schrodinger.application.desmond.mdpose.mdpose_analysis module¶
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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
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format
()¶
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run
()¶
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class
schrodinger.application.desmond.mdpose.mdpose_analysis.
ContactCmd
(input_fname, st, contact1_asl, contact2_asl)¶ -
atidToResname
(atid)¶
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cmd_template
= '\n entryimport %s\n contactset1 %s\n contactset2 %s\n propertygeneratecontacts\n writecontact %s\n '¶
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run
()¶
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class
schrodinger.application.desmond.mdpose.mdpose_analysis.
MDPoseAnalysis
(description)¶ -
description
()¶
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name
¶
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run
()¶
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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
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format
()¶
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run
()¶
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class
schrodinger.application.desmond.mdpose.mdpose_analysis.
Tanimoto
(ref_st, avg_st)¶ Bases:
schrodinger.application.desmond.mdpose.mdpose_analysis.MDPoseAnalysis
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run
()¶
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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:
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schrodinger.application.desmond.mdpose.mdpose_analysis.
run_maestro_cmd
(cmd)¶