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This commit is contained in:
Rik Veenboer
2017-10-10 14:11:20 +01:00
commit c1641bda46
18 changed files with 1057 additions and 0 deletions
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47
article.php Normal file
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<?php
set_time_limit(0);
header('Content-Type: text/html;charset=utf-8');
?>
<pre><?php
/* Load dependencies */
require_once 'bibtex.php';
$sDois = <<<DOIS
DOIS;
$sKeys = <<<KEYS
KEYS;
$aKeys = array();
$aDuplicates = array();
foreach (explode("\n", trim($sKeys)) as $sKey) {
$sKey = trim(current((explode('(', $sKey))));
$aMatch = array();
preg_match('~([a-z]+)([\d]+)([[a-z]*)~i', $sKey, $aMatch);
if (isset($aMatch[2])) {
$iYear = intval($aMatch[2]);
$aKeys[$iYear] = isset($aKeys[$iYear]) ? array_merge($aKeys[$iYear], array($aMatch[1])) : array($aMatch[1]);
if (!empty($aMatch[3])) {
if (!isset($aDuplicates[$iYear][$aMatch[1]])) {
$aDuplicates[$iYear][$aMatch[1]] = $aMatch[3];
} else {
$aDuplicates[$iYear][$aMatch[1]] .= sprintf('/%s', $aMatch[3]);
}
}
}
}
$aKeys = array_map('array_unique', $aKeys);
$aDois = explode("\r\n", $sDois);
$aError = array();
foreach ($aDois as $sDoi) {
if ($sDoi == null) continue;
if (($sArticle = doi_bibtex($sDoi, $aKeys, $aDuplicates, $aError)) !== false) {
echo $sArticle;
}
}
if (!empty($aError)) {
print_r($aError);
}

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<?php
/* Configuration */
$sAccount = file_get_contents('.account');
$aTemplate = array(
'article' => "@article{%s,\n%s\n}\n",
'entry' => ' %s = {%s},',
'author' => '%s, %s');
require_once 'remove-accents.php';
function doi_bibtex($sDoi, $mKey = null, $aDuplicates = null, &$aError = null) {
global $sAccount, $aTemplate;
$sUrl = sprintf('http://www.crossref.org/openurl/?id=%s&noredirect=true&pid=%s&format=unixref', urlencode(trim($sDoi)), $sAccount);
if (!($sContents = file_get_contents($sUrl))) {
$aError[] = $sDoi;
return false;
}
$oXml = new SimpleXMLElement($sContents);
$oCrossrefXml = $oXml->doi_record->crossref;
if ($oCrossrefXml === null || isset($oCrossrefXml->error)) {
$aError[] = $sDoi;
return false;
}
$oJournalXml = $oCrossrefXml->journal;
$oArticleXml = $oJournalXml->journal_article;
$aAuthors = array();
if (isset($oArticleXml->contributors)) {
foreach ($oArticleXml->contributors->person_name as $oPersonXml) {
$aAuthors[] = sprintf($aTemplate['author'], $oPersonXml->surname, $oPersonXml->given_name);
}
}
$oIssueXml = $oJournalXml->journal_issue;
$sAuthors = implode(' and ', $aAuthors);
$sAuthorsAccentless = remove_accents($sAuthors);
if (!isset($oIssueXml->publication_date)) {
$aError[] = $sDoi;
return false;
}
$iYear = intval($oIssueXml->publication_date->year);
if (is_string($mKey)) {
$sKey = $mKey;
} else {
$aFound = array();
if (isset($mKey[$iYear])) {
foreach ($mKey[$iYear] as $sAuthor) {
if (strpos(str_replace(' ', null, $sAuthorsAccentless), $sAuthor) !== false) {
$sKey = sprintf('%s%d%s', $sAuthor, $iYear, isset($aDuplicates[$iYear][$sAuthor]) ? $aDuplicates[$iYear][$sAuthor] : null);
$aFound[] = $sKey;
}
}
}
$sKey = empty($aFound) ? md5($sDoi) : implode(';', $aFound);
}
$aEntries = array();
$aEntries[] = sprintf($aTemplate['entry'], 'author', $sAuthors);
$aEntries[] = sprintf($aTemplate['entry'], 'title', trim($oArticleXml->titles->title));
$oMetadataXml = $oJournalXml->journal_metadata;
$aEntries[] = sprintf($aTemplate['entry'], 'journal', $oMetadataXml->full_title);
$aEntries[] = sprintf($aTemplate['entry'], 'year', $iYear);
$aEntries[] = sprintf($aTemplate['entry'], 'volume', $oIssueXml->journal_volume->volume);
$sPages = empty($oArticleXml->pages->last_page)
? $oArticleXml->pages->first_page
: sprintf('%d-%d', $oArticleXml->pages->first_page, $oArticleXml->pages->last_page);
$aEntries[] = sprintf($aTemplate['entry'], 'pages', $sPages);
$aEntries[] = sprintf($aTemplate['entry'], 'number', $oIssueXml->issue);
$aEntries[] = sprintf($aTemplate['entry'], 'month', $oIssueXml->publication_date->month);
$aEntries[] = sprintf($aTemplate['entry'], 'doi', $sDoi);
$aEntries[] = sprintf($aTemplate['entry'], 'url', $oArticleXml->doi_data->resource);
return sprintf($aTemplate['article'], $sKey, implode("\n", $aEntries));
}

