configurePdbFile.html

{% extends "layout.html" %}

{% macro fileinput(id, accept="") %}
    <div class="input-group om-filedrop" data-file-input="{{ id }}">
        <label class="btn btn-default btn-file input-group-addon">
            <span title="Select File"style=" font-weight: 700;">Browse... </span>
            <input type="file" name="{{ id }}" id="{{ id }}" style="display: none" {% if accept %}accept="{{ accept }}"{% endif %} onchange="if (omValidateFileInput(this)) optionChanged()"/>
        </label>
        <span id="{{ id }}_label" class="form-control om-filedrop-label"></span>
    </div>
{% endmacro %}

{% block title %}Select Input Files{% endblock %}
{% block body %}
</style>


Select the pdb input file and options for how to model it.
<p/>

<form method="post" enctype="multipart/form-data" action="{{ url_for('configureFiles') }}" class="form-horizontal">
    <div class="form-group">
    <label for="filename" class="control-label col-md-2">PDB File</label>
        <div class="col-md-10">{{ fileinput('file', accept='.pdb') }}</div>
    </div>
    <div class="form-group">
    <label for="forcefield" class="control-label col-md-2">Force Field</label>
    <div class="col-md-10"><select name="forcefield" id="forcefield" class="form-control" title="CHARMM force field does not support ligands. Select Amber force fields for ligand-protein MD simulations" onchange="optionChanged()">
        <option value="AMBER19" selected>AMBER19</option> 
        <option value="AMBER14">AMBER14</option>
        <option value="AMBER99SB">AMBER99SB</option>
        <option value="AMBER99SB-ILDN">AMBER99SB-ILDN</option>
        <option value="AMBER03">AMBER03</option>
        <option value="AMBER10">AMBER10</option>
        <option value="CHARMM36">CHARMM36</option>
        <option value="CHARMM2024">CHARMM36 2024</option>
    </select></div>
    </div>
    <div id="waterModelRow" class="form-group">
        <label for="waterModel" class="control-label col-md-2">Water Model</label>
        <div class="col-md-10"><select name="waterModel" id="waterModel" class="form-control" title="TIP3P, TIP3P-FB and SPC/E are the most tested water models in OpenMMDL "></select></div>
    </div>
    <p>
    Optional : Add ligand SDF file to the MD simulation (Default: No ligand)
    </p>
    <div class="form-group">
    <label for="filename" class="control-label col-md-2">Ligand File</label>
        <div class="col-md-10" title="The supported formats are SDF, MOL and MOL2"> {{ fileinput('sdfFile', accept='.sdf,.mol,.mol2') }}</div>
    </div>
    <div class="form-group">
    <label for="smallMoleculeForceField" class="control-label col-md-2">Small Molecule Force Field</label>
    <div class="col-md-10"><select name="smallMoleculeForceField" id="smallMoleculeForceField" class="form-control" title="Select the preferred small molecule force field" onchange="optionChanged()">
        <option value="gaff" selected>GAFF</option>
        <option value="smirnoff">SMIRNOFF</option>
    </select></div>
    </div>
    <div id="gaffVersionRow" class="form-group" hidden>
        <label for="gaffVersion" class="control-label col-md-2">GAFF Version</label>
        <div class="col-md-10">
            <select name="gaffVersion" id="gaffVersion" class="form-control" onchange="optionChanged()"></select>
        </div>
    </div>

    <div id="smirnoffConstraintRow" class="form-group" hidden>
        <label for="openffConstraint" class="control-label col-md-2">SMIRNOFF Mode</label>
        <div class="col-md-10">
            <select name="openffConstraint" id="openffConstraint" class="form-control" onchange="optionChanged()">
                <option value="constrained" selected>Constrained</option>
                <option value="unconstrained">Unconstrained</option>
            </select>
        </div>
    </div>

