Schema residue-based-diagram.xsd


schema location:  http://icb.med.cornell.edu/schemas/rbdg/2008/January/residue-based-diagram.xsd
attribute form default: 
element form default:  qualified
 
Elements 
color-scheme 
colors 
control-points 
define 
diagram 
diagram-layout 
direction 
elipses 
exclude 
image 
image-map 
include 
links 
name 
options 
output 
page 
protein 
rbde-diagram 
residue 
residue-background 
residue-codes 
residue-color 
residue-geometry 
secondary-structure 
segment 
shapes 
spacer 
subunit 


element color-scheme
diagram residue-based-diagram_p1.png
properties
content complex
children residue-background
used by
element colors
attributes
Name  Type  Use  Default  Fixed  annotation
namexsd:stringrequired      
annotation
documentation
Selects the color-scheme. Can be either GPCRDB or monotonous.
source <xsd:element name="color-scheme">
  <xsd:annotation>
    <xsd:documentation>Selects the color-scheme. Can be either GPCRDB or monotonous.</xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:sequence>
      <xsd:element ref="residue-background" minOccurs="0"/>
    </xsd:sequence>
    <xsd:attribute name="name" type="xsd:string" use="required"/>
  </xsd:complexType>
</xsd:element>

attribute color-scheme/@name
type xsd:string
properties
isRef 0
use required
source <xsd:attribute name="name" type="xsd:string" use="required"/>

element colors
diagram residue-based-diagram_p2.png
properties
content complex
children define color-scheme residue-color
used by
element diagram
annotation
documentation
Groups color-related options
source <xsd:element name="colors">
  <xsd:annotation>
    <xsd:documentation>Groups color-related options</xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:sequence>
      <xsd:element ref="define" minOccurs="0" maxOccurs="unbounded"/>
      <xsd:element ref="color-scheme"/>
      <xsd:element ref="residue-color" minOccurs="0" maxOccurs="unbounded"/>
    </xsd:sequence>
  </xsd:complexType>
</xsd:element>

element control-points
diagram residue-based-diagram_p3.png
properties
content complex
children cpoint
used by
element subunit
annotation
documentation
Use only when subunit type is FreeLoop, Nterm or Cterm. Provides control points for the shape of the loop (Bezier control points). Control points are defined in a 2D space centered on the position of the first residue of the subunit. Thus, the first control point must have position (0,0). The last control point should be placed such that it matches the spacer of the subunit. The other control points can be placed to control the shape of the path along which residues of the subunit will be laid out.
source <xsd:element name="control-points">
  <xsd:annotation>
    <xsd:documentation>Use only when subunit type is FreeLoop, Nterm or Cterm. Provides control points for the shape of the loop (Bezier control points). Control points are defined in a 2D space centered on the position of the first residue of the subunit. Thus, the first control point must have position (0,0). The last control point should be placed such that it matches the spacer of the subunit. The other control points can be placed to control the shape of the path along which residues of the subunit will be laid out.</xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:sequence>
      <xsd:element name="cpoint" minOccurs="4" maxOccurs="unbounded">
        <xsd:annotation>
          <xsd:documentation>A control point. x and y coordinates are doubles.</xsd:documentation>
        </xsd:annotation>
        <xsd:complexType>
          <xsd:attribute name="x" type="xsd:double" use="required"/>
          <xsd:attribute name="y" type="xsd:double" use="required"/>
        </xsd:complexType>
      </xsd:element>
    </xsd:sequence>
  </xsd:complexType>
</xsd:element>

element control-points/cpoint
diagram residue-based-diagram_p4.png
properties
isRef 0
minOcc 4
maxOcc unbounded
content complex
attributes
Name  Type  Use  Default  Fixed  annotation
xxsd:doublerequired      
yxsd:doublerequired      
annotation
documentation
A control point. x and y coordinates are doubles.
source <xsd:element name="cpoint" minOccurs="4" maxOccurs="unbounded">
  <xsd:annotation>
    <xsd:documentation>A control point. x and y coordinates are doubles.</xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:attribute name="x" type="xsd:double" use="required"/>
    <xsd:attribute name="y" type="xsd:double" use="required"/>
  </xsd:complexType>
</xsd:element>

attribute control-points/cpoint/@x
type xsd:double
properties
isRef 0
use required
source <xsd:attribute name="x" type="xsd:double" use="required"/>

attribute control-points/cpoint/@y
type xsd:double
properties
isRef 0
use required
source <xsd:attribute name="y" type="xsd:double" use="required"/>

element define
diagram residue-based-diagram_p5.png
properties
content complex
used by
element colors
attributes
Name  Type  Use  Default  Fixed  annotation
colorxsd:stringrequired      
redxsd:intrequired      
greenxsd:intrequired      
bluexsd:intrequired      
annotation
documentation
Define a new color. Defined colors can be referenced by name throughout the input file.
source <xsd:element name="define">
  <xsd:annotation>
    <xsd:documentation>Define a new color. Defined colors can be referenced by name throughout the input file. </xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:attribute name="color" type="xsd:string" use="required"/>
    <xsd:attribute name="red" type="xsd:int" use="required"/>
    <xsd:attribute name="green" type="xsd:int" use="required"/>
    <xsd:attribute name="blue" type="xsd:int" use="required"/>
  </xsd:complexType>
</xsd:element>

