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calcglypos.m
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calcglypos.m
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function [plotinfoout,specialoptions] = calcglypos(sgpseq,options,specialoptions)
% CALCGLYPOS: calculate monosaccharide positions of glycan
%
% Syntax:
% [plotinfoout,specialoptions] = calcglypos(sgpseq,options,specialoptions)
%
% Input:
% sgpseq: string, the glycans to be analyzed.
% options: structure, contains global options for drawing glycans. See
% DRAWGLYCAN for details.
% specialoptions: structure, pre-compiled local options. Each field is a
% type of local option, which contains a n x 2 cell array, 1st column is
% the index number of monosac. that's been modified, 2nd column is the
% detail of the modification.
%
% Output:
% plotinfoout: structure containing the following fields:
% "mspos": n x 2 numerical matrices, monosaccharide positions in the glycan.
% n equals to the number of monosaccharides in the glycan.
% "bondmap": n x n numerical matrices, the linkage information of monosac. in glycan.
% "alllinkout": n x 1 cell array of strings, the glycosidic bond information of glycans.
% "allms": n x 1 cell array of strings, the name of the monosaccharides in glycan.
% "directionseq": n x 1 numerical matrices, the orientation of monosaccharides.
% FIELDS BELOW APPEARS ONLY WHEN INPUT "SPECIALOPTIONS" IS NOT EMPTY
% "bonddescription": modification of individual monosaccharides, such as
% -U, -D, and bond modifications, such as -ZIG, -BOLD.
% other fields: all fields of input "specialoptions" will be copied here.
%
% Note:
% Solo perpendicular monosaccharides will be plotted up,
%e.g. the top vertex of a solitary Fuc will point up
% whatever the orientation of the glycan is.
%
% Example:
% N/A. Run examples in DRAWGLYCAN and set breakpoints.
%
% Children function:
% DRAWRAWTREE, BRANCHEQUALIZER, SMARTPMDISPENSER,
% BONEADDPM, ADDSTUBPM
%
% DrawGlycan authors: Kai Cheng, Yusen Zhou, Sriram Neelamegham
%(c) 2019, Research Foundation for State University of New York. All rights reserved
%
sortbranches = false;
if ischar(options.sortbranches)
if strcmpi(options.sortbranches,'yes') || strcmpi(options.sortbranches,'true')
sortbranches = true;
end
elseif isnumeric(options.sortbranches)
if options.sortbranches > 0
sortbranches = true;
end
elseif islogical(options.sortbranches)
sortbranches = options.sortbranches;
end
if sortbranches
[sgpseq,msindfix] = branchreform(sgpseq);
if ~isempty(specialoptions)
fldnms = fieldnames(specialoptions);
for i = 1:length(fldnms)
for j = 1:size(specialoptions.(fldnms{i}),1)
if ~any(strfind(fldnms{i},'pep'))
specialoptions.(fldnms{i}){j,2} = specialoptions.(fldnms{i}){j,2} + msindfix(specialoptions.(fldnms{i}){j,2});
end
end
end
end
end
alllinkout = regexp(sgpseq,DrawGlycanPara.regexp_monosaclinkage,'match');
for i = 1:length(alllinkout)
alllinkout{i} = alllinkout{i}(2:end-1);
end
%% Start calculation
%% sep. monosac. and bond
thisgly = sgpseq;
thisgly = strrep(thisgly,'[','');
thisgly = strrep(thisgly,']','');
indtemp = strfind(thisgly,'{');
levelindex = zeros(2,length(thisgly));
indtemp2 = strfind(thisgly,'}');
if ~ismember(1,indtemp)
error('Did you forget something?');
end
levelindex(1,indtemp) = 1;
levelindex(1,indtemp2) = -1;
levelindex(2,1) = 1;
for j = 2:size(levelindex,2)
levelindex(2,j) = levelindex(2,j-1) + levelindex(1,j);
end
wholestr = zeros(1,length(thisgly));
wholestr(indtemp) = 1;
wholestr(indtemp2) = 1;
readind = 1;
allms = cell(sum(wholestr)/2,1);
writeind = 1;
tempstr = '';
while readind <= length(wholestr)
if wholestr(readind) ~= 1 % gather character to form the monosac. string
tempstr = [tempstr,thisgly(readind)];
else
if ~isempty(tempstr)
bondinfo = strfind(tempstr,')');
if ~isempty(bondinfo) % using parenthesis
allms{writeind} = tempstr(max(bondinfo) + 1:end);
else % No parenthesis means there's only monosac.
