Package schrodinger :: Package application :: Package bioluminate :: Package patch_utils :: Module patch_finder :: Class PreAnalyzer

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Class PreAnalyzer

object --+
         |
        PreAnalyzer

Perform patch finding calculations that only need to be done once per structure. This class is intended to be run under job control.

Instance Methods

[hide private]

__init__(self, struc, asl)
x.__init__(...) initializes x; see help(type(x)) for signature

run(self)
Perform the pre-analysis.

_prepareStructure(self)
Perform necessary calculations on the structure.

_calcCLogP(self)
Calculate cLogP, the partition coefficient, for the entire structure.

_calcPartialCharges(self)
Calculate the partial charge on each atom.

_prepareSurface(self)
Generate the surface and perform necessary calculations on it.

_calculateSurfaceNeighbors(self)
For each vertex on the surface, calculate all neighboring triangles and store the results in self._neighboring_vertices.

_calcSmoothedValues(self)
Smooth the specified atom-level charges for partial charges and slogP-values over the surface.

tuple

_calcResData(self)
Calculate the aggregation, surface area, and reactive residue grouping data for each residue.

ResidueDictionary

_calcAggregation(self, all_seq, all_struc)
Calculate the Zyggregator and Aggrescan values for each residue.

list

_resDataByVertex(self, res_data_by_res)
Create a list of the ResData object corresponding to each surface surface.

_getConnectedComponents(self)
Determine all covalently connected components of self._struc (i.e.

list

_calcZyggregator(self, seq)
Calculate the Zyggregator aggregation score for the specified residues

list

_calcAggrescan(self, seq)
Calculate the Aggrescan aggregation score for the specified residues

_calcSasa(self, res_data_by_res)
Calculate the solvent accessible surface area for each atom and residue.

_calcAccessibility(self, res_data_by_res)
Calculate side chain accessibility (side chain surface area divided by the maximum possible side chain surface area for that residue type).

_calcReactiveResidues(self, res_data_by_res, asa_by_atom, all_struc)
Determine which residues match the reactive residue sites.

list

_genSeqDictsForReactiveResiduesSearch(self, asa_by_atom, all_struc)
Create the sequence dictionaries required for find_generalized_pattern()

_calcDisulfides(self, res_data_by_res)
Determine which residues have a disulfide bond.

bool

_resHasDisulfide(self, res)
Does the specified residue contain a disulfide bond?

_calcAntibodyTopography(self, res_data_by_res)
Determine the antibody topography for each residue.

write(self, basename)
Write out the surface and all calculated values

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Methods

[hide private]

PreAnalyzer

readAndRun(cls, basename)
Read a structure and ASL from the specified files and run the analysis.

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, struc, asl)
(Constructor)

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:

struc (schrodinger.structure.Structure) - The structure to analyze
asl (str) - An ASL describing atoms of struc to analyze

Overrides: object.__init__

readAndRun(cls, basename)
Class Method

Read a structure and ASL from the specified files and run the analysis.

Parameters:

basename (str) - The full path to the file to analyzes except the ".maegz" and ".txt" extensions

Returns: PreAnalyzer

The completed pre-analysis

run(self)

Perform the pre-analysis. The results will be stored in instance attributes and can be written to a pickle file using write.

_prepareStructure(self)

Perform necessary calculations on the structure. The results will be stored in atom-level properties.

_calcCLogP(self)

Calculate cLogP, the partition coefficient, for the entire structure. This measures hydrophobicity. Results will be stored in the CLOGP_PROP atom-level property.

_calcPartialCharges(self)

Calculate the partial charge on each atom. Results will be stored in the PARTIAL_CHARGE_PROP atom-level property.

_prepareSurface(self)

Generate the surface and perform necessary calculations on it. The results will be stored in instance attributes.

_calcResData(self)

Calculate the aggregation, surface area, and reactive residue grouping data for each residue.

Returns: tuple

A tuple of:

A list of residue data for each vertex. The ResData object is given for the residue closest to the vertex.
A list of the solvent accessible surface area for each atom (OneIndexedList)

_calcAggregation(self, all_seq, all_struc)

Calculate the Zyggregator and Aggrescan values for each residue.

Parameters:

all_seq (list) - A list of list of residue names (str). Each list of residue names represents a single covalently connected component.
all_struc (list) - A list of list of schrodinger.structure._Residue objects. This object mirrors the structure of the list of list of residue names.

Returns: ResidueDictionary

A dictionary of ResData objects containing aggregation data

_resDataByVertex(self, res_data_by_res)

Create a list of the ResData object corresponding to each surface surface.