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<?php
set_time_limit(0);
error_reporting(E_ALL ^ E_DEPRECATED);
/* Load dependencies */
chdir(dirname(__FILE__));
set_include_path(implode(PATH_SEPARATOR, array(get_include_path(), '../../', '../../Pear/')));
require_once 'vendor/autoload.php';
/* Configuration */
$sBibtexFile = 'C:\Users\Rik\Git\latex\Report\phd-thesis\Bibliography\reference.bib';
$sEntriesFile = 'C:\Users\Rik\Dropbox\Reference\check.txt';
$sFailFile = 'C:\Users\Rik\Dropbox\Reference\fail.txt';
$sTmpDir = 'C:\tmp';
/* Latex template */
$sLatex = '\documentclass{article}
\usepackage[utf8]{inputenc}
\usepackage[backend=bibtex8,style=chem-angew]{biblatex}
\addbibresource{reference.bib}
\begin{document}
\cite{%s}
\printbibliography
\end{document}';
/* Parse bibtex file */
$bReset = isset($_GET['reset']) || (isset($argc) && $argc == 2 && $argv[1] == 'reset');
if ($bReset || !file_exists($sEntriesFile)) {
$aEntries = array();
$oBibtex = new Structures_BibTex();
if ($oBibtex->loadFile($sBibtexFile) && $oBibtex->parse()) {
foreach ($oBibtex->data as $aEntry) {
if ($aEntry['type'] != 'comment') {
$aEntries[] = $aEntry['cite'];
}
}
}
} else {
$aEntries = explode("\n", file_get_contents($sEntriesFile));
}
/* Prepare temporary directory */
@mkdir($sTmpDir);
chdir($sTmpDir);
copy($sBibtexFile, 'reference.bib');
/* Loop over entries */
@unlink($sFailFile);
foreach ($aEntries as $iKey => $sEntry) {
if (!empty($sEntry)) {
printf('Checking "%s"... ', $sEntry);
command('rm check*.*');
file_put_contents('check.tex', sprintf($sLatex, $sEntry));
command('latex -interaction=nonstopmode check');
command('bibtex check');
command('latex -interaction=nonstopmode check');
$sLog = file_get_contents('check.log');
if (strpos($sLog, 'inputenc Error') === false) {
printf("success!\n");
unset($aEntries[$iKey]);
} else {
printf("fail!\n");
file_put_contents($sFailFile, sprintf("%s\n", $sEntry), FILE_APPEND);
}
}
}
/* Clean up */
command('rm check*.*');
unlink('reference.bib');
/* Keep track of failed files */
file_put_contents($sEntriesFile, implode("\n", $aEntries));
/* Helper functions */
function command($sCommand) {
ob_start();
exec(sprintf('%s 2>&1', $sCommand));
return ob_get_clean();
}

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<pre><?php
set_time_limit(0);
/* Configuration */
$sFiles = 'C:\Users\Rik\Dropbox\Reference';
$sFile = file_get_contents('.reference');
$sDatabase = file_get_contents($sFile);
// define('TEXT_NOLINK', true);
$bLink = !defined('TEXT_NOLINK');
$bDois = defined('TEXT_NOLINK');
$bText = defined('TEXT_NOLINK');
$bLoose = true;
$aIgnore = array('Todo', 'Theses', 'Authors', 'Patent');
//$aIgnore = array();
$aMissing = array(
'file' => array( # entries without citation
'Schmidbaur2002a',
'Anderson2011',
'Cadierno2012',
'Selander2017a'
),
'keys' => array( # entries without file
'Finkelstein1910',
'Williamson1851',
'Ullmann1901',
'Ullmann1904',
'Saito1973',
'Lee1991',
'Hayashi2012',
'Rix1956',
'Sheldrick2008',
'Smykalla1991',
'Kuzmina1994',
'Tanisaki1973',
'Hayton2010',
'Cadierno2013',
'Gutmann1975',
'Schwerdtfeger1993'
),
'type' => array(
'online',
'book',
'inbook',
'incollection',
'phdthesis'));
/* Load dependencies */
set_include_path(implode(PATH_SEPARATOR, array(get_include_path(), '../../')));
require_once 'vendor/autoload.php';
require_once 'explore.php';
require_once 'pdf2text.php';
use ZendPdf\PdfDocument;
use ZendPdf\Exception\CorruptedPdfException;
use ZendPdf\Exception\NotImplementedException;
preg_match_all('~@([^{]+){([^,]+),~i', $sDatabase, $aMatches);
$aEntries = array_combine($aMatches[2], $aMatches[1]);
$aDois = array();
echo "<strong>No entry found for:</strong>\n";
explore($sFiles, '\*.pdf', $aFound);
$aKeys = [];
foreach ($aFound as $sFile) {
$sBase = basename($sFile, '.pdf');
if (ctype_upper(substr($sBase, 0, 1)) && substr($sBase, -2, 1) !== '.' && strpos($sBase, ' ') === false && in_array($sBase, $aMissing['file']) === false) {
$bIgnore = false;
foreach ($aIgnore as $sIgnore) {
if (strpos($sFile, sprintf('%s\\', $sIgnore)) !== false) {
$bIgnore = true;
break;
}
}
if (!$bIgnore) {
$aKeys[] = $sBase;
}
$bEntry = isset($aEntries[$sBase]);
if ($bIgnore || $bEntry) {
unset($aEntries[$sBase]);
} else {
if ($bDois) {
$sDoi = null;
try {
$oPdf = new PdfDocument($sFile, 0, true);
if (isset($oPdf->properties['WPS-ARTICLEDOI'])) {
$sDoi = $oPdf->properties['WPS-ARTICLEDOI'];
}
} catch (CorruptedPdfException $e) {
} catch (NotImplementedException $e) {}
if (isset($sDoi)) {
$aDois[] = $sDoi;
} elseif ($bText) {
$sText = pdf2text($sFile);
if (preg_match('~(dx\.doi\.org/|doi:\s?)(\d+\.\d+/(:?\w+\.)?\w+)~i', $sText, $aMatch)) {
$aDois[] = $aMatch[2];
} else if (preg_match('~\s(\d+\.\d+/(:?\w+\.)?\w+)CCC~i', $sText, $aMatch)) {
$aDois[] = $aMatch[1];
} else if ($bLoose && preg_match('~(\d{2}\.\d+/\s*(:?\w+\.)?\w+)~i', $sText, $aMatch)) {
$aDois[] = str_replace(' ', null, $aMatch[0]);
}
}
}
if ($bLink) {
printf("%-20s (<a href=\"file://%s\" target=\"_blank\">%s</a>)\n", $sBase, $sFile, str_replace(array($sFiles, basename($sFile)), null, $sFile));
} else {
printf("%s\n", $sBase);
}
}
}
}
foreach ($aEntries as $sBase => $sType) {
if (in_array(strtolower($aEntries[$sBase]), $aMissing['type']) || strpos($sBase, 'ange_') === 0) {
unset($aEntries[$sBase]);
}
}
echo "\n<strong>DOIs:</strong>\n";
echo count($aDois) > 0 ? implode("\n", $aDois) . "\n" : null;
echo "\n<strong>File missing for:</strong>\n";
echo implode("\n", array_diff(array_keys($aEntries), $aMissing['keys'])). "\n";
// print_r(array_unique($aKeys));
// print_r(($aKeys));
echo "\n<strong>Duplicate files:</strong>\n";
echo implode("\n", array_diff_assoc($aKeys, array_unique($aKeys)));

