Index in position 1 is invalid. Array indices must be positive integers or logical values?

In the following code I encounter the problem in the last line. How to rectify this? The integer value is positive , i.e., i=1:3, but I am getting this error.

uxc = getpdb('1UXC'); 
isTYR = ({uxc.Model.Atom.resName} == "TYR") 

isTYR = 1×808 logical array
   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0

uxcTYR = uxc.Model.Atom(isTYR)  % Extracts particulars of only TYR

uxcTYR = 1×63 struct array with fields:
    AtomSerNo
    AtomName
    altLoc
    resName
    chainID
    resSeq
    iCode
    X
    Y
    Z
    occupancy
    tempFactor
    segID
    element
    charge
    AtomNameStruct

TyrXYZ = [uxcTYR.X; uxcTYR.Y; uxcTYR.Z]' ; %Coordinates of all Tyrosine residues

Tyrcd = {};
Tyrseq = {};
Tyrmass = {};
sizeTyr = size(TyrXYZ);
numTyr = sizeTyr(1) / 21 ;
for i = 1:numTyr
    Tyrcd{i} = TyrXYZ((21*i-20):(21*i),:);
    Tseq = [uxcTYR.element]' ;
    Tyrseq{i} = Tseq((21*i-20):(21*i),:)
end

Tyrseq = 1×1 cell array
    {21×1 char}

Tyrseq = 1×2 cell array
    {21×1 char}    {21×1 char}

Tyrseq = 1×3 cell array
    {21×1 char}    {21×1 char}    {21×1 char}

%COM
Amac_mass = ["A", 71.0788;"R", 156.1875;"N", 114.1038;"D", 115.0886;"C", 103.1388;"E", 129.1155;"Q", 128.1307;"G", 57.0519;"H", 137.1411;"I", 113.1594;"L", 113.1594;"K", 128.1741;"M", 131.1926;"F", 147.1766;"P", 97.1167;"S", 87.0782;"T", 101.1051;"W", 186.2132;"Y", 163.1760;"V", 99.1326];
Tyrmass = {};
for i = 1:numTyr
[ism2,idx2] = ismember(Tyrseq{i},Amac_mass(:,1));
Tyrmass{i} = [Amac_mass(idx2,:)];
end

Index in position 1 is invalid. Array indices must be positive integers or logical values.

Answer 1

[Walter Roberson]

ismember returns 0 for indices in the case that the value was not found.

Note that the entries in Tyrseq have not had trailing blanks removed.

[Masha]

I tried fixing the trailing blanks but the error is still shown.

Answer 2

[Steven Lord]

If you just want to be able to determine the mass for a specified identifier, I wouldn't use ismember in this case. I'd use a dictionary object. I'm going to start off with a cell array because I don't feel like editing the code further to split this into separate string and numeric arrays.

idAndMass = {"A", 71.0788;"R", 156.1875;"N", 114.1038;"D", 115.0886;"C", 103.1388;...
             "E", 129.1155;"Q", 128.1307;"G", 57.0519;"H", 137.1411;"I", 113.1594;...
             "L", 113.1594;"K", 128.1741;"M", 131.1926;"F", 147.1766;"P", 97.1167;...
             "S", 87.0782;"T", 101.1051;"W", 186.2132;"Y", 163.1760;"V", 99.1326};
D = dictionary([idAndMass{:, 1}], [idAndMass{:, 2}])

D = 
  dictionary (string ⟼ double) with 20 entries:

    "A" ⟼ 71.0788
    "R" ⟼ 156.1875
    "N" ⟼ 114.1038
    "D" ⟼ 115.0886
    "C" ⟼ 103.1388
    "E" ⟼ 129.1155
    "Q" ⟼ 128.1307
    "G" ⟼ 57.0519
    "H" ⟼ 137.1411
    "I" ⟼ 113.1594
    "L" ⟼ 113.1594
    "K" ⟼ 128.1741
    "M" ⟼ 131.1926
    "F" ⟼ 147.1766
    "P" ⟼ 97.1167
    "S" ⟼ 87.0782
    "T" ⟼ 101.1051
    "W" ⟼ 186.2132
    "Y" ⟼ 163.1760
    "V" ⟼ 99.1326

Now to use it I can query the dictionary:

values = D(["M", "A", "T"])

values = 1×3

131.1926 71.0788 101.1051

though I'd check if the identifier I'm searching for isKey of the dictionary first, to guard against your sequence having an identifier for which you haven't specified a mass (like "B" in the example below.)

isInDictionary = isKey(D, ["M", "A", "T", "L", "A", "B"])

isInDictionary = 1×6 logical array
   1   1   1   1   1   0

[Masha]

Thank you for the suggestion!