schrodinger.application.jaguar.macro_pka_utils module

class schrodinger.application.jaguar.macro_pka_utils.RowData(name, mol, pop, pH_pop)

Bases: tuple

__contains__(key, /)

Return key in self.

__len__()

Return len(self).

count(value, /)

Return number of occurrences of value.

index(value, start=0, stop=9223372036854775807, /)

Return first index of value.

Raises ValueError if the value is not present.

mol: rdkit.Chem.rdchem.Mol

Alias for field number 1

name: str

Alias for field number 0

pH_pop: float

Alias for field number 3

pop: float

Alias for field number 2

class schrodinger.application.jaguar.macro_pka_utils.GraphData(x, y, labels)

Bases: tuple

__contains__(key, /)

Return key in self.

__len__()

Return len(self).

count(value, /)

Return number of occurrences of value.

index(value, start=0, stop=9223372036854775807, /)

Return first index of value.

Raises ValueError if the value is not present.

labels: Dict[Tuple[int, int], str]

Alias for field number 2

x: Dict[Tuple[int, int], List[float]]

Alias for field number 0

y: Dict[Tuple[int, int], List[float]]

Alias for field number 1

schrodinger.application.jaguar.macro_pka_utils.register_file(name, logfile=False)
schrodinger.application.jaguar.macro_pka_utils.get_aligned_mols(mols: List[rdkit.Chem.rdchem.Mol]) → List[rdkit.Chem.rdchem.Mol]

Align molecules by the common core of all compounds using RDKit MCS and return new RDKit mol instances.

Parameters

mols – list of molecules

Returns

list of of newly-oriented RDKit mol objects

schrodinger.application.jaguar.macro_pka_utils.get_2Dimage(mol: rdkit.Chem.rdchem.Mol, scaling: int = 30) → Optional[str]

Return image bytes of SVG file depicting a 2D structure. It doesn’t store SVG file in disk.

The optional argument <scaling> allows the image size to be adjusted dynamically according to the span of the 2D coordinates. Else a default size is used for all molecules.

Parameters

  • mol – RDKit mol structure to generate the image file

  • scaling – scale factor to multiply original image size by, where ‘original’ is derived from the span of the X or Y cartesian coordinates.

Returns

image bytes of 2D structure

class schrodinger.application.jaguar.macro_pka_utils.PhPopulations(pops: Dict[int, Dict[int, float]], macro_pkas: Dict[Tuple[int, int], float])

Bases: object

Container for pH-dependent and pH-independent tautomer populations from a Macro-pKa calculation.

__init__(pops: Dict[int, Dict[int, float]], macro_pkas: Dict[Tuple[int, int], float])
Parameters

  • pops – Dict of pH-independent tautomer populations of form {charge: {tautomer_index: population}}

  • macro_pkas – Dict of Macro-pKa equilibrium constants of form {(prot_charge, deprot_charge): pKa}

get_populations_at_pH(pH: float) → Dict[int, Dict[int, float]]

Get populations of each tautomer at a given pH value.

Parameters

pH – pH at which to compute pH-dependent populations

Returns

pH-dependent populations in form {charge: {tautomer_index: population}}

get_pH_population_factors(pH: float) → Dict[int, float]

Get population factors for a given pH value, which may be used to scale the pH-independent tautomer populations to obtain the pH-dependent populations. Note that the factor is the same for all tautomers of a given molecular charge.

Parameters

pH – pH at which to compute population factors.

Returns

dict of population scaling factors keyed by charge.

schrodinger.application.jaguar.macro_pka_utils.write_populations_report(jobname: str, tautomers: Dict[int, Dict[int, rdkit.Chem.rdchem.Mol]], macro_pkas: Dict[Tuple[int, int], float], populations: schrodinger.application.jaguar.macro_pka_utils.PhPopulations, user_pH: float, page_title: Optional[str] = None, cmdline: Optional[str] = None, names: Optional[Dict[int, Dict[int, str]]] = None, scaling: int = 30, cutoff: float = 0.0001) → str

Create a final HTML page summarizing all the dominant tautomers found, the macro-pKa transitions, and pH-dependent and independent populations.

Parameters

  • jobname – name of job to prefix file names.

  • tautomers – tautomers of all charges, indexed by molecular charge and a unique tautomer index.

  • macro_pkas – macro-pKa’s for all charge transitions computed, indexed by prot/deprot charges.

  • populations – pH-dependent and independent tautomer populations, indexed by molecular charge and tautomer index.

  • user_pH – user-requested pH to show populations in table.

  • page_title – title to print at top of report.

  • cmdline – command line string for printing.

  • names – optional unique names for each tautomer, indexed by molecular charge and tautomer index (same as tautomers indices).

  • scaling – scale factor to multiply original image size by, where ‘original’ is derived from the span of the X or Y cartesian coordinates.

  • cutoff – optional cutoff for tautomer populations to include (0 to 1)

Returns

absolute path to HTML file on launch machine

schrodinger.application.jaguar.macro_pka_utils.dump_output_csv_file(jobname: str, pkas: Dict[Tuple[int, int], float])

Write Macro-pKa output to a simple .csv file

Parameters

  • jobname – name of job to prefix file names

  • pkas – Dict of Macro-pKa’s like {(prot_charge, deprot_charge): pKa}