MATLAB Examples

# frame2atom.m

• This function extracts a frame to the trajectory matrix
• Tested 15/04/2017
• Please report bugs to michael.holmboe@umu.se

## Examples

• atom = frame2atom(atom,traj,frame,Box_dim)
• atom = frame2atom(atom,traj,frame,Box_dim,'smooth')
```function new_atom = frame2atom(atom,traj,frame,Box_dim,varargin) ```
```new_atom=atom; XYZ=traj(frame,:); new_XYZ_data=reshape(XYZ,3,[])'; % To smooth out .xtc data due to low precision if nargin>4 new_XYZ_data=new_XYZ_data+(rand(size(new_XYZ_data))-.5)/100; end for i=1:size(new_XYZ_data,1); new_atom(i).x=new_XYZ_data(i,1); new_atom(i).y=new_XYZ_data(i,2); new_atom(i).z=new_XYZ_data(i,3); end % new_atom=update_atom(new_atom); % function atom = atom_frame(atom,frame) % %% This function is used to extract a frame to the atom struct % % X=num2cell(arrayfun(@(x) x.x(frame,:), atom)); % Y=num2cell(arrayfun(@(x) x.y(frame,:), atom)); % Z=num2cell(arrayfun(@(x) x.z(frame,:), atom)); % % [atom.x]=deal(X{:}); % [atom.y]=deal(Y{:}); % [atom.z]=deal(Z{:}); %assignin('caller','frame',frame); ```