mkuhn · December 21, 2015 17:19 · Aug 26, 2013 · Oct 26, 2011 · Oct 25, 2011 · Oct 25, 2011
diff --git a/_smiles_inchi_annotated.js b/_smiles_inchi_annotated.js
@@ -1,10 +1,21 @@
 //SMILES, Inchi Regex , by lo sauer - lsauer.com
 //Here's a PREG version for SMILES validation (JavaScript) beyond a length of 5:
 var x = "OC[C@@H](O1)[C@@H](O)[C@H](O)[C@@H]2[C@@H]1c3c(O)c(OC)c(O)cc3C(=O)O2"
+var y = "Not=a=SMILES=String"
 
 x.trim().match(/^([^J][a-z0-9@+\-\[\]\(\)\\\/%=#$]{6,})$/ig)[0]
 >"OC[C@@H](O1)[C@@H](O)[C@H](O)[C@@H]2[C@@H]1c3c(O)c(OC)c(O)cc3C(=O)O2"
 
+y.trim().match(/^([^J][a-z0-9@+\-\[\]\(\)\\\/%=#$]{6,})$/ig)[0]
+>"Not=a=SMILES=String"
+
+// explicitely search for all elements
+x.trim().match(/^(A[cglmrstu]|B[aehikr]?|C[adeflmorsu]?|D[bsy]|E[rsu]|F[emr]?|G[ade]|H[efgos]?|I[nr]?|Kr?|L[airu]|M[dgnot]|N[abdeiop]?|Os?|P[abdmortu]?|R[abefghnu]|S[bcegimnr]?|T[abcehilm]|U|Uu.|V|W|Xe|Yb?|Z[nr]|[0-9@+\-\[\]\(\)\\\/%=#$]){6,}$/ig)                                                               )
+>"OC[C@@H](O1)[C@@H](O)[C@H](O)[C@@H]2[C@@H]1c3c(O)c(OC)c(O)cc3C(=O)O2"
+
+y.trim().match(/^(A[cglmrstu]|B[aehikr]?|C[adeflmorsu]?|D[bsy]|E[rsu]|F[emr]?|G[ade]|H[efgos]?|I[nr]?|Kr?|L[airu]|M[dgnot]|N[abdeiop]?|Os?|P[abdmortu]?|R[abefghnu]|S[bcegimnr]?|T[abcehilm]|U|Uu.|V|W|Xe|Yb?|Z[nr]|[0-9@+\-\[\]\(\)\\\/%=#$]){6,}$/ig)                                                               )
+> null
+
 //for the most frequent organic molecules
 x.trim().match(/^([^J][0-9BCOHNSOPrIFla@+\-\[\]\(\)\\\/%=#$]{6,})$/ig)
 

diff --git a/_smiles_inchi_annotated.js b/_smiles_inchi_annotated.js
@@ -27,7 +27,7 @@ x.toLowerCase().split('').map(function(v,k){return 'c'==v|0;})
   0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 0, 1, 1, 0, 1, 0, 0, 0, 0, 0, 0]
 if(!Array.prototype.hasOwnProperty('sum'))
 {
-    function (){return this.reduce(function(a,b){return a+b})}
+    Array.prototype.sum = function (){return this.reduce(function(a,b){return a+b})}
 }
 
 x.toLowerCase().split('').map(function(v,k){return 'c'==v|0;}).sum()

diff --git a/InChiKey.js b/InChiKey.js
@@ -2,7 +2,7 @@
 // The InChIKey, or hashed InChI, is a fixed length (25 character) condensed digital representation 
 // of the InChI, which tries to be unique but is not human-comprehensible. It uses a BASE26  alphabet (Hexavigesimal)!
 // The last character of an InChIKey is computed from the rest of the InChIKey 
-// The InChIKey specification facilitates web searches for chemical compounds, owing to unqiue referencing 
+// The InChIKey specification facilitates web searches for chemical compounds, owing to sufficiently unqiue referencing 
 // of compounds with a concise key, which is problematic with the full-length InChI (e.g. GET url limit is 1600 chars)
 
