[Dock-fans] 6.2 bugfix 2
Scott Brozell
sbrozell at scripps.edu
Tue May 6 00:01:56 PDT 2008
http://dock.compbio.ucsf.edu/DOCK_6/bugfixes.htm
********>Bugfix 2:
Author: Scott Brozell and Terry Lang
Date: May 5, 2008
Program: dock
Description: Flexible ligand pruning without clustering
(flexible_ligand=yes and pruning_use_clustering=no) ignored input parameter
pruning_conformer_score_cutoff increasing the number of conformations.
In addition, the use of an unitialized variable with clustering
was corrected.
Fix: make the following changes to the files src/dock/conf_gen.cpp
install/test/anchor_and_grow/flex5.dockout.save
and
install/test/anchor_and_grow/flex5_scored.mol2.save
-------------------------------------------------------------------------
*** src/dock/conf_gen.cpp 27 Feb 2008 20:31:40 -0000 1.31
--- src/dock/conf_gen.cpp 6 May 2008 02:12:21 -0000
***************
*** 77,82 ****
--- 77,83 ----
}
anchor_score_cutoff = atof(parm.query_param("pruning_orient_score_cutoff", "25.0").c_str());
num_growth_poses = atoi(parm.query_param("pruning_max_conformers", "75").c_str());
+ growth_cutoff = true;
growth_score_cutoff = atof(parm.query_param("pruning_conformer_score_cutoff", "25.0").c_str());
}
***************
*** 703,709 ****
// initialize
bool valid_orient = false;
int num_layers = layers.size();
- float RMSD_CUTOFF = (float) nc;
// /////////////////////////// ANCHORS //////////////////////////////
// add anchors to seed list
--- 704,709 ----
***************
*** 741,746 ****
--- 741,747 ----
// remove confs that fail the rank/rmsd test
if(cluster){
+ float RMSD_CUTOFF = nc;
for (j = 0; j < exp_seeds.size(); j++) {
if (!exp_seeds[j].used) {
for (k = j + 1; k < exp_seeds.size(); k++) {
***************
*** 846,851 ****
--- 847,853 ----
// remove confs that fail the rank/rmsd test
if(cluster){
+ float RMSD_CUTOFF = nc;
for (j = 0; j < exp_seeds.size(); j++) {
if (!exp_seeds[j].used) {
for (k = j + 1; k < exp_seeds.size(); k++) {
===================================================================
*** install/test/anchor_and_grow/flex5.dockout.save 4 Mar 2008 03:34:07 -0000 1.7
--- install/test/anchor_and_grow/flex5.dockout.save 6 May 2008 02:43:20 -0000
***************
*** 76,82 ****
Anchors: 1
Orientations: 50
! Conformations: 60
--- 76,82 ----
Anchors: 1
Orientations: 50
! Conformations: 30
===================================================================
*** install/test/anchor_and_grow/flex5_scored.mol2.save 5 Dec 2006 21:51:54 -0000 1.1
--- install/test/anchor_and_grow/flex5_scored.mol2.save 6 May 2008 02:47:59 -0000
***************
*** 9,67 ****
@<TRIPOS>ATOM
