Class Scaffold

Create a Scaffold object

Parameters:

• struct (schrodinger.structure.Structure or None) - The scaffold structure, or None if there is no scaffold for the cell.

Overrides: object.__init__

Causes scaffold objects to evaluate to False if the scaffold structure evaluates to False

Returns: bool

A boolean cast of the scaffold property

Computes the approximate volume of the scaffold molecule using a Monte
Carlo sampling algorithm. The alogorithm:
    1) define a box that fully encloses the structure
    2) randomly pick a point inside the box
    3) check if the point lies inside the VDW radius of an atom
    4) iterate over steps 2 & 3 a bunch
    5) The volume is box_volume * fraction of points inside VDW radii

@type vdw_scale: float
@param vdw_scale: The VdW scale factor to apply to VdW radii when
checking to see if a point is "inside" an atom

@rtype: float
@return: The approximate volume of a molecule

@note: This is expensive, so is only done at class initialization. After
that, call getExcludedVolume to obtain the cached volume.

Return a new structure that contains the scaffold molecule. If there is scaffold structure, the returned structure is empty

Returns: schrodinger.structure.Structure

A structure object that is either empty or contains the scaffold structure, depending on whether a scaffold structure exists or not.

Get the amount of volume the scaffold occupies

Returns: bool

The volume computed by approximateVolume when this object was created.

The default implementation is to define a cube with all sides equal that is centered on the scaffold centroid.

Parameters:

• volume (float) - The volume of the desired cube

Returns: Box

The Box object for this scaffold

Add periodic boundary condition properties to the structure. This method overwrites any existing periodic boundary condition properties, including Desmond chorus, PDB space group and Crystal Builder BC_BOX properties.

Parameters:

• struct (schrodinger.structure.Structure) - The structure to add the properties to
• volume (float) - The volume of the cubic periodic boundary condition

Add properties to the structure that define the periodic boundary condition in the way Desmond wants it defined.

Parameters:

• struct (schrodinger.structure.Structure) - The structure to add the properties to
• ax - The value of the ax box property
• ay - The value of the ay box property. Defaults to 0.
• az - The value of the az box property. Defaults to 0.
• bx - The value of the bx box property. Defaults to 0.
• by - The value of the by box property. If not given, this value is set the same as ax.
• bz - The value of the bz box property. Defaults to 0.
• cx - The value of the cx box property. Defaults to 0.
• cy - The value of the cy box property. Defaults to 0.
• cz - The value of the cz box property. If not given, this value is set the same as ax.

Add properties to the structure that define the periodic boundary condition in the way Crystal wants it defined.

Parameters:

• struct (schrodinger.structure.Structure) - The structure to add the properties to
• side (float) - The length of one side of the cubic periodic boundary condition

Add properties to the structure that define the periodic boundary condition in the way Crystal wants it defined.

Parameters:

• struct (schrodinger.structure.Structure) - The structure to add the properties to
• aval (float) - The length of lattice vector a
• bval (float) - The length of lattice vector b
• cval (float) - The length of lattice vector c
• alpha (float) - The angle between the b & c vectors (degrees)
• beta (float) - The angle between the a & c vectors (degrees)
• gamma (float) - The angle between the a & b vectors (degrees)
• vectors (list) - A list of length three, each item is a list or array of length three which gives the x, y and z values of a lattice vector. If not supplied, will be computed from a, b, c, alpha, beta and gamma

Get the length of one side of the periodic boundary condition

Parameters:

• cell (schrodinger.structure.Structure) - The current cell with structures that have already been placed

Returns: list

A six item list that defines the min and max value of X, Y and Z. The six values in order are: Xmin, Ymin, Zmin, Xmax, Ymax, Zmax. If not PBC box has been created, a list of all 0.0 is returned

Get a point in a random position in the box

Returns: list

[x, y, z] coordinates of a random point in the box