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<!DOCTYPE html>
<html lang="en">
<head>
<!-- Google tag (gtag.js) -->
<script async src="https://www.googletagmanager.com/gtag/js?id=G-LKDPNXKFMR"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'G-LKDPNXKFMR');
</script>
<script type="application/ld+json">
{
"@context": "http://schema.org/",
"@type": "SoftwareApplication",
"name": "PyChelator",
"applicationCategory": ["Web application", "Script"],
"discussionUrl": "https://github.com/AmruteLab/PyChelator/discussions",
"downloadUrl": "https://zenodo.org/doi/10.5281/zenodo.10674753",
"identifier": ["https://pubmed.ncbi.nlm.nih.gov/39014298/", "https://identifiers.org/pubmed:39014298", "https://bio.tools/pychelator", "https://research-software-directory.org/software/pychelator"],
"isAccessibleForFree": "True",
"citation": {
"@type": "CreativeWork",
"name": "PyChelator: a Python-based Colab and web application for metal chelator calculations",
"url": "https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-024-05858-8",
"sameAs": "https://doi.org/10.1186/s12859-024-05858-8"
},
"description": "Pychelator is a helpful tool for researchers, scientists, and professionals working with metal-chelator interactions who need to obtain critical data related to these complexes. PyChelator Colab offers the Python version and extensive new features of the well-established Maxchelator developed by Chris Patton and colleagues. The JavaScript version is served in Github Pages PyChelator Web.",
"url": "https://amrutelab.github.io/PyChelator/",
"featureList": ["http://edamontology.org/operation_3645", "http://edamontology.org/operation_3438"],
"softwareVersion": "1.1.0",
"operatingSystem": "Any",
"softwareHelp": {
"@type": "CreativeWork",
"Name": "Tutorial",
"url": "https://amrutelab.github.io/PyChelator/",
"description": "Tutorial popup"
},
"dateCreated": "2023-07-23",
"dateModified": "2024-07-24",
"Keywords": ["http://edamontology.org/topic_3307", "metal", "chelator", "PyChelator", "web application", "python", "calcium", "EGTA", "ligand", "colab", "maxchelator"],
"license": [{
"@type": "CreativeWork",
"name": "GPL-2.0",
"url": "https://www.gnu.org/licenses/old-licenses/gpl-2.0-standalone.html",
"description": "GNU GENERAL PUBLIC LICENSE"
}],
"publisher": [{
"@type": "Organization",
"name": "MHH",
"description": "Hannover Medical School"
},
{
"@type": "Person",
"name": "Emrulla Spahiu",
"email": "spahiu.emrulla@mh‑hannover.de"
},
{
"@type": "Person",
"name": "Esra Kastrati",
"email": "esra.kastrati6@gmail.com"
},
{
"@type": "Person",
"name": "Mamta Amrute‑Nayak",
"email": "amrute.mamta@mh‑hannover.de"
}
],
"potentialAction": {
"@type": "ControlAction",
"object": {
"@type": "Dataset",
"name":"Input of data",
"additionalType": ["http://edamontology.org/data_2140", "http://edamontology.org/data_3108"],
"license": "https://www.gnu.org/licenses/old-licenses/gpl-2.0-standalone.html",
"description":"The data is provided by the user, depending on the experimental conditions",
"creator":{
"@type":"Organization",
"name": "Sub dataset 01 creator"
}
},
"result": {
"@type": "Dataset",
"name":"Output of data",
"additionalType": ["http://edamontology.org/format_2331", "http://edamontology.org/data_2048", "http://edamontology.org/format_3620"],
"license": "https://www.gnu.org/licenses/old-licenses/gpl-2.0-standalone.html",
"description":"The data is provided by the user, depending on the experimental conditions",
"creator":{
"@type":"Organization",
"name": "Sub dataset 01 creator"
}
}
}
}
</script>
<script src="pychelator.js"></script>
<link rel="stylesheet" href="pychelator.css">
<script src="https://unpkg.com/xlsx/dist/xlsx.full.min.js"></script>
