1406 lines
49 KiB
XML
1406 lines
49 KiB
XML
<?xml version="1.0" encoding="UTF-8"?>
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<ui version="4.0">
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<class>Form</class>
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<widget class="QWidget" name="Form">
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<property name="geometry">
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<rect>
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<x>0</x>
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<width>530</width>
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<property name="baseSize">
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<size>
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<width>200</width>
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<height>200</height>
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</size>
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</property>
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<property name="windowTitle">
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<string notr="true">APBS Electrostatics</string>
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</property>
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<layout class="QVBoxLayout" name="verticalLayout">
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<item>
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<widget class="QTabWidget" name="tabWidget">
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<property name="currentIndex">
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<number>0</number>
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<widget class="QScrollArea" name="scrollArea">
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</property>
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<property name="styleSheet">
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<string notr="true">QWidget[transparent_background=true] {background-color:transparent}</string>
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</property>
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<property name="frameShape">
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<enum>QFrame::NoFrame</enum>
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</property>
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<property name="horizontalScrollBarPolicy">
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<enum>Qt::ScrollBarAlwaysOff</enum>
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</property>
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<property name="widgetResizable">
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<bool>true</bool>
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</property>
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<property name="transparent_background" stdset="0">
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<bool>true</bool>
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</property>
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<attribute name="title">
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<string notr="true">Main</string>
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</attribute>
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<widget class="QWidget" name="scrollAreaWidgetContents">
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<property name="geometry">
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<rect>
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<x>0</x>
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<y>0</y>
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<width>485</width>
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<height>965</height>
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</rect>
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</property>
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<property name="transparent_background" stdset="0">
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<bool>true</bool>
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</property>
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<layout class="QVBoxLayout" name="verticalLayout_16">
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<property name="leftMargin">
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<number>10</number>
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</property>
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<property name="topMargin">
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<number>12</number>
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</property>
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<property name="rightMargin">
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<number>10</number>
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</property>
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<property name="bottomMargin">
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<number>10</number>
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</property>
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<item>
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<layout class="QHBoxLayout" name="horizontalLayout_4">
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<item>
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<widget class="QLabel" name="label">
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<property name="text">
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<string notr="true">Selection:</string>
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</property>
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<property name="buddy">
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<cstring>input_sele</cstring>
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</property>
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</widget>
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</item>
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<item>
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<widget class="QComboBox" name="input_sele">
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<property name="sizePolicy">
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<sizepolicy hsizetype="Expanding" vsizetype="Fixed">
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<horstretch>0</horstretch>
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</property>
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<property name="editable">
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<bool>true</bool>
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</property>
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<item>
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<property name="text">
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<string notr="true">polymer</string>
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</property>
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</item>
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</widget>
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</item>
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</layout>