    <div id="smirnoffVersionRow" class="form-group" hidden>
        <label for="openffVersion" class="control-label col-md-2">SMIRNOFF Version</label>
        <div class="col-md-10">
            <select name="openffVersion" id="openffVersion" class="form-control" onchange="optionChanged()"></select>
        </div>
    </div>
    <div class="form-group">
    <label for="ligandMinimization" class="control-label col-md-2">Ligand Minimization</label>
    <div class="col-md-10"><select name="ligandMinimization" id="ligandMinimization" class="form-control" title="Minimize ligand with MMFF94 rdkit without protein" onchange="optionChanged()">
        <option value="False" selected>No</option>
        <option value="True">Yes</option>
    </select></div>
    </div>
    <div class="form-group">
    <label for="ligandSanitization" class="control-label col-md-2">
        <span style=" font-weight: 700" title="Depending on the ligand the Sanitization can be required for OpenMM or may lead to errors in case of specific ligand substructures (example: Thiopene)"">Ligand Sanitization</span>
    </label>
    <div class="col-md-10"><select name="ligandSanitization" id="ligandSanitization" class="form-control" title="Sanitize ligand with rdkit" onchange="optionChanged()">
        <option value="False" selected>No</option>
        <option value="True">Yes</option>
    </select></div>
    </div>
    <br/>
    <button type="button" class="btn btn-default btn-back-red"
            onclick="window.location.href='{{ url_for('showSelectFileType') }}'">Back</button>
    <input type="submit" value="Continue" id="continue" class="btn" disabled="true"/>
</form>
<script>
var newAmberWaterModels = [
        ["TIP3P", "TIP3P", true],
        ["TIP3P-FB", "TIP3P-FB", false],
        ["SPC/E", "SPC/E", false],
        ["TIP4P-Ew", "TIP4P-Ew", false],
        ["TIP4P-FB", "TIP4P-FB", false],
        ["OPC3", "OPC3", false],
        ["OPC", "OPC", false],
]

var charmmWaterModels = [
        ["CHARMM default", "CHARMM default", true],
        ["TIP3P-PME-B", "TIP3P-PME-B", false],
        ["TIP3P-PME-F", "TIP3P-PME-F", false],
        ["SPC/E", "SPC/E", false],
        ["TIP4P-Ew", "TIP4P-Ew", false],
        ["TIP4P-2005", "TIP4P-2005", false],
        ["TIP5P", "TIP5P", false],
        ["TIP5P-Ew", "TIP5P-Ew", false],
]

var gaffVersions = [
        ["gaff-2.2.20", "GAFF 2.2.20", true],
        ["gaff-2.11", "GAFF 2.11", false],
        ["gaff-2.1", "GAFF 2.1", false],
        ["gaff-1.81", "GAFF 1.81", false],
        ["gaff-1.8", "GAFF 1.8", false],
        ["gaff-1.4", "GAFF 1.4", false],
]

var openffVersionsDefault = [
        ["openff_no_water-3.0.0-alpha0.offxml", "OpenFF 3.0 no water (ALPHA version – may be unstable)", false],
        ["openff-2.2.1.offxml", "OpenFF 2.2.1", true],
        ["openff-2.2.0.offxml", "OpenFF 2.2.0", false],
        ["openff-2.1.1.offxml", "OpenFF 2.1.1", false],
        ["openff-2.1.0.offxml", "OpenFF 2.1.0", false],
        ["openff-2.0.0.offxml", "OpenFF 2.0.0", false],
        ["openff-1.3.1.offxml", "OpenFF 1.3.1", false],
        ["openff-1.3.0.offxml", "OpenFF 1.3.0", false],
        ["openff-1.2.1.offxml", "OpenFF 1.2.1", false],
        ["openff-1.2.0.offxml", "OpenFF 1.2.0", false],
        ["openff-1.1.1.offxml", "OpenFF 1.1.1", false],
        ["openff-1.1.0.offxml", "OpenFF 1.1.0", false],
        ["openff-1.0.1.offxml", "OpenFF 1.0.1", false],
        ["openff-1.0.0.offxml", "OpenFF 1.0.0", false],
]