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<?php
set_time_limit(0);
$sList = 'C:\Users\Rik\Downloads\OHBF3.gcd';
$sData = 'C:\Users\Rik\Downloads\data-OHBF3.csv';
$aList = explode("\n", trim(file_get_contents($sList)));
$bHead = false;
$aHead = [];
$aEntries = [];
foreach ($aList as $sEntry) {
$sUrl = sprintf('https://summary.ccdc.cam.ac.uk/structure-summary?refcode=%s', trim($sEntry));
$sContents = file_get_contents($sUrl);
$aParts = explode('<script>', $sContents);
if (!isset($aParts[3])) continue;
$sJavascript = trim(current(explode('</script>', $aParts[3])));
preg_match_all('~"([\w]+)":\s*"([^"]+)"~', $sJavascript, $aMatches, PREG_PATTERN_ORDER);
$aData = [];
$aHead = array_unique(array_merge($aHead, $aMatches[1]));
foreach ($aMatches[1] as $iKey => $sKey) {
$aData[$sKey] = $aMatches[2][$iKey];
}
$aEntries[] = $aData;
printf("%s\n", $aData['RefCode']);
}
file_put_contents($sData, implode("\t", $aHead) . PHP_EOL);
$aEmpty = array_flip($aHead);
foreach ($aEntries as $aEntry) {
$aEntry = array_merge($aEmpty, $aEntry);
file_put_contents($sData, implode("\t", $aEntry) . PHP_EOL, FILE_APPEND);
}

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<pre><?php
$sDirectory = 'C:\Users\Rik\Git\latex\Report\phd-thesis';
$oDirectory = new RecursiveDirectoryIterator($sDirectory);
$oIterator = new RecursiveIteratorIterator($oDirectory);
define('NEED', 'Notes.tex');
$aCites = [];
foreach ($oIterator as $oFile) {
$sFile = (string) $oFile;
if (strpos($sFile, '.tex') && !strpos($sFile, '-tmp')) {
$sFilePath = substr(str_replace($sDirectory, null, $sFile), 1);
$sContents = file_get_contents($sFile);
preg_match_all('~cite\{([^\}]+)\}~', $sContents, $aMatches, PREG_SET_ORDER);
foreach ($aMatches as $aCite) {
$sCites = str_replace(', ', ',', $aCite[1]);
foreach (explode(',', $sCites) as $sCite) {
if (isset($aCites[$sCite])) {
$aCites[$sCite][] = $sFilePath;
$aCites[$sCite] = array_unique($aCites[$sCite]);
} else {
$aCites[$sCite] = array($sFilePath);
}
}
}
}
}
$iRepeated = 0;
$sBuffer = null;
ksort($aCites);
foreach ($aCites as $sCite => $aFiles) {
$iCount = count($aFiles);
if ($iCount > 1) {
if (defined('NEED')) {
$bFound = false;
foreach ($aFiles as $sFile) {
if (basename($sFile) == NEED) {
$bFound = true;
}
}
if (!$bFound) {
continue;
}
}
++$iRepeated;
$sBuffer .= sprintf("<strong>%s=%d</strong>\n", $sCite, $iCount);
foreach ($aFiles as $sFile) {
$sBuffer .= sprintf(" - %s\n", $sFile);
}
}
if (isset($aStats[$iCount])) {
++$aStats[$iCount];
} else {
$aStats[$iCount] = 1;
}
}
printf("<em>Total number of unique citations: %d</em>\n\n", count($aCites));
printf("<em>Number of repeated citations: %d</em>\n\n", $iRepeated);
printf("%s\n\n", $sBuffer);
ksort($aStats);
foreach ($aStats as $iCount => $iNumber) {
printf("%d > %d\n", $iCount, $iNumber);
}

