chemcalc - npm Package Compare versions

Comparing version 1.0.8 to 2.0.0

package.json

 {
   "name": "chemcalc",
-  "version": "1.0.8",
+  "version": "2.0.0",
   "description": "Analyse molecular formula",
@@ -5,0 +5,0 @@ "main": "lib.js",

README.md

@@ -1,17 +0,19 @@
-chemcalc-js
-===========
+# chemcalc-js
 
-Use chemcalc in javascript !
+Library allowing to manipulate and find molecular formula.  
+This library contains 2 main functions: <b>analyzeMF</b> and <b>mfFromMonoisotopicMass</b>.  
+In all the molecular formula you are allowed to use groups like Phe, Ala, Gly, Ph, ...
 
-Installation
------------
+## Installation
 
-npm install chemcalc
+`npm install chemcalc`  
+OR  
+`bower install chemcalc`  
+OR just include in a script tag
 
-Usage
------------
+## Usage
 
 ### In NodeJS
-```javascript
-var chemcalc = require('chemcalc').Chemcalc;
+```js
+var chemcalc = require('chemcalc');
 var result = chemcalc.analyseMF('CaSO4.1/2H2O');
@@ -22,10 +24,102 @@ ```
 #### By default
-```javascript
-var result = CI.Chemcalc.analyseMF('PhNH2.HCl');
+```js
+var result = Chemcalc.analyseMF('PhNH2.HCl');
 ```
 #### Using an AMD loader
-```javascript
-require(['lib/chemcalc'], function(CI) { 
-	var result = CI.Chemcalc.analyseMF('Ph(CO)C(CH3)3');
+```js
+require(['lib/chemcalc'], function(Chemcalc) { 
+	var result = Chemcalc.analyseMF('Ph(CO)C(CH3)3');
 });
 ```
+
+## Documentation
+
+### Molecular formula
+
+#### analyseMF(mf, [options])
+
+Get various information about a molecular formula as an object.  
+From a molecular formula and different options, this function will return an object that may contain
+the monoisotopic mass, molecular weight, element analysis, isotopic distribution (as a JDX of XY).  
+Molecular formula can be entered using groups, parenthesis, isotopes, combinatorial elements, enriched isotopic elements, ...
+
+__Arguments__
+
+* `mf` - string with the molecular formula to analyse
+
+__Options__
+
+* `isotopomers` - Should we calculate the isotompers, possible values are xy, jcamp, array or any combination (default: false). The use of "array" allows to get back a javascript array for further processing.
+* `resolution` - Specify the resolution to calculate the information (default: 0.001)
+* `threshold` - Intensity cutoff (default: 1e-5)
+* `gaussianWidth` - Define the number of point (default: 0). A good value is 10 which means that the width at half the height will be 10 points.
+* `gaussianResolution` - Define resolution that corresponds the width at half-height (default: resolution * gaussianWidth).
+* `joiningAlgorithm` - May take 2 values: "center" (center of mass) or "main" (keep the main peak) (default: main)
+* `typedResult` - The result field will be typed like "mf" "jcamp" ... so instead of having "mf":"C10H12" the json will contain "mf":{type:"mf",value:"C10H12"} (default: false)
+
+__Examples__
+
+`Chemcalc.analyzeMF("CH3CH2Cl")` Retrieve a JSON containing the information about all the parts of this molecular formula. In this case there is only one part.  
+`Chemcalc.analyzeMF("CH3CH2Cl",{isotopomers:"xy,jcamp",reolustion:0.0001})` Retrieve a JSON containing the information for a molecular formula with a resolution of 0.0001 and calculate also the isotopomers as a jcamp and xy.  
+`Chemcalc.analyzeMF("RuClH(CO)(PPh3)3")` MF containing groups (like "Ph") and parenthesis.  
+`Chemcalc.analyzeMF("CuSO4.5H2O")` MF containing many parts.  
+`Chemcalc.analyzeMF("{Ph,Me}Me")` MF containing a mixture of groups (like in combinatorial chemistry), ie 0.5PhMe+0.5MeMe.  
