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Add Wikipedia fallback for SMILES lookup

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This commit is contained in:
Saul Johnson
2017-08-27 17:22:29 +01:00
parent f09e4a1934
commit 7b6c069c06
6 changed files with 253 additions and 50 deletions
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composer.json
+2 -1
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@@ -15,7 +15,8 @@
"mustangostang/spyc": "^0.5.1",
"intervention/image": "^2.4",
"guzzlehttp/guzzle": "^6.3",
"lambdacasserole/condense": "^1.1"
"lambdacasserole/condense": "^1.1",
"tburry/pquery": "^1.1"
},
"autoload": {
"psr-4": {
composer.lock
Generated
+53 -1
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@@ -4,7 +4,7 @@
"Read more about it at https://getcomposer.org/doc/01-basic-usage.md#composer-lock-the-lock-file",
"This file is @generated automatically"
],
"content-hash": "414181a9b439757b16b4938d109a80bd",
"content-hash": "18fab38459b21165a1075c73d836e92c",
"packages": [
{
"name": "defuse/php-encryption",
@@ -1056,6 +1056,58 @@
],
"time": "2016-06-29T05:41:56+00:00"
},
{
"name": "tburry/pquery",
"version": "v1.1.1",
"source": {
"type": "git",
"url": "https://github.com/tburry/pquery.git",
"reference": "872339ffd38d261c4417ea1855428b1b4ff9abf1"
},
"dist": {
"type": "zip",
"url": "https://api.github.com/repos/tburry/pquery/zipball/872339ffd38d261c4417ea1855428b1b4ff9abf1",
"reference": "872339ffd38d261c4417ea1855428b1b4ff9abf1",
"shasum": ""
},
"require": {
"php": ">=5.3.0"
},
"require-dev": {
"htmlawed/htmlawed": "dev-master"
},
"type": "library",
"autoload": {
"classmap": [
"IQuery.php",
"gan_formatter.php",
"gan_node_html.php",
"gan_parser_html.php",
"gan_selector_html.php",
"gan_tokenizer.php",
"gan_xml2array.php",
"pQuery.php"
]
},
"notification-url": "https://packagist.org/downloads/",
"license": [
"LGPL-2.1"
],
"authors": [
{
"name": "Todd Burry",
"email": "todd@vanillaforums.com",
"role": "developer"
}
],
"description": "A jQuery like html dom parser written in php.",
"keywords": [
"dom",
"ganon",
"php"
],
"time": "2016-01-14T20:55:00+00:00"
},
{
"name": "twig/twig",
"version": "v1.24.1",
src/CactusSmilesConverter.php
+15 -47
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@@ -6,55 +6,26 @@ use Condense\Database;
use \GuzzleHttp\Client;
/**
* Provides a conversion service between compound names and SMILES strings.
* Provides a conversion service between compound names and SMILES strings that uses a dedicated lookup service.
*
* @author Saul Johnson <saul.a.johnson@gmail.com>
* @since 06/08/2017
* @package Avogadrio
*/
class CactusSmilesConverter
class CactusSmilesConverter extends SmilesConverter
{
/**
* The compound name/SMILES cache database.
*
* @var Database
*/
private $db;
/**
* Initializes a new instance of a conversion service between compound names and SMILES strings.
*
* @param Database $db the database in which to cache lookup results
* @param Database $db the database in which to cache lookup results
* @param SmilesConverter $fallback the conversion service to fall back to in case of error
*/
public function __construct($db = null) {
$this->db = $db;
public function __construct($db = null, $fallback = null) {
parent::__construct($db, $fallback);
}
/**
* Gets whether or not the API result cache is enabled.
*
* @return bool true if the cache is enabled, otherwise false
*/
public function isCacheEnabled() {
return $this->db !== null;
}
/**
* Attempts to fix any errors in a SMILES string and returns the result.
*
* @param string $smiles the SMILES string to fix
* @return string the fixed SMILES string
*/
private static function fixSmiles($smiles) {
$output = str_replace('|', '', $smiles); // Zap vertical bars.
return $output;
}
/**
* Converts a compound name to SMILES notation.
*
* @param string $name the name of the compound
* @return null|string the SMILES notation for the named compound or null if not found
* @inheritdoc
*/
public function nameToSmiles($name)
{
@@ -62,11 +33,9 @@ class CactusSmilesConverter
$encoded = rawurlencode($name);
// Check if we've got the name cached already.
if ($this->isCacheEnabled()) {
$cachedSmiles = $this->db->get('smiles', 'name', $encoded);
if ($cachedSmiles !== null) {
return self::fixSmiles($cachedSmiles);
}
$cached = $this->getIfCachedAndValid($encoded);
if ($cached !== null) {
return $cached;
}
// Convert chemical name to SMILES if we can using API.
@@ -76,13 +45,12 @@ class CactusSmilesConverter
// If request was successful.
if ($response->getStatusCode() === 200) {
$smiles = $response->getBody()->getContents();
if ($this->isCacheEnabled()) {
$this->db->insert(['name' => $encoded, 'smiles' => $smiles]); // Cache name for future.
if (self::isValidSmiles($smiles)) {
$this->cache($encoded, $smiles);
return $smiles;
}
return self::fixSmiles($smiles);
}
// Request failed.
return null;
return $this->fallback($name); // Fall back.
}
}
src/SmilesConverter.php
+111
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@@ -0,0 +1,111 @@
<?php
namespace Avogadrio;
use Condense\Database;
/**
* Provides a conversion service between compound names and SMILES strings.
