Navigating through the structure's hierarchy

Loading a structure and traversing the structure/chain/residue hierarchy, outputting some information.

" Copyright 2003-2006 Alexander V. Diemand
This file is part of MolTalk.
MolTalk is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
MolTalk is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with MolTalk; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
"

[ |

" traverses the structure/chain/residue hierarchy
 at the end it prints out the count of residues
 with CA distances in the range from 3.5 to 4.1
 grouped by tenth of Angstroms
"

 

main

   | arg strxcode |

   strxcode := nil.
   1 to: (ARGS count) - 1 do: [ :argc |
      arg := (ARGS objectAtIndex:(argc intValue)).
      (arg = '-strx' ) ifTrue: [ targc := argc + 1. strxcode := (ARGS objectAtIndex:(targc)). ].
   ].
   (strxcode isNil) ifTrue: [ self usage. ]
      ifFalse: [ self continue:strxcode. ].
   ^self

 

!
usage

   Transcript showLine: 'Usage: MolTalk scripts/traverseHierarchy.st -strx [strxcode]' .
   Transcript showLine: '' .
   ^self

 

!
continue:strxcode

   | strx CAatm1 CAatm2 dist idx distr val |

   strx := MTStructureFactory newStructureFromPDBDirectory: strxcode.     " MTStructure 3.2     "
   (strx notNil) ifTrue: [
      distr := NSMutableArray arrayWithArray: #(0 0 0 0 0 0).     " NSArray 9.3     "
      Transcript showLine:( 'have structure:' ,strx pdbcode).
      Transcript showLine:( 'header: ' ,strx header).
      Transcript showLine:( 'title: ' ,strx title).
      Transcript showLine:( 'date: ' ,strx date description).
      (strx allChains allObjects) do: [ :chain |     " MTChain 3.4     "
         Transcript showLine:( ' have chain:',chain description,'´#' ,chain code stringValue).
         Transcript showLine:( ' E.C. code: ' ,chain eccode).
         Transcript showLine:( ' compound: ' ,chain compound).
         Transcript showLine:( ' source: ' ,chain source).
         Transcript showLine:( ' #aa: ' ,chain allResidues allObjects count stringValue).
         Transcript showLine:( ' #het:' ,chain allHeterogens allObjects count stringValue).
         Transcript showLine:( ' #sol:' ,chain allSolvent allObjects count stringValue).
         CAatm2 := nil.
         (chain allResidues allObjects) do: [ :residue |     " MTResidue 3.6     "
            CAatm1 := residue getCA.     " MTAtom 3.8     "
            (CAatm2 notNil) ifTrue: [
               dist := CAatm1 distanceTo: CAatm2.
               idx := ((dist - 3.5) * 10) intValue.
               ((idx >= 0) and: (idx < 6)) ifTrue: [
                  val := distr objectAtIndex:idx.
                  distr replaceObjectAtIndex:idx withObject:(val + 1).
               ].
               (dist > 4.0) ifTrue: [
                  Transcript showLine:( 'CA-CA distance > 4.0 A between residues: ' ,presidue description, ' and ' ,residue description, ' distance=' ,dist stringValue).
               ].
            ].     " if we know the previous CA atom "
            presidue := residue.     " remember this residue in next iteration as previous residue "
            CAatm2 := CAatm1.     " remember this CA atom "
         ].     " for all residues "
         Transcript showLine: '' .
      ].     " for all chains "
   ]     " if strx "
   ifFalse: [ Transcript showLine: 'I do not know this structure.' . ].

   0 to: 5 do: [ :index |
      Transcript showLine:( 'count of residues with CA distance between ' ,
         ((35 + index) / 10.0) stringValue, ' and ' ,
         ((36 + index) / 10.0) stringValue, ' are: ' ,
         (distr objectAtIndex:index) stringValue).
   ].
   ^self
]