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</item>
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<item>
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<widget class="QLabel" name="label_sele_has">
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<property name="font">
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<font>
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<italic>true</italic>
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</font>
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</property>
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<property name="styleSheet">
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<string notr="true">background: #f66; padding: 5;</string>
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</property>
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<property name="text">
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<string notr="true">Selection has ...</string>
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</property>
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</widget>
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</item>
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<item>
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<widget class="QFrame" name="groupBox">
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<property name="frameShape">
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<enum>QFrame::StyledPanel</enum>
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</property>
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<layout class="QVBoxLayout" name="verticalLayout_2">
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<item>
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<layout class="QHBoxLayout" name="horizontalLayout">
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<item>
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<widget class="QCheckBox" name="do_prepare">
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<property name="toolTip">
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<string notr="true">uncheck if the selected molecule already has partial charges and radii ("elec_radius" property) assigned, e.g. if you have loaded a PQR file</string>
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</property>
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<property name="text">
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<string notr="true">Prepare Molecule</string>
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</property>
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<property name="checked">
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<bool>true</bool>
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</property>
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</widget>
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</item>
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<item>
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<spacer name="horizontalSpacer">
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<property name="orientation">
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<enum>Qt::Horizontal</enum>
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</property>
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<property name="sizeHint" stdset="0">
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<size>
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<width>40</width>
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<height>20</height>
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</size>
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</property>
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</spacer>
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</item>
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<item>
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<widget class="QPushButton" name="optbutton_prepare">
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<property name="text">
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<string notr="true">Options >></string>
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</property>
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<property name="checkable">
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<bool>true</bool>
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</property>
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</widget>
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</item>
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</layout>
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</item>
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<item>
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<widget class="QWidget" name="optarea_prep" native="true">
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<property name="enabled">
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<bool>true</bool>
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</property>
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<property name="sizePolicy">
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<sizepolicy hsizetype="Preferred" vsizetype="Minimum">
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<horstretch>0</horstretch>
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<verstretch>0</verstretch>
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</sizepolicy>
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</property>
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<layout class="QGridLayout" name="gridLayout">
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<property name="sizeConstraint">
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<enum>QLayout::SetDefaultConstraint</enum>
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</property>
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<property name="leftMargin">
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<number>0</number>
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</property>
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<property name="topMargin">
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<number>0</number>
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</property>
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<property name="rightMargin">
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<number>0</number>
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</property>
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<property name="bottomMargin">
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<number>0</number>
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</property>
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<item row="0" column="0">
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<widget class="QLabel" name="label_2">
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<property name="text">
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<string notr="true">Method:</string>
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</property>
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<property name="buddy">
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<cstring>prep_method</cstring>
