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//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) | |
//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')) | |
{ | |
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() | |
>14 | |
Array.prototype.atomCount = function(t){ return this.map(function(v,k){return t==v|0;}).reduce(function(a,b){return a+b}) }; |
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// 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 |
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// 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 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 ): | |
// "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 | |
//Collisions do occurs: | |
//see http://www.chemconnector.com/2011/09/01/an-inchikey-collision-is-discovered-and-not-based-on-stereochemistry/ |
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// 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+++] | |
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 | |
/** | |
* 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 |
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