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Conop Functions
=======================================================================
.. currentmodule:: ost.conop
.. function:: 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 :attr:`~ost.mol.ResidueHandle.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.
:param prev: The amino acid before *res*
:type prev: :class:`~ost.mol.ResidueHandle`
:param res: The central amino acid. Must be a valid handle.
:type res: :class:`~ost.mol.ResidueHandle`
:param next: The amino acid after *res*
:type next: :class:`~ost.mol.ResidueHandle`
:param chain: Chain to process.
:type chain: :class:`~ost.mol.ChainHandle`
:param residues: List of residues to process.
:type residues: :class:`~ost.mol.ResidueHandleList`
.. function:: IsBondFeasible(atom_a, atom_b)
:return: True, if *atom_a* and *atom_b* are within a reasonable distance for
a bond to be present, namely if the distance between the two atoms
is between 0.0625 and 0.375 times the square of the sum of the
:attr:`van der Waals radii <ost.mol.AtomHandle.radius>` of the two
atom.
:rtype: :class:`bool`
:param atom_a: Atom to be checked.
:type atom_a: :class:`~ost.mol.AtomHandle`
:param atom_b: Atom to be checked.
:type atom_b: :class:`~ost.mol.AtomHandle`
.. function:: GetUnknownAtomsOfResidue(residue, compound, strict_hydrogens=False)
Returns the list of atoms present in *residue* that are not part of the
atom specifications in *compound*.
:param residue: The residue to analyze.
:type residue: :class:`~ost.mol.ResidueHandle`
:param compound: Chemical compound to compare with.
:type compound: :class:`Compound`
:param strict_hydrogens: When set to True, hydrogen atoms are checked as well.
:type strict_hydrogens: :class:`bool`
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