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</property>
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</widget>
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</item>
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<item row="0" column="1" colspan="2">
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<widget class="QComboBox" name="prep_method">
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<item>
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<property name="text">
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<string notr="true">pdb2pqr</string>
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</property>
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</item>
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<item>
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<property name="text">
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<string notr="true" comment="what's disambiguation?" extracomment="prepwizard adds hydrogens and missing sidechain atoms, and assigns partial charges. PyMOL's vdw radii will be used. Requires Schrodinger Suite.">prepwizard (SCHRODINGER)</string>
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</property>
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</item>
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<item>
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<property name="text">
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<string notr="true">protein_assign_charges_and_radii</string>
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</property>
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</item>
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<item>
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<property name="text">
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<string notr="true">use formal_charge and vdw</string>
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</property>
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</item>
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<item>
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<property name="text">
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<string notr="true">use CB-pseudocharge and vdw</string>
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</property>
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</item>
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<item>
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<property name="text">
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<string notr="true">use CA-pseudocharge and radius=3.0</string>
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</property>
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</item>
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<item>
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<property name="text">
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<string notr="true">use vdw</string>
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</property>
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</item>
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</widget>
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</item>
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<item row="0" column="3">
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<spacer name="horizontalSpacer_4">
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<property name="orientation">
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<enum>Qt::Horizontal</enum>
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</property>
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<property name="sizeHint" stdset="0">
|
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<size>
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|
<width>40</width>
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|
<height>20</height>
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</size>
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</property>
|
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</spacer>
|
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</item>
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<item row="2" column="2" colspan="2">
|
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<widget class="QLineEdit" name="prep_name">
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|
<property name="text">
|
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<string/>
|
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</property>
|
|
<property name="placeholderText">
|
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<string notr="true">prepared</string>
|
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</property>
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</widget>
|
|
</item>
|
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<item row="2" column="0" colspan="2">
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<widget class="QLabel" name="label_3">
|
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<property name="text">
|
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<string notr="true">Output Molecule Object:</string>
|
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</property>
|
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<property name="buddy">
|
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<cstring>prep_name</cstring>
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</property>
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</widget>
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</item>
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<item row="1" column="0" colspan="4">
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<widget class="QStackedWidget" name="stackedWidget">
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<property name="currentIndex">
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<number>0</number>
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</property>
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<widget class="QWidget" name="widget_2">
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<layout class="QVBoxLayout" name="verticalLayout_8">
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<property name="leftMargin">
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<number>0</number>
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</property>
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<property name="topMargin">
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<number>0</number>
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</property>
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<property name="rightMargin">
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<number>0</number>
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</property>
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<property name="bottomMargin">
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<number>0</number>
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</property>
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<item>
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<widget class="QLabel" name="label_21">
