Template:MassBank/Matrix

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{{MassBank/Header}}
 
{{MassBank/Header}}
−
 
+
{{#def:MASSBANKID|{{#substring:{{PAGENAME}}|0|{{#expr:{{#length:{{PAGENAME}}}}-1}}}}}}
 +
{{#def:dataline|{{#SearchLine:{{PAGENAME}}|Index|MassBank/Molecules}}}}
 
<!---化合物組成式の正規表現--------->{{#def:FORMULA_PAT|(C?[1-9]?[0-9]?)(H?[1-9]?[0-9]?)(C?l?[2-9]?)(F?[2-9]?)(I?[2-9]?)(N?[1-9]?[0-9]?)(O?[1-9]?[0-9]?)(P?[2-9]?)(S?[2-9]?)}}
 
<!---化合物組成式の正規表現--------->{{#def:FORMULA_PAT|(C?[1-9]?[0-9]?)(H?[1-9]?[0-9]?)(C?l?[2-9]?)(F?[2-9]?)(I?[2-9]?)(N?[1-9]?[0-9]?)(O?[1-9]?[0-9]?)(P?[2-9]?)(S?[2-9]?)}}
−
<!---化合物組成式に出てくる文字列--->{{#def:FORMULA_CHAR|CHFINOPSl0-9}}
+
<!---化合物組成式に出てくる文字列--->{{#def:FORMULA_CHAR|CHFINOPSl0-9%*}}
 
<!---化合物組成式に使われる原子----->{{#def:ATOM|{"C", "H", "Cl", "F", "I", "N", "O", "P", "S"} }}
 
<!---化合物組成式に使われる原子----->{{#def:ATOM|{"C", "H", "Cl", "F", "I", "N", "O", "P", "S"} }}
 
<!---各原子の質量(上のリスト)------->{{#def:MASS|{12, 1, 35, 19, 127, 14, 16, 31, 32} }}
 
<!---各原子の質量(上のリスト)------->{{#def:MASS|{12, 1, 35, 19, 127, 14, 16, 31, 32} }}
 +
<!---化合物の名前------------------->{{#def:NAME|{{#nth:{{#var:dataline}}|6|&&}}}}
  
−
=Top 10 Similar Molecules of {{#cdr:{{#cdddr:{{#SearchLine:{{PAGENAME}}|Index|MassBank/Molecules}}|&&}}|&&}}=
+
<span style="float:right;">
−
{{Twocolumn|
+
[[Image:{{#var:MASSBANKID}}.png|150px]]<br/>
−
Similarity score is defined as the sum of Shannon entropy of shared ionic formulas.
+
<big>{{#var:NAME}}</big><br/>
 +
</span>
 +
 
 +
<div>
 +
{| class="wikitable nowraplinks" border="1" cellpadding="2" cellspacing="1" style="float: right; clear: none; margin: 1em 1em 1em 1em"
 +
|-
 +
! colspan="2" | IDs and Links
 +
|- class
 +
| style="width: 35%;" | [http://massbank.jp/ MassBank]
 +
| style="width: 65%;" | [http://www.massbank.jp/jsp/FwdRecord.jsp?id={{#var:MASSBANKID}} {{#var:NAME}}]
 +
|- class{{#nth:{{#var:dataline}}|3|&&}}="hiddenStructure"
 +
| style="width: 35%;" | [https://scifinder.cas.org/ CAS]
 +
| style="width: 65%;" | {{#nth:{{#var:dataline}}|3|&&}}
 +
|- class
 +
| style="width: 35%;" | Keio ID
 +
| style="width: 65%;" | {{#nth:{{#var:dataline}}|4|&&}}
 +
|}
 +
 
 +
==Top 10 Similar Molecules of {{#var:NAME}}==
 +
{| class="wikitable collapsible collapsed"
 +
! Ranking
 +
! About scoring
 +
|-
 
|
 
|
−
類似度スコアはスペクトル間で共有するイオン式のシャノン情報量の総和です。
+
{{#repeat:MassBank/Matrix/RankingLink|1|
−
}}
+
 
{{#lua:
 
{{#lua:
 
   function intersection(x, y)
 
   function intersection(x, y)
Line 35: Line 58:
 
   total = 0
 
   total = 0
 
   ---Register Ions---
 
   ---Register Ions---
 +
  ---全ページのイオンヘッダーにおける頻度を登録。最初の要素はページ名---
 
   for id, frag in stdin:gmatch("&&([%a%d]+)&&([%S]+)") do
 
   for id, frag in stdin:gmatch("&&([%a%d]+)&&([%S]+)") do
 
     table.insert(Name, id)
 
     table.insert(Name, id)
Line 63: Line 87:
 
