center_atom.m

This function centers the atom with respect to the resname molecule. newBox_dim could be a new or old Box_dim
atom is the atom struct
Box_dim is the box dimension vector
resname is the Resnames ofthe atoms ou want to move, can be 'all'
dim is a string containing for example x, xy, xyz

Version
Contact

Version

2.11

Contact

Please report problems/bugs to michael.holmboe@umu.se

atom = center_atom(atom,Box_dim) % Basic input arguments
atom = center_atom(atom,Box_dim,'Na') % Will center with respect to all residues named Na
atom = center_atom(atom,Box_dim,'all','xy') % Will center woth respect to all sites in x and y, resp.

function atom = center_atom(atom,Box_dim,varargin)
disp('Centering')

nAtoms=size(atom,2);

if nargin == 2
    resname='all';
    dim='xyz';
elseif nargin == 3
    resname=varargin{1};
    dim='xyz';
elseif nargin == 4
    resname=varargin{1};
    dim=varargin{2};
end

tric_Box_dim=Box_dim;
if numel(Box_dim)==1
    Box_dim(2)=Box_dim;
    Box_dim(3)=Box_dim(2);
    Box_dim(1)=Box_dim(2);
else
    if size(tric_Box_dim(1,:),2)>3
        atom=orto_atom(atom,Box_dim);
        Box_dim=orto_Box_dim;
    end
end


% Box_dim=newBox_dim;

% atom = wrap_atom(atom,Box_dim);

if strcmpi(resname,'all')
    ind_resname=1:nAtoms;
else
    if sum(find(strcmp([atom.resname],resname)))>0
        ind_resname=find(strcmp([atom.resname],resname));
    elseif sum(find(strcmp([atom.type],resname)))>0
        ind_resname=find(strcmp([atom.type],resname));
    end
end

if strfind(dim,'x') | strfind(dim,'X')
    disp('centering along x')
    x_shift=num2cell([atom.x]-median([atom(ind_resname).x])+Box_dim(1)/2); [atom(:).x]=deal(x_shift{:});
    x_shift=num2cell([atom.x]-mean([atom(ind_resname).x])+Box_dim(1)/2); [atom(:).x]=deal(x_shift{:});
end
if strfind(dim,'y') | strfind(dim,'Y')
    disp('centering along y')
    y_shift=num2cell([atom.y]-median([atom(ind_resname).y])+Box_dim(2)/2); [atom(:).y]=deal(y_shift{:});
    y_shift=num2cell([atom.y]-mean([atom(ind_resname).y])+Box_dim(2)/2); [atom(:).y]=deal(y_shift{:});
end
if strfind(dim,'z') | strfind(dim,'Z')
    disp('centering along z')
    median([atom(ind_resname).z])
    z_shift=num2cell([atom.z]-median([atom(ind_resname).z])+Box_dim(3)/2);   [atom(:).z]=deal(z_shift{:});
    z_shift=num2cell([atom.z]-mean([atom(ind_resname).z])+Box_dim(3)/2); [atom(:).z]=deal(z_shift{:});
end

if size(tric_Box_dim(1,:),2)>3
    xy=tric_Box_dim(6); xz=tric_Box_dim(8); yz=tric_Box_dim(9);
    atom=triclinic_atom(atom,Box_dim,[xy xz yz],'tilt');
    Box_dim=tric_Box_dim;

    if sum(abs(triclinic_Box_dim-tric_Box_dim))>0.01
        disp('Canged box dimensions between initial and temp triclinic cell')
        triclinic_Box_dim
        tric_Box_dim
        pause
    end
end

assignin('caller','Box_dim',Box_dim);
assignin('caller','XYZ_data',[[atom.x]' [atom.y]' [atom.z]']);
assignin('caller','XYZ_labels',[atom.type]');

center_atom.m

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