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<property name="sizePolicy">
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<sizepolicy hsizetype="Preferred" vsizetype="Minimum">
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<horstretch>0</horstretch>
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<verstretch>0</verstretch>
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</sizepolicy>
|
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</property>
|
|
<property name="text">
|
|
<string notr="true">"pdb2pqr" adds hydrogens and missing sidechain atoms, assigns partial charges and radii. REMOVES ligands and modified residues.</string>
|
|
</property>
|
|
<property name="alignment">
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<set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignTop</set>
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</property>
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<property name="wordWrap">
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<bool>true</bool>
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</property>
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</widget>
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</item>
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<item>
|
|
<widget class="QCheckBox" name="pdb2pqr_ignore_warnings">
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|
<property name="text">
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|
<string notr="true">Ignore warnings</string>
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|
</property>
|
|
</widget>
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</item>
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</layout>
|
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</widget>
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<widget class="QWidget" name="widget">
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<layout class="QVBoxLayout" name="verticalLayout_9">
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<property name="leftMargin">
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<number>0</number>
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</property>
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<property name="topMargin">
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<number>0</number>
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</property>
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<property name="rightMargin">
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<number>0</number>
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</property>
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<property name="bottomMargin">
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<number>0</number>
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</property>
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<item>
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<widget class="QLabel" name="label_22">
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<property name="sizePolicy">
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<sizepolicy hsizetype="Preferred" vsizetype="Minimum">
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<horstretch>0</horstretch>
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<verstretch>0</verstretch>
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</sizepolicy>
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</property>
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<property name="text">
|
|
<string notr="true">"prepwizard" adds hydrogens and missing sidechain atoms, and assigns partial charges. Can handle ligands and modified residues. PyMOL's vdw radii will be used. Requires Schrodinger Suite.</string>
|
|
</property>
|
|
<property name="alignment">
|
|
<set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignTop</set>
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</property>
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<property name="wordWrap">
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<bool>true</bool>
|
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</property>
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</widget>
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</item>
|
|
<item>
|
|
<widget class="QLineEdit" name="prepwizard_args">
|
|
<property name="toolTip">
|
|
<string>Additional command line options for prepwizard, for example "-r 2.0" or "-fix"</string>
|
|
</property>
|
|
<property name="placeholderText">
|
|
<string notr="true">extra command line options</string>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
</layout>
|
|
</widget>
|
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<widget class="QWidget" name="page_3">
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<layout class="QVBoxLayout" name="verticalLayout_10">
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<property name="leftMargin">
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<number>0</number>
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</property>
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<property name="topMargin">
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<number>0</number>
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</property>
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<property name="rightMargin">
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<number>0</number>
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</property>
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<property name="bottomMargin">
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<number>0</number>
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</property>
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<item>
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<widget class="QLabel" name="label_23">
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<property name="sizePolicy">
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|
<sizepolicy hsizetype="Preferred" vsizetype="Minimum">
|
|
<horstretch>0</horstretch>
|
|
<verstretch>0</verstretch>
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|
</sizepolicy>
|
|
</property>
|
|
<property name="text">
|
|
<string notr="true">"protein_assign_charges_and_radii" REMOVES incomplete or modified residues, adds missing C-terminus, and assigns AMBER99 partial charges and radii</string>
|
|
</property>
|
|
<property name="alignment">
|
|
<set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignTop</set>
|
|
</property>
|
|
<property name="wordWrap">
|
|
<bool>true</bool>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
</layout>
|
|
</widget>
|
|
<widget class="QWidget" name="page_4">
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<layout class="QVBoxLayout" name="verticalLayout_11">
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<property name="leftMargin">
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<number>0</number>
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</property>
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<property name="topMargin">
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<number>0</number>