   ---Output Similarity---
 
   ---Output Similarity---
 
   for i=table.getn(Score), math.max(table.getn(Score)-9,1), -1 do
 
   for i=table.getn(Score), math.max(table.getn(Score)-9,1), -1 do
−
     print("# [[MassBank:" .. Name[ Rank[Score[i]] ] .. "]] Score:" ..math.floor(Score[i])/100)
+
     print(Name[ Rank[Score[i]] ] .. " Score:" ..math.floor(Score[i])/100)
 
   end
 
   end
 
|
 
|
−
&&{{PAGENAME}}{{#car:{{{data}}}}}
+
&&{{PAGENAME}}&&{{#car:{{{data}}}}}
 
{{#SearchLine:^&&_%&&|MassBank}}
 
{{#SearchLine:^&&_%&&|MassBank}}
 
}}
 
}}
 +
}}
 +
|valign="top"|
 +
The similarity score between two molecules is defined as the sum of Shannon entropy of ionic formulas shared by the molecules:
 +
<math>\textstyle - \sum_{p\in shared} \log(\mbox{frequency}(p))</math>
 +
<br/>
 +
代謝物間の類似度スコアは、それらのスペクトルで共有される（アノテートされた）イオン式のシャノン情報量の総和です。
 +
|}
 +
  
 
=Links=
 
=Links=
 +
{| class="wikitable collapsible collapsed"
 +
! Page list for each fragment
 +
|-
 +
|
 
{{#repeat:MassBank/SearchFgmt|1|
 
{{#repeat:MassBank/SearchFgmt|1|
 
{{#lua:
 
{{#lua:
−
   ---find and print Ruler---  
+
   ---find and print Ruler---
 +
  ---ヘッダー部分を分解するだけ---
 
   for line in stdin:gmatch("[%S ,]+") do
 
   for line in stdin:gmatch("[%S ,]+") do
 
     if (string.find(line, "^&&[&%a%d]+&&$") ~= nil) then
 
     if (string.find(line, "^&&[&%a%d]+&&$") ~= nil) then
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|{{{data|CHClFINOPS}}}
 
|{{{data|CHClFINOPS}}}
 
}}|&&}}
 
}}|&&}}
 +
|}
  
−
=Annotations=
+
==Annotations==
 +
{{#ifeq:{{NAMESPACE}}|Ojima|
 +
<div style="float:right">
 +
{{#ifexists:Image:Fragmentation:{{PAGENAME}}.png|[[Image:Fragmentation:{{PAGENAME}}.png]]}}
 +
</div>
 +
}}
 
{{#replace:
 
{{#replace:
 
{{#lua:
 
{{#lua:
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     if (h ~= nil and t ~= nil) then
 
     if (h ~= nil and t ~= nil) then
 
       if (comment ~= "") then
 
       if (comment ~= "") then
−
         ret = ret .."~-\n~~"..head.." ('''"..mass(tail).."''')".." ~~ "..tail.." ('''"..mass(tail).."''')".."\n~~ "..comment.."\n"
+
         ret = ret .."~-\n~~"..head.." ('''"..mass(head).."''')".." ~~ "..tail.." ('''"..mass(tail).."''')".."\n~~ "..comment.."\n"
 
         comment = ""
 
         comment = ""
 
       end
 
       end
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|~|{{#bar:}}}}
 
|~|{{#bar:}}}}
  
−
=Precursor-Product Relationship=
+
==Precursor-Product Relationship==
−
{{Twocolumn|
+
{| class="collapsible collapsed"
−
The matrix is viewed columnwise. The topmost precursor ion in bold face produces the product ions beneath it.
+
! colspan="2"| About the PP Table (行列表示について)
 +
|-
 +
|The matrix is viewed columnwise. The topmost precursor ion in bold face produces the product ions beneath it.
 
Each formula in matrix cells corresponds to the neutral loss. Blackout cells indicate products that cannot be derived, and orange cells indicate a structurally plausible link produced by cleaving a single chemical bond (in cases of ring-opening, two bonds).
 