! 1 C1 20.6278 15.0111 58.8770 C.3 1 C1 -0.0688
! 2 C10 20.8700 13.4801 58.7974 C.3 1 C1 -0.0061
! 3 C19 19.5150 12.6836 58.9186 C.3 1 C1 -0.0852
! 4 H27 19.5548 12.0452 59.7627 H 1 C1 0.0425
! 5 H26 19.3666 12.1044 58.0449 H 1 C1 0.0431
! 6 H25 18.7132 13.3664 59.0298 H 1 C1 0.0371
! 7 C9 21.9048 13.0869 59.9163 C.3 1 C1 -0.0507
! 8 C11 21.3622 13.4134 61.3318 C.3 1 C1 -0.0759
! 9 C12 22.3776 13.0457 62.4495 C.3 1 C1 -0.0674
! 10 C13 22.7753 11.5554 62.3740 C.3 1 C1 -0.0294
! 11 C18 21.5755 10.5936 62.6892 C.3 1 C1 -0.0933
! 12 H24 21.8141 9.9965 63.5305 H 1 C1 0.0514
! 13 H23 21.3938 9.9691 61.8530 H 1 C1 0.0407
! 14 H22 20.7091 11.1664 62.8971 H 1 C1 0.0348
! 15 C17 24.0221 11.1378 63.2219 C.3 1 C1 -0.1667
! 16 C20 23.7392 10.8984 64.7147 C.2 1 C1 0.5766
! 17 C21 22.4135 10.3644 65.1330 C.3 1 C1 -0.2023
! 18 H30 21.9427 11.0561 65.7817 H 1 C1 0.0708
! 19 H29 22.5470 9.4429 65.6370 H 1 C1 0.0687
! 20 H28 21.8075 10.2140 64.2771 H 1 C1 0.0522
! 21 O2 24.5870 11.1508 65.5440 O.2 1 C1 -0.5371
! 22 H21 24.7007 11.9488 63.2756 H 1 C1 0.0636
! 23 C16 24.6412 9.9145 62.4585 C.3 1 C1 -0.0771
! 24 H20 25.6963 9.9959 62.4070 H 1 C1 0.0442
! 25 H19 24.3797 9.0032 62.9302 H 1 C1 0.0728
! 26 C15 24.0420 9.9432 61.0057 C.3 1 C1 -0.0764
! 27 H18 24.7843 9.8649 60.2544 H 1 C1 0.0469
! 28 H17 23.3040 9.1989 60.8519 H 1 C1 0.0487
! 29 C14 23.3846 11.3440 60.9387 C.3 1 C1 -0.0579
! 30 H16 24.2020 12.0088 60.8349 H 1 C1 0.0514
! 31 C8 22.3734 11.5986 59.8160 C.3 1 C1 -0.0473
! 32 H10 21.5409 10.9494 59.8975 H 1 C1 0.0616
! 33 C7 23.0555 11.3951 58.4384 C.3 1 C1 -0.0791
! 34 H9 23.9116 12.0171 58.4122 H 1 C1 0.0444
! 35 H8 23.3542 10.3814 58.3777 H 1 C1 0.0440
! 36 C6 22.1391 11.7325 57.2469 C.3 1 C1 -0.0520
! 37 H7 22.7261 11.7110 56.3661 H 1 C1 0.0559
! 38 H6 21.3895 10.9867 57.1890 H 1 C1 0.0564
! 39 C5 21.4842 13.1018 57.3880 C.2 1 C1 -0.0433
! 40 C4 21.4849 13.9144 56.3470 C.2 1 C1 -0.2513
! 41 H5 22.0111 13.6072 55.4589 H 1 C1 0.1514
! 42 C3 20.7977 15.1964 56.3784 C.2 1 C1 0.5626
! 43 O1 20.8183 15.9463 55.3867 O.2 1 C1 -0.5423
! 44 C2 19.9714 15.5909 57.5987 C.3 1 C1 -0.1812
! 45 H4 19.9300 16.6466 57.6710 H 1 C1 0.0778
! 46 H3 18.9902 15.2054 57.4998 H 1 C1 0.0723
! 47 H15 21.9423 13.2316 63.3962 H 1 C1 0.0407
! 48 H14 23.2505 13.6347 62.3405 H 1 C1 0.0413
! 49 H13 20.4722 12.8661 61.5034 H 1 C1 0.0476
! 50 H12 21.1584 14.4507 61.4008 H 1 C1 0.0408
! 51 H11 22.7420 13.7275 59.8205 H 1 C1 0.0482
! 52 H2 21.5525 15.5081 59.0155 H 1 C1 0.0551
! 53 H1 19.9868 15.2251 59.6921 H 1 C1 0.0453
@<TRIPOS>BOND
1 1 2 1
2 1 44 1
--- 9,67 ----
@<TRIPOS>ATOM
! 1 C1 23.7517 13.3012 63.6203 C.3 1 C1 -0.0688
