htmd.builder.loopmodeler module#

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

Model missing loops in a Molecule using the Modeller software.

Parameters:

  • mol (Molecule) – The molecule containing the gap to fill.

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

  • seq (str) – The one-letter amino acid sequence of residues to insert into the gap.

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

  • movstart (int | None) – The resid after which residues are allowed to move during Modeller refinement. If None, defaults to startresid.

  • movend (int | None) – The resid before which residues are allowed to move during Modeller refinement. If None, defaults to movstart + len(seq) + 1.

  • modellerexe (str) – Path or name of the Modeller executable on PATH.

Returns:

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

Return type:

Molecule

Examples

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