org.xmlcml.cml.base.attributes.xsd Maven / Gradle / Ivy
Abbreviation.
Abbreviation for units, terms, etc.
Describes whether child elements are sequential or parallel.
There is no default.
The type of an alternative.
This adds semantics to an _alternative_ and might be used by an RDF or related engine.
Restricts units to radians or degrees.
An array of atom IDs.
Normally an attribute of an array-based element.
A reference to a map providing mappings between atoms
The map will normally be contained within the same document and referenced by its ID. It will contain a list of links with from and to attributes linking atoms. The topology of the linking is defined by the application - it could be overlay of molecular fragments, reactant/product mapping, etc. The reserved phrase "USE_IDS" assume that the sets of atoms are of equal size and have 1:1 mapping between each id. This is another way of saying that the atoms mapped by a given ID are "the same atom".
A reference to an atom.
Used by bond, electron, etc.
The first atoms in each bond.
Currently only used in bondArray in CML2 array mode.
The second atoms in each bond.
Only used in bondArray in CML2 array mode.
An array of references to atoms.
Typical use would be to atoms defining a plane.
A reference to a list of atoms.
Used by bonds, electrons, atomSets, etc.
References to two different atoms.
Available for any reference to atoms but normally will be the normal reference attribute on the bond element. The order of atoms is preserved and may matter for some conventions (e.g. wedge/hatch or donor bonds.
A list of three references to atoms.
Typically used for defining angles, but could also be used to define a three-centre bond.
A list of 4 references to atoms.
Typically used for defining torsions and atomParities, but could also be used to define a four-centre bond.
An atomSet describing the region.
Any point falling within atomOffset of any atom in the set lies within the region. This means the region could consist of disjoint fragments.
The IDs for an array of bond.
Required in CML2 array mode.
A reference to a map providing mappings between bonds
The map will normally be contained within the same document and referenced by its ID. It will contain a list of links with from and to attributes linking bonds. The topology of the linking is defined by the application - it could be overlay of molecular fragments, reactant/product mapping, etc. The reserved phrase "USE_IDS" assume that the sets of bonds are of equal size and have 1:1 mapping between each id. This is another way of saying that the bonds mapped by a given ID are "the same bond".
A reference to a bond.
used by electron, etc.
A reference to a list of bonds.
Used by electrons, bondSets, etc.
A parallelipiped box.
By default the box uses isometric Cartesians axes but can also be linked to lattice Vector. Any point falling within the box or on a boundary is within the regio.
builtin children.
CML1-only - now deprecated.
Error array for cellParameter
3 numbers giving error limits on paremters.
The type of a cellParameter.
length or angle
The chirality of a system or molecule.
This is being actively investigated by a IUPAC committee (2002) so the convention is likely to change. No formal default.
Number of columns.
A concise formula.
The string represents an (unstructured) formula i.e. no submolecules. Recommended to use the format "H 2 O 1", etc.
The constant to add to the raw data.
add *after* applying any multiplier.
Additive constant to generate SI equivalent.
The amount to add to a quantity in non-SI units to convert its representation to SI Units. This is applied *after* multiplierToSI. It is necessarily zero for SI units.
Constraint on a parameter.
Semantics not yet finalised. We anticipate "fixed", "none" and symbolic relationships to other parameters.
content of metadata.
A reference to a convention.
There is no controlled vocabulary for conventions, but the author must ensure that the semantics are openly available and that there are mechanisms for implementation. The convention is inherited by all the subelements, so that a convention for
molecule would by default extend to its
bond and
atom children. This can be overwritten if necessary by an explicit
convention .
It may be useful to create conventions with namespaces (e.g.
iupac:name ). Use of
convention will normally require non-STMML semantics, and should be used with caution. We would expect that conventions prefixed with "ISO" would be useful, such as ISO8601 for dateTimes.
There is no default, but the conventions of STMML or the related language (e.g. CML) will be assumed.
The value of an element with a _convention_.
When convention is used this attribute must be present and element content must be empty.
The count of the object.
No fixed semantics or default, normally integers. It is presumed that the element can be multiplied by the count value.
Array of object counts.
No fixed semantics or default, normally integral. It is presumed that the element can be multiplied by the count value.
General formula for the repeat count of the element.
Experimental. No fixed semantics or default.
The cyclic nature of a bond.
This is an assertion by a human or program about the cyclic nature of a bond. It need not correspond to what is deducible from the connection table (e.g. a bond in a ring might be labelled as 'acyclic' or 'unknown')
The data type of the object.
Normally applied to scalar/array objects but may extend to more complex one.
default value in an enumeration.
