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

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Masha
Masha 2023-2-24
评论： Masha 2023-2-28
Ran in:
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.

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回答（2 个）

Walter Roberson
Walter Roberson 2023-2-24
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.
Steven Lord
Steven Lord 2023-2-24
Ran in:
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

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