<script src="https://code.jquery.com/jquery-3.6.0.min.js"></script>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>PyChelator: Metal chelator calculations</title>
<meta name="description" content="PyChelator performs metal chelator calculations taking into account pH, temperature, and ionic strength, using the algorithms of Maxchelator. Python based PyChelator Colab notebook is also provided.">
<meta name="keywords" content="metal, chelator, calcium, egta, fabiato, maxchelator, python, javascript">
<meta name="google-site-verification" content="5GzaYXH87VpG9VvQGPOJyhmJMa22v-QaaxlUqzE6ptg" />
</head>
<body onLoad="setup()">
<div id="container">
<div id="popup-tabs" class="popup-tabs">
<div class="popup-content">
<span class="close" onclick="closePopupTabs()">×</span>
<div class="tab">
<button class="tablinks" onclick="openTab(event, 'tab1')">Find Free Mode - Example</button>
<button class="tablinks" onclick="openTab(event, 'tab2')">Manual entry of stability constants - Example</button>
<button class="tablinks" onclick="openTab(event, 'tab3')">Build-in stability constants</button>
</div>
<div id="tab1" class="tabcontent">
<h2>Find Free Mode - Example Calcium calculation</h2>
<p>Solution A with a pH 7.4 with ionic equivalent 100 mM at 20°C containing:</p>
<ul>
<li>5 mM EGTA (98% purity)</li>
<li>1 mM CaCl2</li>
<li>2 mM MgATP (97% purity)</li>
<li>2 mM MgCl2</li>
</ul>
<p>Steps for free Calcium calculation in PyChelator:</p>
<ol>
<li>From "Constants" dropdown, select the preferred constants' source (ex.NIST)</li>
<li>Select mM as Input unit.</li>
<li>Write the Temperature as 20°C.</li>
<li>Write the pH as 7.4.</li>
<li>Write the Ionic (Ie) equivalent as 100 mM. If you do not know the ionic equivalent, you can calculate by using the "Calculate Ie" button.</li>
<li>Select the parameters to "Show in report", or keep defaults.</li>
<li>Using the top panel, write the Chelator concentration of ATP to 2 mM (97% purity), and EGTA to 5 mM (98% purity).</li>
<li>Write the Total metals given to the solution; Ca²⁺ as 2 mM and Mg²⁺ as 4 mM</li>
<li>Click Calculate. You can copy the Free (M) concentration for Ca²⁺ or the -log10[free]. Alternatively, click Download to have a local copy of the results.</li>
</ol>
</div>
<div id="tab2" class="tabcontent">
<h2>Manual entry of stability constants - Example</h2>
<p>Using the stability constants for Zinc and Calcium buffered using EDTA and EGTA, from <a href="https://www.semanticscholar.org/paper/NIST-Critically-Selected-Stability-Constants-of-Smith-Martell/4d1e936ecb2cd7c641ada4f9db589ad5b50072ba" target="_blank">NIST Critical Stability Constants</a>. A useful table of frequently used chelators and metals can also be found under <a href="https://owamoosa.com/maxchelator/xlsconstants.htm" target="_blank">Maxchelator</a>.</p>
<p>Steps for manual entry of constants in PyChelator:</p>
<ol>
<li>From "Constants" dropdown, select "Write custom constants"</li>
<li>Write the Ligands (L1, L2) comma-separated as: EDTA, EGTA.</li>
<li>Write the Metals (M1, M2) comma-separated as: Zn, Ca.</li>
<li>Write the temperature that the constants were determined (Et) in °C: 20.</li>
<li>Write the ionic equivalent that the constants were determined (Ei) in mM: 100.</li>
<li>Write the protonation constant H1 (logK) for L1 and L2: 10.3, 9.5</li>
<li>Write the ΔH1 enthalpy (kcal/mol) for H1 for L1 and L2: -5.6, -5.9</li>
<li>Repeat steps 6 and 7 for all protonation constants.</li>
<li>Write the stability constant ML (logK) for M1-L1,M1-L2,M2-L1,M2-L2: 16.6, 12.7, 10.7, 10.9</li>
<li>Write the ΔML enthalpy (kcal/mol) for M1-L1,M1-L2,M2-L1,M2-L2: -4.7, -4.3, -6.1, -8.4</li>