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<pre><?php
set_time_limit(0);
/* Configuration */
$sFiles = 'C:\Users\Rik\Dropbox\Reference';
$sBibliography = file_get_contents('.reference');
$sDatabase = file_get_contents($sBibliography);
/* Load dependencies */
set_include_path(implode(PATH_SEPARATOR, array(get_include_path(), '../../')));
require_once 'explore.php';
$aFound = [];
explore($sFiles, '\*.pdf', $aFound);
foreach ($aFound as $sFile) {
$sBase = basename($sFile, '.pdf');
if (strpos($sBase, '.') === false) {
$aFiles[$sBase] = ltrim(str_replace($sFiles, null, $sFile), '\\/');
}
}
preg_match_all('~@[\w]+\{(.*?),.*?\},?[\s]*\}~s', $sDatabase, $aMatches);
foreach ($aMatches[0] as $i => $sOriginal) {
$sKey = $aMatches[1][$i];
if (isset($aFiles[$sKey])) {
$sFile = str_replace('\\', '\\\\', $aFiles[$sKey]);
$sField = sprintf(':%s:PDF', $sFile);
$sNew = preg_replace('~[\s]*file[\s]*=[\s]*\{[^\}]*\},?([\n\r])+~', '$1', $sOriginal);
$aFields = explode(',', $sNew);
$sNew = rtrim($sNew, "\n\r}");
if (substr($sNew, -1) !== ',') {
$sNew .= '},';
}
$sNew = sprintf("%s\nfile = {%s}\n}", $sNew, $sField);
$sDatabase = str_replace($sOriginal, $sNew, $sDatabase);
}
}
file_put_contents($sBibliography, $sDatabase);

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<pre><?php
$sFile = file_get_contents('.reference');
$sDatabase = file_get_contents($sFile);
preg_match_all('~@[\w]+\{(.*?),.*?\}(?!,)~s', $sDatabase, $aMatches);
foreach ($aMatches[0] as $i => $sOriginal) {
preg_match_all('~[\s]+volume[\s]*=[\s]*\{.*?\},~si', $sOriginal, $aVolumes);
$iCount = count($aVolumes[0]);
if ($iCount > 1) {
printf("Deleting %d volume fields from %s!\n", $iCount, $aMatches[1][$i]);
$sNew = str_replace($aVolumes[0], null, $sOriginal);
$sDatabase = str_replace($sOriginal, $sNew, $sDatabase);
}
}
file_put_contents($sFile, $sDatabase);

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<?php
$sWebMO = 'C:\Program Files\WebMO\user';
$sTarget = 'D:\Computations\WebMO';
$aJobs = glob(sprintf('%s\*', $sWebMO));
foreach ($aJobs as $sJob) {
$iJob = basename($sJob);
$sChk = sprintf('%s\output.chk', $sJob);
$sFch = sprintf('%s\output.fch', $sJob);
if (file_exists($sChk)) {
if (!file_exists($sFch)) {
system(printf('formchk "%s"', $sChk));
}
copy($sFch, sprintf('%s\%d.fch', $sTarget, $iJob));
}
}

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<pre><?php
$sFile = file_get_contents('.reference');
$sContents = file_get_contents($sFile);
$aEntries = array();
preg_match_all('~@(?:article|(?:phd|master)thesis)\{(.+?)\}\s*\}~is', $sContents, $aMatches);
foreach ($aMatches[1] as $sArticle) {
$sKey = current(explode(',', $sArticle));
if (preg_match('~pdf[^=]*=[^\{]*\{([^\}]+)~si', $sArticle, $aMatch) > 0) {
$aEntries[$sKey] = $aMatch[1];
}
}
preg_match_all('~@comment\{([^\}]+)\}~s', $sContents, $aMatches);
$aGroups = array();
foreach ($aMatches[1] as $sComment) {
$aParts = explode(';', $sComment);
$aType = explode(':', array_shift($aParts));
if (trim($aType[0]) == 'jabref-meta' && trim($aType[1]) == 'groupstree') {
foreach ($aParts as $sPart) {
$sPart = str_replace(array('\\', "\r", "\n"), null, trim($sPart));
if (!empty($sPart)) {
if (preg_match('~group:(.+)~i', $sPart, $aMatch) > 0) {
$sGroup = $aMatch[1];
$sSearch = $sGroup;//str_replace(array('Thesis'), array('Theses'), $sGroup);
$aGroup = array($sPart . '\\;0\\');
foreach ($aEntries as $sKey => $sPdf) {
if (strpos($sPdf, $sSearch) !== false) {
$aGroup[] = $sKey . '\\';
}
}
$aGroup[] = null;
$aGroups[] = implode(';', $aGroup);
}
}
}
}
}
echo implode(";\n", $aGroups);