Each formula in matrix cells corresponds to the neutral loss. Blackout cells indicate products that cannot be derived, and orange cells indicate a structurally plausible link produced by cleaving a single chemical bond (in cases of ring-opening, two bonds).
−
|
+
|行列は列方向に見ます。最上段太字の前駆イオン(precursor ion)が直下の生成イオン群(product ions)になると解釈します。
−
行列は列方向に見ます。最上段太字の前駆イオン(precursor ion)が直下の生成イオン群(product ions)になると解釈します。
+
 
行列要素に書かれている組成式はニュートラルロスです。黒は前駆イオンから生成しえない関係、オレンジは分子構造における共有結合1本の切断（開環の場合は2本）で生じる関係を意味します。
 
行列要素に書かれている組成式はニュートラルロスです。黒は前駆イオンから生成しえない関係、オレンジは分子構造における共有結合1本の切断（開環の場合は2本）で生じる関係を意味します。
−
}}
+
|}
 
{{#replace:
 
{{#replace:
 
{{#lua:
 
{{#lua:
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   ---Main Program---
 
   ---Main Program---
−
   local ruler = nil;
+
   local ruler = nil; ---first line (list of fragments)---
−
   local fragments = {};
+
   local fragments = {}; ---following lines (head : tail style)---
 +
  local focus = {}; ---formulas that should be highlighted---
 
   local x, y;
 
   local x, y;
 
   ---Read Data---
 
   ---Read Data---
Line 208: Line 253:
 
       ---register fragments---
 
       ---register fragments---
 
       head, tail = string.match(line, "^&&(["..FORMULA_CHAR.."]+) *: *(["..FORMULA_CHAR.." ]+)$")
 
       head, tail = string.match(line, "^&&(["..FORMULA_CHAR.."]+) *: *(["..FORMULA_CHAR.." ]+)$")
 +
      if (string.match(head,"*")) then
 +
        head = string.gsub(head,"*", "")
 +
        focus[head] = head
 +
      end
 
       if (head ~= nil and tail ~= nil) then
 
       if (head ~= nil and tail ~= nil) then
−
         if (fragments[head] == nil) then y = {} else y = fragments[head] end
+
         if (fragments[head] == nil)
 +
          then y = {} else y = fragments[head] end
 
         for x in string.gmatch(tail,"["..FORMULA_CHAR.."]+") do
 
         for x in string.gmatch(tail,"["..FORMULA_CHAR.."]+") do
−
           y[x] = x
+
          z = string.gsub(x,"*", "")
 +
           y[x] = z
 +
          y[z] = z
 
         end
 
         end
 
         fragments[head] = y
 
         fragments[head] = y
Line 225: Line 277:
 
   end
 
   end
 
   x = nil
 
   x = nil
−
   y = {}
+
   inRuler = {}
 
   for formula in string.gmatch(ruler, "([%S]+)") do
 
   for formula in string.gmatch(ruler, "([%S]+)") do
 
     if (x ~= nil and mass(formula) > mass(x)) then
 
     if (x ~= nil and mass(formula) > mass(x)) then
Line 231: Line 283:
 
     end
 
     end
 
     x = formula
 
     x = formula
−
     y[formula] = true
+
     inRuler[formula] = true
 
   end
 
   end
 
   ---Check Fragments---
 
   ---Check Fragments---
 
   for i,v in pairs(fragments) do
 
   for i,v in pairs(fragments) do
−
     if (not y[i]) then print('<span style="color:red">Parent ion '..i..' does not exist.</span>') end
+
    ---i is head, v is a list of fragments---
 +
     if (not inRuler[i]) then print('<span style="color:red">Parent ion '..i..' does not exist.</span>') end
 
     for j,w in pairs(v) do
 
     for j,w in pairs(v) do
−
       if (not y[j]) then print('<span style="color:red">Fragment ion '..j..' does not exist.</span>') end
+
      j = string.gsub(j,"*","")
 +
       if (not inRuler[w]) then print('<span style="color:red">Fragment ion '..w..' does not exist.</span>') end
 
     end
 
     end
 
   end
 
   end
 
   ---Write Matrix---
 
   ---Write Matrix---
 
   print("<small>")
 
   print("<small>")
−
   print('{# class ="wikitable"')
+
   print('{# class ="wikitable collapsible" style="margin:0 0 0 0"')
 
   local axis  = {};
 
   local axis  = {};
 
   local i = 1;
 
   local i = 1;
Line 251: Line 305:
 
