schrodinger.application.desmond.automatic_analysis_generator module¶
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schrodinger.application.desmond.automatic_analysis_generator.
removeAminoAcids
(ligand_list)¶ This function iterates over ligand structures in the given list and removes those that have amino acid names in their pdb residue name.
Parameters: ligand_list (list) – list of ligand structures Returns: a list of Ligand
instancesReturn type: list
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schrodinger.application.desmond.automatic_analysis_generator.
getLigand
(cms_st)¶ This parses a CMS for the ligand to use. :param cms_st: A CMS to find a ligand within :type cms_st: cms.Cms object
Returns: (ligand structure, ligand asl) Return type: (Structure, str)
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schrodinger.application.desmond.automatic_analysis_generator.
getASLExcludingLigand
(asl_type, protein_asl='(protein)', ligand_asl='')¶ This gives an ASL for a subsection of the protein without the ligand. :param asl_type: Type of protein wanted, Heavy, Backbone, etc :type asl_type: str
Parameters: - protein_asl (str) – The ASL to describe the entire protein
- ligand_asl (str) – The ASL to describe the ligand
Returns: ASL for the protein component minus the ligand
Return type: str
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schrodinger.application.desmond.automatic_analysis_generator.
getRMSDKeywords
(protein_asl, ligand_asl, ref_struct_fname=None, frame=0)¶ Returns keywords for RMSD analysis of protein components. :param protein_asl: The ASL to describe the entire protein :type protein_asl: str
Parameters: - ligand_asl (str or None) – The ASL to describe the ligand
- ref_struct_fname (None or
str
) – Path to the structure to do the RMSD against - frame (int) – The frame to take the RMSD against, ignored if ref_struct_fname!=None
Returns: Keyword(s) for calculation
Return type:
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schrodinger.application.desmond.automatic_analysis_generator.
getRMSDLigandKW
(ligand_asl, fitby, ref_struct_fname=None, frame=0)¶ Returns keywords for RMSD analysis of the ligand. :param ligand_asl: The ASL to describe the ligand :type ligand_asl: str
Parameters: - fitby (None or str) – None or an ASL to describe what portion of the CMS to fit
- ref_struct_fname (None or
str
) – Path to the structure to do the RMSD against - frame (int) – The frame to take the RMSD against, ignored if ref_struct_fname!=None
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schrodinger.application.desmond.automatic_analysis_generator.
getRMSFProtKeywords
(protein_asl, ligand_asl, ref_struct_fname=None, frame=0)¶ Returns keywords for RMSF analysis of protein components. :param protein_asl: The ASL to describe the entire protein :type protein_asl: str
Parameters: - ligand_asl (str) – The ASL to describe the ligand
- ref_struct_fname (None or schrodinger.structure.Structure) – A structure to do the RMSF against
- frame (int) – The frame to take the RMSF against, ignored if ref_struct_fname!=None
Returns: Keyword(s) for calculation
Return type:
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schrodinger.application.desmond.automatic_analysis_generator.
getSSEProtKeywords
(protein_asl, ligand_asl)¶ Returns keywords for SSE analysis :param protein_asl: The ASL to describe the entire protein :type protein_asl: str
Parameters: ligand_asl (str) – The ASL to describe the ligand Returns: Keyword(s) for calculation Return type: sea.Map
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schrodinger.application.desmond.automatic_analysis_generator.
getRMSFLigandKW
(fitby_asl, ligand_asl, ref_struct_fname=None, frame=0)¶ Returns keywords for RMSF analysis of the ligand. :param ligand_asl: The ASL to describe the ligand :type ligand_asl: str
Parameters: - fitby (None or str) – None or an ASL to describe what portion of the CMS to fit
- ref_struct_fname (None or schrodinger.structure.Structure) – A structure to do the RMSF against
- frame (int) – The frame to take the RMSF against, ignored if ref_struct_fname!=None
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schrodinger.application.desmond.automatic_analysis_generator.
getProtLigInterKW
(protein_asl, ligand_asl, metal_asl=None)¶ Returns keywords for PLI analysis :param protein_asl: The ASL to describe the entire protein :type protein_asl: str
Parameters: - ligand_asl (str) – The ASL to describe the ligand
- metal_asl (str or None) – The ASL to describe metals or ions. If None, use all metals and ions in the input structure.