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<pre><?php
$sData = <<<NMR
0015 616.623 2.4652 0.0250 2264538
0016 614.244 2.4557 0.0502 4537255
0017 611.862 2.4462 0.0265 2399964
NMR;
/*
2.54 (q, J=1.2 Hz, H, )
2.52 (q, J=1.3 Hz, H, )
*/
$aData = explode("\n", trim($sData));
process($aData, $aFreqs, $aShifts);
switch (count($aData)) {
case 2:
echo doublet($aFreqs, $aShifts, false);
break;
case 3:
echo triplet($aFreqs, $aShifts, false);
break;
case 4:
echo quartet($aFreqs, $aShifts, false);
echo doubletdoublet($aFreqs, $aShifts, false);
break;
case 6:
//echo doubletriplet($aFreqs, $aShifts, false);
echo tripletdoublet($aFreqs, $aShifts, false);
break;
}
function process($aData, &$aFreqs, &$aShifts) {
foreach ($aData as $sRow) {
$aRow = explode(' ', $sRow);
$aFreqs[] = next($aRow);
$aShifts[] = next($aRow);
}
}
function average($aData) {
return array_sum($aData) / count($aData);
}
function doublet($aFreqs, $aShifts, $bValues = true) {
$aValues = array(
($aShifts[0] + $aShifts[1]) / 2,
$aFreqs[0] - $aFreqs[1]);
return $bValues
? $aValues
: vsprintf('%.2f (d, J=%.1f Hz, H, )', $aValues);
}
function triplet($aFreqs, $aShifts, $bValues = true) {
$aValues = array(
$aShifts[1],
average(array(
$aFreqs[0] - $aFreqs[1],
$aFreqs[1] - $aFreqs[2],
($aFreqs[0] - $aFreqs[2]) / 2)));
return $bValues
? $aValues
: vsprintf('%.2f (t, J=%.1f Hz, H, )', $aValues);
}
function quartet($aFreqs, $aShifts, $bValues = true) {
$aValues = array(
average($aShifts),
average(array(
$aFreqs[0] - $aFreqs[1],
$aFreqs[1] - $aFreqs[2],
$aFreqs[2] - $aFreqs[3])));
return $bValues
? $aValues
: vsprintf('%.2f (q, J=%.1f Hz, H, )', $aValues);
}
function doubletdoublet($aFreqs, $aShifts, $bValues = true) {
$aFirstDoublet = doublet(
array_slice($aFreqs, 0, 2),
array_slice($aShifts, 0, 2));
$aSecondDoublet = doublet(
array_slice($aFreqs, 2, 2),
array_slice($aShifts, 2, 2));
$aDoublet = doublet(
array(($aFreqs[0] + $aFreqs[1]) / 2, ($aFreqs[2] + $aFreqs[3]) / 2),
array($aFirstDoublet[0], $aSecondDoublet[0]));
$aValues = array(
$aDoublet[0],
$aDoublet[1],
($aFirstDoublet[1] + $aSecondDoublet[1]) / 2);
return $bValues
? $aValues
: vsprintf("%.2f (dd, J=%.1f Hz, %.1f Hz, H, )", $aValues);
}
function doubletriplet($aFreqs, $aShifts, $bValues = true) {
$aFirstTriplet = triplet(
array_slice($aFreqs, 0, 3),
array_slice($aShifts, 0, 3));
$aSecondTriplet = triplet(
array_slice($aFreqs, 3, 3),
array_slice($aShifts, 3, 3));
$aDoublet = doublet(
array($aFreqs[1], $aFreqs[4]),
array($aFirstTriplet[0], $aSecondTriplet[0]));
$aValues = array(
$aDoublet[0],
$aDoublet[1],
($aFirstTriplet[1] + $aSecondTriplet[1]) / 2);
return $bValues
? $aValues
: vsprintf('%.2f (dt, J=%.1f Hz, J=%.1f Hz, H, )', $aValues);
}
function tripletdoublet($aFreqs, $aShifts, $bValues = true) {
$aFirstDoublet = doublet(
array_slice($aFreqs, 0, 2),
array_slice($aShifts, 0, 2));
$aSecondDoublet = doublet(
array_slice($aFreqs, 2, 2),
array_slice($aShifts, 2, 2));
$aThirdDoublet = doublet(
array_slice($aFreqs, 4, 2),
array_slice($aShifts, 4, 2));
$aFirstTriplet = triplet(
array($aFreqs[0], $aFreqs[2], $aFreqs[4]),
array($aShifts[0], $aShifts[2], $aShifts[4]));
$aSecondTriplet = triplet(
array($aFreqs[1], $aFreqs[3], $aFreqs[5]),
array($aShifts[1], $aShifts[3], $aShifts[5]));
$aValues = array(
($aFirstTriplet[0] + $aSecondTriplet[0]) / 2,
($aFirstTriplet[1] + $aSecondTriplet[1]) / 2,
average(array(
$aFirstDoublet[1],
$aSecondDoublet[1],
$aThirdDoublet[1])));
return $bValues
? $aValues
: vsprintf('%.2f (td, J=%.1f Hz, J=%.1f Hz, H, )', $aValues);
}

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<?php
set_time_limit(0);
header('Content-Type: text/html;charset=utf-8');
?>
<pre><?php
/* Configuration */
error_reporting(E_ALL ^ E_DEPRECATED);
$sFile = file_get_contents('.reference');
$sAccount = file_get_contents('.account');
$bUpdateDoi = true;
/* Load dependencies */
set_include_path(implode(PATH_SEPARATOR, array(get_include_path(), '../../')));
require_once 'vendor/autoload.php';
$sDatabase = file_get_contents($sFile);
$oBibtex = new Structures_BibTex();
if ($oBibtex->loadFile($sFile) && $oBibtex->parse()) {
foreach ($oBibtex->data as $aEntry) {
$bPages = isset($aEntry['pages']);
if ($aEntry['type'] == 'article' && isset($aEntry['doi'])) {
$bDoi = $bPages && strpos($aEntry['pages'], 'doi') !== false;
if (!$bUpdateDoi || ($bPages && $aEntry['pages'] != '0-0' && $aEntry['pages'] != '0' && (is_numeric($aEntry['pages']) ? $aEntry['pages'] < 1000000 : true) && !$bDoi)) {
continue;
}
$sCite = $aEntry['cite'];
$sDoi = $aEntry['doi'];
printf("Processing %s (%s)...\n", $sCite, $bPages ? $aEntry['pages'] : null);
preg_match(sprintf('~@article\{%s,.*?\}[\s]*\}~si', $sCite), $sDatabase, $aMatch);
if (!isset($aMatch[0])) {
printf("Entry not found!\n");
continue;
}
$sOriginal = $aMatch[0];
$sUrl = sprintf('http://www.crossref.org/openurl/?id=%s&noredirect=true&pid=%s&format=unixref', urlencode(trim($sDoi)), $sAccount);
if (!($sContents = file_get_contents($sUrl))) {
printf("Failed to fetch reference!\n");
continue;
}
if (strpos($sContents, 'Malformed DOI') !== false) {
echo "error!\n";
continue;
}
$oXml = new SimpleXMLElement($sContents);
$oCrossrefXml = $oXml->doi_record->crossref;
$oJournalXml = $oCrossrefXml->journal;
$oArticleXml = $oJournalXml->journal_article;
if ($oCrossrefXml === null || isset($oCrossrefXml->error)) {
printf("Corrupt reference!\n");
continue;
}
$oArticleXml = $oJournalXml->journal_article;
$sPages = ($bSingle = empty($oArticleXml->pages->last_page))
? $oArticleXml->pages->first_page
: sprintf('%d-%d', $oArticleXml->pages->first_page, $oArticleXml->pages->last_page);
if ($sPages == '0-0' || $sPages == '0' || empty($sPages) || ($bSingle && $sPages > 100000)) {
if ($bDoi) {
continue;
}
$sPages = sprintf('doi: %s', $sDoi);
}
printf("Set to: %s\n", $sPages);
if (isset($aEntry['pages'])) {
$sNew = str_replace(
$aEntry['pages'],
$sPages,
$sOriginal);
} else {
$sNew = str_replace(
sprintf('%s,', $sCite),
sprintf("%s,\npages = {%s},", $sCite, $sPages),
$sOriginal);
}
$sDatabase = str_replace($sOriginal, $sNew, $sDatabase);
}
}
}
file_put_contents($sFile, $sDatabase);