 // From the official documents ( http://chemdata.nist.gov/InChI/inchi-hash.pdf ):

diff --git a/InChiKey.js b/InChiKey.js
@@ -50,3 +50,7 @@ var x = 'RYGMFSIKBFXOCR-UHFFFAOYSA-N'
 27===x.length && '-'===x[14] && '-'===x[25]
 && !!x.match(/^([0-9A-Z\-]+)$/)
 >true
+
+
+//Collisions do occurs:
+//see http://www.chemconnector.com/2011/09/01/an-inchikey-collision-is-discovered-and-not-based-on-stereochemistry/
diff --git a/InChiKey → InChiKey.js b/InChiKey → InChiKey.js
diff --git a/InChiKey b/InChiKey
@@ -0,0 +1,52 @@
+// International Chemical Identifier KEY Regex, by lo sauer - lsauer.com
+// The InChIKey, or hashed InChI, is a fixed length (25 character) condensed digital representation 
+// of the InChI, which tries to be unique but is not human-comprehensible. It uses a BASE26  alphabet (Hexavigesimal)!
+// The last character of an InChIKey is computed from the rest of the InChIKey 
+// The InChIKey specification facilitates web searches for chemical compounds, owing to unqiue referencing 
+// of compounds with a concise key, which is problematic with the full-length InChI (e.g. GET url limit is 1600 chars)
+
+// From the official documents ( http://chemdata.nist.gov/InChI/inchi-hash.pdf ):
+	// "The InChIKey is a character signature based on a hash code of the InChI string. Also, this hash
+	 // may serve as a checksum for verifying InChI, for example, after transmission over a network."
+
+	 // InChIKey has four (4) distinct components: a 14-character hash of the basic (Mobile-H)
+	// InChI layer (without /p segment accounting for added or removed protons); a 8-character
+	// hash of the remaining layers; a 1 character is a flag indicating selected features (e.g.
+	// presence of fixed-H layer); a 1 character is a “check” character. The overall length of
+	// InChIKey is fixed at 25 characters, including separator:
+	// AAAAAAAAAAAAAA-BBBBBBBBCD
+
+	// This is significantly shorter than a typical InChI string (for example, the average length
+	// of InChI string for Pubchem collection is 146 characters).
+	// --------------------------------
+	// InChIKey layout is as follows:
+	// --------------------------------
+	// AAAAAAAAAAAAAA
+	// First block (14 letters)
+	// Encodes molecular skeleton (connectivity)
+	// BBBBBBBB
+	// Second block (8 letters)
+	// Encodes proton positions (tautomers), stereochemistry, isotopomers, reconnected layer
+	// C
+	// Flag character
+	// Indicates InChI version, presence of a fixed-H layer, isotopes, and stereochemical
+	// information.
+	// D
+	// Check character, obtained from all symbols except delimiters, i.e. from
+	// AAAAAAAAAAAAAABBBBBBBBC
+
+	// All symbols except the delimiter (a dash, that is, a minus) are uppercase English letters
+	// representing a “base-26” encoding.
+// see also:http://en.wikipedia.org/wiki/Hexavigesimal
+
+//InChiKey v1.2 length: 14-10-1
+//InChIKey v1.2 for morphine is BQJCRHHNABKAKU-KBQPJGBKSA-N
+var x = 'BQJCRHHNABKAKU-KBQPJGBKSA-N'
+25===x.length && '-'===x[14]
+&& !!x.match(/^([0-9A-Z\-]+)$/)
+>false
+//enzyme ligand Copper - InchiKey: RYGMFSIKBFXOCR-UHFFFAOYSA-N
+var x = 'RYGMFSIKBFXOCR-UHFFFAOYSA-N'
+27===x.length && '-'===x[14] && '-'===x[25]
+&& !!x.match(/^([0-9A-Z\-]+)$/)
+>true
diff --git a/InChi.js b/InChi.js
@@ -0,0 +1,11 @@
+// International Chemical Identifier Regex, by lo sauer - lsauer.com
+// Morphine InchI:
+var x="InChI=1S/C17H19NO3/c1-18-7-6-17-10-3-5-13(20)16(17)21-15-12(19)4-2-9(14(15)17)8-11(10)18/h2-5,10-11,13,16,19-20H,6-8H2,1H3/t10-,11+,13-,16-,17-/m0/s1"
+
+// applying an organic character-subset
+// we could check for the length property, but in case of 0 matches 'null' is returned -> hence !!.. \ generally equal to Boolean(..) 
+!!x.trim().match(/^((InChI=)?[^J][0-9BCOHNSOPrIFla+\-\(\)\\\/,pqbtmsih]{6,})$/ig)
+>true
+//generic:
+x.trim().match(/^((InChI=)?[^J][0-9a-z+\-\(\)\\\/,]+)$/ig)
+>true
diff --git a/_smiles_inchi_annotated.js b/_smiles_inchi_annotated.js
@@ -1,6 +1,6 @@
 //SMILES, Inchi Regex , by lo sauer - lsauer.com
 //Here's a PREG version for SMILES validation (JavaScript) beyond a length of 5:
-x = "OC[C@@H](O1)[C@@H](O)[C@H](O)[C@@H]2[C@@H]1c3c(O)c(OC)c(O)cc3C(=O)O2"
+var x = "OC[C@@H](O1)[C@@H](O)[C@H](O)[C@@H]2[C@@H]1c3c(O)c(OC)c(O)cc3C(=O)O2"
 