A non-whitespace string (value is irrelevant) indicates that the content of this enumeration is the default value (usually of a scalar). It is an error to have more than one default. If the scalar in an instance document has no value (i.e. is empty or contains only whitespace) its value is given by the default. If the scalar in the instance is empty and no enumerations have a default attribute, an application may throw an error.
A flag indicated that the element can detach/delete itself.
An element containg this attribute may only have a transient existence (e.g. a template to create other elements) and this attribute shows that the element can be deleted at the appropriate stage. The time at which this is called is application dependent. At present the presence of the attribute is sufficient to trigger this; later a controlled vocabulary will be developed.
2006-05-21: PMR added attribute.
A delimiter character for arrays and matrices.
By default array components ('elements' in the non-XML sense) are whitespace-separated. This fails for components with embedded whitespace or missing completely:
Example: In the protein database ' CA' and 'CA' are different atom types, and and array could be: <array delimiter="/" dictRef="pdb:atomTypes">/ N/ CA/CA/ N/</array> Note that the array starts and ends with the delimiter, which must be chosen to avoid accidental use. There is currently no syntax for escaping delimiters.
The namespacePrefix for a data item.
The dictionaryPrefix is associated with elements such as dictionaries and units and allows them to be referenced namespaces. The dictionaryPrefix is normally unbound but it may be necessary to hardcode them occasionally. Thus if a value is fixed (e.g. "xsd:double") the prefix must be identified and fixed.
A reference to a dictionary entry.
Elements in data instances such as _scalar_ may have a
dictRef attribute to point to an entry in a dictionary. To avoid excessive use of (mutable) filenames and URIs we recommend a namespace prefix, mapped to a namespace URI in the normal manner. In this case, of course, the namespace URI must point to a real XML document containing _entry_ elements and validated against STMML Schema.
Where there is concern about the dictionary becoming separated from the document the dictionary entries can be physically included as part of the data instance and the normal XPointer addressing mechanism can be used.
This attribute can also be used on _dictionary_ elements to define the namespace prefix
Dimensionality of a coordinate system.
Note that this means that coordinates of higher dimensionality are ignored or an error is flagged. Thus z3 and dimensionality='2' are incompatible. At present higher dimensionalities than 3 (cf. Wondratschek) are not supported. The labelling of the axes id not controlled. ?? should we have an explicit attribute for labelling convention?.
The basis of the dimension.
Normally taken from the seven SI types but possibly expandable.
The duration of the action.
Semantics undefined.
The orientation of the eigenvector matrix.
Describes whether the vectors are columns or rows. No default, so effectively mandatory unless you want to make implementers guess and break applications.
A reference to a map providing mappings between electrons
The map will normally be contained within the same document and referenced by its ID. It will contain a list of links with from and to attributes linking electrons. The topology of the linking is defined by the application - it could be reactant/product mapping, etc. The reserved phrase "USE_IDS" assume that the sets of electrons are of equal size and have 1:1 mapping between each id. This is another way of saying that the electrons mapped by a given ID are "the same electron".
The identity of a chemical element.
Normally mandatory on _atom_, _isotope_, etc.
The identity of a chemical element.
Normally mandatory on _atom_, _isotope_, etc.
The end value.
The end value in any allowable XSD representation of data.
The end condition.
At present a human-readable string describing some condition when the ac tion should end. As XML develops it may be possible to add machine-processable semantics in this field.
Basis of the error estimate.
Value of the error.
Reports the author's estimate of the error in a scalar value. Only meaningful for dataTypes mapping to real number.
Array of error values.
Reports the author's estimate of the error in an array of values. Only meaningful for dataTypes mapping to real number.
A flag on 'arg' to indicate that the value can be calculated.
This is still experimental. if eval="_ijk_+3" and the value of the ijk was 2, this would change the value of the arg to 5. Only + and - are currently allowed
2006-05-21: PMR added attribute.
Information identifying the name of a file or other resource.
This allows an element (such as cml) to carry limited information about provenance such as the name of the document used to provide the content. It is not a complete solution but can help to protect a document becoming separated from its external metadata. It is restricted to the basic XML character set (printable ANSI) and whitespace (which should anyway be discouraged) is normalized to single space (attribute values cannot carry newlines). Quotation marks and other horrors (as used in some OS) should be avoided.
A reference to a functional form.
Currently used for potential.
The formalCharge on the object.
NOT the calculated charge or oxidation state. No formal default, but assumed to be zero if omitted. It may become good practice to include it.
An array of formalCharges.
