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

Class steric_clash_data_set

Report.data_set --+
                  |
                 Report.steric_clash_data_set

Class to compute and hold data for Steric Clashes.

Data point descriptor is atoms involved, values are "Distance", "Min Allowed", "Delta".

Summary is N/A

See parent class data_set for additional documenation

Nested Classes

[hide private]

Inherited from data_set: data_point

Instance Methods

[hide private]

__init__(self, *args, **kwargs)

bool

within_three_bonds(self, protein, iatom, target_atom)
Method to determine whether two atoms are within three bonds of each other.

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

run_analysis(self, protein)
Iterate over the atom pairs and check record clashes

analyze_pair(self, protein, atom1, atom2)
Test a pair of atoms and record data if they clash.

check_hbond(self, protein, atom1, atom2, clash=None, distance=None, require_hydrogen=True)
Test and atom pair to see if they can be considered a hydrogen bond.

find_hbond_hydrogen(self, protein, donor, acceptor, distance=None)
Locate a hydrogen that is bound to the donor that is closer to the acceptor than the donor is.

Inherited from data_set: add_point, 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__

within_three_bonds(self, protein, iatom, target_atom)

Method to determine whether two atoms are within three bonds of each other.

Parameters:

parent - The Report object that this is for
iatom (int) - atom number of first atom
target_atom (int) - atom number of the second atom
protein (Report.local_protein)

Returns: bool

True if atoms are within 3 bonds of each other, False if not

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

run_analysis(self, protein)

Iterate over the atom pairs and check record clashes

Parameters:

protein (Report.local_protein) - the protein

analyze_pair(self, protein, atom1, atom2)

Test a pair of atoms and record data if they clash. Order does not matter.

Parameters:

protein (Report.local_protein) - The protein
atom1 (Report.local_atom) - One atom of the pair
atom2 (Report.local_atom) - The second atom of the pair

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

Test and atom pair to see if they can be considered a hydrogen bond. The presence of a H-bond makes permissible atom proximity that would normally be considered a clash. Atom order does not matter.

Parameters:

protein (Report.local_protein) - The protein
atom1 (Report.local_atom) - atom 1
atom2 (Report.local_atom) - atom 2
clash (float or None) - Pre-computed clash ratio
distance (float or None) - Pre-computed distance
require_hydrogen (bool) - Whether an intervening hydrogen must be found to qualify as an H-bond.

find_hbond_hydrogen(self, protein, donor, acceptor, distance=None)

Locate a hydrogen that is bound to the donor that is closer to the acceptor than the donor is.

Parameters:

protein (Report.local_protein) - the protein
donor (Report.local_atom) - donor atom
acceptor (Report.local_atom) - acceptor atom
distance (float or None) - pre-computed distance between donor and acceptor

Class steric_clash_data_set

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

within_three_bonds(self, protein, iatom, target_atom)

analyze(self, parent)

run_analysis(self, protein)

analyze_pair(self, protein, atom1, atom2)

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

find_hbond_hydrogen(self, protein, donor, acceptor, distance=None)

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