Topological Descriptors

A topological_descriptor allows selection of atoms based upon the topology (connectedness) of the molecule.

"topological_descriptors" = bonded_neighbor     
                          = connected_fragment 
                          = non-bonded fragment

The PSL currently supports the following types of topological descriptors:

Connected Fragment

 uniqatom1->uniqatom2--uniqatom3    
[uniqatom1]->uniqatom2--uniqatom3   
 uniqatom1->uniqatom2--[uniqatom3]  
[uniqatom1]->uniqatom2--[uniqatom3]

uniqatom3 = * 
          = uniqatom

uniqatom is any mol_chains:residues.atoms specifier which evaluates to a single atom or is "*" which means "entire fragment to the end of the chain. The square brackets denote optional punctuation marks rather than denoting patameters which can be optionally omitted.

A connected fragment denotes a specific bonded path of atoms starting from a pair of bonded atoms (uniqatom1 and uniqatom2) and continuing through to a terminating atom (uniqatom3) and includes all atoms connected to the interior atoms. Either uniqatom1 or uniqatom3 may be omitted from the path by enclosing the specification for that atom in square brackets ( [uniqatom] ).

Connected Fragment      Description

C1->C2--N5              the connected fragment of atoms starting with 
                           atom C1 in the direction of bonded atom C2 
                           and thence to atom N5.
[C1]->C2--[N5]          as above, but excluding atoms C1 and N5.
                        C1->C2--*the connected fragment of atoms
                           starting with atom C1 in the direction of
                           bonded atom C2 and thence to the end of
                           the chain.

Bonded Neighbor

  atom_specification;N 
  atom_specification;

  N = a positive integer, or zero.

atom_specification is any mol_chain:residue.atoms specifier. It does not have to evaluate to a single atom, and can use all the features of the selection_list (excluding FILTERS).

atom_specification will be evaluated according to the following three rules:

• All the atoms in the atom_specification are found.
• For each of these atoms, all heavy atoms within "N" bonds, plus all attached hydrogens and lone pairs are returned.
• If the atom_specification is included in square brackets [], the atom itself in rule 2 is not returned.

These rules may produce lengthy lists, and some atoms may be included in the list more than once.

Bonded Neighbor     Description

N5;                 atom N5 with any attached hydrogens and
                       lone pairs
N5;3                as above, but including any heavy atoms within 3 
                       bonds of N5 and including any attached
                       hydrogens 
                       and lone pairs on those heavy atoms.
O*;                 all oxygen atoms with any attached hydrogens and 
                       lone pairs.
 
 


Nonbonded Fragment

<uniqatom> 
<!uniqatom>

   uniqatom = atomname


uniqatom is any mol_chains:residues.atoms specifier which evaluates 
to a single atom. The angle brackets denote required punctuation 
marks. The non-bonded fragment specification returns all atoms in an 
isolated portion (no connecting bonds) of a molecule. The ! 
punctuation before the uniqatom instructs the PSL to return all atom 
NOT in the fragment specified by the input atom.

Nonbonded Fragment     Description

<N1>                   all atoms in molecule fragment containing 
                          atom N1.
<!N1>                  all atoms in molecule fragment not containing 
                          atom N1.



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