Used in CML2 Array mode. NOT the calculated charge or oxidation state. No formal defaults, but assumed to be zero if omitted. It may become good practice to include it.
Format of a spectrum.
The data structure of the spectrum. (Not the format of the data). This describes how the data structure is to be interpreted.
Simple chemical formula.
This attribute should only be used for simple formulae (i.e. without brackets or other nesting for which a _formula_ child element should be used. The attribute might be used as a check on the child elements or for ease of representation. Essentially the same as _concise_ attribute on _formula.
Number of digits after the point.
This is used in dictionaries to define precision. However it might be replaced by xsd:facet.
The base of one or more links.
On link elements the value is the single id of an element within the document or context specified in map@fromRef attributes. It must identify the element uniquely. The reserved value 'null' implies that no mapping has been provided for the object(s) in the 'to' attribute. This implies no semantics but may be used by software to keep count of which elements have been mapped. For multiple targets use 'fromSet'.
2005-06-18: updated docs
The context for the 'from' links in a map.
A reference to the unique 'id' attribute of an element defining the context for links in a map. This may be required when id attributes may not be unique within a document. The id should either reference an element uniquely or should be taken as the first ancestor (of the map) with such an id.
This is fairly horrid but may be required when documents are assembled without establishing unique ids (e.g. concatenation of files). As an example a map referencing linked atoms in two molecules might use the containing 'reaction' element as its uniquifying context.
2005-06-18: created
A set of ids representing the base of a link.
For a partial mapping where a number of 'from' elements are known to link to a number of 'to' elements it can be useful to aggregate these into a single attribute value. The primary use is to assert that n links exist between a set of n 'from' elements and n 'to' elements but that the precise links are unknown. The semantics of the reference are the same as for 'from' and all the elements must be of the same type (which can be specified with 'fromType' either on the link or the containing map). No order information is implied. In general there will be the same number of idRefs in the 'toSet' and all implicit links will share the same attributes (e.g. 'role'). In many cases the sets will be later split into discrete links thorugh further calculation or experiment (e.g. peak assignment). Sets should never be used as a lazy or concise alternative where the all the links are explicitly known.
2005-06-18: created
The type of the base of a link.
The local tagname of the referenced element (e.g. 'molecule' or 'peakGroup'). This acts as a partial check on the integrity of the link. Software can assume that the referenced element is of a given tytpe and can create an object supporting that type.
This attribute can be attached to the 'map' attribute and requires all contained links to be of this type. This can be overridden by a 'toType' attribute on indivdual links, but it may also be useful to split the map into maps od different link types.
2005-06-18: created
Domain of an FT spectrum.
Indicates whether a spectrum is raw FID or has been transforme.
address of a resource.
Links to another element in the same or other file. For dictionary/@dictRef requires the prefix and the physical URI address to be contained within the same file. We can anticipate that better mechanisms will arise - perhaps through XMLCatalogs. At least it works at present.
Number of hydrogens.
The total number of hydrogens bonded to the atom or molecule. It is preferable to include hydrogens explicitly, and where this is done their count represents the minimum (and may thus override this attribute). It is dangerous to use this attribute for electron-deficient molecules (e.g. diborane) or hydrogen bonds. There is NO DEFAULT and the absence of this attribute must not be given any meaning.
Array of hydrogenCounts.
Normally used in CML2 array mode. The total number of hydrogens bonded to the atom or molecule. It is preferable to include hydrogens explicitly, and where this is done their count represents the minimum (and may thus override this attribute). It is dangerous to use this attribute for electron-deficient molecules (e.g. diborane) or hydrogen bonds. There is NO DEFAULT and the absence of this attribute must not be given any meaning.
A unique ID for an element.
Id is used for machine identification of elements and in general should not have application semantics. It is similar to the XML ID type as containing only alphanumerics, '_', ',' and '-' and and must start with an alphabetic character. Ids are case sensitive. Ids should be unique within local scope, thus all atoms within a molecule should have unique ids, but separated molecules within a document (such as a published article) might have identical ids. Software should be able to search local scope (e.g. all atoms within a molecule). However this is under constant review.
Allows a referring element to generate a unique id.
idgen can hold a unique identifier which is copied into the id attribute of the referenced element. This avoids multiple copies of the referenced object with duplicate ids. EXPERIMENTAL
2006-05-22: PMR added.
Inheritance mechanism.
