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Re: [IMP-dev] Q) How to correlate atoms and residue in IMP molecular hierarchy?

MolecularHierarchy inherits from Hierachy, so you can do operations like get_parent and get_child. And by default, atoms are children of residues. So you can do atomdecorator.get_parent().get_index() to find which residue a given atom belongs to. Does that answer things? 
On Jan 7, 2009, at 7:34 PM, Seung Joong Kim wrote:


Hi all,
This can be a very simple question, but I'm just wondering how to correlate atoms and a residue in IMP molecular hierarchy. 
First of all, I get "IMP::core::MolecularHierarchyDecorator mp" by  
calling read_pdb function defined in IMP modeller module.  It simply  
reads contents of a pdb file and generates the molecular hierarchy.

  mp = IMP.modeller.read_pdb('single_protein.pdb', m)



Then, I load particles by calling "molecular_hierarchy_get_by_type"  
function as follows.

  ps_ = IMP::core::molecular_hierarchy_get_by_type(mp_,  
IMP::core::MolecularHierarchyDecorator::ATOM);
  IMP::core::AtomDecorator ad =  
IMP::core::AtomDecorator::cast(ps_[i]);

  IMP::core::AtomType at = ad.get_type()


  residues = IMP.core.molecular_hierarchy_get_by_type(mp,  
IMP.core.MolecularHierarchyDecorator.RESIDUE);
  IMP::core::ResidueDecorator rd =  
IMP::core::ResidueDecorator::cast(residues_[i]);

  IMP::core::ResidueType rt = rd.get_type();


By doing this, I get only independent particle arrays of atom and  
residue, without any relation between them.



What I want to know is a piece of linked information between atom  
index and residue index, such that a Nitrogen atom (atom index 458)  
is positioned at a LYS residue (residue index 56).

ATOM    458  N   LYS    56      38.397  16.302  23.700  1.00  
18.45         N
Is there any simple function defined in MolecularHierarchyDecorator  
class for this purpose?  (Input : atom index & Output : residue  
index, and vice versa.)  Or is there any other simple way to do this?

Thanks a lot!
Seung Joong Kim
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