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|&&}}}}
  
−
{{#def:dataline|{{#SearchLine:{{PAGENAME}}|Index|MassBank/Molecules}}}}
 
 
<span style="float:right;">
 
<span style="float:right;">
−
[[Image:{{PAGENAME}}.png|150px]]<br/>
+
[[Image:{{#var:MASSBANKID}}.png|150px]]<br/>
−
<big>{{#nth:{{#var:dataline}}|5|&&}}</big><br/>
+
<big>{{#var:NAME}}</big><br/>
 
</span>
 
</span>
  
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|- class
 
|- class
 
| style="width: 35%;" | [http://massbank.jp/ MassBank]
 
| style="width: 35%;" | [http://massbank.jp/ MassBank]
−
| style="width: 65%;" | [http://www.massbank.jp/jsp/FwdRecord.jsp?id={{PAGENAME}} {{PAGENAME}}]
+
| style="width: 65%;" | [http://www.massbank.jp/jsp/FwdRecord.jsp?id={{#var:MASSBANKID}} {{#var:NAME}}]
 
|- class{{#nth:{{#var:dataline}}|3|&&}}="hiddenStructure"
 
|- class{{#nth:{{#var:dataline}}|3|&&}}="hiddenStructure"
 
| style="width: 35%;" | [https://scifinder.cas.org/ CAS]
 
| style="width: 35%;" | [https://scifinder.cas.org/ CAS]
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|}
 
|}
  
−
=Top 10 Similar Molecules of {{MassBank/getName|{{PAGENAME}}}}=
+
==Top 10 Similar Molecules of {{#var:NAME}}==
−
{{Twocolumn|
+
{| class="wikitable collapsible collapsed"
−
Similarity score is defined as the sum of Shannon entropy of shared ionic formulas.
+
! 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|
 
{{#repeat:MassBank/Matrix/RankingLink|1|
 
{{#lua:
 
{{#lua:
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}}
 
}}
 
}}
 
}}
 +
|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:
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|{{{data|CHClFINOPS}}}
 
|{{{data|CHClFINOPS}}}
 
}}|&&}}
 
}}|&&}}
 +
|}
  
−
=Annotations=
+
==Annotations==
 +
{{#ifeq:{{NAMESPACE}}|Ojima|
 
<div style="float:right">
 
<div style="float:right">
 
{{#ifexists:Image:Fragmentation:{{PAGENAME}}.png|[[Image:Fragmentation:{{PAGENAME}}.png]]}}
 
{{#ifexists:Image:Fragmentation:{{PAGENAME}}.png|[[Image:Fragmentation:{{PAGENAME}}.png]]}}
 
</div>
 
</div>
 +
}}
 
{{#replace:
 
{{#replace:
 
{{#lua:
 
{{#lua:
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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---
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       ---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
 
           z = string.gsub(x,"*", "")
 
           z = string.gsub(x,"*", "")
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   ---Check Fragments---
 
   ---Check Fragments---
 
   for i,v in pairs(fragments) do
 
   for i,v in pairs(fragments) do
 +
    ---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
 
     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
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   print("! {{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;height:0em'# '''" .. mass(axis[i]) .. "''' " .. 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
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               print('#style="background-color:skyblue"# ' .. s)
 
               print('#style="background-color:skyblue"# ' .. s)
 
             elseif (fragments[axis[j]][axis[i].."**"] ~= nil) then
 
             elseif (fragments[axis[j]][axis[i].."**"] ~= nil) then
−
               print('#style="background-color:lightgray"# ' .. s)
+
               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
 
             else
 
               print('#style="background-color:orange"# ' .. s)
 
               print('#style="background-color:orange"# ' .. s)
Line 321: Line 353:
  
 
<!---- next/prev links at the page bottom---->
 
<!---- next/prev links at the page bottom---->
−
{{#def:KeioID|{{#nth:{{#SearchLine:{{PAGENAME}}|Index|MassBank/Molecules}}|4|&&}}}}
+
{{#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:

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

 [hide] 

[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)&&...&&

[hide] MassBank/Matrix 210
CHClFIONSP
210 CHClFIONSP



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