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Re-implement rigid body docking #41

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merged 17 commits into from
Jul 29, 2021
Merged

Re-implement rigid body docking #41

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026bce0
Update .gitignore
rvhonorato Jul 26, 2021
30a8eb2
add cns protocols for rigidbody
rvhonorato Jul 26, 2021
b03e4da
refactor topology
rvhonorato Jul 26, 2021
1823d69
move generic cns functions
rvhonorato Jul 26, 2021
e4150ca
implement rigidbody docking
rvhonorato Jul 26, 2021
9689ef7
add rigidbody examples
rvhonorato Jul 26, 2021
c9438b8
adapt scoring to refactored topology
rvhonorato Jul 26, 2021
2d1c08c
clean unused cns scripts for rigidbody
rvhonorato Jul 27, 2021
d2b4ce2
rename module
rvhonorato Jul 27, 2021
f6d54ec
propagate renaming
rvhonorato Jul 27, 2021
1d09373
refactor to use relative files
rvhonorato Jul 27, 2021
3e5293b
implement docking with ambig restraints
rvhonorato Jul 27, 2021
1e6196c
add multiple functions to add restraints
rvhonorato Jul 27, 2021
cc19a48
cleaning
rvhonorato Jul 27, 2021
1e066c5
move generate_topology to correct location
rvhonorato Jul 27, 2021
fbba75b
keep prepare_run modular
joaomcteixeira Jul 27, 2021
8c33e50
Merge pull request #2 from joaomcteixeira/41comments
rvhonorato Jul 29, 2021
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1 change: 0 additions & 1 deletion .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -139,4 +139,3 @@ tags
bin/cns
# ignore generated data of the examples
examples/*/run*

1,643 changes: 1,643 additions & 0 deletions examples/rigid_body_docking/1a2k_l_u.pdb
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1,982 changes: 1,982 additions & 0 deletions examples/rigid_body_docking/1a2k_r_u.pdb
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378 changes: 378 additions & 0 deletions examples/rigid_body_docking/ambig.tbl
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Original file line number Diff line number Diff line change
@@ -0,0 +1,378 @@