 x.trim().match(/^([^J][a-z0-9@+\-\[\]\(\)\\\/%=#$]{6,})$/ig)[0]
 >"OC[C@@H](O1)[C@@H](O)[C@H](O)[C@@H]2[C@@H]1c3c(O)c(OC)c(O)cc3C(=O)O2"
@@ -31,4 +31,6 @@ if(!Array.prototype.hasOwnProperty('sum'))
 }
 
 x.toLowerCase().split('').map(function(v,k){return 'c'==v|0;}).sum()
->14
+>14
+
+Array.prototype.atomCount = function(t){ return this.map(function(v,k){return t==v|0;}).reduce(function(a,b){return a+b}) };
diff --git a/smiles_inchi_annotated.js b/smiles_inchi_annotated.js
@@ -1,4 +1,4 @@
-//SMILES Regex annotated, by lo sauer - lsauer.com
+// Simplified Molecular Input Line Entry Specification (SMILES) Regex annotated, by lo sauer - lsauer.com
 /^(    //starting with
 [^J]   //must not contain J, which is the only letter absent from the periodic table
 [0-9   // number for cyclic connection quantifiers and charge; e.g. [Co+3] or [Co+++]
@@ -14,4 +14,32 @@ BCOHNSOPrIFla  //"organic subset": B, C, N, O, P, S, F, Cl, Br, I -> do not requ
 $      // quadruple bonds e.g.  [Ga-]$[As+] (gallium arsenide)
 ]{6,}  // length must be > 5
 )$
-/ig   //ending with, search global, case-insensitive
+/ig   //ending with, search global, case-insensitive
+
+/**
+ * SMARTS
+*/
+// SMARTS...Smiles arbitrary target specification has commas in addition to the SMILES character-set
+// bonds are defined as:  '-' (single), '=' (double), '#' (triple), ':' (aromatic) and '~' (any)
+// logic operators: 
+//       OR operator ',' 
+//       AND operator '&' (lower priority ';')
+//       NOT operator  '!'
+// more information: http://en.wikipedia.org/wiki/Smiles_arbitrary_target_specification
+
+//REGEX
+/^([^J][0-9BCOHNSOPrIFla@+\-\[\]\(\)\\\/%=#$,.~&!]{6,})$/
+
+
+//examples 
+// definitions of hydrogen bond donors and acceptors used to apply Lipinski's Rule of Five:
+var x="[N,n,O;!H0]"
+var y="[#7,#8;!H0]"
+
+!!x.trim().match(/^([^J][0-9BCOHNSOPrIFla@+\-\[\]\(\)\\\/%=#$,.~;&!]{6,})$/ig)
+>true
+y.trim().match(/^([^J][0-9BCOHNSOPrIFla@+\-\[\]\(\)\\\/%=#$,.~;&!]{6,})$/ig)
+>true
+// definition of aliphatic amines, likely to protonate at physiological pH:
+var x="[$([NH2][CX4]),$([NH]([CX4])[CX4]),$[NX3]([CX4])([CX4])[CX4])]"
+>true
diff --git a/_smiles_inchi_annotated.js b/_smiles_inchi_annotated.js
@@ -17,9 +17,14 @@ x.trim().match(/^([^J][0-9BCOHNSOPrIFla@+\-\[\]\(\)\\\/%=#$]{6,})$/ig)
 
