Module automatic_analysis_generator

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: list

a list of Ligand instances

This parses a CMS for the ligand to use.

Parameters:

• cms_st (schrodinger.trajectory.cmsstructure.CmsStructure object) - A CMS to find a ligand within

Returns: (Structure, str)

(ligand structure, ligand asl)

This gives an ASL for a subsection of the protein without the ligand.

Parameters:

• asl_type (str) - Type of protein wanted, Heavy, Backbone, etc
• protein_asl (str) - The ASL to describe the entire protein
• ligand_asl (str) - The ASL to describe the ligand

Returns: str

ASL for the protein component minus the ligand

Returns keywords for RMSD analysis of protein components.

Parameters:

• protein_asl (str) - The ASL to describe the entire protein
• ligand_asl (str) - The ASL to describe the ligand
• reference_struct (None or schrodinger.structure.Structure) - A structure to do the RMSD against
• frame (int) - The frame to take the RMSD against, ignored if reference_struct!=None

Returns: sea.Map

Keyword(s) for calculation

Returns keywords for RMSD analysis of the ligand.

Parameters:

• ligand_asl (str) - The ASL to describe the ligand
• fitby (None or str) - None or an ASL to describe what portion of the CMS to fit
• reference_struct (None or schrodinger.structure.Structure) - A structure to do the RMSD against
• frame (int) - The frame to take the RMSD against, ignored if reference_struct!=None

Returns keywords for RMSF analysis of protein components.

Parameters:

• protein_asl (str) - The ASL to describe the entire protein
• ligand_asl (str) - The ASL to describe the ligand
• reference_struct (None or schrodinger.structure.Structure) - A structure to do the RMSF against
• frame (int) - The frame to take the RMSF against, ignored if reference_struct!=None

Returns: sea.Map

Keyword(s) for calculation

Returns keywords for SSE analysis

Parameters:

• protein_asl (str) - The ASL to describe the entire protein
• ligand_asl (str) - The ASL to describe the ligand

Returns: sea.Map

Keyword(s) for calculation

Returns keywords for RMSF analysis of the ligand.

Parameters:

• ligand_asl (str) - The ASL to describe the ligand
• fitby (None or str) - None or an ASL to describe what portion of the CMS to fit
• reference_struct (None or schrodinger.structure.Structure) - A structure to do the RMSF against
• frame (int) - The frame to take the RMSF against, ignored if reference_struct!=None

Returns keywords for PLI analysis

Parameters:

• protein_asl (str) - The ASL to describe the entire protein
• ligand_asl (str) - The ASL to describe the ligand

This will get the atoms index associated with an asl index

Parameters:

• ligand_st (structure) - ligand structure
• lig_idx (int

  @return : atom_index of the asl selection for that atom @rtype : atom_index

  ) - ligand atom index

Given an atom (a_id), return the mass of all the atoms that are connected to it

Parameters:

• st (structure) - small molecule structure
• a_id (inta

  @rtype float @return the mass of all the atoms that are connected to a_id

  ) - index of the atom whose bonded atoms you want to return

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

@param a_id: index of the atom whose bonded atoms you want to return
@type a_id: int

@exclude_atom_id: remove that atom from the list
@type exclude_atom_id: int

@param for_fep: if this options is ture, then return only atoms that is
                mapped to another atoms (contains i_fep_mapping prop)
@type for_fep: bool
@rtype int
@return The index of the first heavy atom a_id, that is bounded, and that
    isn't exclude_atom_id

returns all rotatable bonds, defined as torsions. returns original atoms indeces.

Parameters:

• st (structure) - structure of a ligand

Returns: list

a list of four atoms that define a rotatable bond

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

Parameters:

• st (structure) - structure of a ligand

Returns: structure

a structure file with reordered atoms according to unique SMILES

Returns keywords for ligand-specific analysis * Intramolecular Hbonds * Molecular Surface Area (Cannolly surface) * Solvent Accessible Surface Area * Polar Surface area * Radius of Gyration

Parameters:

• ligand_asl (str) - The ASL to describe the ligand
• calcRMSD (bool) - Bool to also set up RMSD jobs

Returns: sea.Map

Keyword(s) for calculation

Returns keywords for ligand torsion analysis

Parameters:

• ligand_st (schrodinger.structure.Structure) - Structure of the ligand
• ligand_asl (str) - The ASL to describe the ligand

Returns: sea.Map

Keyword(s) for calculation

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 (None or schrodinger.structure.Structure) - A structure to do RMSD/RMSF calcs against
• frame (int) - The frame to take the RMSF/RMSD against, ignored if ref_struct!=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_ltorsion (bool) - Whether to add a ligand torsions keyword
• want_lprops (bool) - Whether to add ligand properties keyword

Returns: sea.Map

Keyword(s) for calculation