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scfix behaviour change #621

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merged 8 commits into from
Oct 24, 2024
+2,479 −17
Merged

scfix behaviour change #621

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e23fb3e
Initial change in argument
csbrasnett Oct 21, 2024
ec15581
Update defaults and correct commands. Merge with #622
csbrasnett Oct 21, 2024
38229f5
add extra integration test to make sure new defaults are applied
csbrasnett Oct 21, 2024
09283b8
fixed failing name_moltype test
csbrasnett Oct 21, 2024
5550cfd
removed superfluous flag in an integration test
csbrasnett Oct 21, 2024
24fb8fa
changed -cys default argument to 'auto' and corrected tests
csbrasnett Oct 21, 2024
bdcc1bc
changing scfix behaviour
csbrasnett Oct 21, 2024
acb158d
nitpick changes
csbrasnett Oct 21, 2024
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6 changes: 3 additions & 3 deletions bin/martinize2
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Original file line number Diff line number Diff line change
Expand Up @@ -472,7 +472,7 @@ def entry():
"-ef",
dest="rb_force_constant",
type=float,
default=500,
default=700,
help="Elastic bond force constant Fc in kJ/mol/nm^2",
)
rb_group.add_argument(
Expand Down Expand Up @@ -628,9 +628,9 @@ def entry():
prot_group.add_argument(
"-scfix",
dest="scfix",
action="store_true",
action="store_false",
default=True,
help="Apply side chain corrections.",
help="[don't] apply side chain corrections.",
)
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prot_group.add_argument(
"-cys",
Expand Down
1 change: 1 addition & 0 deletions vermouth/tests/data/integration_tests/tier-0/dipro-termini/martinize2/command
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Original file line number Diff line number Diff line change
Expand Up @@ -4,3 +4,4 @@ martinize2
-o topol.top
-ff martini3001
-nt
-scfix
2 changes: 2 additions & 0 deletions vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/martinize2/command
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Expand Up @@ -5,3 +5,5 @@ martinize2
-ff martini22
-dssp
-cys auto
-ef 2500
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-scfix
2 changes: 2 additions & 0 deletions vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/martinize2/command
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Original file line number Diff line number Diff line change
Expand Up @@ -6,3 +6,5 @@ martinize2
-ss CCSHHHHHHHHHHCCCCHHHHHHHHHHHTSCHHHHHHHTCCCC
-nter NH2-ter
-cter COOH-ter
-ef 500
-scfix
1 change: 1 addition & 0 deletions vermouth/tests/data/integration_tests/tier-0/mini-protein3_trp-cage/martinize2/command
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Original file line number Diff line number Diff line change
Expand Up @@ -6,3 +6,4 @@ martinize2
-dssp
-eu 0.7
-ef 800.0
-scfix