<li>Repeat Steps 9 and 10 for MHL and ΔMHL, respectively.</li>
<li>Download the JSON file. You can use this file the next time using the command Upload constants under Constants dropdown.</li>
</ol>
</div>
<div id="tab3" class="tabcontent">
<h2>Stability constant references</h2>
<p></p>
<p></p>
<ol>
<li>NIST: The National Institute of Standards and Technology Database #46 v8. These constants are used in <a href="https://owamoosa.com/maxchelator/" target="_blank">MaxChelator</a></li>
<li>Chelator by Schoenmakers et al. These constants are used in MaxChelator from <a href="https://web.math.princeton.edu/~sswang/GECI/CHELATOR_biotechniques12_870.pdf" target="_blank">Ref.</a></li>
<li>SPECS by Fabiato. Taken from <a href="https://www.sciencedirect.com/science/article/pii/001048259598886I" target="_blank">Fujushiro et al. 1995</a> and compared to the reported constants in <a href="https://owamoosa.com/maxchelator/" target="_blank">McGuigan et al.</a>. The ATP ML and MHL constants were corrected for 20°C.</li>
<li>Calcium by <a href="https://www.sciencedirect.com/science/article/abs/pii/007668799321014Y" target="_blank">Föhr et al. 1993</a></li>
<li>Bapta-ATP_Ca-Mg. Bapta constants (20°C) taken from <a href="https://somapp.ucdmc.ucdavis.edu/pharmacology/bers/maxchelator/xlsconstants.htm" target="_blank">MaxChelator</a> , NIST constants of ATP were adapted from 25°C to 20°C</li>
<li>Zn-Ca_EDTA-EGTA. <a href="https://onlinelibrary.wiley.com/doi/10.1111/apha.12988" target="_blank">Neumaier et al.</a></li>
</ol>
</div>
</div>
</div>
<td class="constants" id="constants" colspan="4" style="width: 100%;">
<!-- Second Modal -->
<div class="overlay" id="overlay2"></div>
<div class="modal" id="modal2">
<!-- File upload option -->
<div class="custom-field">
<label for="fileUpload">Upload Constants File:</label>
<div id="fileInputContainer">
<input type="file" id="fileInput" />
<div id="output"></div>
</div>
</div>
<input value="Submit" name="processit" onclick="readFile()" type="button">
<button onclick="closeSecondModal()">Close</button>
</div>
<!-- Modal -->
<div class="overlay" id="overlay1"></div>
<div class="modal" id="modal1">
<div class="input-container">
<div class="custom-field">
<label for="namesOfChelators">Ligands (L1, L2):</label>
<input type="text" id="namesOfChelators" placeholder="L1,L2 (e.g., ATP, EGTA)">
</div>
<div class="custom-field">
<label for="namesOfMetals">Metals (M1, M2):</label>
<input type="text" id="namesOfMetals" placeholder="M1,M2 (e.g., Ca²⁺, Mg²⁺)">
</div>
</div>
<div class="input-container">
<div class="custom-field">
<label for="customEt">E<sub>t</sub>:</label>
<input type="text" id="customEt" placeholder="Temperature (e.g., 25°C)">
</div>
<div class="custom-field">
<label for="customEi">E<sub>i</sub>:</label>
<input type="text" id="customEi" placeholder="Ionic Strength (e.g., 0.1 M)">
</div>
</div>
<hr>
<p><b>Protonation constants (logK) & enthalpy (kcal/mol), comma-separated as: L1,L2</b></p>
<div class="input-container">
<div class="custom-field">
<label for="hydrogen1">H1:</label>
<input type="text" id="hydrogen1" placeholder="e.g., 6.48,9.4">
</div>
<div class="custom-field">
<label for="deltaH1">ΔH1:</label>
<input type="text" id="deltaH1" placeholder="e.g., 0.5,-5.6">
</div>
</div>
<div class="input-container">
<div class="custom-field">
<label for="hydrogen2">H2:</label>
<input type="text" id="hydrogen2" placeholder="e.g., 3.99,8.79">
</div>
<div class="custom-field">
<label for="deltaH2">ΔH2:</label>
<input type="text" id="deltaH2" placeholder="e.g., -3.6,-5.6">
</div>
</div>
<div class="input-container">
<div class="custom-field">
<label for="hydrogen3">H3:</label>
<input type="text" id="hydrogen3" placeholder="e.g., 1.9,2.7">
