MATLAB Examples

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import_atom_gro.m - This function import .gro files into the atom struct

function atom = import_atom_gro_test(filenamegro)
tic
C = textread(filenamegro, '%s','delimiter', '\n');
Title=C{1}; nAtoms=str2num(cell2mat(C(2)));
startRow = 3; endRow = 2+nAtoms;

Box_dim=str2double(strsplit(C{endRow+1}))*10;

if size(Box_dim,2)==3;
    Box_dim=[Box_dim 0 0 0];
end

fileID = fopen(filenamegro,'r');

Read columns of data as strings:

formatSpec = '%5s%5s%5s%5.0f%8.3f%8.3f%8.3f%8.4f%8.4f%8.4f%[^\n\r]';

Open the text file.

fileID = fopen(filenamegro,'r');
dataArray = textscan(fileID, formatSpec, endRow-startRow+1, 'Delimiter', '', 'WhiteSpace', '', 'EmptyValue' ,NaN,'HeaderLines', startRow-1, 'ReturnOnError', false);
fclose(fileID);

AtomID ResName

nAtoms=size(dataArray{:,5}(:),1);
MolID = str2double((dataArray{:,1})); % Converts to double
Resname = strtrim(dataArray{:,2});
Atomtype = strtrim(dataArray{:,3});
ind=find(dataArray{:,4}(:)>99999);
dataArray{1,4}(ind)=dataArray{1,4}(ind)-100000;
AtomID = dataArray{:,4}; % Converts to double
X_coord = dataArray{:,5}*10;
Y_coord = dataArray{:,6}*10;
Z_coord = dataArray{:,7}*10;
X_velo = dataArray{:,8}*10;
Y_velo = dataArray{:,9}*10;
Z_velo = dataArray{:,10}*10;

% atom = struct('atom',struct('molid',cell(1,nAtoms),'resname',cell(1,nAtoms),'type',cell(1,nAtoms),'fftype',cell(1,nAtoms),...
%      'index',cell(1,nAtoms),'x',cell(1,nAtoms),'y',cell(1,nAtoms),'z',cell(1,nAtoms),'vx',cell(1,nAtoms),'vy',cell(1,nAtoms),'vz',cell(1,nAtoms)));
nmol=1;first_in=[1];last_in=[];
for i=1:nAtoms;
    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=1;
    end
    atom(i).resname=Resname(i);
    atom(i).type=Atomtype(i);
    atom(i).fftype=Atomtype(i);
    atom(i).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=X_coord(i);
    atom(i).y=Y_coord(i);
    atom(i).z=Z_coord(i);
%     atom(i).fx=X_coord(i)/Box_dim(1);
%     atom(i).fy=Y_coord(i)/Box_dim(2);
%     atom(i).fz=Z_coord(i)/Box_dim(3);
    atom(i).vx=X_velo(i);
    atom(i).vy=Y_velo(i);
    atom(i).vz=Z_velo(i);
end

last_in(atom(end).molid,1)=nAtoms;

XYZ_data=[[atom.x]' [atom.y]' [atom.z]'];
XYZ_labels=[atom.type]';

assignin('caller','XYZ_labels',XYZ_labels)
assignin('caller','XYZ_data',XYZ_data)
assignin('caller','atom',atom)
assignin('caller','nAtoms',nAtoms)
assignin('caller','Box_dim',Box_dim)
assignin('caller','MolID',MolID)

disp('.gro file imported')
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