1 275 1 0.137573 0.337573 1.33757 1
11 12 1 285 1 0.164203 0.364203 1.3642 1
11 15 1 288 1 0.0938608 0.293861 1.29386 1
11 18 1 291 1 0.0941391 0.294139 1.29414 1
11 20 1 293 1 0.14253 0.34253 1.34253 1
12 13 1 308 1 0.162857 0.362857 1.36286 1
12 14 1 309 1 0.157101 0.357101 1.3571 1
15 19 1 374 1 0.0914262 0.291426 1.29143 1
15 20 1 375 1 0.0896022 0.289602 1.2896 1
15 22 1 377 1 0.0916612 0.291661 1.29166 1
15 30 1 385 1 0.16326 0.36326 1.36326 1
15 31 1 386 1 0.141698 0.341698 1.3417 1
15 32 1 387 1 0.157672 0.357672 1.35767 1
16 19 1 392 1 0.0910602 0.29106 1.29106 1
16 22 1 395 1 0.0902998 0.2903 1.2903 1
16 24 1 397 1 0.089119 0.289119 1.28912 1
16 25 1 398 1 0.0876886 0.287689 1.28769 1
16 28 1 401 1 0.163936 0.363936 1.36394 1
16 29 1 402 1 0.155229 0.355229 1.35523 1
16 30 1 403 1 0.163032 0.363032 1.36303 1
16 31 1 404 1 0.140828 0.340828 1.34083 1
17 21 1 411 1 0.0864457 0.286446 1.28645 1
17 33 1 423 1 0.164492 0.364492 1.36449 1
18 20 1 426 1 0.0894281 0.289428 1.28943 1
18 21 1 427 1 0.088218 0.288218 1.28822 1
18 23 1 429 1 0.091575 0.291575 1.29158 1
18 26 1 432 1 0.0902998 0.2903 1.2903 1
18 27 1 433 1 0.13728 0.33728 1.33728 1
18 32 1 438 1 0.162939 0.362939 1.36294 1
18 33 1 439 1 0.152555 0.352555 1.35255 1
18 34 1 440 1 0.159488 0.359488 1.35949 1
19 22 1 443 1 0.136588 0.336588 1.33659 1
19 31 1 452 1 0 0.197252 1.19725 1
20 31 1 466 1 0.163167 0.363167 1.36317 1
20 32 1 467 1 0 0.197929 1.19793 1
21 27 1 475 1 0.161973 0.361973 1.36197 1
21 33 1 481 1 0 0.198438 1.19844 1
22 30 1 490 1 0 0.198051 1.19805 1
23 26 1 497 1 0.136332 0.336332 1.33633 1
23 27 1 498 1 0 0.194345 1.19435 1
24 28 1 509 1 0 0.199106 1.19911 1
25 29 1 519 1 0 0.196732 1.19673 1
25 31 1 521 1 0.162734 0.362734 1.36273 1
26 34 1 532 1 0 0.196468 1.19647 1
#endif
#ifdef ClayNoOHSheets
[ distance_restraints ]
; i j ? label funct lo up1 up2 weight
1 5 1 3 1 0.061459 0.261459 1.26146 1
1 14 1 12 1 0.0616818 0.261682 1.26168 1
2 8 1 22 1 0.0588899 0.25889 1.25889 1
2 11 1 25 1 0.0607607 0.260761 1.26076 1
2 12 1 26 1 0.0624407 0.262441 1.26244 1
2 14 1 28 1 0.0625977 0.262598 1.2626 1
3 12 1 41 1 0.0616075 0.261608 1.26161 1
3 13 1 42 1 0.0619537 0.261954 1.26195 1
4 6 1 49 1 0.060826 0.260826 1.26083 1
4 7 1 50 1 0.0621542 0.262154 1.26215 1
4 9 1 52 1 0.0604151 0.260415 1.26042 1
4 13 1 56 1 0.061558 0.261558 1.26156 1
5 14 1 70 1 0.164367 0.364367 1.36437 1
5 17 1 73 1 0.0920989 0.292099 1.2921 1
5 18 1 74 1 0.093902 0.293902 1.2939 1
6 7 1 75 1 0.164127 0.364127 1.36413 1
6 9 1 77 1 0.16889 0.36889 1.36889 1
6 13 1 81 1 0.166874 0.366874 1.36687 1
6 16 1 84 1 0.0930932 0.293093 1.29309 1
7 9 1 88 1 0.157101 0.357101 1.3571 1
7 13 1 92 1 0.158884 0.358884 1.35888 1
8 11 1 100 1 0.164571 0.364571 1.36457 1
8 12 1 101 1 0.158884 0.358884 1.35888 1
8 14 1 103 1 0.162724 0.362724 1.36272 1
9 10 1 108 1 0.163911 0.363911 1.36391 1
9 13 1 111 1 0.162724 0.362724 1.36272 1
10 16 1 122 1 0.0922446 0.292245 1.29224 1
11 12 1 125 1 0.164203 0.364203 1.3642 1
11 15 1 128 1 0.0938608 0.293861 1.29386 1
11 18 1 131 1 0.0941391 0.294139 1.29414 1
12 13 1 132 1 0.162857 0.362857 1.36286 1
12 14 1 133 1 0.157101 0.357101 1.3571 1
#endif
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