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<property name="rightMargin">
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<number>0</number>
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</property>
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<property name="bottomMargin">
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<number>0</number>
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</property>
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<item>
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<widget class="QLabel" name="label_24">
|
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<property name="sizePolicy">
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|
<sizepolicy hsizetype="Preferred" vsizetype="Minimum">
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<horstretch>0</horstretch>
|
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<verstretch>0</verstretch>
|
|
</sizepolicy>
|
|
</property>
|
|
<property name="text">
|
|
<string notr="true">Coarse grained charge model: use formal charges (-1/0/1) and PyMOL's vdw radii. Note that missing sidechains of charged residues (e.g. GLU) will not contribute any charge!</string>
|
|
</property>
|
|
<property name="alignment">
|
|
<set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignTop</set>
|
|
</property>
|
|
<property name="wordWrap">
|
|
<bool>true</bool>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
</layout>
|
|
</widget>
|
|
<widget class="QWidget" name="page">
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<layout class="QVBoxLayout" name="verticalLayout_12">
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<property name="leftMargin">
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<number>0</number>
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</property>
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<property name="topMargin">
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<number>0</number>
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</property>
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<property name="rightMargin">
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<number>0</number>
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</property>
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<property name="bottomMargin">
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<number>0</number>
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</property>
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<item>
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<widget class="QLabel" name="label_25">
|
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<property name="sizePolicy">
|
|
<sizepolicy hsizetype="Preferred" vsizetype="Minimum">
|
|
<horstretch>0</horstretch>
|
|
<verstretch>0</verstretch>
|
|
</sizepolicy>
|
|
</property>
|
|
<property name="text">
|
|
<string notr="true">Coarse grained charge model for proteins with "stub" side chains: place a pseudo charge on the CB atom of GLU, ASP, ARG and LYS</string>
|
|
</property>
|
|
<property name="alignment">
|
|
<set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignTop</set>
|
|
</property>
|
|
<property name="wordWrap">
|
|
<bool>true</bool>
|
|
</property>
|
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</widget>
|
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</item>
|
|
</layout>
|
|
</widget>
|
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<widget class="QWidget" name="page_2">
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<layout class="QVBoxLayout" name="verticalLayout_13">
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<property name="leftMargin">
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<number>0</number>
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</property>
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<property name="topMargin">
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<number>0</number>
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<property name="rightMargin">
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<number>0</number>
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</property>
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<property name="bottomMargin">
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<number>0</number>
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</property>
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<item>
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<widget class="QLabel" name="label_26">
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<property name="sizePolicy">
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<sizepolicy hsizetype="Preferred" vsizetype="Minimum">
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<horstretch>0</horstretch>
|
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<verstretch>0</verstretch>
|
|
</sizepolicy>
|
|
</property>
|
|
<property name="text">
|
|
<string notr="true">Coarse grained charge model for CA-only models: place a pseudo charge on the CA atom of GLU, ASP, ARG and LYS and set a radius of 3.0 for all atoms</string>
|
|
</property>
|
|
<property name="alignment">
|
|
<set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignTop</set>
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</property>
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<property name="wordWrap">
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<bool>true</bool>
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</property>
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</widget>
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</item>
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</layout>
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</widget>
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<widget class="QWidget" name="page_5">
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<layout class="QVBoxLayout" name="verticalLayout_14">
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<property name="leftMargin">
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<number>0</number>
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<property name="topMargin">
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<number>0</number>
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|
|
<property name="rightMargin">
|
|
<number>0</number>
|
|
</property>
|
|
<property name="bottomMargin">
|
|
<number>0</number>
|
|
</property>
|
|
<item>
|
|
<widget class="QLabel" name="label_27">
|
|
<property name="sizePolicy">
|
|
<sizepolicy hsizetype="Preferred" vsizetype="Minimum">
|
|
<horstretch>0</horstretch>
|
|
<verstretch>0</verstretch>
|
|
</sizepolicy>
|
|
</property>
|
|
<property name="text">
|
|
<string notr="true">Use existing "partial_charge", use vdw as "elec_radius"</string>
|
|
</property>
|
|
<property name="alignment">
|
|
<set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignTop</set>
|
|
</property>
|
|
<property name="wordWrap">
|
|
<bool>true</bool>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
</layout>
|
|
</widget>
|
|
</widget>
|
|
</item>
|
|
</layout>
|
|
</widget>
|
|
</item>
|
|
</layout>
|
|
</widget>
|
|
</item>
|
|
<item>
|
|
<widget class="QFrame" name="groupBox_2">
