schrodinger.application.desmond.mdpose.mdpose_analysis module

class schrodinger.application.desmond.mdpose.mdpose_analysis.Contact(ref_st, avg_st, ref_fname, avg_fname, contact1_asl, contact2_asl, description)

Bases: schrodinger.application.desmond.mdpose.mdpose_analysis.MDPoseAnalysis

format()
run()
class schrodinger.application.desmond.mdpose.mdpose_analysis.ContactCmd(input_fname, st, contact1_asl, contact2_asl)
atidToResname(atid)
cmd_template = '\n entryimport %s\n contactset1 %s\n contactset2 %s\n propertygeneratecontacts\n writecontact %s\n '
run()
class schrodinger.application.desmond.mdpose.mdpose_analysis.MDPoseAnalysis(description)
description()
name
run()
class schrodinger.application.desmond.mdpose.mdpose_analysis.RMSD(ref_st, avg_st, lig_asl='(mol.atoms 10-120)', cutoff=6.0)

Bases: schrodinger.application.desmond.mdpose.mdpose_analysis.MDPoseAnalysis

format()
run()
class schrodinger.application.desmond.mdpose.mdpose_analysis.Tanimoto(ref_st, avg_st)

Bases: schrodinger.application.desmond.mdpose.mdpose_analysis.MDPoseAnalysis

run()
schrodinger.application.desmond.mdpose.mdpose_analysis.get_active_site_asl(base_asl, lig_asl, cutoff=6.0, fillres=True)

Returns an ASL expression defining binding site atoms based on the ligand molecule number and cutoff distance. This ASL specifically identifies the C-alpha atoms.

Parameters:
  • cutoff (float) – Cutoff from ligand used to asign binding site atoms
  • molnum (int) – The molecule number fo the ligand. If None the ligand will be automatically detected.
  • fillres (bool) – Use all atoms in a residue if any atom is found
Returns:

ASL expression for binding site atoms

Return type:

str

schrodinger.application.desmond.mdpose.mdpose_analysis.run_maestro_cmd(cmd)