update_atom.m

This function updates the molid index and the atoms index in the atom struct
Multiple atom structs can be also concatenated by using this format atom = update_atom({atom1 atom2 atom3})

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Contact
Examples

Version

2.11

Contact

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

Examples

atom = update_atom(atom) % Basic input arguments
atom = update_atom({atom1 atom2 atom3}) % Will append atom1 and atom2 and atom3 and update their MolID's, respectively

function atom = update_atom(atom,varargin)

if iscell(atom)

    % In case first struct is empty
    if size(atom,2)>1 && size(atom{1},2)==0 % Was 1?
        for i=2:size(atom,2)
            newatom{i-1}=atom{i};
        end
        atom=newatom;
    end

    size_ind=zeros(size(atom,2),1);
    for i=1:size(atom,2)
        if size(atom{i},2)>0
            size_ind(i)=1;
        end
    end

    keepfieldnames=fieldnames(atom{1}); % Orig line
    if size(atom,2) > 1
        for i=1:size(atom,2)
            if numel(atom{i})
                keepfieldnames=intersect(keepfieldnames,fieldnames(atom{i}));
            end
        end
        for i=1:size(atom,2)
            if numel(atom{i})
                rmfieldnames=setdiff(fieldnames(atom{i}),keepfieldnames);
                for j=1:numel(rmfieldnames)
                    atom{i}=rmfield(atom{i},rmfieldnames(j));
                end
            end
        end
    end

    atom=atom(logical(size_ind));
    atom_Tot=atom{1}; % Orig line
    if size(atom,2) > 1
        for i=2:size(atom,2)
            atom_temp=atom{i};
            if size(atom_temp,2)>0
                if numel(unique([atom_temp.molid]))==1
                    molid=num2cell(([atom_temp.molid]+[atom_Tot(end).molid]));
                    [atom_temp.molid]=deal(molid{:});
                elseif numel(unique([atom_temp.molid]))==size(atom_temp,2)
                    molid=num2cell(([1:size(atom_temp,2)]+[atom_Tot(end).molid]));
                    [atom_temp.molid]=deal(molid{:});
                end
            end
            atom_Tot=[atom_Tot atom_temp];
        end
    end
    atom=atom_Tot;
end

nAtoms=size(atom,2);

MolID=[atom.molid];

if length(MolID) < nAtoms
    MolID=[MolID;[MolID(end)+1:nAtoms]'];
end

% Update Molid and index
nmol=1;first_in=[1];last_in=[];
for i=1:nAtoms
    if i > 1 && MolID(i) ~= MolID(i-1) | strcmp([atom(i).resname],[atom(i-1).resname]) == 0
        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=1;
    end
    atom(i).index=mod(i,100000);
end

atom=order_attributes(atom); % Order all attributes

% assignin('base','atom1',atom);

% atom = resname_atom(atom);

if nargin>1
    [atom.molid]=deal(varargin{1});
end

assignin('caller','nAtoms',nAtoms);

update_atom.m

Contents

Version

Contact

Examples