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remove-accents.php Normal file
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<?php
function remove_accents($sString) {
if (!preg_match('/[\x80-\xff]/', $sString)) {
return $sString;
}
$aChars = array(
// Decompositions for Latin-1 Supplement
chr(195).chr(128) => 'A', chr(195).chr(129) => 'A',
chr(195).chr(130) => 'A', chr(195).chr(131) => 'A',
chr(195).chr(132) => 'A', chr(195).chr(133) => 'A',
chr(195).chr(135) => 'C', chr(195).chr(136) => 'E',
chr(195).chr(137) => 'E', chr(195).chr(138) => 'E',
chr(195).chr(139) => 'E', chr(195).chr(140) => 'I',
chr(195).chr(141) => 'I', chr(195).chr(142) => 'I',
chr(195).chr(143) => 'I', chr(195).chr(145) => 'N',
chr(195).chr(146) => 'O', chr(195).chr(147) => 'O',
chr(195).chr(148) => 'O', chr(195).chr(149) => 'O',
chr(195).chr(150) => 'O', chr(195).chr(153) => 'U',
chr(195).chr(154) => 'U', chr(195).chr(155) => 'U',
chr(195).chr(156) => 'U', chr(195).chr(157) => 'Y',
chr(195).chr(159) => 's', chr(195).chr(160) => 'a',
chr(195).chr(161) => 'a', chr(195).chr(162) => 'a',
chr(195).chr(163) => 'a', chr(195).chr(164) => 'a',
chr(195).chr(165) => 'a', chr(195).chr(167) => 'c',
chr(195).chr(168) => 'e', chr(195).chr(169) => 'e',
chr(195).chr(170) => 'e', chr(195).chr(171) => 'e',
chr(195).chr(172) => 'i', chr(195).chr(173) => 'i',
chr(195).chr(174) => 'i', chr(195).chr(175) => 'i',
chr(195).chr(177) => 'n', chr(195).chr(178) => 'o',
chr(195).chr(179) => 'o', chr(195).chr(180) => 'o',
chr(195).chr(181) => 'o', chr(195).chr(182) => 'o',
chr(195).chr(182) => 'o', chr(195).chr(185) => 'u',
chr(195).chr(186) => 'u', chr(195).chr(187) => 'u',
chr(195).chr(188) => 'u', chr(195).chr(189) => 'y',
chr(195).chr(191) => 'y',
// Decompositions for Latin Extended-A
chr(196).chr(128) => 'A', chr(196).chr(129) => 'a',
chr(196).chr(130) => 'A', chr(196).chr(131) => 'a',
chr(196).chr(132) => 'A', chr(196).chr(133) => 'a',
chr(196).chr(134) => 'C', chr(196).chr(135) => 'c',
chr(196).chr(136) => 'C', chr(196).chr(137) => 'c',
chr(196).chr(138) => 'C', chr(196).chr(139) => 'c',
chr(196).chr(140) => 'C', chr(196).chr(141) => 'c',
chr(196).chr(142) => 'D', chr(196).chr(143) => 'd',
chr(196).chr(144) => 'D', chr(196).chr(145) => 'd',
chr(196).chr(146) => 'E', chr(196).chr(147) => 'e',
chr(196).chr(148) => 'E', chr(196).chr(149) => 'e',
chr(196).chr(150) => 'E', chr(196).chr(151) => 'e',
chr(196).chr(152) => 'E', chr(196).chr(153) => 'e',
chr(196).chr(154) => 'E', chr(196).chr(155) => 'e',
chr(196).chr(156) => 'G', chr(196).chr(157) => 'g',
chr(196).chr(158) => 'G', chr(196).chr(159) => 'g',
chr(196).chr(160) => 'G', chr(196).chr(161) => 'g',
chr(196).chr(162) => 'G', chr(196).chr(163) => 'g',
chr(196).chr(164) => 'H', chr(196).chr(165) => 'h',
chr(196).chr(166) => 'H', chr(196).chr(167) => 'h',
chr(196).chr(168) => 'I', chr(196).chr(169) => 'i',
chr(196).chr(170) => 'I', chr(196).chr(171) => 'i',
chr(196).chr(172) => 'I', chr(196).chr(173) => 'i',
chr(196).chr(174) => 'I', chr(196).chr(175) => 'i',
chr(196).chr(176) => 'I', chr(196).chr(177) => 'i',
chr(196).chr(178) => 'IJ',chr(196).chr(179) => 'ij',
chr(196).chr(180) => 'J', chr(196).chr(181) => 'j',
chr(196).chr(182) => 'K', chr(196).chr(183) => 'k',
chr(196).chr(184) => 'k', chr(196).chr(185) => 'L',
chr(196).chr(186) => 'l', chr(196).chr(187) => 'L',
chr(196).chr(188) => 'l', chr(196).chr(189) => 'L',
chr(196).chr(190) => 'l', chr(196).chr(191) => 'L',
chr(197).chr(128) => 'l', chr(197).chr(129) => 'L',
chr(197).chr(130) => 'l', chr(197).chr(131) => 'N',
chr(197).chr(132) => 'n', chr(197).chr(133) => 'N',
chr(197).chr(134) => 'n', chr(197).chr(135) => 'N',
chr(197).chr(136) => 'n', chr(197).chr(137) => 'N',
chr(197).chr(138) => 'n', chr(197).chr(139) => 'N',
chr(197).chr(140) => 'O', chr(197).chr(141) => 'o',
chr(197).chr(142) => 'O', chr(197).chr(143) => 'o',
chr(197).chr(144) => 'O', chr(197).chr(145) => 'o',
chr(197).chr(146) => 'OE',chr(197).chr(147) => 'oe',
chr(197).chr(148) => 'R',chr(197).chr(149) => 'r',
chr(197).chr(150) => 'R',chr(197).chr(151) => 'r',
chr(197).chr(152) => 'R',chr(197).chr(153) => 'r',
chr(197).chr(154) => 'S',chr(197).chr(155) => 's',
chr(197).chr(156) => 'S',chr(197).chr(157) => 's',
chr(197).chr(158) => 'S',chr(197).chr(159) => 's',
chr(197).chr(160) => 'S', chr(197).chr(161) => 's',
chr(197).chr(162) => 'T', chr(197).chr(163) => 't',
chr(197).chr(164) => 'T', chr(197).chr(165) => 't',
chr(197).chr(166) => 'T', chr(197).chr(167) => 't',
chr(197).chr(168) => 'U', chr(197).chr(169) => 'u',
chr(197).chr(170) => 'U', chr(197).chr(171) => 'u',
chr(197).chr(172) => 'U', chr(197).chr(173) => 'u',
chr(197).chr(174) => 'U', chr(197).chr(175) => 'u',
chr(197).chr(176) => 'U', chr(197).chr(177) => 'u',
chr(197).chr(178) => 'U', chr(197).chr(179) => 'u',
chr(197).chr(180) => 'W', chr(197).chr(181) => 'w',
chr(197).chr(182) => 'Y', chr(197).chr(183) => 'y',
chr(197).chr(184) => 'Y', chr(197).chr(185) => 'Z',
chr(197).chr(186) => 'z', chr(197).chr(187) => 'Z',
chr(197).chr(188) => 'z', chr(197).chr(189) => 'Z',
chr(197).chr(190) => 'z', chr(197).chr(191) => 's'
);
$sString = strtr($sString, $aChars);
return $sString;
}