</div>
<div class="custom-field">
<label for="deltaH3">ΔH3:</label>
<input type="text" id="deltaH3" placeholder="e.g., 2.3,-2.6">
</div>
</div>
<div class="input-container">
<div class="custom-field">
<label for="hydrogen4">H4:</label>
<input type="text" id="hydrogen4" placeholder="e.g., 0,0">
</div>
<div class="custom-field">
<label for="deltaH4">ΔH4:</label>
<input type="text" id="deltaH4" placeholder="e.g., 0,0">
</div>
</div>
<hr>
<p><b>Stability constants (logK) & enthalpy (kcal/mol), as: M1-L1,M1-L2,M2-L1,M2-L2</b></p>
<div class="input-container">
<div class="custom-field">
<label for="metal1">ML:</label>
<input type="text" id="metal1" placeholder="e.g., 3.86,10.86,4.19,5.28">
</div>
<div class="custom-field">
<label for="deltaMetal1">ΔML:</label>
<input type="text" id="deltaMetal1" placeholder="e.g., 3.2,-7.9,4.4,5.5">
</div>
</div>
<div class="input-container">
<div class="custom-field">
<label for="metalchelator2">MHL:</label>
<input type="text" id="metalchelator2" placeholder="e.g., 2.16,5.307,2.32,3.47">
</div>
<div class="custom-field">
<label for="deltaMetalChelator2">ΔMHL:</label>
<input type="text" id="deltaMetalChelator2" placeholder="e.g., 1.9,0,2.3,0">
</div>
</div>
<input value="Submit and Download" name="processit" onclick="submitConstants()" type="button">
<input value="Load Sample Constants" name="load" onclick="loadSampleConstants()" type="button">
<button onclick="closeModal()">Close</button>
</div>
<div id="iePopup" class="popup">
<div id="m_form-container">
<div class="ionic-modal">
<h1>Ionic Equivalent Calculator</h1>
<h3><i>I</i>e=0.5∑C<sub>i</sub>|z<sub>i</sub>|</h3>
<label for="m_buffer-name">Buffer Name (optional):</label>
<input type="text" id="m_buffer-name" placeholder="e.g., Buffer A">
<label for="m_ions">Ion Names (comma-separated, optional):</label>
<input type="text" id="m_ions" placeholder="e.g., Na, Cl">
<label for="m_concentrations">Concentration of ions (comma-separated, mM):</label>
<input type="text" id="m_concentrations" placeholder="e.g., 25, 25">
<label for="m_charges">Charges of ions (comma-separated):</label>
<input type="text" id="m_charges" placeholder="e.g., 1, -1">
<label for="m_num-atoms">Number of atoms (comma-separated):</label>
<input type="text" id="m_num-atoms" placeholder="e.g., 1, 1">
<button id="calculateBtn" onClick="calculateAndStoreIonicEquivalent()" type="button">Calculate</button>
<div id="m_result"></div>
<button id="downloadBtn" onClick="downloadIeResults()" type="button">Download All Results</button>
</div>
</div>
<button id="closePopupBtn" onClick="closeIonicModal()" class="popup-close">Close</button>
</div>
</td>
<div id="left-panel">
<h2>PyChelator v1.2.0 </h2>
<h3>Metal chelator calculations - <span class="doc-icon" onclick="openPopup()">📃 Tutorial </span></h3>
<br>
<div>
<form name="WMXC2">
Find:
<input
name="TYPECALC"
value="F"
onClick="switchActiveState()"
type="radio"
checked="checked"
id="free_metals"
/>
<label for="free_metals"> Free (M) </label>
<input
name="TYPECALC"
value="T"
onClick="switchActiveState()"
type="radio"
id="total_metals"
/>
<label for="total_metals"> Total (M)</label>
</form>
</div>
<!-- Constants section -->
<div>
<span class="input-label"> Constants:
<div class="tooltip-container">
<div class="circle">i</div>
<span class="tooltiptext">Check Tutorial and Github Readme for more info</span>
</div>
</span>
<select name="constantsSource" id="constantsSource" onchange="updateConstants()">
<optgroup label="Calcium - Magnesium">
<option value="NIST" selected>EGTA-ATP (NIST)</option>
<option value="Schoenmakers">EGTA-ATP (Schoenmakers)</option>
<option value="Fabiato">EGTA-ATP (Fabiato)</option>
