Skip to content

Commit

Permalink
Adding example for paired_batch mode
Browse files Browse the repository at this point in the history
  • Loading branch information
@envidian
envidian committed Jan 12, 2024
1 parent 3bbf2e0 commit 5def756
Show file tree
Hide file tree
Showing 12 changed files with 8,389 additions and 0 deletions.
76 changes: 76 additions & 0 deletions unidock/example/paired_batch/actives1.pdbqt
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,76 @@
REMARK Name = CHEMBL417870
REMARK 12 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: C_1 and C_5
REMARK 2 A between atoms: N_3 and C_19
REMARK 3 A between atoms: C_5 and N_6
REMARK 4 A between atoms: C_5 and C_14
REMARK 5 A between atoms: N_9 and O_12
REMARK 6 A between atoms: C_14 and C_15
REMARK 7 A between atoms: C_15 and C_16
REMARK 8 A between atoms: C_16 and C_18
REMARK 9 A between atoms: C_19 and C_20
REMARK 10 A between atoms: C_19 and C_30
REMARK 11 A between atoms: CA_26 and C_27
REMARK 12 A between atoms: C_27 and O_28
REMARK x y z vdW Elec q Type
REMARK _______ _______ _______ _____ _____ ______ ____
ROOT
ATOM 1 C UNK A 1 -4.250 -4.409 0.280 0.00 0.00 +0.560 C
ATOM 2 O UNK A 1 -4.774 -4.759 -0.756 0.00 0.00 -0.457 OA
ATOM 3 N UNK A 1 -4.883 -4.601 1.454 0.00 0.00 -0.676 N
ATOM 4 H UNK A 1 -4.464 -4.321 2.283 0.00 0.00 +0.343 HD
ENDROOT
BRANCH 1 5
ATOM 5 C UNK A 1 -2.890 -3.760 0.255 0.00 0.00 +0.135 C
BRANCH 5 6
ATOM 6 N UNK A 1 -2.217 -4.083 -1.006 0.00 0.00 -0.731 N
ATOM 7 C UNK 1 -2.773 -3.720 -2.179 0.00 0.00 +0.831 C
ATOM 8 O UNK 1 -3.833 -3.124 -2.190 0.00 0.00 -0.472 OA
ATOM 9 N UNK 1 -2.155 -4.018 -3.338 0.00 0.00 -0.494 N
ATOM 10 H UNK A 1 -1.372 -4.559 -0.996 0.00 0.00 +0.338 HD
ATOM 11 H UNK 1 -1.309 -4.493 -3.329 0.00 0.00 +0.302 HD
BRANCH 9 12
ATOM 12 O UNK 1 -2.739 -3.636 -4.571 0.00 0.00 -0.427 OA
ATOM 13 H UNK 1 -2.222 -3.893 -5.347 0.00 0.00 +0.334 HD
ENDBRANCH 9 12
ENDBRANCH 5 6
BRANCH 5 14
ATOM 14 C UNK A 1 -3.047 -2.243 0.374 0.00 0.00 +0.039 C
BRANCH 14 15
ATOM 15 C UNK A 1 -1.666 -1.593 0.475 0.00 0.00 +0.029 C
BRANCH 15 16
ATOM 16 C UNK A 1 -1.823 -0.076 0.594 0.00 0.00 +0.024 C
BRANCH 16 18
ATOM 17 C UNK A 1 -0.599 2.091 0.814 0.00 0.00 +0.034 C
ATOM 18 C UNK A 1 -0.441 0.574 0.694 0.00 0.00 +0.017 C
ENDBRANCH 16 18
ENDBRANCH 15 16
ENDBRANCH 14 15
ENDBRANCH 5 14
