Template:MassBank/Matrix2 - Revision history

Adm at 06:31, 7 April 2011

2011-04-07T06:31:15Z

Adm at 06:28, 7 April 2011

2011-04-07T06:28:05Z

Adm at 06:19, 7 April 2011

2011-04-07T06:19:39Z

Adm at 06:07, 7 April 2011

2011-04-07T06:07:11Z

Adm at 06:05, 7 April 2011

2011-04-07T06:05:44Z

Adm at 06:03, 7 April 2011

2011-04-07T06:03:51Z

Adm: Created page with "{{MassBank/Header}} {{#def:MASSBANKID|{{#substring:{{PAGENAME}}|0|{{#expr:{{#length:{{PAGENAME}}}}-1}}}}}} {{#def:dataline|{{#SearchLine:{{PAGENAME}}|Index|MassBank/Molecules}}}}..."

2011-04-07T06:02:21Z

Created page with "{{MassBank/Header}} {{#def:MASSBANKID|{{#substring:{{PAGENAME}}|0|{{#expr:{{#length:{{PAGENAME}}}}-1}}}}}} {{#def:dataline|{{#SearchLine:{{PAGENAME}}|Index|MassBank/Molecules}}}}..."

New page

{{MassBank/Header}}
{{#def:MASSBANKID|{{#substring:{{PAGENAME}}|0|{{#expr:{{#length:{{PAGENAME}}}}-1}}}}}}
{{#def:dataline|{{#SearchLine:{{PAGENAME}}|Index|MassBank/Molecules}}}}
{{#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]?)}}
{{#def:FORMULA_CHAR|CHFINOPSl0-9%*}}
{{#def:ATOM|{"C", "H", "Cl", "F", "I", "N", "O", "P", "S"} }}
{{#def:MASS|{12, 1, 35, 19, 127, 14, 16, 31, 32} }}
{{#def:NAME|{{#nth:{{#var:dataline}}|6|&&}}}}


[[Image:{{#var:MASSBANKID}}.png|150px]] 
<big>{{#var:NAME}}</big> 


<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="collapsible collapsed"
! About the comparison measure
|-
|The similarity score between two molecules is defined as the sum of Shannon entropy of ionic formulas shared by the molecules:
<math>- \sum_{p\in shared} \log(\mbox{frequency}(p))</math>
|
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。
|}
{{#repeat:MassBank/Matrix/RankingLink|1|
{{#lua:
function intersection(x, y)
local z = {}
local i = 1
local j = 1
repeat
if (x[i] == y[j])
then table.insert(z, x[i]) i = i + 1 j = j + 1 end
if (i > table.getn(x) or j > table.getn(y))
then break end
if (x[i] > y[j]) then j = j + 1 end
if (j > table.getn(y)) then break end
if (x[i] < y[j]) then i = i + 1 end
if (i > table.getn(x)) then break end
until false
return z
end

Name = {}
Ions = {}
Freq = {}
total = 0
---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
table.insert(Name, id)
T = {}
for f in string.gmatch(frag,"([%a%d]+)&&") do
table.insert(T, f)
if (Freq[f]) then Freq[f] = Freq[f] + 1 else Freq[f] = 1 total = total + 1 end
end
table.sort(T)
table.insert(Ions, T)
end
---Compute Similarity---
Rank = {}
Score = {}
for i=2, table.getn(Ions) do
R = intersection(Ions[i], Ions[1])
if (table.getn(R) > 0) then
inf = 0
for _,v in pairs(R) do
inf = inf - math.log(Freq[v]/total)
end
inf = math.floor(inf*100) + i * 0.0001
table.insert(Score, inf)
Rank[inf] = i
end
end
table.sort(Score)
---Output Similarity---
for i=table.getn(Score), math.max(table.getn(Score)-9,1), -1 do
print(Name[ Rank[Score[i]] ] .. " Score:" ..math.floor(Score[i])/100)
end
|
&&{{PAGENAME}}&&{{#car:{{{data}}}}}
{{#SearchLine:^&&_%&&|MassBank}}
}}
}}