A reference to an existing element can be used to supplement values such as coordinates. The
inheritance attribute determines whether the values are supplemented, overwritten or deleted. In the example:
<molecule id="m1" view="initial"> <atomArray> <atom id="a1" x3="0.1"/> </atomArray> </molecule> <!-- this adds more information --> <molecule ref="m1" view="initial" inherit="supplement"> <atomArray> <atom id="a1" hydrogenCount="1"/> </atomArray> </molecule> <!-- this will overwrite the previous values --> <molecule ref="m1" inherit="overwrite" view="final" id="m2"> <atomArray> <atom id="a1" x3="0.1"/> </atomArray> </molecule> <!-- this will delete the previous values --> <molecule ref="m1" inherit="delete" view="restart"> <atomArray> <atom id="a1" hydrogenCount=""/> </atomArray> </molecule>
The first
molecule/@ref adds complementary information, the second changes the values. Software is allowed to generate two independent copies of the molecule and reference them by different IDs (
m1 and
m2 ).
This mechanism is necessary to manage the implied inheritance of partial information during minimisations and dynamics. It requires careful software implementation.
An inline representation of the object.
This can represent a wide range of information from formal serialization as ASCII through to domain-specific textual representations. It will often be used in conjunction with the "convention" attribute. For example it could be used to represent IUPAC formula, SMILES strings, TeX equations, etc. Characters should conforma to the XML character set, and XML markup (lt and amp) should be escaped.
IT SHOULD NEVER BE USED FOR INLINE XML
Area under a peak.
Unfortunately units are usually arbitrary and not related to the x- and y- axis units, and in this case _peakUnits_ should be use.
A symmetry species.
No fixed semantics, though we may provide a controlled-extensible list in the future.
The isotope for an element.
A real number describing the isotope. Probably obsolet.
Reference to a description of the isotopic composition of an atom.
Used when more than one atom shares the same isotopic composition (e.g. when H/D have been scrambled over some or all of the atoms in a molecule..
The integer number for an isotope.
The number representing the isotope. By default it does not point to a fuller description of the isotope (use isotopeRef).
Reference to a fuller description of the isotope.
The description may be found in an external collection (e.g. IUPAC) or within the current document.
indicates whether a unit is an SI or derived SI unit.
required on SI unit elements with value 'true'. Optional on other units with attribute 'false'. A unitList should contain either SI units or non-SI units but not both.
The k vector.
The k-vector with 3 components.
A reference to a kpoint.
Used by band, etc.
2006-01-21: PMR. Created
The secondary quantum number.
takes values 0, 1, etc.
A label.
The semantics of label are not defined in the schema but are normally commonly used standard or semi-standard text strings. This attribute has the the same semantics as the more common _label_ element.
The primitivity of a lattice.
No default. The semantics of this are software-dependent (i.e. this Schema does not check for consistency between spacegroups, symmetry operators, etc.
Length of an array or .
Probably will be replaced with xsd:schema tool.
The type of the link.
A list of values.
Normally for iterations.
2006-06-09: PMR Created..
symbolic represention of l amd m.
takes avlues of s, p, px, dxy, dx2y2, f, etc.
The azimuthal quantum number.
takes values -1, 0, 1, etc.
An attribute providing a mandatory unique ID for an element.
This is a horrible hack. It should be possible to add 'required' to the attributeGroup where used... (Maybe it is and I am still fighting Schema Wars.
Type of matrix.
Mainly square, but extensible through the _xsd:union_ mechanis.
Maximum value allowed for an element or attribute.
maximum exclusive value.
by analogy with xsd:schema.
minimum inclusive value.
by analogy with xsd:schem.
maximum length of a scalar.
by analogy with xsd:schem.
Maximum values for numeric _matrix_ or _array.
A whitespace-separated list of the same length as the array in the parent element.
Type of spectral measurement.
The nature of the measured data. This is not an exhaustive list and should only be used if it affects the storage or immediate processing.
The metadata type.
This is likely to be the Dublin Core name or something similar. The use of "type" is an infelicitous misnomer and we shall try to remove it.
The minimum value allowed for an element or attribute.
minimum exclusive value.
by analogy with xsd:schema.
minimum inclusive value.
by analogy with xsd:schema.
minimum length of a scalar.
by analogy with xsd:schema.
Minimum values for numeric _matrix_ or _array.
A whitespace-separated lists of the same length as the array in the parent element.
A reference to a molecule.
Used by spectrum, etc.
A reference to one or more molecules.
Uses the id attribute as the target identification. The order of molecules is preserved. It is not necessarily an error to have repeated references to the same molecule
2005-11-22: PMR. added this attribute.
References to two different molecules.
Available for any reference to molecules but normally will be the normal reference attribute on the join element. The order of molecules is preserved and may matter.
