htmd.builder.loopmodeler module

htmd.builder.loopmodeler.loopModeller(mol, segid, seq, startresid, movstart=None, movend=None, modellerexe='mod9.18')

Uses the Modeller software to predict missing loops in a Molecule.

Parameters
  • mol (Molecule object) – A Molecule object.

  • segid (str) – The name of the segment containing the gap.

  • seq (str) – The sequence of residues to be added by the loop modeller.

  • startresid (int) – The resid of the residue before the gap.

  • movstart (int) – The resid after which the residues will be allowed to move in modeller.

  • movend (int) – The resid before which the residues will be allowed to move in modeller.

  • modellerexe (str) – The path to the modeller executable.

Returns

newmol – A new Molecule object containing the protein with the modelled loop.

Return type

Molecule object

Examples

>>> mol = Molecule('1qg8')
>>> mol2 = loopModeller(mol, '0', 'ENR', 133)