attribute define/@color
type xsd:string
properties
isRef 0
use required
source <xsd:attribute name="color" type="xsd:string" use="required"/>

attribute define/@red
type xsd:int
properties
isRef 0
use required
source <xsd:attribute name="red" type="xsd:int" use="required"/>

attribute define/@green
type xsd:int
properties
isRef 0
use required
source <xsd:attribute name="green" type="xsd:int" use="required"/>

attribute define/@blue
type xsd:int
properties
isRef 0
use required
source <xsd:attribute name="blue" type="xsd:int" use="required"/>

element diagram
diagram residue-based-diagram_p6.png
properties
content complex
children colors shapes elipses links options output
used by
element rbde-diagram
annotation
documentation
Groups the main sections that determine how the diagram will appear.
source <xsd:element name="diagram">
  <xsd:annotation>
    <xsd:documentation>Groups the main sections that determine how the diagram will appear.</xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:sequence>
      <xsd:element ref="colors" minOccurs="0"/>
      <xsd:element ref="shapes" minOccurs="0"/>
      <xsd:element ref="elipses" minOccurs="0"/>
      <xsd:element ref="links" minOccurs="0"/>
      <xsd:element ref="options" minOccurs="0"/>
      <xsd:element ref="output" minOccurs="0"/>
    </xsd:sequence>
  </xsd:complexType>
</xsd:element>

element diagram-layout
diagram residue-based-diagram_p7.png
properties
content complex
children tm-bundle subunit
used by
element rbde-diagram
annotation
documentation
Describes the graphical arrangement of secondary structure units on the 2D page.
source <xsd:element name="diagram-layout">
  <xsd:annotation>
    <xsd:documentation>Describes the graphical arrangement of secondary structure units on the 2D page. </xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:sequence>
      <xsd:annotation>
        <xsd:documentation>Defines the graphical subunits of the diagram.</xsd:documentation>
      </xsd:annotation>
      <xsd:choice>
        <xsd:element name="tm-bundle" minOccurs="0">
          <xsd:annotation>
            <xsd:documentation>Use the bundle to layout integral membrane proteins. Specify the number of transmembrane (TM) segment to display, and the bundle will automatically calculate the layout of the diagram. Attributes of the bundle include the direction the N-term will take (up or down). Ids must also be generated for each subunit the tm-bundle contains, so that subunits can be referenced by the secondary -structure section of the diagram. The N and C-term X and Y attributes relate to the spacer values that can be used when drawing the diagram.</xsd:documentation>
          </xsd:annotation>
          <xsd:complexType>
            <xsd:attribute name="tm-number" type="xsd:int" use="required"/>
            <xsd:attribute name="tm-id-prefix" type="xsd:string" use="optional" default="TM"/>
            <xsd:attribute name="nterm-id" type="xsd:string" use="optional" default="N-term"/>
            <xsd:attribute name="cterm-id" type="xsd:string" use="optional" default="C-term"/>
            <xsd:attribute name="direction" type="xsd:string" use="optional" default="up"/>
            <xsd:attribute name="N-termX" type="xsd:int" use="optional"/>
            <xsd:attribute name="N-termY" type="xsd:int" use="optional"/>
            <xsd:attribute name="C-termX" type="xsd:int" use="optional"/>
            <xsd:attribute name="C-termY" type="xsd:int" use="optional"/>
          </xsd:complexType>
        </xsd:element>
        <xsd:element ref="subunit" maxOccurs="unbounded"/>
      </xsd:choice>
    </xsd:sequence>
  </xsd:complexType>
</xsd:element>

element diagram-layout/tm-bundle
diagram residue-based-diagram_p8.png
properties
isRef 0
minOcc 0
maxOcc 1
content complex
attributes
Name  Type  Use  Default  Fixed  annotation
tm-numberxsd:intrequired      
tm-id-prefixxsd:stringoptional  TM    
nterm-idxsd:stringoptional  N-term    
cterm-idxsd:stringoptional  C-term    
directionxsd:stringoptional  up    
N-termXxsd:intoptional      
N-termYxsd:intoptional      
C-termXxsd:intoptional      
C-termYxsd:intoptional      
annotation
documentation
Use the bundle to layout integral membrane proteins. Specify the number of transmembrane (TM) segment to display, and the bundle will automatically calculate the layout of the diagram. Attributes of the bundle include the direction the N-term will take (up or down). Ids must also be generated for each subunit the tm-bundle contains, so that subunits can be referenced by the secondary -structure section of the diagram. The N and C-term X and Y attributes relate to the spacer values that can be used when drawing the diagram.
source <xsd:element name="tm-bundle" minOccurs="0">
  <xsd:annotation>
    <xsd:documentation>Use the bundle to layout integral membrane proteins. Specify the number of transmembrane (TM) segment to display, and the bundle will automatically calculate the layout of the diagram. Attributes of the bundle include the direction the N-term will take (up or down). Ids must also be generated for each subunit the tm-bundle contains, so that subunits can be referenced by the secondary -structure section of the diagram. The N and C-term X and Y attributes relate to the spacer values that can be used when drawing the diagram.</xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:attribute name="tm-number" type="xsd:int" use="required"/>
    <xsd:attribute name="tm-id-prefix" type="xsd:string" use="optional" default="TM"/>
    <xsd:attribute name="nterm-id" type="xsd:string" use="optional" default="N-term"/>
    <xsd:attribute name="cterm-id" type="xsd:string" use="optional" default="C-term"/>
    <xsd:attribute name="direction" type="xsd:string" use="optional" default="up"/>
    <xsd:attribute name="N-termX" type="xsd:int" use="optional"/>
    <xsd:attribute name="N-termY" type="xsd:int" use="optional"/>
    <xsd:attribute name="C-termX" type="xsd:int" use="optional"/>
    <xsd:attribute name="C-termY" type="xsd:int" use="optional"/>
  </xsd:complexType>
</xsd:element>

