CML element atom

Abstract	false (This can be used in an instance)
Nillable	false (Instance values cannot use xsi:nil)
Target Namespace	http://www.xml-cml.org/schema/cml2/core
Declared Namespaces	xmlns:val=http://www.w3.org/1999/XSL/TransformX xmlns:stm=http://www.xml-cml.org/schema/stmml xmlns:xsd=http://www.w3.org/2001/XMLSchema xmlns:xlink=http://www.w3.org/1999/xlink xmlns:cml=http://www.xml-cml.org/schema/cml2/core xmlns=http://www.xml-cml.org/schema/cml2/core

<xsd:element name="atom" id="el.atom">
    <xsd:annotation>
        <xsd:documentation>
            <div class="summary">An atom.</div>
            <div documentation="general">
                <p>Usually within a
                    <tt>molecule</tt>
.
It is almost always contained within
                    <tt>atomArray</tt>
.
</p>
            </div>
            <div class="example">
                <pre>
<cml title="single atom example">
<atom id="a1" title="O3'" elementType="O"
formalCharge="1" hydrogenCount="1"
isotope="17" occupancy="0.7"
x2="1.2" y2="2.3"
x3="3.4" y3="4.5" z3="5.6"
convention="ABC" dictRef="chem:atom"
>
<scalar title="dipole" dictRef="d:dip"
units="units:debye">0.2</scalar>
<atomParity atomRefs4="a3 a7 a2 a4">1</atomParity>
<electron id="e1" atomRef="a1" count="2"/>
</atom>
</cml>
                </pre>
            </div>
        </xsd:documentation>
        <xsd:appinfo/>
    </xsd:annotation>
    <xsd:complexType>
        <xsd:choice>
            <xsd:choice minOccurs="0" maxOccurs="unbounded">
                <xsd:annotation>
                    <xsd:documentation>
                        <div class="general">
                            <p>the electron children: One or more electrons associated with the atom. The
                                <a href="st.atomRefType">atomRef</a>
on the
                                <tt>electron</tt>
should
point to the id on the atom. We may relax this later and allow
reference by context.
                            </p>
                        </div>
                    </xsd:documentation>
                </xsd:annotation>
                <xsd:element ref="name"/>
                <xsd:element ref="array"/>
                <xsd:element ref="matrix"/>
                <xsd:element ref="scalar"/>
                <xsd:element ref="atomParity"/>
                <xsd:element ref="electron">

                </xsd:element>
            </xsd:choice>

            <xsd:choice minOccurs="0" maxOccurs="unbounded">
                <xsd:element ref="float" minOccurs="0" maxOccurs="unbounded"/>
                <xsd:element ref="integer" minOccurs="0" maxOccurs="unbounded"/>
                <xsd:element ref="string" minOccurs="0" maxOccurs="unbounded"/>
            </xsd:choice>
        </xsd:choice>
        <xsd:attributeGroup ref="id"/>

