Within a for loop, you can read one line at a time using fgetl. Once you have the line, it looks like you need to determine where the % is in the line to know whether the data is before the % or if the data is on the next line. You could use find to find the index of the first %:
ind = find(str == '%',1);
if ind == 1
% Read next line for data
else
% Data is earlier in the line.
end
To determine the parameter name, I think regexp is the only option. For example:
out = regexp(str,'^(?<value>[^%]*)%(?<type>Parameter|Matrix) (?<name>[\S]+)','once','names')
The output from that statement should be a structure with three fields: value (the part before the %), type (the part immediately after the %), and name (the characters after either Parameter or Matrix). It won't work on the line that includes "Temperature Initial/Final/Step". You can either use a different pattern match for that (for example, you could just use contains or strfind to determine if the word 'Temperature' is in the line), or you can try to modify the expression I proposed. It isn't clear which would be easier.
Once you've separated those pieces, you can work with them all individually. You can use sscanf or str2num to convert the strings into doubles.
The last part you may need is how to use a variable to access a struct field. For example:
fieldname = out.name; % This is the 'F' or 'Y' or 'A' from above.
A.(fieldname) = str2num(out.value); % Store the value in the field of the struct.
That might be enough to get you started.