attribute diagram-layout/tm-bundle/@tm-number
type xsd:int
properties
isRef 0
use required
source <xsd:attribute name="tm-number" type="xsd:int" use="required"/>

attribute diagram-layout/tm-bundle/@tm-id-prefix
type xsd:string
properties
isRef 0
default TM
use optional
source <xsd:attribute name="tm-id-prefix" type="xsd:string" use="optional" default="TM"/>

attribute diagram-layout/tm-bundle/@nterm-id
type xsd:string
properties
isRef 0
default N-term
use optional
source <xsd:attribute name="nterm-id" type="xsd:string" use="optional" default="N-term"/>

attribute diagram-layout/tm-bundle/@cterm-id
type xsd:string
properties
isRef 0
default C-term
use optional
source <xsd:attribute name="cterm-id" type="xsd:string" use="optional" default="C-term"/>

attribute diagram-layout/tm-bundle/@direction
type xsd:string
properties
isRef 0
default up
use optional
source <xsd:attribute name="direction" type="xsd:string" use="optional" default="up"/>

attribute diagram-layout/tm-bundle/@N-termX
type xsd:int
properties
isRef 0
use optional
source <xsd:attribute name="N-termX" type="xsd:int" use="optional"/>

attribute diagram-layout/tm-bundle/@N-termY
type xsd:int
properties
isRef 0
use optional
source <xsd:attribute name="N-termY" type="xsd:int" use="optional"/>

attribute diagram-layout/tm-bundle/@C-termX
type xsd:int
properties
isRef 0
use optional
source <xsd:attribute name="C-termX" type="xsd:int" use="optional"/>

attribute diagram-layout/tm-bundle/@C-termY
type xsd:int
properties
isRef 0
use optional
source <xsd:attribute name="C-termY" type="xsd:int" use="optional"/>

element direction
diagram residue-based-diagram_p9.png
properties
content complex
used by
element subunit
attributes
Name  Type  Use  Default  Fixed  annotation
xxsd:intrequired      
yxsd:intrequired      
annotation
documentation
Direction is a vector(x,y) which indicates the orientation of a subunit (helix or loop) within the plane.
source <xsd:element name="direction">
  <xsd:annotation>
    <xsd:documentation>Direction is a vector(x,y) which indicates the orientation of a subunit (helix or loop) within the plane.</xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:attribute name="x" type="xsd:int" use="required"/>
    <xsd:attribute name="y" type="xsd:int" use="required"/>
  </xsd:complexType>
</xsd:element>

attribute direction/@x
type xsd:int
properties
isRef 0
use required
source <xsd:attribute name="x" type="xsd:int" use="required"/>

attribute direction/@y
type xsd:int
properties
isRef 0
use required
source <xsd:attribute name="y" type="xsd:int" use="required"/>

element elipses
diagram residue-based-diagram_p10.png
properties
content complex
children exclude include
used by
element diagram
annotation
documentation
Groups elipses related options
source <xsd:element name="elipses">
  <xsd:annotation>
    <xsd:documentation>Groups elipses related options</xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:sequence>
      <xsd:element ref="exclude" minOccurs="0" maxOccurs="unbounded"/>
      <xsd:element ref="include" minOccurs="0" maxOccurs="unbounded"/>
    </xsd:sequence>
  </xsd:complexType>
</xsd:element>

element exclude
diagram residue-based-diagram_p11.png
properties
content complex
used by
element elipses
attributes
Name  Type  Use  Default  Fixed  annotation
residueRangederived by: xsd:stringrequired      
annotation
documentation
Excludes elipses from a range of residues.
source <xsd:element name="exclude">
  <xsd:annotation>
    <xsd:documentation>Excludes elipses from a range of residues.</xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:attribute name="residueRange" use="required">
      <xsd:simpleType>
        <xsd:restriction base="xsd:string">
          <xsd:minLength value="1"/>
        </xsd:restriction>
      </xsd:simpleType>
    </xsd:attribute>
  </xsd:complexType>
</xsd:element>

attribute exclude/@residueRange
type restriction of xsd:string
properties
isRef 0
use required
facets
minLength 1
source <xsd:attribute name="residueRange" use="required">
  <xsd:simpleType>
    <xsd:restriction base="xsd:string">
      <xsd:minLength value="1"/>
    </xsd:restriction>
  </xsd:simpleType>
</xsd:attribute>

