[IMP-dev] Q) How to correlate atoms and residue in IMP molecular hierarchy?
To: List for IMP development <>
Subject: [IMP-dev] Q) How to correlate atoms and residue in IMP molecular hierarchy?
From: Seung Joong Kim <>
Date: Wed, 07 Jan 2009 19:34:55 -0800
Reply-to: List for IMP development <>
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.
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
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?