=Links=
{{#repeat:MassBank/SearchFgmt|1|
{{#lua:
---find and print Ruler---
---ヘッダー部分を分解するだけ---
for line in stdin:gmatch("[%S ,]+") do
if (string.find(line, "^&&[&%a%d]+&&$") ~= nil) then
print(line) return
end
end
|{{{data|CHClFINOPS}}}
}}|&&}}

=Annotations=
{{#ifeq:{{NAMESPACE}}|Ojima|
<div style="float:right">
{{#ifexists:Image:Fragmentation:{{PAGENAME}}.png|[[Image:Fragmentation:{{PAGENAME}}.png]]}}
</div>
}}
{{#replace:
{{#lua:
---print comments---
FORMULA_PAT = "{{#var:FORMULA_PAT}}"
FORMULA_CHAR = "{{#var:FORMULA_CHAR}}"
ATOM = {{#var:ATOM}}
MASS = {{#var:MASS}}

function toFormula(t)
for i,v in pairs(t) do
if (v == "")
then t[i] = 0
else if (v == ATOM[i])
then t[i] = 1
else t[i]=tonumber(string.sub(v,1+string.len(ATOM[i])))
end
end
end
return t
end

function mass(str)
local t = toFormula({string.match(str,FORMULA_PAT)})
ret = 0;
for i,v in pairs(t) do
ret = ret + t[i] * MASS[i]
end
return ret;
end

ret = ""
comment = "";
head = "";
tail = "";
for line in stdin:gmatch("[%S ,]+") do
repeat
if (string.find(line, "^&&[&%a%d]+&&$") ~= nil) then break end
local h, t = string.match(line, "^&&(["..FORMULA_CHAR.."]+) *: *(["..FORMULA_CHAR.." ]+)$");
if (h ~= nil and t ~= nil) then
if (comment ~= "") then
ret = ret .."~-\n~~"..head.." ('''"..mass(head).."''')".." ~~ "..tail.." ('''"..mass(tail).."''')".."\n~~ "..comment.."\n"
comment = ""
end
head = h; tail = t
break
end
---comment lines---
comment = comment .. line.."\n"
until true
end
---process the last comment (head=precursor, tail=product)---
if (comment ~= "") then
ret = ret .. "~-\n~~"..head.." ('''"..mass(head).."''')".." ~~ "..tail.." ('''"..mass(tail).."''')".."\n~~ "..comment.."\n"
end
if (ret ~= "") then
ret = '{~ class="wikitable sortable"\n!Precursor~~Product~~Comments\n'.. ret ..'~}'
print(ret)
end
|{{{data|CHClFINOPS}}}
}}
|~|{{#bar:}}}}

=Precursor-Product Relationship=
{| class="collapsible collapsed"
! 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).
|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。
|}
{{#replace:
{{#lua:
FORMULA_PAT = "{{#var:FORMULA_PAT}}"
FORMULA_CHAR = "{{#var:FORMULA_CHAR}}"
ATOM = {{#var:ATOM}}
MASS = {{#var:MASS}}

function toFormula(t)
for i,v in pairs(t) do
if (v == "")
then t[i] = 0
else if (v == ATOM[i])
then t[i] = 1
else t[i]=tonumber(string.sub(v,1+string.len(ATOM[i])))
end
end
end
return t
end

function mass(str)
local t = toFormula({string.match(str,FORMULA_PAT)})
ret = 0;
for i,v in pairs(t) do
ret = ret + t[i] * MASS[i]
end
return ret;
end

function diff(str1, str2)
---computes str1 - str2. If negative, returns nil.---
local t1 = toFormula({string.match(str1,FORMULA_PAT)})
local t2 = toFormula({string.match(str2,FORMULA_PAT)})
for i,_ in pairs(t1) do
if (t1[i] < t2[i]) then return nil else t1[i] = t1[i]-t2[i] end
end
local ret = "";
for i,v in pairs(t1) do
if (v >= 1) then ret = ret .. ATOM[i] end
if (v > 1) then ret = ret .. v end
end
return ret
end

