Package schrodinger :: Package trajectory :: Module desmondsimulation :: Class _DesmondFrame
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Class _DesmondFrame

_DesmondFrame contains simulation data at a particular time.

Each raw frame may contain position and velocity of pseudo atoms. Data for pseudo atoms can appear behind component ct or solvent ct. We don't want to expose them in most cases.

Instance Methods [hide private]
 
__init__(self, rawframe, natom=None, frame_id=None, cst=None)
 
getId(self)
 
getStructure(self)
Get a Structure associated with this frame.
 
getMinimalDifference(self, pos1, pos2)
Calculate the smallest difference between two sets of points in the frame, paying attention to periodic boundary conditions.
 
getCellDiff(self, pos1, pos2)
 
position(self)
Position of the real atoms in the frame.
 
pseudo_position(self)
Position of pseudo particles in the frame.
 
velocity(self)
Velocity of the real atoms in the frame.
 
particle_position(self)
Position for all particles in the frame, including pseudo atoms.
 
particle_velocity(self)
Velocity for all particles in the frame, including pseudo atoms.
 
atom_total(self)
Number of real atoms in this frame.
 
particle_total(self)
Number of particles in this frame, including atoms and pseudo atoms.
 
__copy__(self)
 
duplicateFrame(self)
 
__len__(self)
Return the number of atoms in the frame.
a numpy array with shape (9,).
box(self)
The simulation box for the frame.
a BoundaryCondition instance
boundary_condition(self)
The periodic boundary condition for this frame.
 
time(self)
Chemical time (ps) for this frame.
 
charge(self)
Numpy array of atom charges with shape (self._nparticles, 1).
 
mass(self)
Numpy array of atom masses with shape (self._nparticles, 1).
 
total_mass(self)
Total mass of all atoms in the frame.
 
set_pseudo_position(self)
Update positions on the pseudo particles Only works when all pseudo particles are in a single CT
Method Details [hide private]

getMinimalDifference(self, pos1, pos2)

 

Calculate the smallest difference between two sets of points in the frame, paying attention to periodic boundary conditions. Return an array of vectors.

Parameters:
  • pos2 (numpy array with shape (N, 3))
  • pos1 (numpy array with shape (N, 3))
Returns:
numpy array with shape (N, 3).

getCellDiff(self, pos1, pos2)

 
Parameters:
  • pos2 - reference position

position(self)

 

Position of the real atoms in the frame.

Decorators:
  • @property

pseudo_position(self)

 

Position of pseudo particles in the frame.

Decorators:
  • @property

velocity(self)

 

Velocity of the real atoms in the frame.

Decorators:
  • @property

particle_position(self)

 

Position for all particles in the frame, including pseudo atoms.

Decorators:
  • @property

particle_velocity(self)

 

Velocity for all particles in the frame, including pseudo atoms.

Decorators:
  • @property

atom_total(self)

 

Number of real atoms in this frame.

Decorators:
  • @property

particle_total(self)

 

Number of particles in this frame, including atoms and pseudo atoms.

Decorators:
  • @property

box(self)

 

The simulation box for the frame.

Returns: a numpy array with shape (9,).
Decorators:
  • @property

boundary_condition(self)

 

The periodic boundary condition for this frame.

Returns: a BoundaryCondition instance
Decorators:
  • @property

time(self)

 

Chemical time (ps) for this frame.

Decorators:
  • @property

charge(self)

 

Numpy array of atom charges with shape (self._nparticles, 1).

Decorators:
  • @property

mass(self)

 

Numpy array of atom masses with shape (self._nparticles, 1).

Decorators:
  • @property

total_mass(self)

 

Total mass of all atoms in the frame.

Decorators:
  • @property

set_pseudo_position(self)

 

Update positions on the pseudo particles Only works when all pseudo particles are in a single CT

Decorators:
  • @property