! HADDOCK AIR restraints for 1st partner
!
assign ( resid 69 and segid A)
(
( resid 39 and segid B)
or
( resid 41 and segid B)
or
( resid 42 and segid B)
or
( resid 44 and segid B)
or
( resid 67 and segid B)
or
( resid 69 and segid B)
or
( resid 71 and segid B)
or
( resid 76 and segid B)
) 2.0 2.0 0.0
!
assign ( resid 242 and segid A)
(
( resid 39 and segid B)
or
( resid 41 and segid B)
or
( resid 42 and segid B)
or
( resid 44 and segid B)
or
( resid 67 and segid B)
or
( resid 69 and segid B)
or
( resid 71 and segid B)
or
( resid 76 and segid B)
) 2.0 2.0 0.0
!
assign ( resid 259 and segid A)
(
( resid 39 and segid B)
or
( resid 41 and segid B)
or
( resid 42 and segid B)
or
( resid 44 and segid B)
or
( resid 67 and segid B)
or
( resid 69 and segid B)
or
( resid 71 and segid B)
or
( resid 76 and segid B)
) 2.0 2.0 0.0
!
assign ( resid 260 and segid A)
(
( resid 39 and segid B)
or
( resid 41 and segid B)
or
( resid 42 and segid B)
or
( resid 44 and segid B)
or
( resid 67 and segid B)
or
( resid 69 and segid B)
or
( resid 71 and segid B)
or
( resid 76 and segid B)
) 2.0 2.0 0.0
!
assign ( resid 292 and segid A)
(
( resid 39 and segid B)
or
( resid 41 and segid B)
or
( resid 42 and segid B)
or
( resid 44 and segid B)
or
( resid 67 and segid B)
or
( resid 69 and segid B)
or
( resid 71 and segid B)
or
( resid 76 and segid B)
) 2.0 2.0 0.0
!
assign ( resid 294 and segid A)
(
( resid 39 and segid B)
or
( resid 41 and segid B)
or
( resid 42 and segid B)
or
( resid 44 and segid B)
or
( resid 67 and segid B)
or
( resid 69 and segid B)
or
( resid 71 and segid B)
or
( resid 76 and segid B)
) 2.0 2.0 0.0
!
assign ( resid 295 and segid A)
(
( resid 39 and segid B)
or
( resid 41 and segid B)
or
( resid 42 and segid B)
or
( resid 44 and segid B)
or
( resid 67 and segid B)
or
( resid 69 and segid B)
or
( resid 71 and segid B)
or
( resid 76 and segid B)
) 2.0 2.0 0.0
!
assign ( resid 321 and segid A)
(
( resid 39 and segid B)
or
( resid 41 and segid B)
or
( resid 42 and segid B)
or
( resid 44 and segid B)
or
( resid 67 and segid B)
or
( resid 69 and segid B)
or
( resid 71 and segid B)
or
( resid 76 and segid B)
) 2.0 2.0 0.0
!
assign ( resid 323 and segid A)
(
( resid 39 and segid B)
or
( resid 41 and segid B)
or
( resid 42 and segid B)
or
( resid 44 and segid B)
or
( resid 67 and segid B)
or
( resid 69 and segid B)
or
( resid 71 and segid B)
or
( resid 76 and segid B)
) 2.0 2.0 0.0
!
assign ( resid 324 and segid A)
(
( resid 39 and segid B)
or
( resid 41 and segid B)
or
( resid 42 and segid B)
or
( resid 44 and segid B)
or
( resid 67 and segid B)
or
( resid 69 and segid B)
or
( resid 71 and segid B)
or
( resid 76 and segid B)
) 2.0 2.0 0.0
!
! HADDOCK AIR restraints for 2nd partner
!
assign ( resid 39 and segid B)
(
( resid 69 and segid A)
or
( resid 242 and segid A)
or
( resid 259 and segid A)
or
( resid 260 and segid A)
or
( resid 292 and segid A)
or
( resid 294 and segid A)
or
( resid 295 and segid A)
or
( resid 321 and segid A)
or
( resid 323 and segid A)
or
( resid 324 and segid A)
) 2.0 2.0 0.0
!
assign ( resid 41 and segid B)
(
( resid 69 and segid A)
or
( resid 242 and segid A)
or
( resid 259 and segid A)
or
( resid 260 and segid A)
or
( resid 292 and segid A)
or
( resid 294 and segid A)
or
( resid 295 and segid A)
or
( resid 321 and segid A)
or
( resid 323 and segid A)
or
( resid 324 and segid A)
) 2.0 2.0 0.0
!
assign ( resid 42 and segid B)
(
( resid 69 and segid A)
or
( resid 242 and segid A)
or
( resid 259 and segid A)
or
( resid 260 and segid A)
or
( resid 292 and segid A)
or
( resid 294 and segid A)
or
( resid 295 and segid A)
or
( resid 321 and segid A)
or
( resid 323 and segid A)
or
( resid 324 and segid A)
) 2.0 2.0 0.0
!
assign ( resid 44 and segid B)
(
( resid 69 and segid A)
or
( resid 242 and segid A)
or
( resid 259 and segid A)
or
( resid 260 and segid A)
or
( resid 292 and segid A)
or
( resid 294 and segid A)
or
( resid 295 and segid A)
or
( resid 321 and segid A)
or
( resid 323 and segid A)
or
( resid 324 and segid A)
) 2.0 2.0 0.0
!
assign ( resid 67 and segid B)
(
( resid 69 and segid A)
or
( resid 242 and segid A)
or
( resid 259 and segid A)
or
( resid 260 and segid A)
or
( resid 292 and segid A)
or
( resid 294 and segid A)
or
( resid 295 and segid A)
or
( resid 321 and segid A)
or
( resid 323 and segid A)
or
( resid 324 and segid A)
) 2.0 2.0 0.0
!
assign ( resid 69 and segid B)
(
( resid 69 and segid A)
or
( resid 242 and segid A)
or
( resid 259 and segid A)
or
( resid 260 and segid A)
or
( resid 292 and segid A)
or
( resid 294 and segid A)
or
( resid 295 and segid A)
or
( resid 321 and segid A)
or
( resid 323 and segid A)
or
( resid 324 and segid A)
) 2.0 2.0 0.0
!
assign ( resid 71 and segid B)
(
( resid 69 and segid A)
or
( resid 242 and segid A)
or
( resid 259 and segid A)
or
( resid 260 and segid A)
or
( resid 292 and segid A)
or
( resid 294 and segid A)
or
( resid 295 and segid A)
or
( resid 321 and segid A)
or
( resid 323 and segid A)
or
( resid 324 and segid A)
) 2.0 2.0 0.0
!
assign ( resid 76 and segid B)
(
( resid 69 and segid A)
or
( resid 242 and segid A)
or
( resid 259 and segid A)
or
( resid 260 and segid A)
or
( resid 292 and segid A)
or
( resid 294 and segid A)
or
( resid 295 and segid A)
or
( resid 321 and segid A)
or
( resid 323 and segid A)
or
( resid 324 and segid A)
) 2.0 2.0 0.0
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