element image
diagram residue-based-diagram_p12.png
properties
content complex
used by
element output
attributes
Name  Type  Use  Default  Fixed  annotation
formatderived by: xsd:NMTOKENrequired      
filenamexsd:stringrequired      
annotation
documentation
Select options for an image output of the diagram.
source <xsd:element name="image">
  <xsd:annotation>
    <xsd:documentation>Select options for an image output of the diagram.</xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:attribute name="format" use="required">
      <xsd:simpleType>
        <xsd:restriction base="xsd:NMTOKEN">
          <xsd:enumeration value="GIF"/>
          <xsd:enumeration value="JPG"/>
          <xsd:enumeration value="SVG"/>
        </xsd:restriction>
      </xsd:simpleType>
    </xsd:attribute>
    <xsd:attribute name="filename" type="xsd:string" use="required"/>
  </xsd:complexType>
</xsd:element>

attribute image/@format
type restriction of xsd:NMTOKEN
properties
isRef 0
use required
facets
enumeration GIF
enumeration JPG
enumeration SVG
source <xsd:attribute name="format" use="required">
  <xsd:simpleType>
    <xsd:restriction base="xsd:NMTOKEN">
      <xsd:enumeration value="GIF"/>
      <xsd:enumeration value="JPG"/>
      <xsd:enumeration value="SVG"/>
    </xsd:restriction>
  </xsd:simpleType>
</xsd:attribute>

attribute image/@filename
type xsd:string
properties
isRef 0
use required
source <xsd:attribute name="filename" type="xsd:string" use="required"/>

element image-map
diagram residue-based-diagram_p13.png
properties
content complex
used by
element output
attributes
Name  Type  Use  Default  Fixed  annotation
filenamexsd:stringrequired      
annotation
documentation
Output an image map document. Currently not supported. (maps are embedded in the XML produced.)
source <xsd:element name="image-map">
  <xsd:annotation>
    <xsd:documentation>Output an image map document. Currently not supported. (maps are embedded in the XML produced.)</xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:attribute name="filename" type="xsd:string" use="required"/>
  </xsd:complexType>
</xsd:element>

attribute image-map/@filename
type xsd:string
properties
isRef 0
use required
source <xsd:attribute name="filename" type="xsd:string" use="required"/>

element include
diagram residue-based-diagram_p14.png
properties
content complex
used by
element elipses
attributes
Name  Type  Use  Default  Fixed  annotation
residueRangederived by: xsd:stringrequired      
annotation
documentation
Allows elipses to be included in a range of residues.
source <xsd:element name="include">
  <xsd:annotation>
    <xsd:documentation>Allows elipses to be included in a range of residues.</xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:attribute name="residueRange" use="required">
      <xsd:simpleType>
        <xsd:restriction base="xsd:string">
          <xsd:minLength value="1"/>
        </xsd:restriction>
      </xsd:simpleType>
    </xsd:attribute>
  </xsd:complexType>
</xsd:element>

attribute include/@residueRange
type restriction of xsd:string
properties
isRef 0
use required
facets
minLength 1
source <xsd:attribute name="residueRange" use="required">
  <xsd:simpleType>
    <xsd:restriction base="xsd:string">
      <xsd:minLength value="1"/>
    </xsd:restriction>
  </xsd:simpleType>
</xsd:attribute>

element links
diagram residue-based-diagram_p15.png
properties
content complex
children residue subunitRef
used by
element diagram
annotation
documentation
Describes hyperlinks attached to various components of the diagram.
source <xsd:element name="links">
  <xsd:annotation>
    <xsd:documentation>Describes hyperlinks attached to various components of the diagram.</xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:sequence>
      <xsd:element ref="residue" minOccurs="0" maxOccurs="unbounded"/>
      <xsd:element name="subunitRef" id="subunit" minOccurs="0" maxOccurs="unbounded">
        <xsd:annotation>
          <xsd:documentation>Links a subunit to a URL. The subunit is referenced by id. The url attribute provides the URL. For non-SVG outputs, only subunits of type edu.mssm.crover.domain2d.ProteinSegmentDomain can be linked to a URL. the SVG export supports this feature for any type of subunit.  </xsd:documentation>
        </xsd:annotation>
        <xsd:complexType>
          <xsd:attribute name="id" type="xsd:string" use="required"/>
          <xsd:attribute name="url" type="xsd:string" use="required"/>
        </xsd:complexType>
      </xsd:element>
    </xsd:sequence>
  </xsd:complexType>
</xsd:element>

element links/subunitRef
diagram residue-based-diagram_p16.png
properties
isRef 0
minOcc 0
maxOcc unbounded
content complex
id subunit
attributes
Name  Type  Use  Default  Fixed  annotation
idxsd:stringrequired      
urlxsd:stringrequired      
annotation
documentation
Links a subunit to a URL. The subunit is referenced by id. The url attribute provides the URL. For non-SVG outputs, only subunits of type edu.mssm.crover.domain2d.ProteinSegmentDomain can be linked to a URL. the SVG export supports this feature for any type of subunit. 
source <xsd:element name="subunitRef" id="subunit" minOccurs="0" maxOccurs="unbounded">
  <xsd:annotation>
    <xsd:documentation>Links a subunit to a URL. The subunit is referenced by id. The url attribute provides the URL. For non-SVG outputs, only subunits of type edu.mssm.crover.domain2d.ProteinSegmentDomain can be linked to a URL. the SVG export supports this feature for any type of subunit.  </xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:attribute name="id" type="xsd:string" use="required"/>
    <xsd:attribute name="url" type="xsd:string" use="required"/>
  </xsd:complexType>
</xsd:element>

