Package schrodinger :: Package protein :: Module analysis :: Class Report :: Class primex_steric_clash_data_set

Class primex_steric_clash_data_set

         Report.data_set --+    
                           |    
Report.steric_clash_data_set --+
                               |
                              Report.primex_steric_clash_data_set

A subclass of steric_clash_data_set that computes clashes using a different set of criteria used by PrimeX Polish.

Nested Classes

[hide private]

Inherited from data_set: data_point

Instance Methods

[hide private]

__init__(self, *args, **kwargs)

analyze(self, parent)
compute and store the data for this class

check_hbond(self, protein, atom1, atom2, clash=None, distance=None)
Runs a number of quick checks first before calling the super class' method.

add_point(self, descriptor, values, atoms)
Makes changes to how the output data is recorded relative to the super class.

Inherited from steric_clash_data_set: analyze_pair, find_hbond_hydrogen, run_analysis, within_three_bonds

Inherited from data_set: report, report_data_points

Instance Variables

[hide private]

Inherited from data_set: fields, label, points, summary, title

Method Details

[hide private]

init(self, *args, **kwargs)
(Constructor)

Overrides: data_set.__init__

analyze(self, parent)

compute and store the data for this class

Parameters:

parent (l{report} object) - the report object that this is for

Overrides: data_set.analyze

check_hbond(self, protein, atom1, atom2, clash=None, distance=None)

Runs a number of quick checks first before calling the super class' method. See the super class for more information.

Parameters:

protein - The protein
atom1 - atom 1
atom2 - atom 2
clash - Pre-computed clash ratio
distance - Pre-computed distance
require_hydrogen - Whether an intervening hydrogen must be found to qualify as an H-bond.

Overrides: steric_clash_data_set.check_hbond

add_point(self, descriptor, values, atoms)

Makes changes to how the output data is recorded relative to the super class.

Parameters:

descriptor - Label for this point - typically the user-friendly names of the atom or residues involved
values - The values at this point - varies by subclass
atoms - The atoms involved in this point

Overrides: data_set.add_point

Class primex_steric_clash_data_set

__init__(self, *args, **kwargs) (Constructor)

analyze(self, parent)

check_hbond(self, protein, atom1, atom2, clash=None, distance=None)

add_point(self, descriptor, values, atoms)

init(self, *args, **kwargs)
(Constructor)