ENDBRANCH 1 5
BRANCH 3 19
ATOM 19 C UNK A 1 -6.205 -5.233 1.478 0.00 0.00 +0.173 C
BRANCH 19 20
ATOM 20 C UNK A 1 -6.428 -5.880 2.821 0.00 0.00 +0.488 C
ATOM 21 O UNK A 1 -5.838 -5.469 3.797 0.00 0.00 -0.487 OA
ATOM 22 N PRO A 2 -7.283 -6.916 2.936 0.00 0.00 -0.461 N
ATOM 23 CD PRO A 2 -7.986 -7.577 1.822 0.00 0.00 +0.179 C
ATOM 24 CG PRO A 2 -9.240 -8.217 2.468 0.00 0.00 +0.017 C
ATOM 25 CB PRO A 2 -8.681 -8.682 3.839 0.00 0.00 +0.033 C
ATOM 26 CA PRO A 2 -7.663 -7.577 4.192 0.00 0.00 +0.169 C
BRANCH 26 27
ATOM 27 C PRO A 2 -6.428 -8.195 4.850 0.00 0.00 +0.221 C
BRANCH 27 28
ATOM 28 O PRO A 2 -5.917 -9.239 4.019 0.00 0.00 -0.549 OA
ATOM 29 H PRO A 2 -5.131 -9.676 4.375 0.00 0.00 +0.327 HD
ENDBRANCH 27 28
ENDBRANCH 26 27
ENDBRANCH 19 20
BRANCH 19 30
ATOM 30 C UNK A 1 -7.281 -4.172 1.238 0.00 0.00 -0.013 C
ATOM 31 C UNK A 1 -7.111 -3.035 2.248 0.00 0.00 +0.060 C
ATOM 32 C UNK A 1 -7.144 -3.618 -0.181 0.00 0.00 +0.113 C
ENDBRANCH 19 30
ENDBRANCH 3 19
TORSDOF 12
66 changes: 66 additions & 0 deletions unidock/example/paired_batch/actives3.pdbqt
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,66 @@
REMARK Name = CHEMBL91903
REMARK 10 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: C_1 and C_5
REMARK 2 A between atoms: N_3 and C_16
REMARK 3 A between atoms: C_5 and C_6
REMARK 4 A between atoms: C_5 and C_10
REMARK 5 A between atoms: C_6 and C_7
REMARK 6 A between atoms: C_7 and C_9
REMARK 7 A between atoms: C_10 and N_11
REMARK 8 A between atoms: N_11 and O_14
REMARK 9 A between atoms: C_16 and C_17
REMARK 10 A between atoms: C_16 and C_25
REMARK x y z vdW Elec q Type
REMARK _______ _______ _______ _____ _____ ______ ____
ROOT
ATOM 1 C UNL A 1 0.937 -3.560 -3.204 0.00 0.00 +0.568 C
ATOM 2 O UNL A 1 0.352 -3.902 -2.198 0.00 0.00 -0.493 OA
ATOM 3 N UNL A 1 1.645 -4.463 -3.911 0.00 0.00 -0.677 N
ATOM 4 H UNL A 1 2.113 -4.190 -4.715 0.00 0.00 +0.347 HD
ENDROOT
BRANCH 1 5
ATOM 5 C UNL A 1 0.873 -2.126 -3.663 0.00 0.00 -0.095 C
BRANCH 5 6
ATOM 6 C UNL A 1 0.013 -1.317 -2.690 0.00 0.00 +0.099 C
BRANCH 6 7
ATOM 7 C UNL A 1 0.698 -1.266 -1.323 0.00 0.00 +0.048 C
BRANCH 7 9
ATOM 8 C UNL A 1 0.579 -0.317 0.985 0.00 0.00 +0.059 C
ATOM 9 C UNL A 1 -0.107 -0.368 -0.382 0.00 0.00 +0.038 C
ENDBRANCH 7 9
ENDBRANCH 6 7
ENDBRANCH 5 6
BRANCH 5 10
ATOM 10 C UNL A 1 0.257 -2.066 -5.061 0.00 0.00 +0.177 C