        <xsd:attribute id="el.atom.count" name="count" type="countType">

            <xsd:annotation>
                <xsd:documentation>
                    <div class="summary">The occurrence count of the atom.</div>
                    <div class="description">Most useful in
                        <tt>formula</tt>
but possibly useful in
                        <tt>atomArray</tt>
where coordinates and
connectivity is not defined. No formal default, but assumed to be 1.
                    </div>
                </xsd:documentation>
            </xsd:annotation>
        </xsd:attribute>
        <xsd:attribute id="el.atom.elementType" name="elementType" type="elementTypeType">
            <xsd:annotation>
                <xsd:documentation>
                    <div class="general">
                        <p>The elementType. Almost mandatory</p>
                    </div>
                </xsd:documentation>
            </xsd:annotation>
        </xsd:attribute>
        <xsd:attribute id="el.atom.formalCharge" name="formalCharge" type="formalChargeType">
            <xsd:annotation>
                <xsd:documentation>
                    <div class="summary">The formalCharge on the atom (in electrons).</div>
                    <div class="description">NOT the calculated charge or oxidation state. No formal default, but its absence implies 0. It may be good practice to include it explicitly.</div>
                </xsd:documentation>
            </xsd:annotation>
        </xsd:attribute>
        <xsd:attribute id="el.atom.hydrogenCount" name="hydrogenCount" type="hydrogenCountType">
            <xsd:annotation>
                <xsd:documentation>
                    <div class="general">
                        <p>The explicit hydrogen count</p>
                    </div>
                </xsd:documentation>
            </xsd:annotation>
        </xsd:attribute>
        <xsd:attribute id="el.atom.nonHydrogenCount" name="nonHydrogenCount"
            type="nonHydrogenCountType">
            <xsd:annotation>
                <xsd:documentation>
                    <div class="general">
                        <p>The non-hydrogen count (obsolete - moved to CML Query)</p>
                    </div>
                </xsd:documentation>
            </xsd:annotation>
        </xsd:attribute>
        <xsd:attribute id="el.atom.isotope" name="isotope" type="isotopeType">
            <xsd:annotation>
                <xsd:documentation>
                    <div class="general">
                        <p>The isotopic mass. Default implies "natural abundance"</p>
                    </div>
                </xsd:documentation>
            </xsd:annotation>
        </xsd:attribute>
        <xsd:attribute id="el.atom.occupancy" name="occupancy" type="occupancyType">
            <xsd:annotation>
                <xsd:documentation>
                    <div class="general">
                        <p>The occupancy (mainly from crystallography)</p>
                    </div>
                </xsd:documentation>
            </xsd:annotation>
        </xsd:attribute>
        <xsd:attribute id="el.atom.x2" name="x2" type="xsd:float">
            <xsd:annotation>
                <xsd:documentation>
                    <div class="general">
                        <p>
The x coordinate (arbitrary units) of a 2-D representation (unrelated to 3-D structure).
Note that x- and y- 2D coordinates are required for graphical stereochemistry
such as wedge/hatch. x- and y- coordinates must be both present or both absent.
                        </p>
                    </div>
                </xsd:documentation>
            </xsd:annotation>
        </xsd:attribute>
        <xsd:attribute id="el.atom.x3" name="x3" type="xsd:float">
            <xsd:annotation>
                <xsd:documentation>
                    <div class="general">
                        <p>
The x coordinate (in Angstrom units) of a 3-D cartesian representation.
x3 y3 and z3 coordinates must be both present or both absent.
                        </p>
                    </div>
                </xsd:documentation>
            </xsd:annotation>
        </xsd:attribute>
        <xsd:attribute id="el.atom.xFract" name="xFract" type="xsd:float">
            <xsd:annotation>
                <xsd:documentation>
                    <div class="general">
                        <p>
The fractional x coordinate in a crystal structure.
xFract, yFract and zFract coordinates must be all present or all absent.
A
                            <tt>crystal</tt>
element is required
</p>
                    </div>
                </xsd:documentation>
            </xsd:annotation>
        </xsd:attribute>
        <xsd:attribute id="el.atom.xy2" name="xy2" type="coordinate2Type">
            <xsd:annotation>
                <xsd:documentation>
                    <div class="general">
                        <p>
The combined x and y coordinates of a 2-D representation (unrelated to 3-D structure).
Note that x- and y- 2D coordinates are required for graphical stereochemistry
such as wedge/hatch.
                        </p>
                    </div>
                </xsd:documentation>
            </xsd:annotation>
        </xsd:attribute>
        <xsd:attribute id="el.atom.xyz3" name="xyz3" type="coordinate3Type">
            <xsd:annotation>
                <xsd:documentation>
                    <div class="general">
                        <p>The combined x, y, z coordinates (in Angstrom units) of a 3-D cartesian representation.</p>
                    </div>
                </xsd:documentation>
            </xsd:annotation>
        </xsd:attribute>
        <xsd:attribute id="el.atom.xyzFract" name="xyzFract" type="coordinate3Type">
            <xsd:annotation>
                <xsd:documentation>
                    <div class="general">
                        <p>
The combined x, y, z fractional coordinates in a crystal structure.
A
                            <tt>crystal</tt>
element is required
</p>
                    </div>
                </xsd:documentation>
            </xsd:annotation>
        </xsd:attribute>
        <xsd:attribute id="el.atom.y2" name="y2" type="xsd:float">
            <xsd:annotation>
                <xsd:documentation>
                    <div class="general">
                        <p>
The y coordinate (arbitrary units) of a 2-D representation (unrelated to 3-D structure).
Note that x2 and y2 coordinates are required for graphical stereochemistry
such as wedge/hatch. x2 and y2 coordinates must be both present or both absent.
                        </p>
                    </div>
                </xsd:documentation>
            </xsd:annotation>
        </xsd:attribute>
        <xsd:attribute id="el.atom.y3" name="y3" type="xsd:float">
            <xsd:annotation>
                <xsd:documentation>
                    <div class="general">
                        <p>
The y coordinate (in Angstrom units) of a 3-D cartesian representation.
x3 y3 and z3 coordinates must be both present or both absent.
                        </p>
                    </div>
                </xsd:documentation>
            </xsd:annotation>
        </xsd:attribute>
        <xsd:attribute id="el.atom.yFract" name="yFract" type="xsd:float">
            <xsd:annotation>
                <xsd:documentation>
                    <div class="general">
                        <p>
The fractional x coordinate in a crystal structure.
xFract, yFract and zFract coordinates must be all present or all absent.
A
                            <tt>crystal</tt>
element is required
</p>
                    </div>
                </xsd:documentation>
            </xsd:annotation>
        </xsd:attribute>
        <xsd:attribute id="el.atom.z3" name="z3" type="xsd:float">
            <xsd:annotation>
                <xsd:documentation>
                    <div class="general">
                        <p>
The z coordinate (in Angstrom units) of a 3-D cartesian representation.
x3 y3 and z3 coordinates must be both present or both absent.
                        </p>
                    </div>
                </xsd:documentation>
            </xsd:annotation>
        </xsd:attribute>
        <xsd:attribute id="el.atom.zFract" name="zFract" type="xsd:float">
            <xsd:annotation>
                <xsd:documentation>
                    <div class="general">
                        <p>
The fractional x coordinate in a crystal structure.
xFract, yFract and zFract coordinates must be all present or all absent.
A
                            <tt>crystal</tt>
element is required
</p>
                    </div>
                </xsd:documentation>
            </xsd:annotation>
        </xsd:attribute>
        <xsd:attributeGroup ref="title"/>
        <xsd:attributeGroup ref="convention"/>
        <xsd:attributeGroup ref="dictRef"/>
        <xsd:attributeGroup ref="ref"/>
        <xsd:attribute name="role" type="xsd:string">
            <xsd:annotation>
                <xsd:documentation>
                    <div class="general">
                        <p>This can be used to describe the purpose of atoms whose
                            <tt>elementType</tt>
s are
                            <tt>dummy</tt>
or
                            <tt>locant</tt>
.
</p>
                    </div>
                </xsd:documentation>
            </xsd:annotation>
        </xsd:attribute>



    </xsd:complexType>
</xsd:element>

element {http://www.xml-cml.org/schema/cml2/core}atom

Source

Documentation