2006-11-24: PMR created
The scale by which to multiply raw data or a unit.
The scale is applied *before* adding any constant. The attribute may be found on a data item (scalar, array, matrix, etc.) or a user-defined unit.
Multiplier to generate SI equivalent.
The factor by which the non-SI unit should be multiplied to convert a quantity to its representation in SI Units. This is applied *before* _constantToSI_. Necessarily unity for SI unit.
The principal quantum number.
Takes values 1, 2, 3, etc.
Name of the object.
A string by which the object is known. Often a required attribute. The may or may not be a semi-controlled vocabulary.
The namespace for a data item.
The namespace is associated with elements such as dictionaries and units and allows them to be referenced through free namespace prefixes.
A number determined by context
Used for isotope number in isotope, and rotational symmetry number in symmetry for calculation of entropy, etc.
2003-03-30: added number attribut.
The class of an object.
The type of this information. This is not controlled, but examples might include:
label
summary
note
usage
qualifier
It might be used to control display or XSL filtering.
The attribute is named 'objectClass' to avoid clashes with other class attributes and inappropriate conversion to foo.getClass().
Occupancy for an atom.
Normally only found in crystallography. Defaults to 1.0. The occupancy is required to calculate the molecular formaula from the atoms.
Array of occupancies.
Normally only found in crystallography. Defaults to 1.0. The occupancy is required to calculate the molecular formula from the atoms.
The order of the bond.
There is NO default. This order is for bookkeeping only and is not related to length, QM calculations or other experimental or theoretical calculations.
The order of the bond.
There is NO default. This order is for bookkeeping only and is not related to length, QM calculations or other experimental or theoretical calculations.
parameter name passed to an element
This is still experimental.
2006-06-09: PMR added attribute.
raplaces attribute on parent
This is still experimental. Creates, overwriting if necessary, an attribute on parent. Example:
<foo> <arg parentAttribute="bar">zubbo</arg> will create an attribute bar="zubbo" on <foo>
2006-06-09: PMR added attribute.
A dictRef-like reference to the id of the parent SI unit.
This parent should occur in this or another dictionary and be accessible through the dictRef mechanism. This attribute is forbidden for SI Units themselves. The mechanism holds for base SI units (7) and all compound (derived) units made by combinations of base Units.
Pattern constraint.
Based on xsd:schema.
Height of a peak.
For 1-dimensional data (e.g. y vs x) hould use the same units as the appropriate axis (e.g. y).
Multiplicity of a peak.
Uses a semi-controlled vocabulary.
Shape of a peak.
Semi-controlled vocabulary such as broad or sharp.
Type of this structure.
Semi-controlled vocabulary such as coupling or splitting.
Units for a peak or peak integral.
For 2-dimensional spectra the units represent the observation. For an integral they are usually arbitrary and not related to the x- and y- axis units. Thus NMR spectra may use hydrogen count as the units for the peak area.
Is the axis periodic.
Any or all of the axes may be periodic or aperiodic. An example could be a surface where 2 periodic axes (not necessarily orthogonal) are used to describe the coordinates in the surface, perhaps representing lattice vectors of a 3D crystal or 2D layer. The third vector is orthogonal and represents coordinates normal to the surface. In this case only the direction, not the magnitude of the vector is important.
Periodicity of the system.
This represents the number of dimensions (or coordinate axes) along periodic behaviour occurs and can be supported by symmetry operators or other transformations. Periodicity must never exceed dimensionality.
A point in 3 dimensions.
can be used for any complex geometrical object, such as line.
A point group.
No fixed semantics, though Schoenflies is recommended over Hermann-Mauguin. We may provide a controlled-extensible list in the future.
SpaceGroup multiplicity.
Normally for an atom. This attribute gives the pointGroup multiplicity of the molecule and is independent of any atomic information. No default, and it may take any positive integer value (though values are normally between 1 and 60 (for icosahedral). It represents the number of symmetry operations (without any translations) that transform the atom into itself. Thus an atom on a centre of symmetry can have a pointGroupMultiplicity of 2. The pointGroupMultiplicity can be deduced from a knowledge of the coordinates and the pointGroup operators and so is formally redundant but this is a useful convenience operator. Distinguish carefully from occupancy which represents incomplete occupation of a site.
The power to which a dimension should be raised.
Normally an integer. Must be included, even if unity.
The power to which a dimension should be raised.
Normally an integer. Must be included, even if unity.
Is the dimension preserved during algebra.
Experimental. The idea is to support concepts like volume/volume where algebraically these cancel out. preserve="yes" is intending to support preservation during derivation of new unitTypes.