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rss-science.php Normal file
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<?php
header('Content-Type: text/xml');
$sUrl = 'http://www.sciencemag.org/rss/current.xml';
$oXml = new SimpleXMLElement(file_get_contents($sUrl));
for ($i = count($oXml->item) - 1; $i >= 0; --$i) {
$oItemXml = $oXml->item[$i];
if (strpos($oItemXml->title, 'Chemistry:') === false) {
unset($oXml->item[$i]);
}
}
echo $oXml->asXML();

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<pre><?php
// $sData = file_get_contents('C:\Users\Rik\Downloads\data.txt');
// preg_match_all('~"([^"]+)"\n\n([^\n]+)\n~', $sData, $aMatches);
// $aData = array_combine($aMatches[1], $aMatches[2]);
// var_export($aData);
$sDir = 'C:\Users\Rik\Seafile\PhD\Project\Organogolds\Crystals\Danila\asdg19';
$aParts = array('ligand', 'substrate', 'complex');
$aDeleteGold = array(true, false);
foreach ($aDeleteGold as $bDeleteGold) {
foreach ($aParts as $sPart) {
$sFile = sprintf('%s\%s.xyz', $sDir, $sPart);
$sResponse = execute($sFile, $bDeleteGold);
preg_match_all('~<strong>([^\<]+)</strong>~', $sResponse, $aMatches);
$fValue = isset($aMatches[1][1]) ? $aMatches[1][1] : 0;
printf("%s (%s) = %.1f\n", $sPart, $bDeleteGold ? 'true' : 'false', $fValue);
}
}
function execute($sFile, $bDeleteGold = true) {
$aData = array (
'action' => 'upload',
'xyzinput' => 'upload',
'radii' => 'bondi2',
'atom_center' => '1',
'atom_axis' => '2',
'atom_plane' => '2',
'propC2' => '1.80',
'propC3' => '2.00',
'propN2' => '1.65',
'propN3' => '1.87',
'propP' => '1.90',
'propH' => '1.20',
'atom_coord' => '0',
'atom_indexes' => '0 1',
'which_axis' => '6',
'plane_indexes' => '0 2',
'atom_todelete' => $bDeleteGold ? 0 : null,
'atoms_radius' => '1',
'radius' => '3.5',
'distance' => '0.0',
'i_step' => '0.10',
'submit_button' => 'submit',
);
$sUrl = 'https://www.molnac.unisa.it/OMtools/sambvca2.0/process/sambvca_result.php';
$aData['input_file'] = trim(file_get_contents($sFile));
$aData['input_file_handle'] = new CURLFile(realpath($sFile));
$rCurl = curl_init();
curl_setopt($rCurl, CURLOPT_URL, $sUrl);
curl_setopt($rCurl, CURLOPT_FOLLOWLOCATION, true);
curl_setopt($rCurl, CURLOPT_SSL_VERIFYPEER, false);
curl_setopt($rCurl, CURLOPT_RETURNTRANSFER, true);
curl_setopt($rCurl, CURLOPT_POST, true);
curl_setopt($rCurl, CURLOPT_POSTFIELDS, $aData);
$sResponse = curl_exec($rCurl);
curl_close($rCurl);
// file_put_contents('result.html', $sResponse);
// $sResponse = file_get_contents('result.html');
$sResponse = str_replace(
array('<head>'),
array('<head><base href="https://www.molnac.unisa.it/OMtools/sambvca2.0/process/" rel="canonical" />'),
$sResponse);
// $sResponse = preg_replace('#<script(.*?)>(.*?)</script>#is', '', $sResponse);
return $sResponse;
}