attribute links/subunitRef/@id
type xsd:string
properties
isRef 0
use required
source <xsd:attribute name="id" type="xsd:string" use="required"/>

attribute links/subunitRef/@url
type xsd:string
properties
isRef 0
use required
source <xsd:attribute name="url" type="xsd:string" use="required"/>

element name
diagram residue-based-diagram_p17.png
type xsd:string
properties
content simple
used by
element protein
annotation
documentation
Name of the protein
source <xsd:element name="name" type="xsd:string">
  <xsd:annotation>
    <xsd:documentation>Name of the protein</xsd:documentation>
  </xsd:annotation>
</xsd:element>

element options
diagram residue-based-diagram_p18.png
properties
content complex
children residue-shape
used by
element diagram
annotation
documentation
Groups options that can affect how the diagram is rendered.
source <xsd:element name="options">
  <xsd:annotation>
    <xsd:documentation>Groups options that can affect how the diagram is rendered.</xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:sequence>
      <xsd:element name="residue-shape" minOccurs="0" maxOccurs="unbounded">
        <xsd:annotation>
          <xsd:documentation>Determines how individual residues will be rendered. Attributes determine when and what type of shape is used to render a residue. When can be either linked or nothing. "linked" selects residues that are hyperlinked. "other" select all the other residues. Three shapes are supported: rectangular, circular, and octagonal</xsd:documentation>
        </xsd:annotation>
        <xsd:complexType>
          <xsd:attribute name="when" type="xsd:string" use="required">
            <xsd:annotation>
              <xsd:documentation>When to use the shape. Values can be linked (when residue is linked), or nothing (when residue is not linked).</xsd:documentation>
            </xsd:annotation>
          </xsd:attribute>
          <xsd:attribute name="shape" type="xsd:string" use="required">
            <xsd:annotation>
              <xsd:documentation>Must be "circular", "rectangular", or "octagonal"',</xsd:documentation>
            </xsd:annotation>
          </xsd:attribute>
        </xsd:complexType>
      </xsd:element>
    </xsd:sequence>
  </xsd:complexType>
</xsd:element>

element options/residue-shape
diagram residue-based-diagram_p19.png
properties
isRef 0
minOcc 0
maxOcc unbounded
content complex
attributes
Name  Type  Use  Default  Fixed  annotation
whenxsd:stringrequired      
documentation
When to use the shape. Values can be linked (when residue is linked), or nothing (when residue is not linked).
shapexsd:stringrequired      
documentation
Must be "circular", "rectangular", or "octagonal"',
annotation
documentation
Determines how individual residues will be rendered. Attributes determine when and what type of shape is used to render a residue. When can be either linked or nothing. "linked" selects residues that are hyperlinked. "other" select all the other residues. Three shapes are supported: rectangular, circular, and octagonal
source <xsd:element name="residue-shape" minOccurs="0" maxOccurs="unbounded">
  <xsd:annotation>
    <xsd:documentation>Determines how individual residues will be rendered. Attributes determine when and what type of shape is used to render a residue. When can be either linked or nothing. "linked" selects residues that are hyperlinked. "other" select all the other residues. Three shapes are supported: rectangular, circular, and octagonal</xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:attribute name="when" type="xsd:string" use="required">
      <xsd:annotation>
        <xsd:documentation>When to use the shape. Values can be linked (when residue is linked), or nothing (when residue is not linked).</xsd:documentation>
      </xsd:annotation>
    </xsd:attribute>
    <xsd:attribute name="shape" type="xsd:string" use="required">
      <xsd:annotation>
        <xsd:documentation>Must be "circular", "rectangular", or "octagonal"',</xsd:documentation>
      </xsd:annotation>
    </xsd:attribute>
  </xsd:complexType>
</xsd:element>

attribute options/residue-shape/@when
type xsd:string
properties
isRef 0
use required
annotation
documentation
When to use the shape. Values can be linked (when residue is linked), or nothing (when residue is not linked).
source <xsd:attribute name="when" type="xsd:string" use="required">
  <xsd:annotation>
    <xsd:documentation>When to use the shape. Values can be linked (when residue is linked), or nothing (when residue is not linked).</xsd:documentation>
  </xsd:annotation>
</xsd:attribute>

attribute options/residue-shape/@shape
type xsd:string
properties
isRef 0
use required
annotation
documentation
Must be "circular", "rectangular", or "octagonal"',
source <xsd:attribute name="shape" type="xsd:string" use="required">
  <xsd:annotation>
    <xsd:documentation>Must be "circular", "rectangular", or "octagonal"',</xsd:documentation>
  </xsd:annotation>
</xsd:attribute>

element output
diagram residue-based-diagram_p20.png
properties
content complex
children image page image-map
used by
element diagram
annotation
documentation
Groups options related to the diagram output.
source <xsd:element name="output">
  <xsd:annotation>
    <xsd:documentation>Groups options related to the diagram output. </xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:sequence>
      <xsd:element ref="image" maxOccurs="unbounded"/>
      <xsd:element ref="page"/>
      <xsd:element ref="image-map"/>
    </xsd:sequence>
  </xsd:complexType>
</xsd:element>