Keyword signifying how object is to be processed.
Semantics depend on the parent element
2006-05-20: PMR added
A ratio in the range 0 to 1.
Currently used for ratios between brached reactions but re-usable for other concepts.
Format of the reaction component.
Indicates how the components of reactionScheme, reactionStepList, etc. should be processed. No controlled vocabulary. One example is format="cmlSnap" asserts that the processor can assume that the reactants and products can be rendered using the CMLSnap design. Note that the reaction can be interpreted without reference to the format, which is primarily a processing instruction.
Role of the reaction.
The sequence of steps in a reactionStepList.
By default the reactions in a reactionStepList are assumed to take place in sequence (e.g. one or more products of reaction n are used in reaction n+1 or later. However there are cases where it is known that reactions take place in parallel (e.g. if there is no overlap of molecular identities). Alternatively there are points at which there are two or more competing reactions which may depend on conditions or concentrations. A small semi-controlled vocabulary is suggested.
The semantic of these are not fully explored, but we suggest that consecutive and simultaneous should be the first to be supported
Type of the reaction.
Recommended unit.
a facet on a numeric dictionary entry.
A reference to an element of given type.
ref modifies an element into a reference to an existing element of that type within the document. This is similar to a pointer and it can be thought of a strongly typed hyperlink. It may also be used for "subclassing" or "overriding" elements.
When referring to an element most of the "data" such as attribute values and element content will be on the full instantiated element. Therefore ref (and possibly id) will normally be the only attributes on the pointing element. However there may be some attributes (title, count, etc.) which have useful semantics, but these are element-specific
A list of regions creating a union.
The union of a series of regions produces a larger region (possibly disjoint). Any point belonging to any of the referenced regions is a member of this region.
Type of relatedEntry.
Type represents a the type of relationship in a relatedEntry element.
Role of the object.
How the object functions or its position in the architecture. No controlled vocabulary.
Number of rows.
The sequence of steps in a reactionList.
By default the reactions in a reactionStepList are assumed to take place in sequence (e.g. one or more products of reaction n are used in reaction n+1 or later. However there are cases where it is known that reactions take place in parallel (e.g. if there is no overlap of molecular identities). Alternatively there are points at which there are two or more competing reactions which may depend on conditions or concentrations. A small semi-controlled vocabulary is suggested.
Serial number or other id.
Currently only on module. Modules with the same _role_ attribute can be distinguished by _serial_. This is often an integer but other schemes may be used.
shape of object.
Mainly square, but extensible through the _xsd:union_ mechanism.
The namespace for SI Units dictionary.
Main use is on unitList to identify the dictionary holding the SI Units.
Array of namespaces locating SI Units dictionaries.
Main use is on unitList to identify the dictionaries holding the SI Units.
The size of an array or matrix.
A space group.
No fixed semantics, though Hermann-Mauguin or Hall is recommended over Schoenflies. We may provide a controlled-extensible list in the future.
SpaceGroup multiplicity.
Normally for an atom. This attribute gives the spaceGroup multiplicity of the molecule and is independent of any atomic information. No default, and it may take any positive integer value (though values are normally between 1 and 192. It represents the number of symmetry operations (without cell translations) that transform the atom into itself. Thus an atom on a centre of symmetry can have a spaceGroupMultiplicity of 2. The spaceGroupMultiplicity can be deduced from a knowledge of the coordinates and the spaceGroup operators and so is formally redundant but this is a useful convenience operator. Some crystallographic experiments report this attribute as, for example, the IUCr CIF item 'atom_site_symmetry_multiplicity'. Distinguish carefully from occupancy which represents incomplete occupation of a site.
The spaceType of the lattice.
Usually real or reciprocal. No default. The semantics of this are software-dependent (i.e. this Schema does not check for consistency for unitTypes, etc.
The type of the spectrum.
A sphere.
Currently describes a region. Any point falling within the sphere or on its surface is within the region.
The spin of a system.
Supports fractional values. Currently the spin of a nucleus. The normal fraction representing the spin of the isotope.
Spin multiplicity.
Normally for a molecule. This attribute gives the spin multiplicity of the molecule and is independent of any atomic information. No default, and it may take any positive integer value (though values are normally between 1 and 5.
The start value.
The start value in any allowable XSD representation
The start condition.
This can describe the condition(s) that has to be met before an action can begin, such as in a recipe. Semantics are unexplored but could be used to control robotic operations.
The physical state of the substance.
No fixed semantics or default.
The step value.
The step value in any allowable XSD representation
Type of the substanceList.