<option value="Calcium">EGTA-ATP (Föhr)</option>
<option value="Bapta-ATP_Ca-Mg">BAPTA-ATP (NIST)</option>
</optgroup>
<optgroup label="Other">
<option value="Zn-Ca_EDTA-EGTA">Zn-Ca_EDTA-EGTA</option>
<option value="Custom">Write custom constants</option>
<option value="Upload">Upload constants</option>
</optgroup>
</select>
</div>
<hr>
<!-- Input unit section -->
<div>
<p>
<span class="input-label"> Input unit:</span>
<span class="input-option">
<select id="unit_MT1" name="unit_MT1" onchange="updateUnit('MT1')">
<option value="M">M</option>
<option value="mM">mM</option>
<option value="uM">uM</option>
<option value="nM">nM</option>
</select>
</span>
</p>
<p>
<span class="input-label">Temperature:</span>
<span class="input-option">
<input name="TM" id="TM" value="25" type="number" min="0" max="40" /> °C
</span>
</p>
<p>
<span id="tempRangeError" class="error-message" style="display:none;">Temperature must be between 0°C and 40°C</span>
</p>
<p>
<span class="input-label">pH:</span>
<span class="input-option">
<input name="PH" id="PH" value="7.0" type="number" min="0" max="14" step="0.1" />
</span>
</p>
<p>
<span id="pHRangeError" class="error-message" style="display:none;">pH must be between 0 and 14</span>
</p>
<p>
<span class="input-label">Ionic (<i>I</i>e): <span class="tooltip-container">
<span class="circle">i</span>
<span class="tooltiptext">Ionic equivalent <i>I</i>e=0.5∑C<sub>i</sub>|z<sub>i</i></sub>|</span>
</span>
</span>
<span class="input-option">
<input name="IO" id="IO" value="100" type="number" min="0" max="500" /> mM
</span>
<button id="calculateIeBtn" onClick="openIonicModal()">Calculate <i>I</i>e</button>
</p>
<p>
<span id="ionicRangeError" class="error-message" style="display:none;">Ionic equivalents must be between 0 mM and 500 mM</span>
</p>
</div>
<hr>
<!-- Checkbox section -->
<!-- Checkbox section -->
<div class="options-checkbox-container">
<p>Show in report:</p>
<div class="options-checkbox">
<div class="column">
<label>
<input type="checkbox" checked id="showName"> Name
</label>
<label>
<input type="checkbox" checked id="showTotal"> Total
</label>
<label>
<input type="checkbox" checked id="showFree"> Free
</label>
<label>
<input type="checkbox" checked id="showFinalpCa"> -log<sub>10</sub>[free]
<span class="tooltip-container">
<span class="circle">i</span>
<span class="tooltiptext">e.g., pCa for calcium</span>
</span>
</label>
<label>
<input type="checkbox" checked id="includeMetal1"> Metal1 (e.g. Ca²⁺)
</label>
<label>
<input type="checkbox" checked id="includeMetal2"> Metal2 (e.g. Mg²⁺)
</label>
<label>
<input type="checkbox" checked id="includeLigand1"> Ligand1 (e.g. ATP)
</label>
<label>
<input type="checkbox" checked id="includeLigand2"> Ligand2 (e.g. EGTA)
</label>
</div>
<div class="column">
<label>
<input type="checkbox" id="showComplexes"> M-L Complexes
</label>
<label>
<input type="checkbox" id="showPBound"> % Bound
</label>
<label>
<input type="checkbox" id="showBound"> Bound
</label>
<label>
<input type="checkbox" id="showKd"> Kd
</label>
<label>
<input type="checkbox" id="showLowLimit"> Low Limit
</label>
<label>
<input type="checkbox" id="showHighLimit"> High Limit
</label>
</div>
</div>
</div>
<div style="height: 40px;"></div>
</div>
<!-- Right panel start -->
<div id="right-panel">
<!-- Additional row -->
<div class="additional-row">
<div class="section">
<div class="unit-container">
<h3>Chelator</h3>
<input value="ATP" name="CH1" size="7" maxlength="7" disabled="disabled" type="text" />
<input name="AC1" id="AC1" size="10" maxlength="10" value="0" type="text" />
<span class="unit">M</span>
<span class="purity"> with <input name="AC1purity" id="AC1purity" size="10" maxlength="10" value="100" type="text" /> % purity <span class="tooltip-container">