+`Chemcalc.analyzeMF("HAla(H-1Ph)OH")` MF containing a negative atom count. Funny way to represent the phenyl alanine but very practical to describe peptide side-chain modification.  
+`Chemcalc.analyzeMF("C{50,50}10C10")` MF containing atoms with non natural isotopic ratio. ie 10 atoms of enriched C (50% 12C and 50% 13C) and 10 natural abundance carbons.  
+`Chemcalc.analyzeMF("HAla10OH+.HAla10OH++.HAla10OH+++")` MF containing many parts and charges. ie a mixure of mono, di and tri- charged decapeptide, perfect for mass spectra simulation.  
+
+#### mfFromMonoisotopicMass(mass, [options])
+
+Find molecular formulas from a monoisotopic mass.  
+This general method allow to retrieve the possible molecular formula based on a monoisotopic mass and a range of atoms or groups. Various options may be specified.  
+This method is well optimized and can provide possible molecular formula even with huge ranges.  
+It also allows to provide groups of atoms. For example you may allow a possible sequence of amino acids: H2OAla0-20Arg0-20Asn0-20Asp0-20Cys0-20Gln0-20Glu0-20Gly0-20His0-20Ile0-20Leu0-20Lys0-20Met0-20Phe0-20Pro0-20Ser0-20Val0-20Thr0-20Trp0-20Tyr0-20.
+
+__Arguments__
+
+* `mass` - Target monoisotopic mass
+
+__Options__
+
+* `mfRange` - Molecular formula range like for example: 'C1-30H1-60' (default: C0-20H0-40N0-5O0-8F0-3Cl0-3Br0-1). The range may also include groups or non natural isotopic ratio.
+* `minUnsaturation` - Minimal number of unsaturation (default: 0)
+* `maxUnsaturation` - Maximal number of unsaturation (default: 50)
+* `integerUnsaturation` - Integer number of unsaturation (default: true)
+* `useUnsaturation` - Should we use unsaturation as a filter if possible (default: true)
+* `numberOfResultsOnly` - Returns only the number of results found (default: false)
+* `massRange` - Range of mass to analyze (default: 0.5)
+* `maxNumberRows` - Maximum number of results (rows) to retrieve (default: 1000)
+* `typedResult` - The result field will be typed like "mf" "jcamp" ... so instead of having "mf":"C10H12" the json will contain "mf":{type:"mf",value:"C10H12"}
+
+__Examples__
+
+`Chemcalc.mfFromMonoisotopicMass(397.17,{'mfRange':'C1-30F0-10H1-60N0-10O0-10'})` Retrieve all the molecular formula close to 397.17 and within a range of C1-30F0-10H1-60N0-10O0-10. The other options will be used by default. Only integer unsaturation from 0 to 50 and a massRange of +/- 0.5.  
+`Chemcalc.mfFromMonoisotopicMass(1000,{'mfRange':'H2OAla0-20Arg0-20Asn0-20Asp0-20Cys0-20Gln0-20Glu0-20Gly0-20His0-20Ile0-20Leu0-20Lys0-20Met0-20Phe0-20Pro0-20Ser0-20Val0-20Thr0-20Trp0-20Tyr0-20'})` Find a peptide with monoisotopic mass close to 1000. You should note the H2O that is added in order to add the H on the N-terminal and OH on the C-terminal. All the groups like Ala, Gly, Thr, etc. are diradicals.
+
+### Peptides
+
+#### convertAASequence(sequence)
+
+Returns a peptidic sequence from a PDB or one letter code to the internal molecular formula format
+
+__Arguments__
+
+* `sequence` - string with the amino acids sequence
+
+#### chargePeptide(mf)
+
+Add a positive charge on Arg, His and Lys
+
+__Arguments__
+
+* `mf` - string with a molecular formula to charge
+
+#### generatePeptideFragments(mf, [options])
+
+Generate [peptide fragmentation](http://en.wikipedia.org/wiki/Peptide_sequence_tag).  
+Returns an array of molecular formulas with the different fragments. 
+
+__Arguments__
+
+* `mf` - string with the molecular formula
+* `options` - object with requested fragments. Default: `{a:false, b:true, c:false, x:false, y:true, z:false, i:false}`

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