|
|
<property name="frameShape">
|
|
<enum>QFrame::StyledPanel</enum>
|
|
</property>
|
|
<layout class="QVBoxLayout" name="verticalLayout_4">
|
|
<item>
|
|
<layout class="QHBoxLayout" name="horizontalLayout_2">
|
|
<item>
|
|
<widget class="QCheckBox" name="do_apbs">
|
|
<property name="text">
|
|
<string notr="true">Calculate Map with APBS</string>
|
|
</property>
|
|
<property name="checked">
|
|
<bool>true</bool>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
<item>
|
|
<spacer name="horizontalSpacer_2">
|
|
<property name="orientation">
|
|
<enum>Qt::Horizontal</enum>
|
|
</property>
|
|
<property name="sizeHint" stdset="0">
|
|
<size>
|
|
<width>40</width>
|
|
<height>20</height>
|
|
</size>
|
|
</property>
|
|
</spacer>
|
|
</item>
|
|
<item>
|
|
<widget class="QPushButton" name="optbutton_apbs">
|
|
<property name="text">
|
|
<string notr="true">Options >></string>
|
|
</property>
|
|
<property name="checkable">
|
|
<bool>true</bool>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
</layout>
|
|
</item>
|
|
<item>
|
|
<widget class="QWidget" name="optarea_apbs" native="true">
|
|
<layout class="QGridLayout" name="gridLayout_2">
|
|
<property name="leftMargin">
|
|
<number>0</number>
|
|
</property>
|
|
<property name="topMargin">
|
|
<number>0</number>
|
|
</property>
|
|
<property name="rightMargin">
|
|
<number>0</number>
|
|
</property>
|
|
<property name="bottomMargin">
|
|
<number>0</number>
|
|
</property>
|
|
<item row="1" column="0">
|
|
<widget class="QLabel" name="label_5">
|
|
<property name="toolTip">
|
|
<string notr="true">limit the expensive fine grid calculation to a region of interest, e.g. a binding pocket</string>
|
|
</property>
|
|
<property name="text">
|
|
<string notr="true">Focus Selection (optional):</string>
|
|
</property>
|
|
<property name="buddy">
|
|
<cstring>focus_sele</cstring>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
<item row="1" column="1">
|
|
<widget class="QLineEdit" name="focus_sele"/>
|
|
</item>
|
|
<item row="3" column="0">
|
|
<widget class="QLabel" name="label_6">
|
|
<property name="text">
|
|
<string notr="true">Output Map Object:</string>
|
|
</property>
|
|
<property name="buddy">
|
|
<cstring>apbs_map</cstring>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
<item row="3" column="1">
|
|
<widget class="QLineEdit" name="apbs_map">
|
|
<property name="text">
|
|
<string notr="true"/>
|
|
</property>
|
|
<property name="placeholderText">
|
|
<string notr="true">apbs_map</string>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
<item row="2" column="0">
|
|
<widget class="QLabel" name="label_20">
|
|
<property name="toolTip">
|
|
<string notr="true">Grid spacing not guaranteed, will increase grid spacing if grid doesn't fit into memory</string>
|
|
</property>
|
|
<property name="text">
|
|
<string notr="true">Grid Spacing:</string>
|
|
</property>
|
|
<property name="buddy">
|
|
<cstring>apbs_grid</cstring>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
<item row="2" column="1">
|
|
<widget class="QDoubleSpinBox" name="apbs_grid">
|
|
<property name="toolTip">
|
|
<string notr="true">Angstrom</string>
|
|
</property>
|
|
<property name="minimum">
|
|
<double>0.010000000000000</double>
|
|
</property>
|
|
<property name="singleStep">
|
|
<double>0.250000000000000</double>
|
|
</property>
|
|
<property name="value">
|
|
<double>0.500000000000000</double>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
</layout>
|
|
</widget>
|
|
</item>
|
|
</layout>
|
|
</widget>
|
|
</item>
|
|
<item>
|
|
<widget class="QFrame" name="groupBox_3">
|
|
<property name="frameShape">
|
|
<enum>QFrame::StyledPanel</enum>
|
|
</property>
|
|
<layout class="QVBoxLayout" name="verticalLayout_3">
|
|
<item>
|
|
<layout class="QHBoxLayout" name="horizontalLayout_3">
|
|
<item>
|
|
<widget class="QCheckBox" name="do_surface">
|
|
<property name="text">
|
|
<string notr="true">Molecular Surface Visualization</string>
|
|
</property>
|
|
<property name="checked">
|
|
<bool>true</bool>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
<item>
|
|
<spacer name="horizontalSpacer_3">
|
|
<property name="orientation">
|
|
<enum>Qt::Horizontal</enum>
|
|
</property>
|
|
<property name="sizeHint" stdset="0">
|
|
<size>
|
|
<width>40</width>
|
|
<height>20</height>
|
|
</size>
|
|
</property>
|
|
</spacer>
|
|
</item>
|
|
<item>
|
|
<widget class="QPushButton" name="optbutton_surface">
|
|
<property name="text">
|
|
<string notr="true">Options >></string>
|
|
</property>
|
|
<property name="checkable">
|
|
<bool>true</bool>
|
|
</property>
|
|
<property name="flat">
|
|
<bool>false</bool>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
</layout>
|
|
</item>
|
|
<item>
|
|
<widget class="QWidget" name="optarea_surf" native="true">
|
|
<layout class="QGridLayout" name="gridLayout_3">
|
|
<property name="leftMargin">
|
|
<number>0</number>
|
|
</property>
|
|
<property name="topMargin">
|
|
<number>0</number>
|
|
</property>
|
|
<property name="rightMargin">
|
|
<number>0</number>
|
|
</property>
|
|
<property name="bottomMargin">
|
|
<number>0</number>
|
|
</property>
|
|
<item row="1" column="0">
|
|
<widget class="QLabel" name="label_7">
|
|
<property name="text">
|
|
<string notr="true">Map:</string>
|
|
</property>
|
|
<property name="buddy">
|
|
<cstring>surf_map</cstring>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
<item row="1" column="1" colspan="2">
|
|
<widget class="QComboBox" name="surf_map">
|
|
<property name="enabled">
|
|
<bool>false</bool>
|
|
</property>
|
|
<property name="editable">
|
|
<bool>true</bool>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
<item row="2" column="0" colspan="2">
|
|
<widget class="QLabel" name="label_9">
|
|
<property name="text">
|
|
<string notr="true">Range: +/-</string>
|
|
</property>
|
|
<property name="buddy">
|
|
<cstring>surf_range</cstring>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
<item row="2" column="2">
|
|
<widget class="QDoubleSpinBox" name="surf_range">
|
|
<property name="value">
|
|
<double>5.000000000000000</double>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
<item row="3" column="0" colspan="2">
|
|
<widget class="QLabel" name="label_19">
|
|
<property name="text">
|
|
<string notr="true">Output Ramp:</string>
|
|
</property>
|
|
<property name="buddy">
|
|
<cstring>surf_ramp</cstring>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
<item row="3" column="2">
|
|
<widget class="QLineEdit" name="surf_ramp">
|
|
<property name="text">
|
|
<string notr="true"/>
|
|
</property>
|
|
<property name="placeholderText">
|
|
<string notr="true">apbs_ramp</string>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
<item row="4" column="0" colspan="3">
|
|
<widget class="QComboBox" name="surf_type">
|
|
<item>
|
|
<property name="text">
|
|
<string notr="true">Solvent Excluded Surface (Connolly surface)</string>
|
|
</property>
|
|
</item>
|
|
<item>
|
|
<property name="text">
|
|
<string notr="true">Solvent Accessible Surface</string>
|
|
</property>
|
|
</item>
|
|
</widget>
|
|
</item>
|
|
<item row="0" column="0" colspan="3">
|
|
<widget class="QLabel" name="label_15">
|
|
<property name="font">
|
|
<font>
|
|
<italic>true</italic>
|
|
</font>
|
|
</property>
|
|
<property name="text">
|
|
