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 > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev