Conop Functions

AssignBackboneTorsions(prev, res, next)
AssignBackboneTorsions(chain)
AssignBackboneTorsions(residues)

Assigns the backbone torsions PHI, PSI and OMEGA. The backbone atoms are required to be connected for the torsions to be added. In addition, only residues for which peptide_linking is True are considered.

The first signature assigns the torsions to res, assuming prev is the amino acid before, and next is the amino acid next to res. Both next and prev may be invalid residues.

The second and third signature assign the torsions to all peptidic residues of the chain/the residue list. The residues in the chain, the residue list are thought to run from N to C terminus.

Parameters:

  • prev (ResidueHandle) – The amino acid before res

  • res (ResidueHandle) – The central amino acid. Must be a valid handle.

  • next (ResidueHandle) – The amino acid after res

  • chain (ChainHandle) – Chain to process.

  • residues (ResidueHandleList) – List of residues to process.

IsBondFeasible(atom_a, atom_b)
Returns:

True, if atom_a and atom_b are within a reasonable distance for a bond to be present. Depends on radius of atoms and heuristic formulas.

Return type:

bool

Parameters:
GetUnknownAtomsOfResidue(residue, compound, strict_hydrogens=False)

Returns the list of atoms present in residue that are not part of the atom specifications in compound.

Parameters:

  • residue (ResidueHandle) – The residue to analyze.

  • compound (Compound) – Chemical compound to compare with.

  • strict_hydrogens (bool) – When set to True, hydrogen atoms are checked as well.