allms{writeind} = tempstr;
end
tempstr = '';
writeind = writeind + 1;
end
end
readind = readind + 1;
end
%% calculate distance of each monosac
letterindex = zeros(1,length(thisgly));
letterindex(regexp(thisgly,'[^{}]')) = 1;
distance = letterindex.*levelindex(2,:);
distance = distance(indtemp+1); % all monosac's
%% build adjacency matrix "bondmap"
bondmap = zeros(length(distance));
readind = 1;
while readind < length(distance)
if (distance(readind + 1) - distance(readind)) == 1
bondmap(readind,readind + 1) = 1; % consecutive numbers indicate bond
readind = readind + 1;
elseif (distance(readind + 1) - distance(readind)) < 1 % if chain is broken, go back to find its fork point
thisind = distance(readind + 1); % where it's broken
itsforkpt = find(distance(1:readind) == thisind - 1,1,'last'); % where is the fork point
bondmap(itsforkpt,readind + 1) = 1; % mark this bond
readind = readind + 1; % keep going on
end
end
ispm = find(ismember(lower(allms),lower(options.perpendicularmonosac)));
%% new version: monosac. is PM only when it's at the terminal of a branch
isterminal = zeros(size(ispm));
for i = 1:length(ispm)
isterminal(i) = ~any(bondmap(ispm(i),:));
end
ispm = ispm(logical(isterminal));
%% new version end
ispm = [ispm,zeros(size(ispm))]; % 1: perpendicular to the right (default) 2: to the left. Assuming parent structure points upwards
%% customized perpendicular monosac.
ppmopt = {'P','PL','PR'};
ppmlr = [0 1 2];
% specialpm = [];
if ~isempty(specialoptions)
spoptfld = fieldnames(specialoptions);
if any(ismember(ppmopt,upper(spoptfld)))
for i = 1:length(ppmopt)
if ismember(ppmopt{i},upper(spoptfld))
specialpm = specialoptions.(ppmopt{i});
specialpm = cell2mat(specialpm(:,2));
ispm = [[specialpm(:),ones(length(specialpm),1)*ppmlr(i)];ispm];
end
end
end
end
if ~isempty(ispm)
[~,ind,~] = unique(ispm(:,1));
ispm = ispm(ind,:);
end
% ispm = [ispm;specialpm(:)];
directionseq = zeros(size(distance));
%% Decide working mode
if isempty(ispm)
drawglycanmode = 1; % bone only
else
if ismember(1,ispm(:,1))
drawglycanmode = 2; % PMS only
else
drawglycanmode = 3; % bone+PMS
end
end
%% Handling 3 different situations
switch drawglycanmode
case 1
mspos = drawrawtree(bondmap,distance,[]);
mspos = branchequalizer(mspos,bondmap);
case 2
mspos = drawrawtree(bondmap,distance,[]);
mspos = branchequalizer(mspos,bondmap);
case 3
bonebondmap = bondmap; % bone part
bonedistance = distance;
pmchildlist = {}; % Each element in 'pmschildlist' is a sub-tree connected to the main structure,
% the first monosac in each element is 'thispms'
while ~isempty(ispm) % retrieve the monosac index of PMS containing sub-trees
tobetracked = ispm(find(ispm(:,1),1,'first'),1);
temppmchild = [];
while ~isempty(tobetracked)
if any(bondmap(tobetracked(1),:))
tobetracked = [tobetracked find(bondmap(tobetracked(1),:))];
end
temppmchild = [temppmchild;tobetracked(1)];
tobetracked(1) = [];
end
[~,pmchildind] = ismember(ispm(:,1),temppmchild);
pmchildind = pmchildind(pmchildind > 0);
tempispm = ispm(pmchildind,:);
temppmchild = [temppmchild,ones(size(temppmchild))*tempispm(1,2)];
pmchildlist = [pmchildlist;temppmchild];
[~,ispmind] = setdiff(ispm(:,1),temppmchild);
ispm = ispm(ispmind,:);
end
parentms = zeros(size(pmchildlist));
allpmchild = []; % this is used later to draw the bone structure of glycan
for j = 1:size(pmchildlist,1)
parentms(j,1) = find(bondmap(:,pmchildlist{j}(1)));