11 changes: 11 additions & 0 deletions vermouth/tests/data/integration_tests/tier-1/1UBQ/README
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@@ -0,0 +1,11 @@
### DETAILS:

# Ubiquitin 1UBQ

### testing 'new' defaults after -scfix and -ef behaviour changed

### TEST:

# -ff martini 3001
# no -scfix
#
983 changes: 983 additions & 0 deletions vermouth/tests/data/integration_tests/tier-1/1UBQ/aa.pdb
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263 changes: 263 additions & 0 deletions vermouth/tests/data/integration_tests/tier-1/1UBQ/martinize2/cg.pdb
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Original file line number Diff line number Diff line change
@@ -0,0 +1,263 @@
ATOM 1 BB MET A 1 27.168 25.742 3.357 1.00 0.00
ATOM 2 SC1 MET A 1 24.481 24.285 5.673 1.00 0.00
ATOM 3 BB GLN A 2 25.962 28.749 4.446 1.00 0.00
ATOM 4 SC1 GLN A 2 26.776 32.120 2.397 1.00 0.00
ATOM 5 BB ILE A 3 27.033 30.748 7.177 1.00 0.00
ATOM 6 SC1 ILE A 3 26.903 28.414 9.087 1.00 0.00
ATOM 7 BB PHE A 4 26.587 32.877 10.061 1.00 0.00
ATOM 8 SC1 PHE A 4 25.404 34.579 7.877 1.00 0.00
ATOM 9 SC2 PHE A 4 24.102 34.183 5.906 1.00 0.00
ATOM 10 SC3 PHE A 4 25.636 35.236 5.594 1.00 0.00
ATOM 11 BB VAL A 5 28.795 34.925 12.172 1.00 0.00
ATOM 12 SC1 VAL A 5 30.044 32.850 13.157 1.00 0.00
ATOM 13 BB LYS A 6 28.034 36.809 14.994 1.00 0.00
ATOM 14 SC1 LYS A 6 25.484 38.706 14.521 1.00 0.00
ATOM 15 SC2 LYS A 6 23.063 40.721 14.834 1.00 0.00
ATOM 16 BB THR A 7 29.486 39.423 16.577 1.00 0.00
ATOM 17 SC1 THR A 7 31.896 39.157 15.771 1.00 0.00
ATOM 18 BB LEU A 8 29.841 41.902 19.151 1.00 0.00
ATOM 19 SC1 LEU A 8 29.027 40.021 21.711 1.00 0.00
ATOM 20 BB THR A 9 31.098 44.070 16.796 1.00 0.00
ATOM 21 SC1 THR A 9 33.260 43.398 17.341 1.00 0.00
ATOM 22 BB GLY A 10 29.381 43.791 14.001 1.00 0.00
ATOM 23 BB LYS A 11 30.588 41.272 12.826 1.00 0.00
ATOM 24 SC1 LYS A 11 33.571 41.201 11.734 1.00 0.00
ATOM 25 SC2 LYS A 11 35.337 40.430 9.627 1.00 0.00
ATOM 26 BB THR A 12 30.302 39.143 9.931 1.00 0.00
ATOM 27 SC1 THR A 12 27.622 38.894 10.317 1.00 0.00
ATOM 28 BB ILE A 13 30.808 35.743 9.215 1.00 0.00
ATOM 29 SC1 ILE A 13 33.486 35.168 10.482 1.00 0.00
ATOM 30 BB THR A 14 31.524 33.585 6.560 1.00 0.00
ATOM 31 SC1 THR A 14 30.429 34.850 4.854 1.00 0.00
ATOM 32 BB LEU A 15 30.772 30.109 6.105 1.00 0.00
ATOM 33 SC1 LEU A 15 32.488 29.742 9.143 1.00 0.00
ATOM 34 BB GLU A 16 31.830 26.882 5.026 1.00 0.00
ATOM 35 SC1 GLU A 16 31.729 28.107 0.924 1.00 0.00
ATOM 36 BB VAL A 17 29.533 24.119 5.426 1.00 0.00
ATOM 37 SC1 VAL A 17 29.747 25.074 7.920 1.00 0.00
ATOM 38 BB GLU A 18 28.555 21.077 7.047 1.00 0.00
ATOM 39 SC1 GLU A 18 28.860 20.012 3.364 1.00 0.00
ATOM 40 BB PRO A 19 26.326 19.303 8.931 1.00 0.00
ATOM 41 SC1 PRO A 19 24.827 19.858 6.910 1.00 0.00
ATOM 42 BB SER A 20 28.698 17.128 9.627 1.00 0.00
ATOM 43 SC1 SER A 20 28.765 16.177 7.488 1.00 0.00
ATOM 44 BB ASP A 21 29.994 19.105 11.258 1.00 0.00