<string notr="true">Projects the electrostatic potential onto the molecular surface</string>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
</layout>
|
|
</widget>
|
|
</item>
|
|
</layout>
|
|
</widget>
|
|
</item>
|
|
<item>
|
|
<widget class="QFrame" name="groupBox_7">
|
|
<property name="frameShape">
|
|
<enum>QFrame::StyledPanel</enum>
|
|
</property>
|
|
<layout class="QVBoxLayout" name="verticalLayout_6">
|
|
<item>
|
|
<layout class="QHBoxLayout" name="horizontalLayout_6">
|
|
<item>
|
|
<widget class="QLabel" name="label_4">
|
|
<property name="text">
|
|
<string notr="true">Other Visualizations</string>
|
|
</property>
|
|
<property name="buddy">
|
|
<cstring>optbutton_other</cstring>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
<item>
|
|
<spacer name="horizontalSpacer_5">
|
|
<property name="orientation">
|
|
<enum>Qt::Horizontal</enum>
|
|
</property>
|
|
<property name="sizeHint" stdset="0">
|
|
<size>
|
|
<width>40</width>
|
|
<height>20</height>
|
|
</size>
|
|
</property>
|
|
</spacer>
|
|
</item>
|
|
<item>
|
|
<widget class="QPushButton" name="optbutton_other">
|
|
<property name="text">
|
|
<string notr="true">Options >></string>
|
|
</property>
|
|
<property name="checkable">
|
|
<bool>true</bool>
|
|
</property>
|
|
<property name="flat">
|
|
<bool>false</bool>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
</layout>
|
|
</item>
|
|
<item>
|
|
<widget class="QWidget" name="optarea_other" native="true">
|
|
<layout class="QVBoxLayout" name="verticalLayout_7">
|
|
<property name="leftMargin">
|
|
<number>0</number>
|
|
</property>
|
|
<property name="topMargin">
|
|
<number>0</number>
|
|
</property>
|
|
<property name="rightMargin">
|
|
<number>0</number>
|
|
</property>
|
|
<item>
|
|
<widget class="QLabel" name="label_8">
|
|
<property name="sizePolicy">
|
|
<sizepolicy hsizetype="Preferred" vsizetype="Minimum">
|
|
<horstretch>0</horstretch>
|
|
<verstretch>0</verstretch>
|
|
</sizepolicy>
|
|
</property>
|
|
<property name="font">
|
|
<font>
|
|
<italic>true</italic>
|
|
</font>
|
|
</property>
|
|
<property name="text">
|
|
<string notr="true">After the map has been calculated, create additional visualizations using the "Action" items in the object menu panel:</string>
|
|
</property>
|
|
<property name="wordWrap">
|
|
<bool>true</bool>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
<item>
|
|
<widget class="QLabel" name="label_10">
|
|
<property name="text">
|
|
<string notr="true">Isosurface with "A > surface > level +/-1.0"</string>
|
|
</property>
|
|
<property name="indent">
|
|
<number>10</number>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
<item>
|
|
<widget class="QLabel" name="label_13">
|
|
<property name="text">
|
|
<string notr="true">Volume with "A > volume > esp"</string>
|
|
</property>
|
|
<property name="indent">
|
|
<number>10</number>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
<item>
|
|
<widget class="QLabel" name="label_16">
|
|
<property name="text">
|
|
<string notr="true">Field lines with "A > gradient > default"</string>
|
|
</property>
|
|
<property name="indent">
|
|
<number>10</number>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
<item>
|
|
<widget class="QLabel" name="label_12">
|
|
<property name="text">
|
|
<string notr="true">Slice with "A > slice > default"</string>
|
|
</property>
|
|
<property name="indent">
|
|
<number>10</number>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
</layout>
|
|
</widget>
|
|
</item>
|
|
</layout>
|
|
</widget>
|
|
</item>
|
|
<item>
|
|
<spacer name="verticalSpacer_4">
|
|
<property name="orientation">
|
|
<enum>Qt::Vertical</enum>
|
|
</property>
|
|
<property name="sizeHint" stdset="0">
|
|
<size>
|
|
<width>20</width>
|
|
<height>0</height>
|
|
</size>
|
|
</property>
|
|
</spacer>
|
|
</item>
|
|
</layout>
|
|
</widget>
|
|
</widget>
|
|
<widget class="QWidget" name="tab_3">
|
|
<attribute name="title">
|
|
<string notr="true">APBS Template</string>
|
|
</attribute>
|
|
<layout class="QVBoxLayout" name="verticalLayout_15">
|
|
<property name="leftMargin">
|
|
<number>10</number>
|
|
</property>
|
|
<property name="topMargin">
|
|
<number>12</number>
|
|
</property>
|
|
<property name="rightMargin">
|
|
<number>10</number>
|
|
</property>
|
|
<property name="bottomMargin">
|
|
<number>10</number>
|
|
</property>
|
|
<item>
|
|
<widget class="QLabel" name="label_11">
|
|
<property name="text">
|
|
<string notr="true">Documentation: <a href="https://apbs.readthedocs.io/en/latest/using/input/elec/">apbs.readthedocs.io</a></string>
|
|
</property>
|
|
<property name="openExternalLinks">
|
|
<bool>true</bool>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
<item>
|
|
<layout class="QHBoxLayout" name="horizontalLayout_7">
|
|
<item>
|
|
<widget class="QLabel" name="label_28">
|
|
<property name="text">
|
|
<string notr="true">Load existing "apbs.in" file:</string>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
<item>
|
|
<widget class="QPushButton" name="button_load">
|
|
<property name="text">
|
|
<string notr="true">Browse...</string>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
<item>
|
|
<spacer name="horizontalSpacer_6">
|
|
<property name="orientation">
|
|
<enum>Qt::Horizontal</enum>
|
|
</property>
|
|
<property name="sizeHint" stdset="0">
|
|
<size>
|
|
<width>40</width>
|
|
<height>20</height>
|
|
</size>
|
|
</property>
|
|
</spacer>
|
|
</item>
|
|
<item>
|
|
<widget class="QPushButton" name="button_reset">
|
|
<property name="text">
|
|
<string notr="true">Reset</string>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
</layout>
|
|
</item>
|
|
<item>
|
|
<widget class="QPlainTextEdit" name="apbs_template">
|
|
<property name="font">
|
|
<font>
|
|
<family>Monospace</family>
|
|
</font>
|
|
</property>
|
|
<property name="lineWrapMode">
|
|
<enum>QPlainTextEdit::NoWrap</enum>
|
|
</property>
|
|
<property name="plainText">
|
|
<string notr="true"/>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
</layout>
|
|
</widget>
|
|
<widget class="QWidget" name="tab_2">
|
|
<attribute name="title">
|
|
<string notr="true">Advanced Configuration</string>
|
|
</attribute>
|
|
<layout class="QVBoxLayout" name="verticalLayout_18">
|
|
<property name="leftMargin">
|
|
<number>10</number>
|
|
</property>
|
|
<property name="topMargin">
|
|
<number>12</number>
|
|
</property>
|
|
<property name="rightMargin">
|
|
<number>10</number>
|
|
</property>
|
|
<property name="bottomMargin">
|
|
<number>10</number>
|
|
</property>
|
|
<item>
|
|
<widget class="QGroupBox" name="groupBox_5">
|
|
<property name="title">
|
|
<string notr="true">Program Locations</string>
|
|
</property>
|
|
<layout class="QGridLayout" name="gridLayout_9">
|
|
<item row="0" column="0">
|
|
<widget class="QLabel" name="label_14">
|
|
<property name="text">
|
|
<string notr="true">apbs</string>
|
|
</property>
|
|
<property name="buddy">
|
|
<cstring>apbs_exe</cstring>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
<item row="0" column="1">
|
|
<widget class="QLineEdit" name="apbs_exe"/>
|
|
</item>
|
|
<item row="0" column="2">
|
|
<widget class="QPushButton" name="apbs_exe_browse">
|
|
<property name="text">
|
|
<string notr="true">...</string>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
<item row="1" column="0">
|
|
<widget class="QLabel" name="label_17">
|
|
<property name="text">
|
|
