schrodinger.application.jaguar.macro_pka_utils module¶
- class schrodinger.application.jaguar.macro_pka_utils.RowData(smiles, 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.
- pH_pop: float¶
Alias for field number 2
- pop: float¶
Alias for field number 1
- smiles: str¶
Alias for field number 0
- schrodinger.application.jaguar.macro_pka_utils.get_aligned_mols(molecules: List[str]) dict ¶
Align molecules (given as SMILES) by the common core of all compounds using RDKit MCS and return new RDKit mol instances.
- Parameters
molecules – list of SMILES strings
- Returns
dictionary of newly-oriented molecules indexed by SMILES
- schrodinger.application.jaguar.macro_pka_utils.get_2Dimage(name, 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
) – RDKit mol structure to generate the image filescaling – 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
- schrodinger.application.jaguar.macro_pka_utils.get_2Dimage_png(name: str, mol, scaling: int = 30) Optional[str] ¶
Create a PNG image file
name
.png depicting a 2D structure.Note: PNG writing requires graphics libraries, which are not generally available on headless Linux servers. In this case, the method will return None.
- Returns
Filename or None if PNG cannot be written
- schrodinger.application.jaguar.macro_pka_utils.write_html_results_summary(pH: float, macro_pka: Dict[Tuple[int, int], float], populations: Dict[int, List[schrodinger.application.jaguar.macro_pka_utils.RowData]], jobname: str, cmdline: Optional[str] = None, scaling: int = 30, titles: Optional[Dict[str, str]] = None, page_title: Optional[str] = None) str ¶
Create a final HTML page and PDF document summarizing tautomer populations (pH-dependent and independent) and the macro-pKa transitions.
- Parameters
pH – compute populations at this pH
macro_pka – macro-pKa values and (prot_charge, deprot_charge) keys
populations – population data keyed by formal charge. For each charge, a list of tautomer-data should be given with three attributes: (1) smiles: SMILES string denoting tautomer structure (2) pop: pH-independent population (3) pH_pop: pH-dependent population
jobname – name of job to prefix file names
cmdline – command line string for printing
scaling – scale factor to multiply original image size by, where ‘original’ is derived from the span of the X or Y cartesian coordinates.
titles – optional structure titles keyed by SMILES; if provided, this triggers incorporation of a pH-dependent populations graph, which is expected to exist in the CWD as a .png file.
page_title – optional title to print at top of HTML page
- Returns
filename of PDF document if it succeeds, otherwise filename of HTML file. PDF generation will fail if graphics libraries are missing.
- schrodinger.application.jaguar.macro_pka_utils.graph_populations_at_pH(jobname: str, macropKas: List[float], all_label: Dict[Tuple[int, int], str], all_x: Dict[Tuple[int, int], List[float]], all_y: Dict[Tuple[int, int], List[float]], input_abs_charge: int = 0, user_pH: Optional[float] = None)¶
Create pH-dependent populations graph.
- Parameters
jobname – name of job to prefix file names
macropKas – list of macro-pKa values to plot
all_label (dict[tuple, list]) – dict of labels (tautomer name). Must be in the desired order for the legend
all_x – dict of x values (pH) for each tautomer. Must have same keys as
all_label
all_y – dict of y values (% population). Must have same keys as
all_label
input_abs_charge – offset to convert relative to absolute charge
user_pH – user-input pH value for reference