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topspin.php Normal file
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<?php
$sDirectory = 'C:\Users\Rik\Dropbox\PhD\NMR';
$sTopspin = sprintf('C:\Users\Rik\.topspin-%s\prop\browsedir2_Local.prop', gethostname());
$aExclusions = array('mnova');
$aDirectories = array();
foreach (glob(sprintf('%s\*', $sDirectory)) as $sFile) {
$sBase = basename($sFile);
if (is_dir($sFile) && !in_array($sBase, $aExclusions)) {
$aDirectories[] = $sBase;
}
}
natsort($aDirectories);
$aDirectories = array_values($aDirectories);
$aContents = array();
foreach ($aDirectories as $i => $sBase) {
$sFormatted = sprintf('%s:/%s', substr($sDirectory, 0, 1), str_replace('\\', '/', substr($sDirectory, 3)));
$aContents[] = sprintf('%d=%s/%s\=alias\=%3$s', $i, $sFormatted, $sBase, $sBase);
}
file_put_contents($sTopspin, implode("\n", $aContents));

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<?php
set_time_limit(0);
header('Content-Type: text/html;charset=utf-8');
?>
<pre><?php
/* Configuration */
error_reporting(E_ALL ^ E_DEPRECATED);
$sFile = file_get_contents('.reference');
$sAccount = file_get_contents('.account');
$iCount = 0;
/* Load dependencies */
set_include_path(implode(PATH_SEPARATOR, array(get_include_path(), '../../')));
require_once 'vendor/autoload.php';
$sDatabase = file_get_contents($sFile);
$oBibtex = new Structures_BibTex();
if ($oBibtex->loadFile($sFile) && $oBibtex->parse()) {
foreach ($oBibtex->data as $aEntry) {
if ($aEntry['type'] == 'article' && isset($aEntry['doi'])) {
if (isset($aEntry['volume'])) {
continue;
}
$sCite = $aEntry['cite'];
$sDoi = $aEntry['doi'];
printf("Processing %s...\n", $sCite);
preg_match(sprintf('~@article\{%s,.*?\}[\s]*\}~si', $sCite), $sDatabase, $aMatch);
if (!isset($aMatch[0])) {
printf("Entry not found!\n");
continue;
}
$sOriginal = $aMatch[0];
$sUrl = sprintf('http://www.crossref.org/openurl/?id=%s&noredirect=true&pid=%s&format=unixref', urlencode(trim($sDoi)), $sAccount);
if (!($sContents = file_get_contents($sUrl))) {
printf("Failed to fetch reference!\n");
continue;
}
$oXml = new SimpleXMLElement($sContents);
$oCrossrefXml = $oXml->doi_record->crossref;
if ($oCrossrefXml === null || isset($oCrossrefXml->error)) {
printf("Corrupt reference!\n");
continue;
}
$oJournalXml = $oCrossrefXml->journal;
$oArticleXml = $oJournalXml->journal_article;
$oIssueXml = $oJournalXml->journal_issue;
if (isset($oIssueXml->journal_volume->volume)) {
$iVolume = trim($oIssueXml->journal_volume->volume);
$iYear = intval($oIssueXml->publication_date->year);
$oMetadataXml = $oJournalXml->journal_metadata;
$sJournal = $oMetadataXml->full_title;
if ($sJournal == 'Eur. J. Org. Chem.' || $sJournal == 'Eur. J. Inorg. Chem.') {
printf("Notorious journal (%s), skipping!\n", $sJournal);
continue;
}
if ($iVolume == $iYear) {
printf("Volume and year match, skipping!\n", $iVolume);
continue;
}
if (strlen($iVolume) > 0) {
printf("Set to: %s\n", $iVolume);
$sNew = str_replace('doi =', sprintf("volume = {%s},\n doi =", $iVolume), $sOriginal);
$sDatabase = str_replace($sOriginal, $sNew, $sDatabase);
if (++$iCount > 250) {
break;
}
}
}
}
}
}
file_put_contents($sFile, $sDatabase);

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<pre><?php
$sDir = 'C:\Users\Rik\Google Drive\PhD\Project\Tetrafluoroborate\33\Coordinates';
$aMolecules = [];
foreach (glob(sprintf('%s/*.xyz', $sDir)) as $sFile) {
$sName = substr(basename($sFile, '.xyz'), 3);
$sContents = file_get_contents($sFile);
$sContents = str_replace("\r", null, $sContents);
$sContents = str_replace("\n\n", sprintf("\n%s\n", $sName), $sContents);
$aMolecules[] = $sContents;
}
echo implode("\n", $aMolecules);