element page
diagram residue-based-diagram_p21.png
properties
content complex
used by
element output
attributes
Name  Type  Use  Default  Fixed  annotation
templatexsd:stringoptional      
filenamexsd:stringrequired      
diagram-namexsd:stringrequired      
annotation
documentation
Generates an XML document that describes one diagram. This document will contain information suitable to generate HTML pages that embed the diagram images. When provided, the template attribute names an XSL stylesheet that will be set in the document.
source <xsd:element name="page">
  <xsd:annotation>
    <xsd:documentation>Generates an XML document that describes one diagram. This document will contain information suitable to generate HTML pages that embed the diagram images. When provided, the template attribute names an XSL stylesheet that will be set in the document.</xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:attribute name="template" type="xsd:string" use="optional"/>
    <xsd:attribute name="filename" type="xsd:string" use="required"/>
    <xsd:attribute name="diagram-name" type="xsd:string" use="required"/>
  </xsd:complexType>
</xsd:element>

attribute page/@template
type xsd:string
properties
isRef 0
use optional
source <xsd:attribute name="template" type="xsd:string" use="optional"/>

attribute page/@filename
type xsd:string
properties
isRef 0
use required
source <xsd:attribute name="filename" type="xsd:string" use="required"/>

attribute page/@diagram-name
type xsd:string
properties
isRef 0
use required
source <xsd:attribute name="diagram-name" type="xsd:string" use="required"/>

element protein
diagram residue-based-diagram_p22.png
properties
content complex
children name residue-codes secondary-structure
used by
element rbde-diagram
annotation
documentation
Describes the protein to be rendered.
source <xsd:element name="protein">
  <xsd:annotation>
    <xsd:documentation>Describes the protein to be rendered.</xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:sequence>
      <xsd:element ref="name"/>
      <xsd:element ref="residue-codes"/>
      <xsd:element ref="secondary-structure"/>
    </xsd:sequence>
  </xsd:complexType>
</xsd:element>

element rbde-diagram
diagram residue-based-diagram_p23.png
properties
content complex
children diagram-layout protein diagram
annotation
documentation
Input file for construction of one diagram.
source <xsd:element name="rbde-diagram">
  <xsd:annotation>
    <xsd:documentation>Input file for construction of one diagram.</xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:sequence>
      <xsd:element ref="diagram-layout"/>
      <xsd:element ref="protein"/>
      <xsd:element ref="diagram"/>
    </xsd:sequence>
  </xsd:complexType>
</xsd:element>

element residue
diagram residue-based-diagram_p24.png
properties
content complex
used by
element links
attributes
Name  Type  Use  Default  Fixed  annotation
positionxsd:intrequired      
urlxsd:stringrequired      
annotation
documentation
Links a residue to a URL. This feature is supported for all types of export (GIF,JPG, SVG, etc). Residue position numbering starts at 1.
source <xsd:element name="residue">
  <xsd:annotation>
    <xsd:documentation>Links a residue to a URL. This feature is supported for all types of export (GIF,JPG, SVG, etc). Residue position numbering starts at 1.</xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:attribute name="position" type="xsd:int" use="required"/>
    <xsd:attribute name="url" type="xsd:string" use="required"/>
  </xsd:complexType>
</xsd:element>

attribute residue/@position
type xsd:int
properties
isRef 0
use required
source <xsd:attribute name="position" type="xsd:int" use="required"/>

attribute residue/@url
type xsd:string
properties
isRef 0
use required
source <xsd:attribute name="url" type="xsd:string" use="required"/>

element residue-background
diagram residue-based-diagram_p25.png
properties
content complex
used by
element color-scheme
attributes
Name  Type  Use  Default  Fixed  annotation
colorxsd:stringrequired      
annotation
documentation
Fill color for the background of a residue
source <xsd:element name="residue-background">
  <xsd:annotation>
    <xsd:documentation>Fill color for the background of a residue</xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:attribute name="color" type="xsd:string" use="required"/>
  </xsd:complexType>
</xsd:element>

attribute residue-background/@color
type xsd:string
properties
isRef 0
use required
source <xsd:attribute name="color" type="xsd:string" use="required"/>

element residue-codes
diagram residue-based-diagram_p26.png
type xsd:string
properties
content simple
used by
element protein
annotation
documentation
Residues of the protein
source <xsd:element name="residue-codes" type="xsd:string">
  <xsd:annotation>
    <xsd:documentation>Residues of the protein</xsd:documentation>
  </xsd:annotation>
</xsd:element>

element residue-color
diagram residue-based-diagram_p27.png
properties
content complex
used by
element colors
attributes
Name  Type  Use  Default  Fixed  annotation
positionxsd:intrequired      
colorxsd:stringrequired      
annotation
documentation
Color one residue on the sequence. Residue position numbering starts at 1.
source <xsd:element name="residue-color">
  <xsd:annotation>
    <xsd:documentation>Color one residue on the sequence. Residue position numbering starts at 1.</xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:attribute name="position" type="xsd:int" use="required"/>
    <xsd:attribute name="color" type="xsd:string" use="required"/>
  </xsd:complexType>
</xsd:element>