Extension is allowed through the "other" value.
A flag on 'arg' to indicate that the value can be substituted.
This is still experimental. The value may be an XPath expression, at present all attributes (".//@*") are processed. If an attribute contains _ijk_ where the name of the arg is 'ijk' this string is replaced by the value of ijk, e.g. if arg with name ijk has a value of 2 then 'm_ijk__z3' becomes 'm2_z3'. substitute="." replaces this element by its value
2006-05-21: PMR added attribute.
A symbol.
No semantics. However it should contain only ASCII characters and we may have to develop an escaping mechanism. Used on _atomicBasisFunction_, _unit_, etc.
Is the molecule oriented to the symmetry
No formal default, but a molecule is assumed to be oriented according to any _symmetry_ children. This is required for crystallographic data, but some systems for isolated molecules allow specification of arbitrary Cartesian or internal coordinates, which must be fitted or refined to a prescribed symmetry. In this case the attribute value is false.
type of table.
controls content
Indicates whether the structure is a tautomer.
Currently used with IChI _identifier_ element. Semantics, vocabulary and usage are application-dependent.
A term in a dictionary.
The term should be a noun or nounal phrase, with a separate definition and further description.
The test condition on an if element.
No controlled format yet.
2006-06-09: PMR Created..
A title on an element.
No controlled value.
The target of one or more links.
On link elements the value is the single id of an element within the document or context specified in map@toContext attributes. It must identify the element uniquely. The reserved value 'null' implies that no mapping has been provided for the object(s) in the 'from' attribute. This implies no semantics but may be used by software to keep count of which elements have been mapped. For multiple targets use 'toSet'.
2005-06-18: updated docs
The context for the 'from' links in a map.
A reference to the unique 'id' attribute of an element defining the context for links in a map. This may be required when id attributes may not be unique within a document. The id should either reference an element uniquely or should be taken as the first ancestor (of the map) with such an id.
This is fairly horrid but may be required when documents are assembled without establishing unique ids (e.g. concatenation of files). As an example a map referencing linked atoms in two molecules might use the containing 'reaction' element as its uniquifying context.
2005-06-18: created
A set of ids representing the base of a link.
For a partial mapping where a number of 'to' elements are known to link to a number of 'from' elements it can be useful to aggregate these into a single attribute value. The primary use is to assert that n links exist between a set of n 'to' elements and n 'from' elements but that the precise links are unknown. The semantics of the reference are the same as for 'to' and all the elements must be of the same type (which can be specified with 'toType' either on the link or the containing map). No order information is implied. In general there will be the same number of idRefs in the 'fromSet' and all implicit links will share the same attributes (e.g. 'role'). In many cases the sets will be later split into discrete links thorugh further calculation or experiment (e.g. peak assignment). Sets should never be used as a lazy or concise alternative where the all the links are explicitly known.
2005-06-18: created
total digits in a scalar.
based on xsd:schema.
The type of the base of a link.
The local tagname of the referenced element (e.g. 'molecule' or 'peakGroup'). This acts as a partial check on the integrity of the link. Software can assume that the referenced element is of a given tytpe and can create an object supporting that type.
This attribute can be attached to the 'map' attribute and requires all contained links to be of this type. This can be overridden by a 'toType' attribute on indivdual links, but it may also be useful to split the map into maps od different link types.
2005-06-18: created
Type of the object.
A qualifier which may affect the semantics of the object.
A reference to the type of a unit.
Needed to differentiate the rather unhappy polymorphism of unitList/unit and unitList/unitType.
2005-12-17 PMR: Added
Scientific units on an element.
These must be taken from a dictionary of units. There should be some mechanism for validating the type of the units against the possible values of the element.
unitsRef attribute on CML1 elements.
CML1-only - now deprecated.
A reference to the type of a unit.
Used in defining the unit and doing symbolic algebra on the dimensionality.
Value of a scalar object.
The value must be consistent with the dataType of the object.
A vector in 3 dimensions.
can be used for any complex geometrical object, such as line.
The version of the element
cml or identifier elements can currently have versions. They may be dependent on the date of release and this attribute is highly recommended. There is no controlled syntax.
Weight of the element.
Currently the weight of the kPoint, derived from the symmetry such as the inverse of the multiplicity in real space. Thus a point at 0,0,0 in monoclinic space might be 0.25. The lowest value possible is probably 1/48.0 (in m3m).
2003-09-15 (added at suggestion of Jon Wakelin).
Whitespace.
Attached to entry. This may be obsolete.
x2 coordinate for an object.