BRANCH 10 11
ATOM 11 N UNL A 1 0.240 -0.677 -5.528 0.00 0.00 -0.244 N
ATOM 12 C UNL A 1 1.375 -0.101 -5.969 0.00 0.00 +0.476 C
ATOM 13 O UNL A 1 1.362 1.049 -6.355 0.00 0.00 -0.462 OA
BRANCH 11 14
ATOM 14 O UNL A 1 -0.969 0.060 -5.515 0.00 0.00 -0.457 OA
ATOM 15 H UNL A 1 -0.881 0.966 -5.841 0.00 0.00 +0.363 HD
ENDBRANCH 11 14
ENDBRANCH 10 11
ENDBRANCH 5 10
ENDBRANCH 1 5
BRANCH 3 16
ATOM 16 C UNL A 1 1.707 -5.857 -3.465 0.00 0.00 +0.171 C
BRANCH 16 17
ATOM 17 C UNL A 1 2.965 -6.498 -3.992 0.00 0.00 +0.484 C
ATOM 18 O UNL A 1 3.371 -6.216 -5.099 0.00 0.00 -0.479 OA
ATOM 19 N UNL A 1 3.639 -7.385 -3.233 0.00 0.00 -0.464 N
ATOM 20 C UNL A 1 3.110 -7.824 -1.931 0.00 0.00 +0.157 C
ATOM 21 C UNL A 1 3.133 -9.356 -1.893 0.00 0.00 +0.221 C
ATOM 22 O UNL A 1 4.442 -9.816 -2.234 0.00 0.00 -0.457 OA
ATOM 23 C UNL A 1 4.859 -9.469 -3.557 0.00 0.00 +0.224 C
ATOM 24 C UNL A 1 4.922 -7.947 -3.683 0.00 0.00 +0.207 C
ENDBRANCH 16 17
BRANCH 16 25
ATOM 25 C UNL A 1 0.488 -6.617 -3.993 0.00 0.00 -0.026 C
ATOM 26 C UNL A 1 0.467 -6.547 -5.521 0.00 0.00 +0.078 C
ATOM 27 C UNL A 1 0.567 -8.079 -3.550 0.00 0.00 +0.037 C
ATOM 28 C UNL A 1 -0.788 -5.984 -3.436 0.00 0.00 +0.099 C
ENDBRANCH 16 25
ENDBRANCH 3 16
TORSDOF 10
70 changes: 70 additions & 0 deletions unidock/example/paired_batch/actives4.pdbqt
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,70 @@
REMARK Name = CHEMBL364979
REMARK 8 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: C_12 and C_31
REMARK 2 A between atoms: C_16 and C_25
REMARK 3 A between atoms: C_25 and N_26
REMARK 4 A between atoms: N_26 and O_29
REMARK 5 A between atoms: C_31 and C_32
REMARK 6 A between atoms: C_32 and C_33
REMARK 7 A between atoms: C_33 and C_34
REMARK 8 A between atoms: C_34 and N_35
REMARK x y z vdW Elec q Type
REMARK _______ _______ _______ _____ _____ ______ ____
ROOT
ATOM 1 C UNL A 1 0.414 0.964 -0.129 0.00 0.00 +0.014 C
ATOM 2 C UNL A 1 1.860 1.464 -0.117 0.00 0.00 +0.014 C
ATOM 3 C UNL A 1 1.922 2.827 0.577 0.00 0.00 +0.014 C
ATOM 4 C UNL A 1 3.333 3.058 1.122 0.00 0.00 +0.016 C
ATOM 5 C UNL A 1 3.279 4.077 2.261 0.00 0.00 +0.013 C
ATOM 6 C UNL A 1 3.984 3.505 3.492 0.00 0.00 +0.017 C
ATOM 7 C UNL A 1 3.035 3.552 4.691 0.00 0.00 +0.019 C
ATOM 8 C UNL A 1 3.816 3.249 5.972 0.00 0.00 +0.227 C
ATOM 9 N UNL A 1 2.868 2.751 6.996 0.00 0.00 -0.686 N