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schrodinger.application.desmond.automatic_analysis_generator.
get_idx
(ligand_st, lig_idx)¶ This will get the atoms index associated with an asl index :param ligand_st : ligand structure :type ligand_st : structure
:param lig_idx : ligand atom index :type lig_idx : int
:return : atom_index of the asl selection for that atom :rtype : atom_index
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schrodinger.application.desmond.automatic_analysis_generator.
sort_atoms
(st, a_id, exclude_atom_id=None, for_fep=False)¶ Extract atoms that are bonded to a_id atom (excluding the exclude_atom_id atom) and returns a list of atoms in the order such that hydrogens are last :param st: small molecule structure :type st: structure
Parameters: a_id (int) – index of the atom whose bonded atoms you want to return @exclude_atom_id: remove that atom from the list :type exclude_atom_id: int
Parameters: for_fep (bool) – if this options is ture, then return only atoms that is mapped to another atoms (contains i_fep_mapping prop) :rtype int :return The index of the first heavy atom a_id, that is bounded, and that
isn’t exclude_atom_id
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schrodinger.application.desmond.automatic_analysis_generator.
get_rotatable_bonds
(st)¶ returns all rotatable bonds, defined as torsions. returns original atoms indeces. :param st: structure of a ligand :type st: structure
Return type: list Returns: a list of four atoms that define a rotatable bond
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schrodinger.application.desmond.automatic_analysis_generator.
canonicalize_ligand
(st)¶ Use uSMILES to canonicalize the ligand structure, this is so we get the order of the rotatable bonds(torsions) in the same order, regardless of the atom order :param st: structure of a ligand :type st: structure
Return type: structure Returns: a structure file with reordered atoms according to unique SMILES
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schrodinger.application.desmond.automatic_analysis_generator.
getLigandPropsKeywords
(ligand_asl, calcRMSD, ref_struct_fname=None, frame=None)¶ Returns keywords for ligand-specific analysis * Intramolecular Hbonds * Molecular Surface Area (Cannolly surface) * Solvent Accessible Surface Area * Polar Surface area * Radius of Gyration :param ligand_asl: The ASL to describe the ligand :type ligand_asl: str :param calcRMSD: Bool to also set up RMSD jobs :type calcRMSD: bool :param ref_struct_fname: path to the reference structure :param frame: frame index :type frame:
int
Returns: Keyword(s) for calculation Return type: sea.Map
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schrodinger.application.desmond.automatic_analysis_generator.
getFEPTorsionKeywords
(lig1_st, lig2_st, lig1_asl, lig2_asl, fep_lambda=0, is_covalent=False)¶ For a pair for ligands/fragments that, whose atoms are mapped, return sea object of torsions for each rotatable bond.
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schrodinger.application.desmond.automatic_analysis_generator.
lig_to_fullsys_aid
(torsion_list, st)¶ Convert ligand atom IDs to full-system atom IDs
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schrodinger.application.desmond.automatic_analysis_generator.
getTorsionKeywords
(ligand_st, ligand_asl)¶ Returns keywords for ligand torsion analysis :param ligand_st: Structure of the ligand :type ligand_st: schrodinger.structure.Structure
Parameters: ligand_asl (str) – The ASL to describe the ligand Returns: Keyword(s) for calculation Return type: sea.Map
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schrodinger.application.desmond.automatic_analysis_generator.
getPPIKeywords
(protein_asl)¶ Returns keywords for PLI analysis :param protein_asl: The ASL to describe the entire protein :type protein_asl: str
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schrodinger.application.desmond.automatic_analysis_generator.
getPLISKWList
(cms_st, ligand_st, ligand_asl, ref_struct_fname, frame=0, protein_asl='(protein)', want_rmsd=True, want_prmsf=True, want_lrmsf=True, want_pli=True, want_ltorsion=True, want_lprops=True, want_ppi=True, protein_fep=False, metal_asl=None)¶ Generate the entire keyword list for all PLI calculations. Also returns the ligand_asl used in those keywords.
Parameters: - ligand_st (schrodinger.structure.Structure) – Structure of the ligand
- ligand_asl (str) – The ASL to describe the ligand
- ref_struct_fname (None or
str
) – Path to the structure to do the RMSD against - frame (int) – The frame to take the RMSF/RMSD against, ignored if ref_struct_fname!=None
- protein_asl (str) – The ASL to describe the entire protein
- want_rmsd (bool) – Whether to add RMSD keywords
- want_prmsf (bool) – Whether to add RMSF keywords for protein
- want_lrmsf (bool) – Whether to add an RMSF ligand keyword
- want_pli (bool) – Whether to add a PLI keyword
- want_ppi (bool) – Whether to add a PPI keyword
- want_ltorsion (bool) – Whether to add a ligand torsions keyword
- want_lprops (bool) – Whether to add ligand properties keyword
- protein_fep (bool) – Whether the input system is a protein_fep job
- metal_asl (str or None) – The ASL to describe metals or ions. If None, use ‘(ions) or (metals) or (metalloids)’.
Returns: Keyword(s) for calculation
Return type: