mirror of
https://github.com/bckelley/avogadrio.git
synced 2026-08-24 02:04:11 -05:00
Add smiles converter as service
This commit is contained in:
Saul Johnson
@@ -66,3 +66,9 @@ phpunit.phar
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# Compiled code
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/web/js/
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/web/css/
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# Caches
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/db/*.dat
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# Keep files
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!.gitkeep
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+7
-1
@@ -14,6 +14,12 @@
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"twig/twig": "^1.24",
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"mustangostang/spyc": "^0.5.1",
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"intervention/image": "^2.4",
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"guzzlehttp/guzzle": "^6.3"
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"guzzlehttp/guzzle": "^6.3",
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"lambdacasserole/condense": "^1.1"
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},
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"autoload": {
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"psr-4": {
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"Avogadrio\\": "src/"
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}
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}
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}
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Generated
+148
-1
@@ -4,8 +4,71 @@
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"Read more about it at https://getcomposer.org/doc/01-basic-usage.md#composer-lock-the-lock-file",
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"This file is @generated automatically"
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],
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"content-hash": "5e740fc02164dd61e791ba1ae1a34860",
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"content-hash": "414181a9b439757b16b4938d109a80bd",
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"packages": [
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{
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"name": "defuse/php-encryption",
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"version": "v2.1.0",
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"source": {
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"type": "git",
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"url": "https://github.com/defuse/php-encryption.git",
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"reference": "5176f5abb38d3ea8a6e3ac6cd3bbb54d8185a689"
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},
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"dist": {
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"type": "zip",
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"url": "https://api.github.com/repos/defuse/php-encryption/zipball/5176f5abb38d3ea8a6e3ac6cd3bbb54d8185a689",
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"reference": "5176f5abb38d3ea8a6e3ac6cd3bbb54d8185a689",
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"shasum": ""
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},
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"require": {
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"ext-openssl": "*",
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"paragonie/random_compat": "~2.0",
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"php": ">=5.4.0"
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},
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"require-dev": {
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"nikic/php-parser": "^2.0|^3.0",
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"phpunit/phpunit": "^4|^5"
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},
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"bin": [
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"bin/generate-defuse-key"
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],
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"type": "library",
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"autoload": {
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"psr-4": {
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"Defuse\\Crypto\\": "src"
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}
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},
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"notification-url": "https://packagist.org/downloads/",
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"license": [
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"MIT"
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],
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"authors": [
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{
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"name": "Taylor Hornby",
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"email": "taylor@defuse.ca",
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"homepage": "https://defuse.ca/"
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},
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{
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"name": "Scott Arciszewski",
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"email": "info@paragonie.com",
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"homepage": "https://paragonie.com"
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}
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],
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"description": "Secure PHP Encryption Library",
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"keywords": [
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"aes",
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"authenticated encryption",
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"cipher",
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"crypto",
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"cryptography",
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"encrypt",
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"encryption",
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"openssl",
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"security",
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"symmetric key cryptography"
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],
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"time": "2017-05-18T21:28:48+00:00"
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},
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{
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"name": "guzzlehttp/guzzle",
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"version": "6.3.0",
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@@ -257,6 +320,42 @@
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],
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"time": "2017-07-03T15:50:40+00:00"
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},
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{
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"name": "lambdacasserole/condense",
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"version": "v1.1",
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"source": {
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"type": "git",
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"url": "https://github.com/lambdacasserole/condense.git",
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"reference": "dcbe8d7ca5ee0909a0df7c47e493311d130cbe9d"
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},
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"dist": {
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"type": "zip",
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"url": "https://api.github.com/repos/lambdacasserole/condense/zipball/dcbe8d7ca5ee0909a0df7c47e493311d130cbe9d",
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"reference": "dcbe8d7ca5ee0909a0df7c47e493311d130cbe9d",
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"shasum": ""
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},
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"require": {
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"defuse/php-encryption": "^2.0"
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},
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"type": "library",
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"autoload": {
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"psr-4": {
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"Condense\\": "src/"
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}
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},
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"notification-url": "https://packagist.org/downloads/",
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"license": [
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"MIT"
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],
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"authors": [
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{
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"name": "Saul Johnson",
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"email": "saul.a.johnson@gmail.com"
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}
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],
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"description": "Flat-file database in PHP.",
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"time": "2017-01-30T14:35:04+00:00"
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},
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{
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"name": "mustangostang/spyc",
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"version": "0.5.1",
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@@ -304,6 +403,54 @@
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],
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"time": "2013-02-21T10:52:01+00:00"
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},
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{
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"name": "paragonie/random_compat",
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"version": "v2.0.10",
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"source": {
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"type": "git",
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"url": "https://github.com/paragonie/random_compat.git",
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"reference": "634bae8e911eefa89c1abfbf1b66da679ac8f54d"
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},
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"dist": {
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"type": "zip",
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"url": "https://api.github.com/repos/paragonie/random_compat/zipball/634bae8e911eefa89c1abfbf1b66da679ac8f54d",
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"reference": "634bae8e911eefa89c1abfbf1b66da679ac8f54d",
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"shasum": ""
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},
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"require": {
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"php": ">=5.2.0"
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},
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"require-dev": {
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"phpunit/phpunit": "4.*|5.*"
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},
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"suggest": {
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"ext-libsodium": "Provides a modern crypto API that can be used to generate random bytes."
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},
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"type": "library",
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"autoload": {
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"files": [
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"lib/random.php"
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]
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},
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"notification-url": "https://packagist.org/downloads/",
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"license": [
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"MIT"
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],
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"authors": [
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{
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"name": "Paragon Initiative Enterprises",
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"email": "security@paragonie.com",
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"homepage": "https://paragonie.com"
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}
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],
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"description": "PHP 5.x polyfill for random_bytes() and random_int() from PHP 7",
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"keywords": [
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"csprng",
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"pseudorandom",
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"random"
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],
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"time": "2017-03-13T16:27:32+00:00"
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},
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{
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"name": "pimple/pimple",
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"version": "v3.0.2",
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@@ -0,0 +1,59 @@
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<?php
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namespace Avogadrio;
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use Condense\Database;
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use \GuzzleHttp\Client;
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/**
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* Provides a conversion service between compound names and SMILES strings.
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*
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* @author Saul Johnson <saul.a.johnson@gmail.com>
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* @since 06/08/2017
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* @package Avogadrio
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*/
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class SmilesConverter
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{
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/**
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* The compound name/SMILES cache database.
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*
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* @var Database
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*/
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private $db;
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public function __construct($db) {
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$this->db = $db;
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}
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/**
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* Converts a compound name to SMILES notation.
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*
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* @param string $name the name of the compound
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* @return null|string the SMILES notation for the named compound or null if not found
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*/
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public function nameToSmiles($name)
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{
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// Sanitize name for URLs.
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$encoded = urlencode($name);
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// Check if we've got the name cached already.
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$cachedSmiles = $this->db->get('smiles', 'name', $encoded);
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if ($cachedSmiles !== null) {
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return $cachedSmiles;
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}
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// Convert chemical name to SMILES if we can using API.
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$client = new Client(['verify' => false, 'exceptions' => false]);
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$response = $client->request('GET', "https://cactus.nci.nih.gov/chemical/structure/$encoded/smiles");
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// If request was successful.
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if ($response->getStatusCode() === 200) {
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$smiles = $response->getBody()->getContents();
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$this->db->insert(['name' => $encoded, 'smiles' => $smiles]); // Cache name for future.
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return $smiles;
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}
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// Request failed.
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return null;
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}
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}
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+14
-26
@@ -1,6 +1,6 @@
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<?php
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require_once __DIR__.'/../vendor/autoload.php';
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require_once __DIR__ . '/../vendor/autoload.php';
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use Symfony\Component\HttpFoundation\JsonResponse;
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use Symfony\Component\HttpFoundation\Request;
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@@ -8,11 +8,17 @@ use Symfony\Component\HttpKernel\HttpKernelInterface;
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use Intervention\Image\ImageManagerStatic as Image;
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use Condense\Database;
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use Avogadrio\SmilesConverter;
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// Configure GD as image driver.
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Image::configure(array('driver' => 'gd'));
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// Load config.
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$config = Spyc::YAMLLoad(__DIR__.'/../config/config.yaml');
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$config = Spyc::YAMLLoad(__DIR__ . '/../config/config.yaml');
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// Caching SMILES converter.
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$smilesConverter = new SmilesConverter(new Database('names', __DIR__ . '/../db'));
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$app = new Silex\Application();
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@@ -59,24 +65,6 @@ function renderScaledMolecule($canvasWidth, $canvasHeight, $color, $smiles) {
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return $molecule;
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}
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/**
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* Converts a compound name to SMILES notation.
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*
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* @param array $config the configuration settings for the application
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* @param string $name the name of the compound
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* @return null|string the SMILES notation for the named compound or null if not found
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*/
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function nameToSmiles($config, $name) {
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// Convert chemical name to SMILES if we can using API.
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$client = new GuzzleHttp\Client(['verify' => false, 'exceptions' => false]);
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$res = $client->request('GET',
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str_replace('$name', urlencode($name), $config['chem_name_lookup_service']));
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// If request successful return SMILES, otherwise null.
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return $res->getStatusCode() == 200 ? $res->getBody() : null;
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}
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/*
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* Route actions.
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*/
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@@ -104,10 +92,10 @@ $app->get('/api/smiles/{width}/{height}/{bgcolor}/{fgcolor}/{smiles}', function
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);
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});
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$app->get('/api/name/{width}/{height}/{bgcolor}/{fgcolor}/{name}', function ($width, $height, $bgcolor, $fgcolor, $name) use ($app, $twig, $config) {
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$app->get('/api/name/{width}/{height}/{bgcolor}/{fgcolor}/{name}', function ($width, $height, $bgcolor, $fgcolor, $name) use ($app, $smilesConverter) {
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// Convert chemical name to SMILES if we can.
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$smiles = nameToSmiles($config, $name);
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$smiles = $smilesConverter->nameToSmiles($name);
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// Forward to SMILES route.
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if ($smiles !== null) {
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@@ -127,14 +115,14 @@ $app->get('/api/smiles/{width}/{height}/{color}/{smiles}', function ($width, $he
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);
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});
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$app->get('/api/name/exists/{name}', function ($name) use ($config) {
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return new JsonResponse(nameToSmiles($config, $name) === null ? false : true);
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$app->get('/api/name/exists/{name}', function ($name) use ($config, $smilesConverter) {
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return new JsonResponse($smilesConverter->nameToSmiles($name) === null ? false : true);
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});
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$app->get('/api/name/{width}/{height}/{color}/{name}', function ($width, $height, $color, $name) use ($app, $twig, $config) {
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$app->get('/api/name/{width}/{height}/{color}/{name}', function ($width, $height, $color, $name) use ($app, $twig, $config, $smilesConverter) {
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// Convert chemical name to SMILES if we can.
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$smiles = nameToSmiles($config, $name);
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$smiles = $smilesConverter->nameToSmiles($name);
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// Forward to SMILES route.
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if ($smiles !== null) {
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