attribute residue-color/@position
type xsd:int
properties
isRef 0
use required
source <xsd:attribute name="position" type="xsd:int" use="required"/>

attribute residue-color/@color
type xsd:string
properties
isRef 0
use required
source <xsd:attribute name="color" type="xsd:string" use="required"/>

element residue-geometry
diagram residue-based-diagram_p28.png
properties
content complex
used by
element shapes
attributes
Name  Type  Use  Default  Fixed  annotation
positionxsd:intrequired      
shapexsd:stringrequired      
annotation
documentation
Define the shape of one residue on the sequence. Residue position numbering starts at 1.
source <xsd:element name="residue-geometry">
  <xsd:annotation>
    <xsd:documentation>Define the shape of one residue on the sequence. Residue position numbering starts at 1.</xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:attribute name="position" type="xsd:int" use="required"/>
    <xsd:attribute name="shape" type="xsd:string" use="required"/>
  </xsd:complexType>
</xsd:element>

attribute residue-geometry/@position
type xsd:int
properties
isRef 0
use required
source <xsd:attribute name="position" type="xsd:int" use="required"/>

attribute residue-geometry/@shape
type xsd:string
properties
isRef 0
use required
source <xsd:attribute name="shape" type="xsd:string" use="required"/>

element secondary-structure
diagram residue-based-diagram_p29.png
properties
content complex
children start-residue-numbering segment disulfide-bridge
used by
element protein
annotation
documentation
Defines the secondary structure for this protein. The start-residue-numbering is used when the protein sequence that is being represented is only a partial sequence of the whole protein.
source <xsd:element name="secondary-structure">
  <xsd:annotation>
    <xsd:documentation>Defines the secondary structure for this protein. The start-residue-numbering is used when the protein sequence that is being represented is only a partial sequence of the whole protein.</xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:sequence>
      <xsd:element name="start-residue-numbering" type="xsd:int" default="1" minOccurs="0"/>
      <xsd:element ref="segment" maxOccurs="unbounded"/>
      <xsd:element name="disulfide-bridge" minOccurs="0" maxOccurs="unbounded">
        <xsd:annotation>
          <xsd:documentation>Describes a disulfide bridge. A yellow line is drawn on the diagram between the to and from residues. </xsd:documentation>
        </xsd:annotation>
        <xsd:complexType>
          <xsd:attribute name="to" type="xsd:int" use="required"/>
          <xsd:attribute name="from" type="xsd:int" use="required"/>
        </xsd:complexType>
      </xsd:element>
    </xsd:sequence>
  </xsd:complexType>
</xsd:element>

element secondary-structure/start-residue-numbering
diagram residue-based-diagram_p30.png
type xsd:int
properties
isRef 0
minOcc 0
maxOcc 1
content simple
default 1
source <xsd:element name="start-residue-numbering" type="xsd:int" default="1" minOccurs="0"/>

element secondary-structure/disulfide-bridge
diagram residue-based-diagram_p31.png
properties
isRef 0
minOcc 0
maxOcc unbounded
content complex
attributes
Name  Type  Use  Default  Fixed  annotation
toxsd:intrequired      
fromxsd:intrequired      
annotation
documentation
Describes a disulfide bridge. A yellow line is drawn on the diagram between the to and from residues.
source <xsd:element name="disulfide-bridge" minOccurs="0" maxOccurs="unbounded">
  <xsd:annotation>
    <xsd:documentation>Describes a disulfide bridge. A yellow line is drawn on the diagram between the to and from residues. </xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:attribute name="to" type="xsd:int" use="required"/>
    <xsd:attribute name="from" type="xsd:int" use="required"/>
  </xsd:complexType>
</xsd:element>

attribute secondary-structure/disulfide-bridge/@to
type xsd:int
properties
isRef 0
use required
source <xsd:attribute name="to" type="xsd:int" use="required"/>

attribute secondary-structure/disulfide-bridge/@from
type xsd:int
properties
isRef 0
use required
source <xsd:attribute name="from" type="xsd:int" use="required"/>

element segment
diagram residue-based-diagram_p32.png
properties
content complex
used by
element secondary-structure
attributes
Name  Type  Use  Default  Fixed  annotation
startxsd:intrequired      
endxsd:intrequired      
maptoxsd:stringrequired      
annotation
documentation
Defines the limits of of segment of secondary structure. Segments should span non overlapping parts of the sequence.
source <xsd:element name="segment">
  <xsd:annotation>
    <xsd:documentation>Defines the limits of of segment of secondary structure. Segments should span non overlapping parts of the sequence.</xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:attribute name="start" type="xsd:int" use="required"/>
    <xsd:attribute name="end" type="xsd:int" use="required"/>
    <xsd:attribute name="mapto" type="xsd:string" use="required"/>
  </xsd:complexType>
</xsd:element>

attribute segment/@start
type xsd:int
properties
isRef 0
use required
source <xsd:attribute name="start" type="xsd:int" use="required"/>

attribute segment/@end
type xsd:int
properties
isRef 0
use required
source <xsd:attribute name="end" type="xsd:int" use="required"/>

attribute segment/@mapto
type xsd:string
properties
isRef 0
use required
source <xsd:attribute name="mapto" type="xsd:string" use="required"/>