allpmchild = [allpmchild;pmchildlist{j}];
end
[parentmsnum,~,parentmsind] = unique(parentms);
pmgroup = cell(max(parentmsind),2); % The number of elements in 'pmsgroup' equals the number of
for j = 1:size(pmgroup,1)
pmgroup{j,1} = parentmsnum(j); % 1st column contains the parent monosac
pmgroup{j,2} = pmchildlist(parentmsind == j); % 2nd column contains children PMS
end
bonebondmap(:,allpmchild(:,1)) = 0;
bonebondmap(allpmchild(:,1),:) = 0;
bonedistance(allpmchild(:,1)) = 0;
tempbonebondmap = bonebondmap;
tempbonebondmap(allpmchild(:,1),:) = [];
tempbonebondmap(:,allpmchild(:,1)) = [];
mspos = drawrawtree(bondmap,distance,allpmchild(:,1)); % Here mspos contains all pos info of bone monosac
bonemspos = mspos;
bonemspos(allpmchild(:,1),:) = [];
bonemspos = branchequalizer(bonemspos,tempbonebondmap);
mspos(setdiff(1:length(distance),allpmchild(:,1)),:) = bonemspos;
%% start dealing with PM
[pmposstorage,pmindstorage,directionseq] = smartPMdispenser(pmgroup,bondmap,distance,directionseq);
allfork = find(sum(bonebondmap,2) > 1);
if ~isempty(allfork)
% BONEADDPM adds perp. monosac. to branches of the glycan tree structure
[mspos,safezone,PMroot] = boneaddPM(allfork,mspos,bonebondmap,bondmap,pmgroup,pmindstorage,pmposstorage,allpmchild);
stub = min(find(sum(bonebondmap,2) > 1,1,'first')) - 1; % find the operating region for the next step, beyond this point everything stays at where they are now.
% ADDSTUBPM adds perp. monosac. to the "trunk" of the tree structure
mspos = addstubPM(mspos,bondmap,stub,bonebondmap,PMroot,pmposstorage,pmindstorage,safezone,directionseq);
else
safezone = find(bonedistance);
stub = safezone(end);
PMroot = cell2mat(pmgroup(:,1));
[mspos,directionseq] = addstubPM(mspos,bondmap,stub,bonebondmap,PMroot,pmposstorage,pmindstorage,safezone,directionseq);
end
end
mspos(:,2) = -mspos(:,2); % glycan has been drawn upside down, flip it up.
mspos = mspos - repmat(mspos(1,:),size(mspos,1),1); % normalize all coordinates
%% Option: orientation
if strcmpi(options.orientation,'left')
mspos = -mspos;
mspos = mspos - repmat(mspos(1,:),size(mspos,1),1);
elseif strcmpi(options.orientation,'up')
tmp = mspos(:,1);
mspos(:,1) = -mspos(:,2);
mspos(:,2) = tmp;
mspos = mspos - repmat(mspos(1,:),size(mspos,1),1);
elseif strcmpi(options.orientation,'down')
tmp = mspos(:,1);
mspos(:,1) = mspos(:,2);
mspos(:,2) = -tmp;
mspos = mspos - repmat(mspos(1,:),size(mspos,1),1);
end
plotinfoout.mspos = mspos;
plotinfoout.bondmap = bondmap;
plotinfoout.alllinkout = alllinkout(:);
plotinfoout.allms = allms;
plotinfoout.directionseq = directionseq(:);
%% pass info from specialoptions to plotinfoout
if ~isempty(specialoptions)
spfieldnames = fieldnames(specialoptions);
bonddesname = spfieldnames(ismember(spfieldnames,[DrawGlycanPara.intglybondinfo,DrawGlycanPara.intglymodinfo]));
bonddescription = {};
for i = 1:length(bonddesname)
tempbonddes = specialoptions.(bonddesname{i});
if ~isempty(tempbonddes)
bonddescription = [bonddescription;tempbonddes(:,2),repmat(bonddesname(i),size(tempbonddes,1),1),tempbonddes(:,1)];
end
end
plotinfoout.bonddescription = bonddescription;
spfieldnames = setdiff(spfieldnames,bonddesname);
for i = 1:length(spfieldnames)
if strcmpi(spfieldnames{i},'PEPC') || strcmpi(spfieldnames{i},'PEPN')
plotinfoout.(spfieldnames{i}(4)) = specialoptions.(spfieldnames{i});
else
plotinfoout.(spfieldnames{i}) = specialoptions.(spfieldnames{i});
end
end
end
end