Used for displaying the object in 2 dimensions. Unrelated to the 3-D coordinates for the object. The orientation of the axes matters as it can affect the chirality of object.
array of x2 coordinate.
Normally used in CML2 array mode. Used for displaying the object in 2 dimensions. Unrelated to the 3-D coordinates for the object. The orientation of the axes matters as it can affect the chirality of object.
The x coordinate of a 3 dimensional object.
The default units are Angstrom. (The provision for other units is weak at present.) Objects are always described with a right-handed coordinate system.
An array of x3 coordinate.
Normally used in CML2 array mode.
Fractional x coordinate.
normally xFract, yFract and zFract should all be present or absent. If present a _crystal_ element should also occur.
Array of fractional x coordinate.
normally xFract, yFract and zFract should all be present or absent. If present a _crystal_ element should also occur.
Maximum xValue.
Annotates x-axis data with a maximum value. This need not be algorithmically deducible from the data and is typically used for the extent of a _peak_ or _peakGroup_. It uses xUnits or the same units as the data. There may or may not be a _xMin_ attribute but if so xMax should be greater than or equals to it.
Minimum xValue.
Annotates x-axis data with a minimum value. This need not be algorithmically deducible from the data and is typically used for the extent of a _peak_ or _peakGroup_. It uses xUnits or the same units as the data. There may or may not be a _xMax_ attribute but if so xMin should be less than or equals to it.
Units for x axis.
All x-axis data must have unambiguous units. Ideally the data and _xMin_ or _xValue_ should share the same units but different xUnits can be used as long as it is clear..
Value along an x axis.
Annotates x-axis data with a value. It is typically used for the location of a _peak_ or _peakGroup_. It uses xUnits or the same units as the data.
An unsigned interval along an x axis.
It is typically used for the width of a _peak_ or _peakGroup_ but could be used for any range. It uses xUnits or the same units as the data.
y2 coordinate for an object.
Used for displaying the object in 2 dimensions. Unrelated to the 3-D coordinates for the object. The orientation of the axes matters as it can affect the chirality of object.
array of y2 coordinate.
Normally used in CML2 array mode. Used for displaying the object in 2 dimensions. Unrelated to the 3-D coordinates for the object. The orientation of the axes matters as it can affect the chirality of object.
The y coordinate of a 3 dimensional object.
The default units are Angstrom. (The provision for other units is weak at present.) Objects are always described with a right-handed coordinate system.
An array of y3 coordinate.
Normally used in CML2 array mode.
Fractional y coordinate.
normally xFract, yFract and zFract should all be present or absent. If present a _crystal_ element should also occur.
Array of fractional y coordinate.
normally xFract, yFract and zFract should all be present or absent. If present a _crystal_ element should also occur.
Yield of a reaction or reactionStep.
Yields can be given on either element. They should lie in the range 0 to 1 inclusive (i.e. percentages will need to be converted). Software may use yield to calculate amounts of substances created during a reaction or series of reactions.
Maximum yValue.
Annotates y-axis data with a maximum value. This need not be algorithmically deducible from the data and is typically used for the extent of a _peak_ or _peakGroup_. It uses yUnits or the same units as the data. There may or may not be a _yMin_ attribute but if so yMax should be greater than or equals to it.
Minimum yValue.
Annotates y-axis data with a minimum value. This need not be algorithmically deducible from the data and is typically used for the extent of a _peak_ or _peakGroup_. It uses yUnits or the same units as the data. There may or may not be a _yMax_ attribute but if so yMin should be less than or equal to it.
Units for y axis.
All y-axis data must have unambiguous units. Ideally the data and _yMin_ or _yValue_ should share the same units but different yUnits can be used as long as it is clear.
Value along a y axis.
Annotates y-axis data with a value. It is typically used for the location of a _peak_ or _peakGroup_. It uses yUnits or the same units as the data.
An unsigned interval along a y axis.
It is typically used for the width of a _peak_ or _peakGroup_ but could be used for any range. It uses yUnits or the same units as the data.
The number of molecules per cell.
Molecules are defined as the _molecule_ which directly contains the _crystal_ element.
The z coordinate of a 3 dimensional object.
The default units are Angstrom. (The provision for other units is weak at present.) Objects are always described with a right-handed coordinate system.
An array of z3 coordinate.
Normally used in CML2 array mode.
Fractional y coordinate.
normally xFract, yFract and zFract should all be present or absent. If present a _crystal_ element should also occur.
Array of fractional z coordinate.
normally xFract, yFract and zFract should all be present or absent. If present a _crystal_ element should also occur.
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