*
* @author Saul Johnson <saul.a.johnson@gmail.com>
* @since 27/08/2017
* @package Avogadrio
*/
abstract class SmilesConverter
{
/**
* The compound name/SMILES cache database.
*
* @var Database
*/
private $db;
/**
* The conversion service to fall back to in case of error.
*
* @var SmilesConverter
*/
private $fallback;
/**
* Initializes a new instance of a conversion service between compound names and SMILES strings.
*
* @param Database $db the database in which to cache lookup results
* @param SmilesConverter $fallback the conversion service to fall back to in case of error
*/
protected function __construct($db, $fallback) {
$this->db = $db;
$this->fallback = $fallback;
}
/**
* Gets whether or not the API result cache is enabled.
*
* @return bool true if the cache is enabled, otherwise false
*/
public function isCacheEnabled() {
return $this->db !== null;
}
/**
* Attempts to fix any errors in a SMILES string and returns the result.
*
* @param string $smiles the SMILES string to fix
* @return string the fixed SMILES string
*/
protected static function fixSmiles($smiles) {
$output = str_replace('|', '', $smiles); // Zap vertical bars.
return $output;
}
/**
* Returns true if a given SMILES string is valid, otherwise returns false.
*
* @param string $smiles the SMILES string to check
* @return bool true if the string was valid, otherwise false
*/
protected static function isValidSmiles($smiles) {
return preg_match('/^[a-zA-Z0-9@%=\\\\\/\[\]\.\+\-\_\*\(\)]+$/', $smiles) ? true : false;
}
/**
* @param $name
* @return string
*/
protected function getIfCachedAndValid($name) {
if ($this->isCacheEnabled()) {
$cachedSmiles = $this->db->get('smiles', 'name', $name);
if ($cachedSmiles !== null && self::isValidSmiles($cachedSmiles)) {
return $cachedSmiles;
}
}
return null;
}
protected function cache($name, $smiles) {
if ($this->isCacheEnabled()) {
$this->db->insert(['name' => $name, 'smiles' => $smiles]); // Cache name for future.
}
}
/**
* Falls back to another SMILES conversion service.
*
* @param string $name the compound name to convert
* @return null|string the converted compound name or null if not found
*/
protected function fallback($name) {
if ($this->fallback === null) {
return null;
}
return $this->fallback->nameToSmiles($name);
}
/**
* Converts a compound name to SMILES notation.
*
* @param string $name the name of the compound
* @return null|string the SMILES notation for the named compound or null if not found
*/
public abstract function nameToSmiles($name);
}
src/WikipediaSmilesConverter.php
+70
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@@ -0,0 +1,70 @@
<?php
namespace Avogadrio;
use Condense\Database;
use \GuzzleHttp\Client;
use pQuery;
/**
* Provides a conversion service between compound names and SMILES strings that scrapes SMILES strings from Wikipedia.
*
* @author Saul Johnson <saul.a.johnson@gmail.com>
* @since 27/08/2017
* @package Avogadrio
*/
class WikipediaSmilesConverter extends SmilesConverter
{
/**
* Initializes a new instance of a conversion service between compound names and SMILES strings.
*
* @param Database $db the database in which to cache lookup results
* @param SmilesConverter $fallback the conversion service to fall back to in case of error
*/
public function __construct($db = null, $fallback = null) {
parent::__construct($db, $fallback);
}
/**
* @inheritdoc
*/
public function nameToSmiles($name)
{
// Sanitize name for URLs.
$encoded = str_replace(' ', '_', $name);
// Check if we've got the name cached already.
$cached = $this->getIfCachedAndValid($encoded);
if ($cached !== null) {
return $cached;
}
// Get Wikipedia page for compound.
$client = new Client();
$response = $client->request('GET', "https://en.wikipedia.org/wiki/$encoded");
// If there is a page.
if ($response->getStatusCode() === 200) {
// Parse page into DOM.
$page = $response->getBody()->getContents();
$dom = pQuery::parseStr($page);
// Get all hyperlinks.
$links = $dom->select('a');
// Look for the SMILES hyperlink.
foreach ($links as $link) {
if (strstr($link->text(), 'SMILES')) {
$smiles = trim($link->parent->getNextSibling()->text()); // Get actual SMILES string.
if (self::isValidSmiles($smiles)) {
$this->cache($encoded, $smiles);
return $smiles;
}
}
}
}
return $this->fallback($name); // Fall back.
}
}
web/index.php
+2 -1
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@@ -9,6 +9,7 @@ use Symfony\Component\HttpKernel\HttpKernelInterface;
use Condense\Database;
use Avogadrio\CactusSmilesConverter;
use Avogadrio\WikipediaSmilesConverter;
use Avogadrio\MoleculeRenderer;
$app = new Silex\Application();
@@ -20,7 +21,7 @@ $app = new Silex\Application();
$config = Spyc::YAMLLoad(__DIR__ . '/../config/config.yaml');
// Services.
$smilesConverter = new CactusSmilesConverter(new Database('names', __DIR__ . '/../db'));
$smilesConverter = new CactusSmilesConverter(new Database('names', __DIR__ . '/../db'), new WikipediaSmilesConverter());
$moleculeRenderer = new MoleculeRenderer($config['sourire_service']);
$moleculeRenderer->setRenderChiralLabels(false); // Disable chiral labels.