! 2 C10 24.7381 14.0228 62.6638 C.3 1 C1 -0.0061
! 3 C19 24.1254 14.1664 61.2184 C.3 1 C1 -0.0852
! 4 H27 24.7461 13.6672 60.5204 H 1 C1 0.0425
! 5 H26 24.0604 15.1916 60.9626 H 1 C1 0.0431
! 6 H25 23.1578 13.7363 61.2011 H 1 C1 0.0371
! 7 C9 26.0973 13.2291 62.6683 C.3 1 C1 -0.0507
! 8 C11 25.9089 11.7774 62.1566 C.3 1 C1 -0.0759
! 9 C12 27.2386 10.9730 62.1685 C.3 1 C1 -0.0674
! 10 C13 28.3278 11.6828 61.3351 C.3 1 C1 -0.0294
! 11 C18 27.9835 11.7277 59.8044 C.3 1 C1 -0.0933
! 12 H24 28.7389 11.2253 59.2582 H 1 C1 0.0514
! 13 H23 27.9273 12.7359 59.4839 H 1 C1 0.0407
! 14 H22 27.0519 11.2519 59.6380 H 1 C1 0.0348
! 15 C17 29.7884 11.1573 61.5314 C.3 1 C1 -0.1667
! 16 C20 30.1309 9.8852 60.7375 C.2 1 C1 0.5766
! 17 C21 30.7345 10.0076 59.3817 C.3 1 C1 -0.2023
! 18 H30 30.1013 9.5455 58.6701 H 1 C1 0.0708
! 19 H29 31.6810 9.5332 59.3723 H 1 C1 0.0687
! 20 H28 30.8509 11.0321 59.1383 H 1 C1 0.0522
! 21 O2 29.9029 8.7920 61.2099 O.2 1 C1 -0.5371
! 22 H21 29.9088 10.8105 62.5246 H 1 C1 0.0636
! 23 C16 30.7082 12.3935 61.2345 C.3 1 C1 -0.0771
! 24 H20 31.4859 12.4666 61.9504 H 1 C1 0.0442
! 25 H19 31.1265 12.3287 60.2639 H 1 C1 0.0728
! 26 C15 29.7910 13.6667 61.3257 C.3 1 C1 -0.0764
! 27 H18 30.2002 14.4236 61.9431 H 1 C1 0.0469
! 28 H17 29.5585 14.0733 60.3755 H 1 C1 0.0487
! 29 C14 28.5018 13.1085 61.9781 C.3 1 C1 -0.0579
! 30 H16 28.7640 12.9733 62.9948 H 1 C1 0.0514
! 31 C8 27.2344 13.9646 61.8869 C.3 1 C1 -0.0473
! 32 H10 26.9454 14.1128 60.8790 H 1 C1 0.0616
! 33 C7 27.4787 15.3387 62.5625 C.3 1 C1 -0.0791
! 34 H9 27.8172 15.1531 63.5481 H 1 C1 0.0444
! 35 H8 28.2392 15.8318 62.0156 H 1 C1 0.0440
! 36 C6 26.2219 16.2283 62.6105 C.3 1 C1 -0.0520
! 37 H7 26.4397 17.0704 63.2141 H 1 C1 0.0559
! 38 H6 26.0092 16.5480 61.6234 H 1 C1 0.0564
! 39 C5 25.0127 15.4945 63.1790 C.2 1 C1 -0.0433
! 40 C4 24.2731 16.1024 64.0886 C.2 1 C1 -0.2513
! 41 H5 24.5932 17.0662 64.4471 H 1 C1 0.1514
! 42 C3 23.0528 15.5025 64.6060 C.2 1 C1 0.5626
! 43 O1 22.3769 16.0927 65.4669 O.2 1 C1 -0.5423
! 44 C2 22.5458 14.1838 64.0304 C.3 1 C1 -0.1812
! 45 H4 21.9703 13.6775 64.7611 H 1 C1 0.0778
! 46 H3 21.9451 14.3777 63.1804 H 1 C1 0.0723
! 47 H15 27.0726 10.0114 61.7584 H 1 C1 0.0407
! 48 H14 27.5838 10.8771 63.1647 H 1 C1 0.0413
! 49 H13 25.5464 11.7981 61.1620 H 1 C1 0.0476
! 50 H12 25.2134 11.2725 62.7760 H 1 C1 0.0408
! 51 H11 26.3903 13.0977 63.6769 H 1 C1 0.0482
! 52 H2 24.2598 13.0217 64.5062 H 1 C1 0.0551
! 53 H1 23.3689 12.4357 63.1452 H 1 C1 0.0453
@<TRIPOS>BOND
1 1 2 1
2 1 44 1
--------------------------------------------------------------------------
Workaround: none.
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