Parameters:

res_data_by_res (ResidueDictionary) - A dictionary of ResData objects

Returns: list

A list of ResData objects

_getConnectedComponents(self)

Determine all covalently connected components of self._struc (i.e. unbroken chain segments).

Returns:

A tuple of:

A list of list of residue names (str). Each list of residue names represents a single covalently connected component.
A list of list of schrodinger.structure._Residue objects. This object mirrors the structure of the list of list of residue names.

_calcZyggregator(self, seq)

Calculate the Zyggregator aggregation score for the specified residues

Parameters:

seq (list) - A list of residue name for a single covalently connected segment.

Returns: list

A list of the Zyggregator score for each residue.

_calcAggrescan(self, seq)

Calculate the Aggrescan aggregation score for the specified residues

Parameters:

seq (list) - A list of residue name for a single covalently connected segment.

Returns: list

A list of the Aggrescan score for each residue.

_calcSasa(self, res_data_by_res)

Calculate the solvent accessible surface area for each atom and residue.

Parameters:

res_data_by_res (ResidueDictionary) - A dictionary of ResData objects. The values of this dictionary will be updated with the calculated accessible side chain surface area.

Returns:

A tuple of:

The res_data_by_res dictionary
A OneIndexedList of solvent accessible surface area for each atom in the structure

_calcAccessibility(self, res_data_by_res)

Calculate side chain accessibility (side chain surface area divided by the maximum possible side chain surface area for that residue type).

Parameters:

res_data_by_res (ResidueDictionary) - A dictionary of ResData objects. The values of this dictionary will be updated with the calculated accessibility values.

_calcReactiveResidues(self, res_data_by_res, asa_by_atom, all_struc)

Determine which residues match the reactive residue sites. Reactive residue definitions are read from the user's profile, so any changes saved via other panels will be picked up and used here.

Parameters:

res_data_by_res (ResidueDictionary) - A dictionary of ResData objects. The reactive_type dictionary will be created and populated for each ResData object.
asa_by_atom (OneIndexedList) - A list of solvent accessible surface area for each atom in the structure
all_struc (list) - A list of list of schrodinger.structure._Residue objects. Each list of residues represents a single covalently connected component.

_genSeqDictsForReactiveResiduesSearch(self, asa_by_atom, all_struc)

Create the sequence dictionaries required for find_generalized_pattern()

Parameters:

asa_by_atom (OneIndexedList) - A list of solvent accessible surface area for each atom in the structure
all_struc (list) - A list of list of schrodinger.structure._Residue objects. Each list of residues represents a single covalently connected component.

Returns: list

The sequence dictionaries required for find_generalized_pattern()

_calcDisulfides(self, res_data_by_res)

Determine which residues have a disulfide bond.

Parameters:

res_data_by_res (ResidueDictionary) - A dictionary of ResData objects. The disulfide attribute (Boolean) will be set for each ResData object.

_resHasDisulfide(self, res)

Does the specified residue contain a disulfide bond?

Parameters:

res (schrodinger.structure._Residue) - The residue to check

Returns: bool

True if res contains a disulfide bond. False otherwise.

_calcAntibodyTopography(self, res_data_by_res)

Determine the antibody topography for each residue. For non-antibody structures, all values will be None. PANEL-7988

Parameters:

res_data_by_res (ResidueDictionary) - A dictionary of ResData objects. The topography attribute (str) will be set for each ResData object.

write(self, basename)

Write out the surface and all calculated values

Parameters:

basename (str) - The filename to write the output to. The surface will be written to basename.vis and the calculated values will be written to basename.pkl.

Class PreAnalyzer

__init__(self, struc, asl) (Constructor)

readAndRun(cls, basename) Class Method

run(self)

_prepareStructure(self)

_calcCLogP(self)

_calcPartialCharges(self)

_prepareSurface(self)

_calcResData(self)

_calcAggregation(self, all_seq, all_struc)

_resDataByVertex(self, res_data_by_res)

_getConnectedComponents(self)

_calcZyggregator(self, seq)

_calcAggrescan(self, seq)

_calcSasa(self, res_data_by_res)

_calcAccessibility(self, res_data_by_res)

_calcReactiveResidues(self, res_data_by_res, asa_by_atom, all_struc)

_genSeqDictsForReactiveResiduesSearch(self, asa_by_atom, all_struc)

_calcDisulfides(self, res_data_by_res)

_resHasDisulfide(self, res)

_calcAntibodyTopography(self, res_data_by_res)

write(self, basename)

init(self, struc, asl)
(Constructor)

readAndRun(cls, basename)
Class Method