---Main Program---
local ruler = nil; ---first line (list of fragments)---
local fragments = {}; ---following lines (head : tail style)---
local focus = {}; ---formulas that should be highlighted---
local x, y;
---Read Data---
for line in stdin:gmatch("[%S ,]+") do
if (string.find(line, "^&&[&%a%d]+&&$") ~= nil)
then ruler = string.gsub(line, "&&", " ")
elseif (string.match(line,"^&&")) then
---register fragments---
head, tail = string.match(line, "^&&(["..FORMULA_CHAR.."]+) *: *(["..FORMULA_CHAR.." ]+)$")
if (string.match(head,"*")) then
head = string.gsub(head,"*", "")
focus[head] = head
end
if (head ~= nil and tail ~= nil) then
if (fragments[head] == nil)
then y = {} else y = fragments[head] end
for x in string.gmatch(tail,"["..FORMULA_CHAR.."]+") do
z = string.gsub(x,"*", "")
y[x] = z
y[z] = z
end
fragments[head] = y
else
print('Ion in '..line..' does not exist.')
end
end
end
---Check Ruler---
if (ruler == nil) then
print('No "ION INFO" line in the form &&(formula)&&(formula)&&...&&')
ruler = "CHClFIONSP"
end
x = nil
inRuler = {}
for formula in string.gmatch(ruler, "([%S]+)") do
if (x ~= nil and mass(formula) > mass(x)) then
print('Illegal ion order (check mass!): '..x..' < '..formula..' ')
end
x = formula
inRuler[formula] = true
end
---Check Fragments---
for i,v in pairs(fragments) do
---i is head, v is a list of fragments---
if (not inRuler[i]) then print('Parent ion '..i..' does not exist.') end
for j,w in pairs(v) do
j = string.gsub(j,"*","")
if (not inRuler[w]) then print('Fragment ion '..w..' does not exist.') end
end
end
---Write Matrix---
print("")
print('{# class ="wikitable collapsible" style="margin:0 0 0 0"')
local axis = {};
local i = 1;
for formula in string.gmatch(ruler, "([%S]+)") do
axis[i] = formula
i = i + 1
end
---Header---
print("#-\n")
print("! {{PAGENAME}} \n")
for i=1, table.getn(axis) do
---If some fragments are 'focused' then highlight the axis---
if (focused[axis[i]] ~= nil) then
print("#style='text-align:right'# '''" .. mass(axis[i]) .. "''' " .. axis[i])
else
print("#style='text-align:right'# '''" .. mass(axis[i]) .. "''' " .. axis[i])
end
end
---Rows---
for i=1, table.getn(axis) do
print("#-\n")
print("#style='text-align:right'# '''" .. mass(axis[i]) .. "''' " .. axis[i])
for j=1, table.getn(axis) do
if (j < i) then
s = diff(axis[j],axis[i]);
if (s == nil)
then print('#style="background-color:gray"# ')
else
if (fragments[axis[j]] ~= nil and fragments[axis[j]][axis[i]] ~= nil) then
---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
end
else print('#style="background-color:white"# ')
end
end
print("\n")
end
print("#}")
print("")
---End of Matrix---
|
{{{data|CHCFIlNOPS}}}
}}
|#|{{#bar:}}}}


{{#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|
{{#lua:
first = nil
prev = nil
next = nil
last = nil
hit = nil
for word in stdin:gmatch("(%w+)") do
if (first == nil) then first = word end
last = word
if (word == "{{#var:KeioID}}") then
hit = true
if (tmp ~= nil) then
prev = tmp
else
prev = first
end
elseif (hit) then
next = word
hit = false
end
tmp = word
end
if (next == nil) then next = last end
print(first)
print(prev)
print(next)
print(last)
|{{Persist:MassBank/AllPages}}}}
}}