var openffVersionsUnconstrained = [
        ["openff_no_water_unconstrained-3.0.0-alpha0.offxml", "OpenFF 3.0 no water unconstrained (ALPHA version – may be unstable)", false],
        ["openff_unconstrained-2.2.1.offxml", "OpenFF 2.2.1 unconstrained", true],
        ["openff_unconstrained-2.2.0.offxml", "OpenFF 2.2.0 unconstrained", false],
        ["openff_unconstrained-2.1.1.offxml", "OpenFF 2.1.1 unconstrained", false],
        ["openff_unconstrained-2.1.0.offxml", "OpenFF 2.1.0 unconstrained", false],
        ["openff_unconstrained-2.0.0.offxml", "OpenFF 2.0.0 unconstrained", false],
        ["openff_unconstrained-1.3.1.offxml", "OpenFF 1.3.1 unconstrained", false],
        ["openff_unconstrained-1.3.0.offxml", "OpenFF 1.3.0 unconstrained", false],
        ["openff_unconstrained-1.2.1.offxml", "OpenFF 1.2.1 unconstrained", false],
        ["openff_unconstrained-1.2.0.offxml", "OpenFF 1.2.0 unconstrained", false],
        ["openff_unconstrained-1.1.1.offxml", "OpenFF 1.1.1 unconstrained", false],
        ["openff_unconstrained-1.1.0.offxml", "OpenFF 1.1.0 unconstrained", false],
        ["openff_unconstrained-1.0.1.offxml", "OpenFF 1.0.1 unconstrained", false],
        ["openff_unconstrained-1.0.0.offxml", "OpenFF 1.0.0 unconstrained", false],
]

var oldAmberWaterModels = [
        ["TIP3P", "TIP3P", true],
        ["TIP3P-FB", "TIP3P-FB", false],
        ["SPC/E", "SPC/E", false],
        ["TIP4P-Ew", "TIP4P-Ew", false],
        ["TIP5P", "TIP5P", false],
        ["OPC3", "OPC3", false],
        ["OPC", "OPC", false],
]

var amoebaWaterModels = [
        ["Explicit", "Explicit", true],
        ["Implicit", "Implicit", false]
]

function optionChanged() {
    // Update UI elements.

    // -------------------------
    // Forcefield / Water model
    // -------------------------
    forcefield = document.getElementById("forcefield").value;
    waterSelect = document.getElementById("waterModel");

    // If you inject waterModel from the server, use it once; otherwise keep current selection
    currentWater = waterSelect.value;
    if (typeof waterModel !== "undefined" && waterModel) {
        currentWater = waterModel;
    }

    if (forcefield == 'CHARMMPOLAR2019')
        document.getElementById("waterModelRow").hidden = true;
    else {
        document.getElementById("waterModelRow").hidden = false;

        if (forcefield == "AMBER14")
            models = newAmberWaterModels;
        else if (forcefield == "AMBER19")
            models = newAmberWaterModels;
        else if (forcefield == "CHARMM36")
            models = charmmWaterModels;
        else if (forcefield == "CHARMM2024")
            models = charmmWaterModels;
        else if (forcefield == "AMOEBA2018")
            models = amoebaWaterModels;
        else
            models = oldAmberWaterModels;

        while (waterSelect.length > 0)
            waterSelect.remove(0);

        for (i = 0; i < models.length; i++) {
            option = document.createElement("option");
            option.value = models[i][0];
            option.text = models[i][1];
            waterSelect.add(option);
        }

        for (i = 0; i < models.length; i++)
            if (models[i][2])
                waterSelect.selectedIndex = i;

        for (i = 0; i < models.length; i++)
            if (currentWater == models[i][0])
                waterSelect.selectedIndex = i;
    }

    // clear injected waterModel so user changes persist
    if (typeof waterModel !== "undefined" && waterModel) {
        waterModel = "";
    }

    // -------------------------------------
    // Small molecule FF + versions handling
    // -------------------------------------
    smffSelect = document.getElementById("smallMoleculeForceField");

    // If you inject smallMoleculeForceField from the server, apply once
    if (smffSelect && typeof smallMoleculeForceField !== "undefined" && smallMoleculeForceField) {
        smffSelect.value = smallMoleculeForceField;
        smallMoleculeForceField = "";
    }