element shapes
diagram residue-based-diagram_p33.png
properties
content complex
children residue-geometry
used by
element diagram
annotation
documentation
Groups shape-related options
source <xsd:element name="shapes">
  <xsd:annotation>
    <xsd:documentation>Groups shape-related options</xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:sequence>
      <xsd:element ref="residue-geometry" minOccurs="0" maxOccurs="unbounded"/>
    </xsd:sequence>
  </xsd:complexType>
</xsd:element>

element spacer
diagram residue-based-diagram_p34.png
properties
content complex
used by
element subunit
attributes
Name  Type  Use  Default  Fixed  annotation
xxsd:intrequired      
yxsd:intrequired      
annotation
documentation
The separation between the first residue of the subunit and the last, on the page.
source <xsd:element name="spacer">
  <xsd:annotation>
    <xsd:documentation>The separation between the first residue of the subunit and the last, on the page.</xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:attribute name="x" type="xsd:int" use="required"/>
    <xsd:attribute name="y" type="xsd:int" use="required"/>
  </xsd:complexType>
</xsd:element>

attribute spacer/@x
type xsd:int
properties
isRef 0
use required
source <xsd:attribute name="x" type="xsd:int" use="required"/>

attribute spacer/@y
type xsd:int
properties
isRef 0
use required
source <xsd:attribute name="y" type="xsd:int" use="required"/>

element subunit
diagram residue-based-diagram_p35.png
properties
content complex
children direction spacer control-points parameter-search
used by
element diagram-layout
attributes
Name  Type  Use  Default  Fixed  annotation
idxsd:stringrequired      
typexsd:stringrequired      
annotation
documentation
Each subunit is located on the page according to the location and spacer of the subunit that preceeds it. The location of the first subunit is determined so that the complete diagram is visible. At the time of writing, the following types of subunits are available (all types should be entered starting with edu.mssm.crover.domain2d): FreeLoop, ExtremityDomain (for N-terms), CtermDomain,  HelicalDomain, BetaStrandDomain, ProteinSegmentDomain
source <xsd:element name="subunit">
  <xsd:annotation>
    <xsd:documentation>Each subunit is located on the page according to the location and spacer of the subunit that preceeds it. The location of the first subunit is determined so that the complete diagram is visible. At the time of writing, the following types of subunits are available (all types should be entered starting with edu.mssm.crover.domain2d): FreeLoop, ExtremityDomain (for N-terms), CtermDomain,  HelicalDomain, BetaStrandDomain, ProteinSegmentDomain</xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:all>
      <xsd:element ref="direction" minOccurs="0"/>
      <xsd:element ref="spacer" minOccurs="0"/>
      <xsd:element ref="control-points" minOccurs="0"/>
      <xsd:element name="parameter-search" minOccurs="0">
        <xsd:annotation>
          <xsd:documentation>Defines the bound of the parameter search that scales loops when not enough residues can fit in the path. Increase the max attribute to allow loops to grow larger before ellipses are inserted in the sequence. Rendering is appear incorrect if this parameter does not allow the loop to be enlarged, and ellipsis have been restricted  the sequence of this subunit.</xsd:documentation>
        </xsd:annotation>
        <xsd:complexType>
          <xsd:attribute name="max" type="xsd:float" use="optional" default="2"/>
        </xsd:complexType>
      </xsd:element>
    </xsd:all>
    <xsd:attribute name="id" type="xsd:string" use="required"/>
    <xsd:attribute name="type" type="xsd:string" use="required"/>
  </xsd:complexType>
</xsd:element>

attribute subunit/@id
type xsd:string
properties
isRef 0
use required
source <xsd:attribute name="id" type="xsd:string" use="required"/>

attribute subunit/@type
type xsd:string
properties
isRef 0
use required
source <xsd:attribute name="type" type="xsd:string" use="required"/>

element subunit/parameter-search
diagram residue-based-diagram_p36.png
properties
isRef 0
minOcc 0
maxOcc 1
content complex
attributes
Name  Type  Use  Default  Fixed  annotation
maxxsd:floatoptional  2    
annotation
documentation
Defines the bound of the parameter search that scales loops when not enough residues can fit in the path. Increase the max attribute to allow loops to grow larger before ellipses are inserted in the sequence. Rendering is appear incorrect if this parameter does not allow the loop to be enlarged, and ellipsis have been restricted  the sequence of this subunit.
source <xsd:element name="parameter-search" minOccurs="0">
  <xsd:annotation>
    <xsd:documentation>Defines the bound of the parameter search that scales loops when not enough residues can fit in the path. Increase the max attribute to allow loops to grow larger before ellipses are inserted in the sequence. Rendering is appear incorrect if this parameter does not allow the loop to be enlarged, and ellipsis have been restricted  the sequence of this subunit.</xsd:documentation>
  </xsd:annotation>
  <xsd:complexType>
    <xsd:attribute name="max" type="xsd:float" use="optional" default="2"/>
  </xsd:complexType>
</xsd:element>

attribute subunit/parameter-search/@max
type xsd:float
properties
isRef 0
default 2
use optional
source <xsd:attribute name="max" type="xsd:float" use="optional" default="2"/>


XML Schema documentation generated by XMLSpy Schema Editor http://www.altova.com/xmlspy