<string notr="true">pdb2pqr</string>
|
|
</property>
|
|
<property name="buddy">
|
|
<cstring>pdb2pqr_exe</cstring>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
<item row="1" column="1">
|
|
<widget class="QLineEdit" name="pdb2pqr_exe"/>
|
|
</item>
|
|
<item row="1" column="2">
|
|
<widget class="QPushButton" name="pdb2pqr_exe_browse">
|
|
<property name="text">
|
|
<string notr="true">...</string>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
</layout>
|
|
</widget>
|
|
</item>
|
|
<item>
|
|
<widget class="QGroupBox" name="groupBox_4">
|
|
<property name="title">
|
|
<string notr="true">pdb2pqr</string>
|
|
</property>
|
|
<layout class="QGridLayout" name="gridLayout_10">
|
|
<item row="0" column="0">
|
|
<widget class="QLabel" name="label_18">
|
|
<property name="text">
|
|
<string notr="true">command line options:</string>
|
|
</property>
|
|
<property name="buddy">
|
|
<cstring>pdb2pqr_args</cstring>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
<item row="0" column="1">
|
|
<widget class="QLineEdit" name="pdb2pqr_args">
|
|
<property name="text">
|
|
<string notr="true">--ff=AMBER</string>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
<item row="1" column="0" colspan="2">
|
|
<widget class="QCheckBox" name="pdb2pqr_fixrna">
|
|
<property name="text">
|
|
<string notr="true">For RNA, use residue names RA, RC, RG, RU</string>
|
|
</property>
|
|
<property name="checked">
|
|
<bool>true</bool>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
</layout>
|
|
</widget>
|
|
</item>
|
|
<item>
|
|
<widget class="QGroupBox" name="groupBox_6">
|
|
<property name="title">
|
|
<string notr="true">Objects and Files</string>
|
|
</property>
|
|
<layout class="QVBoxLayout" name="verticalLayout_17">
|
|
<item>
|
|
<widget class="QCheckBox" name="check_no_group">
|
|
<property name="text">
|
|
<string notr="true">Don't group new objects</string>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
<item>
|
|
<widget class="QCheckBox" name="check_preserve">
|
|
<property name="text">
|
|
<string notr="true">Don't delete temporary files</string>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
</layout>
|
|
</widget>
|
|
</item>
|
|
<item>
|
|
<spacer name="verticalSpacer">
|
|
<property name="orientation">
|
|
<enum>Qt::Vertical</enum>
|
|
</property>
|
|
<property name="sizeHint" stdset="0">
|
|
<size>
|
|
<width>20</width>
|
|
<height>40</height>
|
|
</size>
|
|
</property>
|
|
</spacer>
|
|
</item>
|
|
</layout>
|
|
</widget>
|
|
</widget>
|
|
</item>
|
|
<item>
|
|
<layout class="QHBoxLayout" name="horizontalLayout_5">
|
|
<item>
|
|
<widget class="QPushButton" name="button_register">
|
|
<property name="text">
|
|
<string notr="true">Register APBS Use</string>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
<item>
|
|
<widget class="QPushButton" name="button_ok">
|
|
<property name="text">
|
|
<string notr="true">Run</string>
|
|
</property>
|
|
</widget>
|
|
</item>
|
|
</layout>
|
|
</item>
|
|
</layout>
|
|
</widget>
|
|
<tabstops>
|
|
<tabstop>input_sele</tabstop>
|
|
<tabstop>do_prepare</tabstop>
|
|
<tabstop>prep_method</tabstop>
|
|
<tabstop>prep_name</tabstop>
|
|
<tabstop>do_apbs</tabstop>
|
|
<tabstop>focus_sele</tabstop>
|
|
<tabstop>apbs_grid</tabstop>
|
|
<tabstop>apbs_map</tabstop>
|
|
<tabstop>do_surface</tabstop>
|
|
<tabstop>surf_map</tabstop>
|
|
<tabstop>surf_range</tabstop>
|
|
<tabstop>surf_ramp</tabstop>
|
|
<tabstop>surf_type</tabstop>
|
|
<tabstop>button_register</tabstop>
|
|
<tabstop>button_ok</tabstop>
|
|
<tabstop>tabWidget</tabstop>
|
|
<tabstop>apbs_exe</tabstop>
|
|
<tabstop>apbs_exe_browse</tabstop>
|
|
<tabstop>pdb2pqr_exe</tabstop>
|
|
<tabstop>pdb2pqr_exe_browse</tabstop>
|
|
<tabstop>pdb2pqr_args</tabstop>
|
|
</tabstops>
|
|
<resources/>
|
|
<connections>
|
|
<connection>
|
|
<sender>optbutton_surface</sender>
|
|
<signal>toggled(bool)</signal>
|
|
<receiver>optarea_surf</receiver>
|
|
<slot>setVisible(bool)</slot>
|
|
<hints>
|
|
<hint type="sourcelabel">
|
|
<x>484</x>
|
|
<y>206</y>
|
|
</hint>
|
|
<hint type="destinationlabel">
|
|
<x>368</x>
|
|
<y>261</y>
|
|
</hint>
|
|
</hints>
|
|
</connection>
|
|
<connection>
|
|
<sender>do_surface</sender>
|
|
<signal>toggled(bool)</signal>
|
|
<receiver>optarea_surf</receiver>
|
|
<slot>setEnabled(bool)</slot>
|
|
<hints>
|
|
<hint type="sourcelabel">
|
|
<x>268</x>
|
|
<y>210</y>
|
|
</hint>
|
|
<hint type="destinationlabel">
|
|
<x>269</x>
|
|
<y>261</y>
|
|
</hint>
|
|
</hints>
|
|
</connection>
|
|
<connection>
|
|
<sender>optbutton_apbs</sender>
|
|
<signal>toggled(bool)</signal>
|
|
<receiver>optarea_apbs</receiver>
|
|
<slot>setVisible(bool)</slot>
|
|
<hints>
|
|
<hint type="sourcelabel">
|
|
<x>484</x>
|
|
<y>51</y>
|
|
</hint>
|
|
<hint type="destinationlabel">
|
|
<x>320</x>
|
|
<y>94</y>
|
|
</hint>
|
|
</hints>
|
|
</connection>
|
|
<connection>
|
|
<sender>do_apbs</sender>
|
|
<signal>toggled(bool)</signal>
|
|
<receiver>optarea_apbs</receiver>
|
|
<slot>setEnabled(bool)</slot>
|
|
<hints>
|
|
<hint type="sourcelabel">
|
|
<x>229</x>
|
|
<y>53</y>
|
|
</hint>
|
|
<hint type="destinationlabel">
|
|
<x>145</x>
|
|
<y>94</y>
|
|
</hint>
|
|
</hints>
|
|
</connection>
|
|
<connection>
|
|
<sender>optbutton_prepare</sender>
|
|
<signal>toggled(bool)</signal>
|
|
<receiver>optarea_prep</receiver>
|
|
<slot>setVisible(bool)</slot>
|
|
<hints>
|
|
<hint type="sourcelabel">
|
|
<x>484</x>
|
|
<y>-155</y>
|
|
</hint>
|
|
<hint type="destinationlabel">
|
|
<x>325</x>
|
|
<y>-89</y>
|
|
</hint>
|
|
</hints>
|
|
</connection>
|
|
<connection>
|
|
<sender>do_prepare</sender>
|
|
<signal>toggled(bool)</signal>
|
|
<receiver>optarea_prep</receiver>
|
|
<slot>setEnabled(bool)</slot>
|
|
<hints>
|
|
<hint type="sourcelabel">
|
|
<x>157</x>
|
|
<y>-163</y>
|
|
</hint>
|
|
<hint type="destinationlabel">
|
|
<x>128</x>
|
|
<y>-90</y>
|
|
</hint>
|
|
</hints>
|
|
</connection>
|
|
<connection>
|
|
<sender>apbs_map</sender>
|
|
<signal>textChanged(QString)</signal>
|
|
<receiver>surf_map</receiver>
|
|
<slot>setEditText(QString)</slot>
|
|
<hints>
|
|
<hint type="sourcelabel">
|
|
<x>442</x>
|
|
<y>163</y>
|
|
</hint>
|
|
<hint type="destinationlabel">
|
|
<x>442</x>
|
|
<y>297</y>
|
|
</hint>
|
|
</hints>
|
|
</connection>
|
|
<connection>
|
|
<sender>do_apbs</sender>
|
|
<signal>toggled(bool)</signal>
|
|
<receiver>surf_map</receiver>
|
|
<slot>setDisabled(bool)</slot>
|
|
<hints>
|
|
<hint type="sourcelabel">
|
|
<x>229</x>
|
|
<y>53</y>
|
|
</hint>
|
|
<hint type="destinationlabel">
|
|
<x>442</x>
|
|
<y>297</y>
|
|
</hint>
|
|
</hints>
|
|
</connection>
|
|
<connection>
|
|
<sender>optbutton_other</sender>
|
|
<signal>toggled(bool)</signal>
|
|
<receiver>optarea_other</receiver>
|
|
<slot>setVisible(bool)</slot>
|
|
<hints>
|
|
<hint type="sourcelabel">
|
|
<x>484</x>
|
|
<y>435</y>
|
|
</hint>
|
|
<hint type="destinationlabel">
|
|
<x>429</x>
|
|
<y>502</y>
|
|
</hint>
|
|
</hints>
|
|
</connection>
|
|
<connection>
|
|
<sender>prep_method</sender>
|
|
<signal>currentIndexChanged(int)</signal>
|
|
<receiver>stackedWidget</receiver>
|
|
<slot>setCurrentIndex(int)</slot>
|
|
<hints>
|
|
<hint type="sourcelabel">
|
|
<x>401</x>
|
|
<y>-119</y>
|
|
</hint>
|
|
<hint type="destinationlabel">
|
|
<x>199</x>
|
|
<y>-38</y>
|
|
</hint>
|
|
</hints>
|
|
</connection>
|
|
</connections>
|
|
</ui>
|