@@ Line 28: / Line 28: @@
 |}
-=Top 10 Similar Molecules of {{#var:NAME}}=
+==Top 10 Similar Molecules of {{#var:NAME}}==
-{| class="collapsible collapsed"
+{| class="wikitable collapsible collapsed"
-! About the comparison measure
+! Ranking
 |-
+|
 {{#repeat:MassBank/Matrix/RankingLink|1|
 {{#lua:
@@ Line 97: / Line 94: @@
 }}
 }}
 =Links=
 {{#repeat:MassBank/SearchFgmt|1|
 {{#lua:
@@ Line 110: / Line 118: @@
 |{{{data|CHClFINOPS}}}
 }}|&&}}
 =Annotations=
@@ Line 300: / Line 309: @@
    ---If some fragments are focused then highlight the axis---
      if (focus[axis[i]] ~= nil) then
-       print("#style='text-align:right;background:orange'# '''" .. mass(axis[i]) .. "'''<br/>" .. axis[i])
+       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])

@@ Line 300: / Line 300: @@
    ---If some fragments are focused then highlight the axis---
      if (focus[axis[i]] ~= nil) then
-       print("#style='text-align:right'# <span style='color:red'>'''" .. mass(axis[i]) .. "'''</span><br/>" .. axis[i])
+       print("#style='text-align:right;background:orange'# '''" .. mass(axis[i]) .. "'''<br/>" .. axis[i])
      else
        print("#style='text-align:right'# '''" .. mass(axis[i]) .. "'''<br/>" .. axis[i])

@@ Line 300: / Line 300: @@
    ---If some fragments are focused then highlight the axis---
      if (focus[axis[i]] ~= nil) then
-       print("#style='text-align:right'# <span style="color:red">'''" .. mass(axis[i]) .. "'''</span><br/>" .. axis[i])
+       print("#style='text-align:right'# <span style='color:red'>'''" .. mass(axis[i]) .. "'''</span><br/>" .. axis[i])
      else
        print("#style='text-align:right'# '''" .. mass(axis[i]) .. "'''<br/>" .. axis[i])

@@ Line 300: / Line 300: @@
    ---If some fragments are focused then highlight the axis---
      if (focus[axis[i]] ~= nil) then
-       print("#style='text-align:right'# '''" .. mass(axis[i]) .. "'''<br/>" .. axis[i])
+       print("#style='text-align:right'# <span style="color:red">'''" .. mass(axis[i]) .. "'''</span><br/>" .. axis[i])
      else
        print("#style='text-align:right'# '''" .. mass(axis[i]) .. "'''<br/>" .. axis[i])

@@ Line 31: / Line 31: @@
 {| class="wikitable collapsible collapsed"
 ! Ranking
-| About scoring
+! About scoring
 |-
+|
@@ Line 94: / Line 94: @@
 }}
 }}
 |valign="top"|
 The similarity score between two molecules is defined as the sum of Shannon entropy of ionic formulas shared by the molecules:
@@ Line 107: / Line 106: @@
 ! Page list for each fragment
 |-
 {{#repeat:MassBank/SearchFgmt|1|
 {{#lua:
@@ Line 120: / Line 120: @@
 |}
-=Annotations=
+==Annotations==
 {{#ifeq:{{NAMESPACE}}|Ojima|
 <div style="float:right">
@@ Line 188: / Line 188: @@
 |~|{{#bar:}}}}
-=Precursor-Product Relationship=
+==Precursor-Product Relationship==
 {| class="collapsible collapsed"
 ! colspan="2"| About the PP Table (行列表示について)

@@ Line 298: / Line 298: @@
    print("! {{PAGENAME}} \n")
    for i=1, table.getn(axis) do
-    ---If some fragments are 'focused' then highlight the axis---
+  ---If some fragments are focused then highlight the axis---
-     if (focused[axis[i]] ~= nil) then
+     if (focus[axis[i]] ~= nil) then
        print("#style='text-align:right'# '''" .. mass(axis[i]) .. "'''<br/>" .. axis[i])
      else