    // If nothing is selected (empty), force the HTML default
    if (smffSelect && !smffSelect.value)
        smffSelect.value = "gaff";

    if (smffSelect) {
        smff = smffSelect.value;

        gaffVersionRow = document.getElementById("gaffVersionRow");
        smirnoffConstraintRow = document.getElementById("smirnoffConstraintRow");
        smirnoffVersionRow = document.getElementById("smirnoffVersionRow");

        gaffVersionSelect = document.getElementById("gaffVersion");
        openffConstraintSelect = document.getElementById("openffConstraint");
        openffVersionSelect = document.getElementById("openffVersion");

        if (smff == "gaff") {
            if (gaffVersionRow) gaffVersionRow.hidden = false;
            if (smirnoffConstraintRow) smirnoffConstraintRow.hidden = true;
            if (smirnoffVersionRow) smirnoffVersionRow.hidden = true;

            if (gaffVersionSelect) {
                // Use injected smallMoleculeForceFieldVersion once if present; otherwise preserve current selection
                currentGaff = gaffVersionSelect.value;
                if (typeof smallMoleculeForceFieldVersion !== "undefined" && smallMoleculeForceFieldVersion)
                    currentGaff = smallMoleculeForceFieldVersion;

                models = gaffVersions;

                while (gaffVersionSelect.length > 0)
                    gaffVersionSelect.remove(0);

                for (i = 0; i < models.length; i++) {
                    option = document.createElement("option");
                    option.value = models[i][0];
                    option.text = models[i][1];
                    gaffVersionSelect.add(option);
                }

                for (i = 0; i < models.length; i++)
                    if (models[i][2])
                        gaffVersionSelect.selectedIndex = i;

                for (i = 0; i < models.length; i++)
                    if (currentGaff == models[i][0])
                        gaffVersionSelect.selectedIndex = i;
            }

            // clear injected version so user changes persist
            if (typeof smallMoleculeForceFieldVersion !== "undefined" && smallMoleculeForceFieldVersion) {
                smallMoleculeForceFieldVersion = "";
            }

        } else if (smff == "smirnoff") {
            if (gaffVersionRow) gaffVersionRow.hidden = true;
            if (smirnoffConstraintRow) smirnoffConstraintRow.hidden = false;
            if (smirnoffVersionRow) smirnoffVersionRow.hidden = false;

            // If we have an injected OpenFF version, set constrained/unconstrained automatically once
            if (openffConstraintSelect && typeof smallMoleculeForceFieldVersion !== "undefined" && smallMoleculeForceFieldVersion) {
                if (smallMoleculeForceFieldVersion.indexOf("unconstrained") != -1)
                    openffConstraintSelect.value = "unconstrained";
                else
                    openffConstraintSelect.value = "constrained";
            }

            mode = "constrained";
            if (openffConstraintSelect)
                mode = openffConstraintSelect.value;

            if (mode == "unconstrained")
                models = openffVersionsUnconstrained;
            else
                models = openffVersionsDefault;

            if (openffVersionSelect) {
                // Use injected smallMoleculeForceFieldVersion once if present; otherwise preserve current selection
                currentOpenff = openffVersionSelect.value;
                if (typeof smallMoleculeForceFieldVersion !== "undefined" && smallMoleculeForceFieldVersion)
                    currentOpenff = smallMoleculeForceFieldVersion;

                while (openffVersionSelect.length > 0)
                    openffVersionSelect.remove(0);

                for (i = 0; i < models.length; i++) {
                    option = document.createElement("option");
                    option.value = models[i][0];
                    option.text = models[i][1];
                    openffVersionSelect.add(option);
                }

                for (i = 0; i < models.length; i++)
                    if (models[i][2])
                        openffVersionSelect.selectedIndex = i;

                for (i = 0; i < models.length; i++)
                    if (currentOpenff == models[i][0])
                        openffVersionSelect.selectedIndex = i;
            }

            // clear injected version so user changes persist
            if (typeof smallMoleculeForceFieldVersion !== "undefined" && smallMoleculeForceFieldVersion) {
                smallMoleculeForceFieldVersion = "";
            }

        } else {
            if (gaffVersionRow) gaffVersionRow.hidden = true;
            if (smirnoffConstraintRow) smirnoffConstraintRow.hidden = true;
            if (smirnoffVersionRow) smirnoffVersionRow.hidden = true;
        }
    }

    // -------------------------
    // File labels + submit state
    // -------------------------
    files = document.getElementById("file").files;
    sdfFile = document.getElementById("sdfFile").files;

    document.getElementById("file_label").textContent = (files.length == 0 ? "" : files[0].name);
    document.getElementById("sdfFile_label").textContent = (sdfFile.length == 0 ? "" : sdfFile[0].name);

    document.getElementById('continue').disabled = !document.getElementById("file").value;
}

optionChanged();
</script>
{% endblock %}