ATOM 10 C UNL A 1 2.668 1.399 6.991 0.00 0.00 +0.550 C
ATOM 11 O UNL A 1 3.243 0.692 6.191 0.00 0.00 -0.479 OA
ATOM 12 C UNL A 1 1.718 0.804 7.998 0.00 0.00 +0.141 C
ATOM 13 N UNL A 1 1.463 -0.606 7.637 0.00 0.00 -0.659 N
ATOM 14 C UNL A 1 0.527 -0.824 6.672 0.00 0.00 +0.567 C
ATOM 15 O UNL A 1 -0.052 0.107 6.155 0.00 0.00 -0.491 OA
ATOM 16 C UNL A 1 0.221 -2.240 6.256 0.00 0.00 -0.092 C
ATOM 17 C UNL A 1 -1.029 -2.253 5.373 0.00 0.00 +0.089 C
ATOM 18 C UNL A 1 -0.679 -2.837 4.003 0.00 0.00 +0.032 C
ATOM 19 C UNL A 1 -1.417 -2.056 2.913 0.00 0.00 +0.026 C
ATOM 20 C UNL A 1 -0.676 -2.214 1.583 0.00 0.00 +0.019 C
ATOM 21 C UNL A 1 -0.915 -0.975 0.717 0.00 0.00 +0.016 C
ATOM 22 C UNL A 1 0.399 -0.555 0.055 0.00 0.00 +0.015 C
ATOM 23 H UNL A 1 2.423 3.341 7.625 0.00 0.00 +0.325 HD
ATOM 24 H UNL A 1 1.936 -1.337 8.065 0.00 0.00 +0.326 HD
ENDROOT
BRANCH 16 25
ATOM 25 C UNL A 1 -0.025 -3.096 7.500 0.00 0.00 +0.159 C
BRANCH 25 26
ATOM 26 N UNL A 1 -0.197 -4.495 7.104 0.00 0.00 -0.249 N
ATOM 27 C UNL A 1 0.874 -5.233 6.750 0.00 0.00 +0.456 C
ATOM 28 O UNL A 1 0.745 -6.415 6.510 0.00 0.00 -0.474 OA
BRANCH 26 29
ATOM 29 O UNL A 1 -1.490 -5.074 7.092 0.00 0.00 -0.467 OA
ATOM 30 H UNL A 1 -1.503 -6.001 6.817 0.00 0.00 +0.353 HD
ENDBRANCH 26 29
ENDBRANCH 25 26
ENDBRANCH 16 25
BRANCH 12 31
ATOM 31 C UNL A 1 2.341 0.874 9.394 0.00 0.00 -0.008 C
BRANCH 31 32
ATOM 32 C UNL A 1 1.326 0.387 10.430 0.00 0.00 +0.018 C
BRANCH 32 33
ATOM 33 C UNL A 1 1.902 0.573 11.835 0.00 0.00 -0.032 C
BRANCH 33 34
ATOM 34 C UNL A 1 0.888 0.086 12.871 0.00 0.00 +0.218 C
BRANCH 34 35
ATOM 35 N UNL A 1 1.441 0.265 14.220 0.00 0.00 -1.044 N
ATOM 36 H UNL A 1 0.772 -0.057 14.904 0.00 0.00 +0.345 HD
ATOM 37 H UNL A 1 2.294 -0.268 14.308 0.00 0.00 +0.346 HD
ATOM 38 H UNL A 1 1.638 1.242 14.376 0.00 0.00 +0.346 HD
ENDBRANCH 34 35
ENDBRANCH 33 34
ENDBRANCH 32 33
ENDBRANCH 31 32
ENDBRANCH 12 31
TORSDOF 8
71 changes: 71 additions & 0 deletions unidock/example/paired_batch/actives5.pdbqt
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,71 @@
REMARK Name = CHEMBL330263
REMARK 12 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: C_1 and C_5
REMARK 2 A between atoms: N_3 and C_16
REMARK 3 A between atoms: C_5 and C_6
REMARK 4 A between atoms: C_5 and C_10
REMARK 5 A between atoms: C_6 and C_7