ATOM 45 SC1 ASP A 21 31.897 20.425 8.722 1.00 0.00
ATOM 46 BB THR A 22 31.696 20.027 13.870 1.00 0.00
ATOM 47 SC1 THR A 22 32.964 17.964 14.694 1.00 0.00
ATOM 48 BB ILE A 23 32.150 22.357 16.298 1.00 0.00
ATOM 49 SC1 ILE A 23 29.691 22.748 17.483 1.00 0.00
ATOM 50 BB GLU A 24 35.221 22.167 16.349 1.00 0.00
ATOM 51 SC1 GLU A 24 37.212 19.122 18.014 1.00 0.00
ATOM 52 BB ASN A 25 35.536 22.822 13.283 1.00 0.00
ATOM 53 SC1 ASN A 25 35.563 21.422 10.874 1.00 0.00
ATOM 54 BB VAL A 26 34.258 25.560 13.239 1.00 0.00
ATOM 55 SC1 VAL A 26 31.632 25.476 13.061 1.00 0.00
ATOM 56 BB LYS A 27 36.267 26.867 15.221 1.00 0.00
ATOM 57 SC1 LYS A 27 34.856 26.242 18.143 1.00 0.00
ATOM 58 SC2 LYS A 27 33.340 26.095 20.889 1.00 0.00
ATOM 59 BB ALA A 28 38.713 26.410 13.302 1.00 0.00
ATOM 60 SC1 ALA A 28 39.285 24.336 13.566 1.00 0.00
ATOM 61 BB LYS A 29 37.669 28.208 10.979 1.00 0.00
ATOM 62 SC1 LYS A 29 35.701 25.986 9.407 1.00 0.00
ATOM 63 SC2 LYS A 29 34.858 24.630 7.053 1.00 0.00
ATOM 64 BB ILE A 30 37.604 30.767 12.684 1.00 0.00
ATOM 65 SC1 ILE A 30 34.773 31.012 14.047 1.00 0.00
ATOM 66 BB GLN A 31 40.554 30.857 13.305 1.00 0.00
ATOM 67 SC1 GLN A 31 42.686 28.923 15.862 1.00 0.00
ATOM 68 BB ASP A 32 41.622 30.874 10.453 1.00 0.00
ATOM 69 SC1 ASP A 32 42.604 28.593 8.949 1.00 0.00
ATOM 70 BB LYS A 33 40.000 33.645 9.631 1.00 0.00
ATOM 71 SC1 LYS A 33 37.395 33.079 8.328 1.00 0.00
ATOM 72 SC2 LYS A 33 36.024 33.483 5.945 1.00 0.00
ATOM 73 BB GLU A 34 40.230 35.519 12.664 1.00 0.00
ATOM 74 SC1 GLU A 34 37.378 37.071 11.301 1.00 0.00
ATOM 75 BB GLY A 35 42.134 34.179 15.169 1.00 0.00
ATOM 76 BB ILE A 36 40.297 32.743 17.186 1.00 0.00
ATOM 77 SC1 ILE A 36 38.067 34.832 17.587 1.00 0.00
ATOM 78 BB PRO A 37 40.452 30.909 19.795 1.00 0.00
ATOM 79 SC1 PRO A 37 42.307 32.248 20.426 1.00 0.00
ATOM 80 BB PRO A 38 38.576 28.222 20.676 1.00 0.00
ATOM 81 SC1 PRO A 38 40.069 27.147 18.801 1.00 0.00
ATOM 82 BB ASP A 39 38.580 28.746 23.873 1.00 0.00
ATOM 83 SC1 ASP A 39 40.554 28.602 25.687 1.00 0.00
ATOM 84 BB GLN A 40 36.961 31.623 23.409 1.00 0.00
ATOM 85 SC1 GLN A 40 40.364 33.805 23.361 1.00 0.00
ATOM 86 BB GLN A 41 34.467 30.166 22.116 1.00 0.00
ATOM 87 SC1 GLN A 41 35.843 30.189 18.265 1.00 0.00
ATOM 88 BB ARG A 42 30.949 30.935 21.949 1.00 0.00
ATOM 89 SC1 ARG A 42 29.843 31.014 24.911 1.00 0.00
ATOM 90 SC2 ARG A 42 27.111 32.424 26.552 1.00 0.00
ATOM 91 BB LEU A 43 28.193 29.117 20.658 1.00 0.00
ATOM 92 SC1 LEU A 43 30.128 28.857 17.747 1.00 0.00
ATOM 93 BB ILE A 44 24.942 30.412 19.404 1.00 0.00
ATOM 94 SC1 ILE A 44 24.811 31.210 22.222 1.00 0.00
ATOM 95 BB PHE A 45 21.716 28.605 19.082 1.00 0.00
ATOM 96 SC1 PHE A 45 21.723 27.916 16.308 1.00 0.00
ATOM 97 SC2 PHE A 45 20.484 28.426 14.315 1.00 0.00
ATOM 98 SC3 PHE A 45 19.953 26.813 15.122 1.00 0.00
ATOM 99 BB ALA A 46 18.627 28.819 19.893 1.00 0.00
ATOM 100 SC1 ALA A 46 17.864 27.977 18.346 1.00 0.00
