Package schrodinger :: Package structutils :: Module sitealign :: Class SiteMatchLookup

Class SiteMatchLookup

Lookup for any reference and mobile structures that have matching binding site atoms. This stores a reference structure and a mobile structure, along with their mapped C-alpha atoms.

The reason the terms reference and mobile are used is because when superimposing 2 structures for RMSD calculations the "reference" structure will always be the stationary structure by default. The "mobile" structure will have it's coordinates changed to get an iteratively lower RMSD.

Instance Methods

[hide private]

__init__(self, ref_st, mobile_st, atom_map)

getMobileStRMSD(self)
Gets the inplace and superimposed RMSDs for the mobile st

_setSuperimposedRMSD(self, new_rmsd)
Sets the superimposed RMSD for the mobile st

_setInPlaceRMSD(self, new_rmsd)
Sets the inplace RMSD for the mobile st

list

ref_keys(self)
Getter for reference keys.

list

mob_keys(self)
Getter for mobile keys.

getMatchingAtomMap(self)

float

getSuperimposedRMSD(self)
Superimpose mobile structure to reference structure.

float

getInPlaceRMSD(self, **kwargs)
Get the in-place RMSD of the reference structure to the mobile structure.

colorByRMSD(self)
Color the reference and mobile structure by per-residue, backbone atom RMSD.

Class Variables

[hide private]

SUPERIMPOSED_PROPERTY = 'r_sitealign_Superimposed_RMSD'

INPLACE_PROPERTY = 'r_sitealign_In_Place_RMSD'

Method Details

[hide private]

init(self, ref_st, mobile_st, atom_map)
(Constructor)

Parameters:

ref_st (structure) - Reference structure
mobile_st (structure) - Mobile structure
atom_map (dict where keys are ref atom indices and values are the mobile atom indices that overlap the ref indices.) - Reference and mobile binding site atom map

ref_keys(self)

Getter for reference keys. The key is a list of residue strings defining the residues belonging to the reference structure.

Returns: list

List of residue strings defining residues in reference structure

Decorators:

@property

mob_keys(self)

Getter for mobile keys. The key is a list of residue strings defining the residues belonging to the mobile structure. If the matching mobile key is None, an empty string is appended.

Returns: list

List of residue strings defining residues in mobile structure

Decorators:

@property

getSuperimposedRMSD(self)

Superimpose mobile structure to reference structure. This will translate the mobile structure to the reference structure.

Returns: float: The RMSD after superimposing

getInPlaceRMSD(self, **kwargs)

Get the in-place RMSD of the reference structure to the mobile structure. No translation happens.

Returns: float: The in-place RMSD

See Also: rmsd.calculate_in_place_rmsd for available kwargs

colorByRMSD(self)

Color the reference and mobile structure by per-residue, backbone atom RMSD. This will change:

Style of all non-het atoms in mobile structure to "element"
Color of all non-het carbons in mobile structure to "user12"
Style of mobile backbone atoms to ball and stick
Color of mobile residues by red-blue scale depending on per-reside RMSD
- blue for RMSD below 0.1
- red for RMSD above 3.4

Class SiteMatchLookup

__init__(self, ref_st, mobile_st, atom_map) (Constructor)

ref_keys(self)

mob_keys(self)

getSuperimposedRMSD(self)

getInPlaceRMSD(self, **kwargs)

colorByRMSD(self)

init(self, ref_st, mobile_st, atom_map)
(Constructor)