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)