Template:MassBank/Matrix
From Metabolomics.JP
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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|&&}}}} | ||
<span style="float:right;"> | <span style="float:right;"> | ||
| − | [[Image:{{ | + | [[Image:{{#var:MASSBANKID}}.png|150px]]<br/> |
| − | <big>{{# | + | <big>{{#var:NAME}}</big><br/> |
</span> | </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 | ||
| + | |- | ||
| | | | ||
| − | |||
| − | |||
{{#repeat:MassBank/Matrix/RankingLink|1| | {{#repeat:MassBank/Matrix/RankingLink|1| | ||
{{#lua: | {{#lua: | ||
| Line 73: | Line 90: | ||
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: | ||
| Line 90: | Line 118: | ||
|{{{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: | ||
| Line 154: | Line 188: | ||
|~|{{#bar:}}}} | |~|{{#bar:}}}} | ||
| − | =Precursor-Product Relationship= | + | ==Precursor-Product Relationship== |
| − | { | + | {| 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: | ||
| Line 207: | Line 242: | ||
---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 217: | 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 | ||
z = string.gsub(x,"*", "") | z = string.gsub(x,"*", "") | ||
| Line 246: | Line 287: | ||
---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 | ||
| Line 254: | Line 296: | ||
---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 263: | Line 305: | ||
---Header--- | ---Header--- | ||
print("#-\n") | print("#-\n") | ||
| − | print(" | + | 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]) .. "''' | + | 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 282: | Line 329: | ||
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: | + | 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 302: | 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 309: | Line 361: | ||
last = nil | last = nil | ||
hit = nil | hit = nil | ||
| − | for | + | for word in stdin:gmatch("(%w+)") do |
| − | if (first == nil) then first = | + | if (first == nil) then first = word end |
| − | last = | + | last = word |
| − | if ( | + | if (word == "{{#var:KeioID}}") then |
hit = true | hit = true | ||
if (tmp ~= nil) then | if (tmp ~= nil) then | ||
| Line 320: | Line 372: | ||
end | end | ||
elseif (hit) then | elseif (hit) then | ||
| − | next = | + | next = word |
hit = false | hit = false | ||
end | end | ||
| − | tmp = | + | 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 | Ion Frequency | Prec.-Product | Neutral Loss | Help |
| IDs and Links | |
|---|---|
| MassBank | [1] |
| CAS | |
| Keio ID | |
Contents |
[edit] Top 10 Similar Molecules of
| Ranking | About scoring |
|---|---|
|
The similarity score between two molecules is defined as the sum of Shannon entropy of ionic formulas shared by the molecules:
|
[edit] Links
| Page list for each fragment |
|---|
[edit] Annotations
| Precursor | Product | Comments |
|---|---|---|
| (0) | (0) | CHClFINOPS |
[edit] Precursor-Product Relationship
| 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). |
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。 |
No "ION INFO" line in the form &&(formula)&&(formula)&&...&&
| MassBank/Matrix | 210 CHClFIONSP |
|---|---|
| 210 CHClFIONSP |
|