 //if you need a carbon count:
 x.toLowerCase().split('').map(function(v,k){return +'c'==v;})
->[false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false]
+>[false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false,
+  false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, 
+  false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, 
+  false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, 
+  false, false, false, false]
 x.toLowerCase().split('').map(function(v,k){return 'c'==v|0;})
->[0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 0, 1, 1, 0, 1, 0, 0, 0, 0, 0, 0]
+>[0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1,
+  0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 0, 1, 1, 0, 1, 0, 0, 0, 0, 0, 0]
 if(!Array.prototype.hasOwnProperty('sum'))
 {
     function (){return this.reduce(function(a,b){return a+b})}

diff --git a/_smiles_inchi_annotated.js b/_smiles_inchi_annotated.js
@@ -1,5 +1,5 @@
 //SMILES, Inchi Regex , by lo sauer - lsauer.com
-Here's a PREG version for SMILES validation (JavaScript) beyond a length of 5:
+//Here's a PREG version for SMILES validation (JavaScript) beyond a length of 5:
 x = "OC[C@@H](O1)[C@@H](O)[C@H](O)[C@@H]2[C@@H]1c3c(O)c(OC)c(O)cc3C(=O)O2"
 
 x.trim().match(/^([^J][a-z0-9@+\-\[\]\(\)\\\/%=#$]{6,})$/ig)[0]

diff --git a/_smiles_inchi_annotated.js b/_smiles_inchi_annotated.js
@@ -0,0 +1,29 @@
+//SMILES, Inchi Regex , by lo sauer - lsauer.com
+Here's a PREG version for SMILES validation (JavaScript) beyond a length of 5:
+x = "OC[C@@H](O1)[C@@H](O)[C@H](O)[C@@H]2[C@@H]1c3c(O)c(OC)c(O)cc3C(=O)O2"
+
+x.trim().match(/^([^J][a-z0-9@+\-\[\]\(\)\\\/%=#$]{6,})$/ig)[0]
+>"OC[C@@H](O1)[C@@H](O)[C@H](O)[C@@H]2[C@@H]1c3c(O)c(OC)c(O)cc3C(=O)O2"
+
+//for the most frequent organic molecules
+x.trim().match(/^([^J][0-9BCOHNSOPrIFla@+\-\[\]\(\)\\\/%=#$]{6,})$/ig)
+
+//generic Perl RegEx:
+/^([^J][A-Za-z0-9@+\-\[\]\(\)\\\/%=#$]+)$/
+
+//Note: The only letter not appearing on the Periodic Table is the letter "J"
+//Annotated
+x.trim().match(/^([^J][0-9BCOHNSOPrIFla@+\-\[\]\(\)\\\/%=#$]{6,})$/ig)
+
+//if you need a carbon count:
+x.toLowerCase().split('').map(function(v,k){return +'c'==v;})
+>[false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false]
+x.toLowerCase().split('').map(function(v,k){return 'c'==v|0;})
+>[0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 0, 1, 1, 0, 1, 0, 0, 0, 0, 0, 0]
+if(!Array.prototype.hasOwnProperty('sum'))
+{
+    function (){return this.reduce(function(a,b){return a+b})}
+}
+
+x.toLowerCase().split('').map(function(v,k){return 'c'==v|0;}).sum()
+>14
diff --git a/smiles_inchi_annotated.js b/smiles_inchi_annotated.js
@@ -0,0 +1,17 @@
+//SMILES Regex annotated, by lo sauer - lsauer.com
+/^(    //starting with
+[^J]   //must not contain J, which is the only letter absent from the periodic table
+[0-9   // number for cyclic connection quantifiers and charge; e.g. [Co+3] or [Co+++]
+BCOHNSOPrIFla  //"organic subset": B, C, N, O, P, S, F, Cl, Br, I -> do not require [] in SMILES; additionally: Na, Cl, Fl 
+@      // Stereocenter configuration descriptor, usually tetrahedral carbon e.g. L-Ala N[C@@H](C)C(=O)O vs. D-Ala N[C@H](C)C(=O)O
+%      // unique labels: C14 is a carbon hold the ring closure labels 1 and 2; C%12 holds the unique label 12
++\-    // +- the charge sign
+\[\]   // [] is used to delinate atoms e.g. [Co+++]
+\(\)   // () branching-descriptors of the sparse-tree (rings are broken in SMILES), e.g. CCC(=O)O for propionic acid 
+\\\/   // /\ for configuration around double bonds e.g. F/C=C/F... trans-difluoroethene,  
+=      // double bonds e.g. O=C=O (carbon dioxide)
+#      // triple bonds e.g. C#N (hydrogen cyanide,)
+$      // quadruple bonds e.g.  [Ga-]$[As+] (gallium arsenide)
+]{6,}  // length must be > 5
+)$
+/ig   //ending with, search global, case-insensitive
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