| ! numtrees.cns |
| ! Define the number of trees for torsion angle MD |
| ! |
| ! *********************************************************************** |
| ! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University. * |
| ! * Originally adapted from Aria 1.2 from Nilges and Linge, EMBL. * |
| ! * All rights reserved. * |
| ! * This code is part of the HADDOCK software and governed by its * |
| ! * license. Please see the LICENSE file that should have been included * |
| ! * as part of this package. * |
| ! *********************************************************************** |
| ! |
|
|
| evaluate ($numtrees = 1) |
| evaluate ($ncount = 0) |
| evaluate ($break=$data.ncomponents) |
|
|
| while ($ncount < $data.ncomponents) loop nsloop |
|
|
| evaluate ($ncount = $ncount + 1) |
|
|
| for $id1 in id ( name C and bondedto(name CA) and segid $prot_segid_$ncount) loop break |
| show (resid) (id $id1) |
| evaluate ($resid1=$result) |
| evaluate ($resid2=encode(decode($resid1)+1)) |
| show sum(1) (id $id1 and known) |
| if ( $result ne 0 ) then |
| identity (store1) ( name N and bondedto(name CA) and segid $prot_segid_$ncount and resid $resid2 ) |
| show element (store1) (attribute store1 > 0) |
| if ( $result ne 0) then |
| evaluate ($id2=$result) |
| show sum(1) (id $id2 and known) |
| if ( $result ne 0 ) then |
| pick bond |
| (name c and segid $prot_segid_$ncount and resid $resid1) |
| (name n and segid $prot_segid_$ncount and resid $resid2) |
| geometry |
| if ( $result > 2.5 ) then |
| evaluate ($break=$break+1) |
| end if |
| else |
| evaluate ($break=$break+1) |
| end if |
| end if |
| end if |
| end loop break |
|
|
| for $id1 in id ( name BB ) loop bbbreak |
| show (resid) (id $id1) |
| evaluate ($resid1=$result) |
| evaluate ($resid2=encode(decode($resid1)+1)) |
| show sum(1) (id $id1 and known) |
| if ( $result ne 0 ) then |
| identity (store1) ( name BB and segid $prot_segid_$ncount and resid $resid2 ) |
| show element (store1) (attribute store1 > 0) |
| if ( $result ne 0) then |
| evaluate ($id2=$result) |
| show sum(1) (id $id2 and known) |
| if ( $result ne 0 ) then |
| pick bond |
| (name BB and segid $prot_segid_$ncount and resid $resid1) |
| (name BB and segid $prot_segid_$ncount and resid $resid2) |
| geometry |
| if ( $result > 8.0 ) then |
| evaluate ($break=$break+1) |
| end if |
| else |
| evaluate ($break=$break+1) |
| end if |
| end if |
| end if |
| end loop bbbreak |
| |
| end loop nsloop |
|
|
| ! check for water molecules |
|
|
| do (store1 = 0) (all) |
| do (store1 = 1) ((resn WAT or resn HOH or resn TIP*) and name OH2) |
| show sum (store1) ((resn WAT or resn HOH or resn TIP*)) |
| evaluate ($numtrees = $numtrees + $break + $result) |
|
|
| evaluate ($numtrees = $numtrees + 300) |
|
|