<span class="circle">i</span>
<span class="tooltiptext">As measured or labelled by the company</span></span>
<br />
<input value="EGTA" name="CH2" size="7" maxlength="7" disabled="disabled" type="text" />
<input name="AC2" id="AC2" size="10" maxlength="10" value="0" type="text" />
<span class="unit">M</span>
<span class="purity"> with <input name="AC2purity" id="AC2purity" size="10" maxlength="10" value="100" type="text" /> % purity <span class="tooltip-container">
<span class="circle">i</span>
<span class="tooltiptext">As measured or labelled by the company</span> </span>
</span>
</div>
</div>
<div class="section">
<div class="unit-container">
<h3>Total Metals</h3>
<input value="Ca²⁺" name="MT1" size="3" maxlength="3" disabled="disabled" type="text" />
<input name="AMT1" size="10" maxlength="10" value="0" type="text" id="AMT1" />
<span class="unit">M</span>
<br />
<input value="Mg²⁺" name="MT2" size="3" maxlength="3" disabled="disabled" type="text" />
<input name="AMT2" size="10" maxlength="10" value="0" type="text" id="AMT2" />
<span class="unit">M</span>
</div>
</div>
<div class="section">
<div class="unit-container">
<h3>Free Metals</h3>
<input value="Ca²⁺" name="MF1" size="3" maxlength="3" disabled="disabled" type="text" id="MF1" />
<input name="AMF1" size="10" maxlength="10" value="0" type="text" id="AMF1" />
<span class="unit">M</span>
<br />
<input value="Mg²⁺" name="MF2" size="3" maxlength="3" disabled="disabled" type="text" id="MF2" />
<input name="AMF2" size="10" maxlength="10" value="0" type="text" id="AMF2" />
<span class="unit">M</span>
</div>
</div>
</div>
<div id="outputDiv">
<form name="WMXC2">
</form>
<div class="output-title">
<span id="name">Name</span>
<span id="total">Total (M)</span>
<span id="free">Free (M) </span>
<span id="pbound">% Bound</span>
<span id="bound">Bound</span>
<span id="finalpCa"> -log<sub>10</sub>[free]</span>
</div>
<div id="output-content">
</div>
</div>
<div class="last-row">
<input
value="Calculate"
name="processit"
onClick="docalc()"
type="button"
/>
<input
value="Download"
name="download"
onClick="downloadOutput()"
type="button"
/>
<a href="https://owamoosa.com/maxchelator/" target="_blank" style="float: right; text-decoration: none; margin-left: 10px;">
<img src="https://owamoosa.com/maxchelator/mclogo.gif" alt="Maxchelator Logo" width="20" height="20" style="vertical-align: middle;">
MaxChelator
</a>
<a href="https://colab.research.google.com/github/AmruteLab/PyChelator/blob/main/PyChelator_Colab.ipynb" target="_blank" style="float: right; text-decoration: none; margin-left: 10px;">
<img src="https://colab.research.google.com/img/colab_favicon.ico" alt="Google Colaboratory Logo" width="20" height="20" style="vertical-align: middle;">
PyChelator Colab
</a>
<a href="https://github.com/AmruteLab/PyChelator/tree/main" target="_blank" class="github-button" style="float: right; text-decoration: none; margin-left: 10px;">
<img src="https://github.githubassets.com/images/modules/logos_page/GitHub-Mark.png" alt="GitHub Logo" width="20" height="20" style="vertical-align: middle;">
Home
</a>
</div>
<div class="citation-row" style="text-align: left; margin-top: 20px;">
Published in: <a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-024-05858-8" target="_blank">BMC Bionformatics</a>.
</div>
<div class="new-row" style="clear: both; text-align: left; margin-top: 10px;">
If you find an error or have suggestions, please file an issue or add a discussion in our <a href="https://github.com/AmruteLab/PyChelator/discussions" target="_blank">GitHub</a>.
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