   ---Header---
 
   ---Header---
 
   print("#-\n")
 
   print("#-\n")
−
   print("## '''ID: {{PAGENAME}}''' \n")
+
   print("! {{PAGENAME}} \n")
 
   for i=1, table.getn(axis) do
 
   for i=1, table.getn(axis) do
−
     print("#style='text-align:right'# '''" .. mass(axis[i]) .. "'''<br/>" .. axis[i])
+
  ---If some fragments are focused then highlight the axis---
 +
     if (focus[axis[i]] ~= nil) then
 +
      print("#style='text-align:right;background:red'# '''" .. mass(axis[i]) .. "'''<br/>" .. axis[i])
 +
    else
 +
      print("#style='text-align:right'# '''" .. mass(axis[i]) .. "'''<br/>" .. axis[i])
 +
    end
 
   end
 
   end
 
   ---Rows---
 
   ---Rows---
 
   for i=1, table.getn(axis) do
 
   for i=1, table.getn(axis) do
 
     print("#-\n")
 
     print("#-\n")
−
     print("#style='text-align:right'# '''" .. mass(axis[i]) .. "'''<br/>" .. axis[i])
+
     print("#style='text-align:right'# '''" .. mass(axis[i]) .. "''' " .. axis[i])
 
     for j=1, table.getn(axis) do
 
     for j=1, table.getn(axis) do
 
       if (j < i) then
 
       if (j < i) then
Line 266: Line 325:
 
         else
 
         else
 
           if (fragments[axis[j]] ~= nil and fragments[axis[j]][axis[i]] ~= nil) then
 
           if (fragments[axis[j]] ~= nil and fragments[axis[j]][axis[i]] ~= nil) then
−
             print('#style="background-color:orange"# ' .. s)
+
             ---記号の有無により色を変更---
 +
            if (fragments[axis[j]][axis[i].."*"] ~= nil) then
 +
              print('#style="background-color:skyblue"# ' .. s)
 +
            elseif (fragments[axis[j]][axis[i].."**"] ~= nil) then
 +
              print('#style="background-color:orange"# ' .. s)
 +
            elseif (fragments[axis[j]][axis[i].."***"] ~= nil) then
 +
              print('#style="background-color:beige"# ' .. s)
 +
            elseif (fragments[axis[j]][axis[i].."****"] ~= nil) then
 +
              print('#style="background-color:coral"# ' .. s)
 +
            else
 +
              print('#style="background-color:orange"# ' .. s)
 +
            end
 
           else print('## ' .. s) end
 
           else print('## ' .. s) end
 
         end
 
         end
Line 283: Line 353:
  
 
<!---- next/prev links at the page bottom---->
 
<!---- next/prev links at the page bottom---->
 +
{{#def:KeioID|{{#ifeq:{{#substring:{{PAGENAME}}|0|2}}|KO|{{#substring:{{#nth:{{#SearchLine:{{PAGENAME}}|Index|MassBank/Molecules}}|4|&&}}|0|4}}|{{#substring:{{PAGENAME}}|0|8}}}}}}
 
{{#repeat:MassBank/PrevNextLink|4|
 
{{#repeat:MassBank/PrevNextLink|4|
 
{{#lua:
 
{{#lua:
Line 290: Line 361:
 
   last = nil
 
   last = nil
 
   hit = nil
 
   hit = nil
−
   for line in stdin:gmatch("(%w+)") do
+
   for word in stdin:gmatch("(%w+)") do
−
     if (first == nil) then first = line end
+
     if (first == nil) then first = word end
−
     last = line
+
     last = word
−
     if (line == "{{PAGENAME}}") then
+
     if (word == "{{#var:KeioID}}") then
 
       hit = true
 
       hit = true
 
       if (tmp ~= nil) then
 
       if (tmp ~= nil) then
Line 301: Line 372:
 
       end
 
       end
 
     elseif (hit) then
 
     elseif (hit) then
−
       next = line
+
       next = word
 
       hit = false
 
       hit = false
 
     end
 
     end
−
     tmp = line
+
     tmp = word
 
   end
 
   end
 
   if (next == nil) then next = last end
 
   if (next == nil) then next = last end

Latest revision as of 16:27, 7 April 2011

General Index

All Molecules
KOX PR PBX COX

Ion Frequency Prec.-Product Neutral Loss Help





150px

IDs and Links
MassBank [1]
CAS
Keio ID

Contents

[edit] Top 10 Similar Molecules of


[edit] Links

[edit] Annotations

Precursor Product Comments
(0) (0) CHClFINOPS

[edit] Precursor-Product Relationship

No "ION INFO" line in the form &&(formula)&&(formula)&&...&&

MassBank/Matrix 210
CHClFIONSP
210 CHClFIONSP



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