ATOM 101 BB GLY A 47 19.668 29.225 23.002 1.00 0.00
ATOM 102 BB LYS A 48 22.231 27.401 22.566 1.00 0.00
ATOM 103 SC1 LYS A 48 20.213 24.827 22.126 1.00 0.00
ATOM 104 SC2 LYS A 48 18.064 24.455 20.590 1.00 0.00
ATOM 105 BB GLN A 49 25.049 25.843 23.458 1.00 0.00
ATOM 106 SC1 GLN A 49 27.856 27.471 25.815 1.00 0.00
ATOM 107 BB LEU A 50 27.608 24.637 21.687 1.00 0.00
ATOM 108 SC1 LEU A 50 25.939 25.527 18.770 1.00 0.00
ATOM 109 BB GLU A 51 29.078 21.449 21.268 1.00 0.00
ATOM 110 SC1 GLU A 51 28.624 19.354 24.704 1.00 0.00
ATOM 111 BB ASP A 52 32.050 20.088 20.010 1.00 0.00
ATOM 112 SC1 ASP A 52 34.187 22.155 21.368 1.00 0.00
ATOM 113 BB GLY A 53 30.918 16.866 19.371 1.00 0.00
ATOM 114 BB ARG A 54 28.848 18.003 17.705 1.00 0.00
ATOM 115 SC1 ARG A 54 26.519 17.453 19.841 1.00 0.00
ATOM 116 SC2 ARG A 54 27.646 14.411 20.672 1.00 0.00
ATOM 117 BB THR A 55 26.733 18.658 15.109 1.00 0.00
ATOM 118 SC1 THR A 55 27.031 16.520 13.692 1.00 0.00
ATOM 119 BB LEU A 56 24.860 20.641 13.180 1.00 0.00
ATOM 120 SC1 LEU A 56 27.152 22.891 11.817 1.00 0.00
ATOM 121 BB SER A 57 22.530 18.578 12.777 1.00 0.00
ATOM 122 SC1 SER A 57 23.548 16.794 11.497 1.00 0.00
ATOM 123 BB ASP A 58 21.786 18.228 15.811 1.00 0.00
ATOM 124 SC1 ASP A 58 24.174 16.003 16.613 1.00 0.00
ATOM 125 BB TYR A 59 20.601 21.380 15.641 1.00 0.00
ATOM 126 SC1 TYR A 59 22.515 22.102 17.183 1.00 0.00
ATOM 127 SC2 TYR A 59 24.662 21.414 18.210 1.00 0.00
ATOM 128 SC3 TYR A 59 22.820 22.032 19.629 1.00 0.00
ATOM 129 SC4 TYR A 59 24.935 21.374 20.693 1.00 0.00
ATOM 130 BB ASN A 60 19.243 22.209 12.952 1.00 0.00
ATOM 131 SC1 ASN A 60 16.554 21.255 12.303 1.00 0.00
ATOM 132 BB ILE A 61 21.241 23.577 10.907 1.00 0.00
ATOM 133 SC1 ILE A 61 23.203 24.990 12.869 1.00 0.00
ATOM 134 BB GLN A 62 20.668 25.662 8.252 1.00 0.00
ATOM 135 SC1 GLN A 62 16.876 23.760 7.212 1.00 0.00
ATOM 136 BB LYS A 63 20.846 27.381 5.691 1.00 0.00
ATOM 137 SC1 LYS A 63 20.703 26.551 2.854 1.00 0.00
ATOM 138 SC2 LYS A 63 18.492 26.227 0.990 1.00 0.00
ATOM 139 BB GLU A 64 21.610 30.746 6.606 1.00 0.00
ATOM 140 SC1 GLU A 64 21.159 30.803 2.737 1.00 0.00
ATOM 141 BB SER A 65 22.366 30.729 9.345 1.00 0.00
ATOM 142 SC1 SER A 65 21.012 28.422 10.185 1.00 0.00
ATOM 143 BB THR A 66 22.828 32.169 12.668 1.00 0.00
ATOM 144 SC1 THR A 66 22.926 34.695 11.648 1.00 0.00
ATOM 145 BB LEU A 67 25.477 32.626 14.755 1.00 0.00
ATOM 146 SC1 LEU A 67 26.234 29.331 14.277 1.00 0.00
ATOM 147 BB HIS A 68 26.716 33.258 18.001 1.00 0.00
ATOM 148 SC1 HIS A 68 24.596 34.843 18.453 1.00 0.00
ATOM 149 SC2 HIS A 68 22.405 35.021 17.454 1.00 0.00
ATOM 150 SC3 HIS A 68 23.309 36.522 17.513 1.00 0.00
ATOM 151 BB LEU A 69 29.616 35.063 19.208 1.00 0.00
ATOM 152 SC1 LEU A 69 32.296 33.940 18.057 1.00 0.00
ATOM 153 BB VAL A 70 31.210 34.555 22.223 1.00 0.00
ATOM 154 SC1 VAL A 70 29.114 35.531 23.778 1.00 0.00
ATOM 155 BB LEU A 71 33.678 35.753 24.378 1.00 0.00
