MATLAB Examples

• This function appends so-called XYZ atomtype labels and XYZ data to an existing atom struct
• XYZ_labels is a nAtoms x 1 (cell) vector of atomtype names
• XYZ_data is a nAtoms x 3 data matrix holding the x,y,z coordinates
• resname is the optional Resname you choose
• in_atom is the optional (requires resname) existing atom struct for which the XYZ data should be appended to
• Tested 15/04/2017
• Please report bugs to michael.holmboe@umu.se

## Examples

```function atom = add2atom(XYZ_labels,XYZ_data,varargin) if numel(XYZ_data)==1 if iscell(XYZ_labels)==0;XYZ_labels={XYZ_labels}; end end if numel(XYZ_data)==1 XYZ_data(1)=XYZ_data(1); XYZ_data(2)=XYZ_data(1); XYZ_data(3)=XYZ_data(1); end if nargin > 2 resname=varargin{1}; if nargin > 3 in_atom=varargin{2}; else in_atom=[]; end else resname=XYZ_labels; in_atom=[]; end nAtoms=length(XYZ_data); nmol=1; MolID=zeros(nAtoms,1); if strncmpi(XYZ_labels(1),'Ow',2) MolID(1:3:end)=ceil((nmol/3):3:nAtoms)'; MolID(2:3:end)=ceil((nmol/3):3:nAtoms)'; MolID(3:3:end)=ceil((nmol/3):3:nAtoms)'; else MolID=nmol:1:nAtoms; end if isfield(in_atom,'molid') MolID=MolID+in_atom(end).molid; index=in_atom(end).index; else in_atom=[]; index=0; end if isfield(in_atom,'molid') == false && sum(size(unique(XYZ_labels),1)) > 3 MolID(:)=1; index=0; elseif isfield(in_atom,'molid') == true && sum(size(unique(XYZ_labels),1)) > 3 MolID(:)=1+in_atom(end).molid; index=in_atom(end).index; end nmol=MolID(1); first_in=[1];last_in=[]; for i=1:size(XYZ_data,1) if i > 1 && MolID(i) ~= MolID(i-1) nmol=nmol+1; atom(i).molid=nmol; first_in(atom(i).molid,1)=i; last_in(atom(i).molid-1,1)=i-1; elseif i > 1 atom(i).molid=atom(i-1).molid; elseif i == 1 atom(i).molid=MolID(1); end if strcmpi(resname,'same') disp('Same resname as type') atom(i).resname=XYZ_labels(i); else atom(i).resname=resname; end atom(i).type=XYZ_labels(i,:); atom(i).fftype=XYZ_labels(i,:); atom(i).index=index+mod(i,100000); atom(i).neigh.type = {}; atom(i).neigh.index = zeros(6,1); atom(i).neigh.dist = zeros(6,1); atom(i).bond.type = zeros(6,1); atom(i).bond.index = zeros(6,1); atom(i).angle.type = zeros(6,1); atom(i).angle.index = zeros(6,1); atom(i).x=XYZ_data(i,1); atom(i).y=XYZ_data(i,2); atom(i).z=XYZ_data(i,3); atom(i).vx=nan; atom(i).vy=nan; atom(i).vz=nan; end if sum(size(unique(XYZ_labels),1)) > 3 [atom.resname]=deal({resname}); end atom=[in_atom atom]; assignin('caller','XYZ_data',[[atom.x]' [atom.y]' [atom.z]']); assignin('caller','XYZ_labels',[atom.type]'); assignin('caller','nAtoms',nAtoms) assignin('caller','MolID',MolID) disp('add2atom done!') ```