REMARK 6 A between atoms: C_7 and C_9
REMARK 7 A between atoms: C_10 and N_11
REMARK 8 A between atoms: N_11 and O_14
REMARK 9 A between atoms: C_16 and C_17
REMARK 10 A between atoms: C_16 and C_22
REMARK 11 A between atoms: C_22 and C_23
REMARK 12 A between atoms: C_23 and S_26
REMARK x y z vdW Elec q Type
REMARK _______ _______ _______ _____ _____ ______ ____
ROOT
ATOM 1 C UNL A 1 1.710 -4.065 -2.416 0.00 0.00 +0.603 C
ATOM 2 O UNL A 1 1.011 -4.567 -1.562 0.00 0.00 -0.477 OA
ATOM 3 N UNL A 1 2.311 -4.842 -3.339 0.00 0.00 -0.581 N
ATOM 4 H UNL A 1 2.871 -4.441 -4.022 0.00 0.00 +0.397 HD
ENDROOT
BRANCH 1 5
ATOM 5 C UNL A 1 1.909 -2.571 -2.446 0.00 0.00 -0.089 C
BRANCH 5 6
ATOM 6 C UNL A 1 1.124 -1.930 -1.299 0.00 0.00 +0.106 C
BRANCH 6 7
ATOM 7 C UNL A 1 1.733 -2.357 0.037 0.00 0.00 +0.061 C
BRANCH 7 9
ATOM 8 C UNL A 1 1.643 -2.042 2.514 0.00 0.00 +0.073 C
ATOM 9 C UNL A 1 1.034 -1.615 1.178 0.00 0.00 +0.044 C
ENDBRANCH 7 9
ENDBRANCH 6 7
ENDBRANCH 5 6
BRANCH 5 10
ATOM 10 C UNL A 1 1.407 -2.016 -3.780 0.00 0.00 +0.276 C
BRANCH 10 11
ATOM 11 N UNL A 1 1.665 -0.575 -3.838 0.00 0.00 -0.248 N
ATOM 12 C UNL A 1 2.917 -0.123 -4.047 0.00 0.00 +0.503 C
ATOM 13 O UNL A 1 3.131 1.070 -4.095 0.00 0.00 -0.457 OA
BRANCH 11 14
ATOM 14 O UNL A 1 0.599 0.342 -3.674 0.00 0.00 -0.449 OA
ATOM 15 H UNL A 1 0.866 1.270 -3.728 0.00 0.00 +0.368 HD
ENDBRANCH 11 14
ENDBRANCH 10 11
ENDBRANCH 5 10
ENDBRANCH 1 5
BRANCH 3 16
ATOM 16 C UNL A 1 2.119 -6.294 -3.310 0.00 0.00 +0.189 C
BRANCH 16 17
ATOM 17 C UNL A 1 3.107 -6.913 -2.355 0.00 0.00 +0.513 C
ATOM 18 O UNL A 1 3.894 -6.211 -1.758 0.00 0.00 -0.457 OA
ATOM 19 N UNL A 1 3.115 -8.248 -2.166 0.00 0.00 -0.483 N
ATOM 20 C UNL A 1 4.076 -8.850 -1.238 0.00 0.00 +0.254 C
ATOM 21 C UNL A 1 2.164 -9.096 -2.888 0.00 0.00 +0.188 C
ENDBRANCH 16 17
BRANCH 16 22
ATOM 22 C UNL A 1 2.338 -6.866 -4.713 0.00 0.00 +0.018 C
BRANCH 22 23
ATOM 23 C UNL A 1 1.232 -6.367 -5.645 0.00 0.00 +0.369 C
ATOM 24 C UNL A 1 1.380 -7.035 -7.014 0.00 0.00 +0.070 C
ATOM 25 C UNL A 1 -0.133 -6.720 -5.051 0.00 0.00 +0.062 C
BRANCH 23 26
ATOM 26 S UNL A 1 1.364 -4.568 -5.832 0.00 0.00 -1.315 S
ATOM 27 C UNL A 1 0.001 -4.142 -6.951 0.00 0.00 +0.463 C
ENDBRANCH 23 26
ENDBRANCH 22 23
ENDBRANCH 16 22
ENDBRANCH 3 16
TORSDOF 12
Loading

0 comments on commit 5def756

Please sign in to comment.