ATOM 156 SC1 LEU A 71 35.644 36.178 21.620 1.00 0.00
ATOM 157 BB ARG A 72 36.072 33.977 26.534 1.00 0.00
ATOM 158 SC1 ARG A 72 35.360 31.797 27.830 1.00 0.00
ATOM 159 SC2 ARG A 72 34.377 29.113 26.651 1.00 0.00
ATOM 160 BB LEU A 73 38.267 35.183 28.623 1.00 0.00
ATOM 161 SC1 LEU A 73 39.151 37.446 26.048 1.00 0.00
ATOM 162 BB ARG A 74 41.535 34.542 30.191 1.00 0.00
ATOM 163 SC1 ARG A 74 41.718 31.351 30.456 1.00 0.00
ATOM 164 SC2 ARG A 74 44.179 29.920 29.559 1.00 0.00
ATOM 165 BB GLY A 75 41.317 37.180 32.109 1.00 0.00
ATOM 166 BB GLY A 76 40.212 39.684 35.087 1.00 0.00
TER 167 GLY A 76
CONECT 1 2 3
CONECT 3 4 5
CONECT 5 6 7
CONECT 7 8 11
CONECT 8 9 10
CONECT 9 10
CONECT 11 12 13
CONECT 13 14 16
CONECT 14 15
CONECT 16 17 18
CONECT 18 19 20
CONECT 20 21 22
CONECT 22 23
CONECT 23 24 26
CONECT 24 25
CONECT 26 27 28
CONECT 28 29 30
CONECT 30 31 32
CONECT 32 33 34
CONECT 34 35 36
CONECT 36 37 38
CONECT 38 39 40
CONECT 40 41 42
CONECT 42 43 44
CONECT 44 45 46
CONECT 46 47 48
CONECT 48 49 50
CONECT 50 51 52
CONECT 52 53 54
CONECT 54 55 56
CONECT 56 57 59
CONECT 57 58
CONECT 59 60 61
CONECT 61 62 64
CONECT 62 63
CONECT 64 65 66
CONECT 66 67 68
CONECT 68 69 70
CONECT 70 71 73
CONECT 71 72
CONECT 73 74 75
CONECT 75 76
CONECT 76 77 78
CONECT 78 79 80
CONECT 80 81 82
CONECT 82 83 84
CONECT 84 85 86
CONECT 86 87 88
CONECT 88 89 91
CONECT 89 90
CONECT 91 92 93
CONECT 93 94 95
CONECT 95 96 99
CONECT 96 97 98
CONECT 97 98
CONECT 99 100 101
CONECT 101 102
CONECT 102 103 105
CONECT 103 104
CONECT 105 106 107
CONECT 107 108 109
CONECT 109 110 111
CONECT 111 112 113
CONECT 113 114
CONECT 114 115 117
CONECT 115 116
CONECT 117 118 119
CONECT 119 120 121
CONECT 121 122 123
CONECT 123 124 125
CONECT 125 126 130
CONECT 126 127 128
CONECT 127 128 129
CONECT 128 129
CONECT 130 131 132
CONECT 132 133 134
CONECT 134 135 136
CONECT 136 137 139
CONECT 137 138
CONECT 139 140 141
CONECT 141 142 143
CONECT 143 144 145
CONECT 145 146 147
CONECT 147 148 151
CONECT 148 149 150
CONECT 149 150
CONECT 151 152 153
CONECT 153 154 155
CONECT 155 156 157
CONECT 157 158 160
CONECT 158 159
CONECT 160 161 162
CONECT 162 163 165
CONECT 163 164
CONECT 165 166
END
2 changes: 2 additions & 0 deletions vermouth/tests/data/integration_tests/tier-1/1UBQ/martinize2/citation
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McGibbon, R T; Beauchamp, K A; Harrigan, M P; Klein, C; Swails, J M; Hernández, C X; Schwantes, C R; Wang, L; Lane, T J; Pande, V S; Biophysical Journal 2015; 10.1016/j.bpj.2015.08.015
Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3
8 changes: 8 additions & 0 deletions vermouth/tests/data/integration_tests/tier-1/1UBQ/martinize2/command
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martinize2
-f ../aa.pdb
-ff martini3001
-x cg.pdb
-o topol.top
-ignore HOH
-dssp
-elastic
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