Package schrodinger :: Package application :: Package jaguar :: Package gui :: Package tabs :: Module scan_tab :: Class ScanCoordinateData

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Class ScanCoordinateData

                object --+    
                         |    
coordinates.CoordinateData --+
                             |
                            ScanCoordinateData

This class stores all data for a single scan coordinate.

Instance Methods

[hide private]

__init__(self, st, atoms, coordinate_type, start_value=None, final_value=None, increment=None)
Initialize coordinates data given a structure, set of atom indices and coordinate type.

float

_getCurrentValue(self)
This function return the current value of coordinate.

_setDefaultValues(self)
This function sets default start, final and increment values for this coordinate.

_setNumberOfSteps(self)
This function sets number of steps between start and final values.

Inherited from coordinates.CoordinateData: validate

Inherited from coordinates.CoordinateData (private): _getAtomName, _getCoordinateName

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

Class Variables

[hide private]

dict COORDINATE_FUNCS = {mm.MMJAG_COORD_CART_X: mm.mmct_atom_get_x,...
dictionary that maps coordinate type to mmct function uses to calculate coordinate value.

COORDINATE_DISTANCE_OFFSET = 0.2

COORDINATE_DISTANCE_INCREMENT = 0.1

COORDINATE_ANGLE_OFFSET = 20.0

COORDINATE_ANGLE_INCREMENT = 5.0

Inherited from coordinates.CoordinateData: COLUMN

Instance Variables

[hide private]

list

atom_indices
indices of atoms, which define this coordinate

str

coordinate_name
name of this coordinate based on atom indices

int

coordinate_type
coordinate type

float

current_value
current value of this coordinate

float

final_value
final coordinate value

float

increment
increment value

int

num_steps
number of steps

schrodinger.structure.Structure

st
ct structure for which coordinates are defined

float

start_value
starting coordinate value

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, st, atoms, coordinate_type, start_value=None, final_value=None, increment=None)
(Constructor)

Initialize coordinates data given a structure, set of atom indices and coordinate type.

Parameters:

st (schrodinger.structure.Structure) - structure
atoms (list) - atom indices
coordinate_type (int) - coordinate type
start_value (float) - starting coordinate value
final_value (float) - final coordinate value
increment (float) - increment value

Overrides: object.__init__

_getCurrentValue(self)

This function return the current value of coordinate.

Returns: float: coordinate current value

_setNumberOfSteps(self)

This function sets number of steps between start and final values. Use the same equation that mmjag's scan.c uses.

Class Variable Details

[hide private]

COORDINATE_FUNCS

dictionary that maps coordinate type to mmct function uses to calculate coordinate value.

Type:: dict

Value:

{mm.MMJAG_COORD_CART_X: mm.mmct_atom_get_x, mm.MMJAG_COORD_CART_Y: mm.
mmct_atom_get_y, mm.MMJAG_COORD_CART_Z: mm.mmct_atom_get_z, mm.MMJAG_C
OORD_DISTANCE: mm.mmct_atom_get_distance, mm.MMJAG_COORD_ANGLE: mm.mmc
t_atom_get_bond_angle, mm.MMJAG_COORD_TORSION: mm.mmct_atom_get_dihedr
al_angle}

Class ScanCoordinateData

__init__(self, st, atoms, coordinate_type, start_value=None, final_value=None, increment=None) (Constructor)

_getCurrentValue(self)

_setNumberOfSteps(self)

COORDINATE_FUNCS

init(self, st, atoms, coordinate_type, start_value=None, final_value=None, increment=None)
(Constructor)