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<!-- ============================================
::DATATOOL:: Generated from "mmdb2.asn"
::DATATOOL:: by application DATATOOL version 1.8.1
::DATATOOL:: on 01/18/2007 23:07:18
============================================ -->
<!-- ============================================ -->
<!-- This section is mapped from module "MMDB-Structural-model"
================================================= -->
<!--
$Revision: 6.0 $
**********************************************************************
Biological Macromolecule 3-D Structure Data Types for MMDB,
A Molecular Modeling Database
Definitions for structural models
By Hitomi Ohkawa, Jim Ostell, Chris Hogue and Steve Bryant
National Center for Biotechnology Information
National Institutes of Health
Bethesda, MD 20894 USA
July, 1996
**********************************************************************
-->
<!-- Elements used by other modules:
Biostruc-model,
Model-id,
Model-coordinate-set-id -->
<!-- Elements referenced from other modules:
Chem-graph-pntrs,
Atom-pntrs,
Chem-graph-alignment,
Sphere,
Cone,
Cylinder,
Brick,
Transform FROM MMDB-Features,
Biostruc-id FROM MMDB,
Pub FROM NCBI-Pub -->
<!-- ============================================ -->
<!--
A structural model maps chemical components into a measured three-
dimensional space. PDB-derived biostrucs generally contain 4 models,
corresponding to "views" of the structure of a biomolecular assemble with
increasing levels of complexity. Model types indicate the complexity of the
view.
The model named "NCBI all atom" represents a view suitable for most
computational biology applications. It provides complete atomic coordinate
data for a "single best" model, omitting statistical disorder information
and/or ensemble structure descriptions provided in the source PDB file.
Construction of the single best model is based on the assumption that the
contents of the "alternate conformation" field from pdb imply no correlation
among the occupancies of multiple sites assigned to sets of atoms: the best
site is chosen only on the basis of highest occupancy. Note, however, that
alternate conformation sets where correlation is implied are generally
constrained in crystallographic refinement to have uniform occupancy, and
will thus be selected as a set. For ensemble models the model which assigns
coordinates to the most atoms is chosen. If numbers of coordinates are the
same, the model occurring first in the PDB file is selected. The single
best model includes complete coordinates for all nonpolymer components, but
omits those classified as "solvent". Model type is 3 for this model.
The model named "NCBI backbone" represents a simple view intended for
graphic displays and rapid transmission over a network. It includes only
alpha carbon or backbone phosphate coordinates for biopolymers. It is based
on selection of alpha-carbon and backbone phosphate atoms from the "NCBI
all atom" model. The model type is set to 2. An even simpler model gives
only a cartoon representation, using cylinders corresponding to secondary
structure elements. This is named "NCBI vector", and has model type 1.
The models named "PDB Model 1", "PDB Model 2", etc. represent the complete
information provided by PDB, including full descriptions of statistical
disorder. The name of the model is based on the contents of the PDB MODEL
record, with a default name of "PDB Model 1" for PDB files which contain
only a single model. Construction of these models is based on the
assumption that contents of the PDB "alternate conformation" field are
intended to imply correlation among the occupancies of atom sets flagged by
the same identifier. The special flag " " (blank) is assumed to indicate
sites occupied in all alternate conformations, and sites flagged otherwise,
together with " ", to indicate a distinct member of an ensemble of
alternate conformations. Note that construction of ensemble members
according to these assumption requires two validation checks on PDB
"alternate conformation" flags: they must be unique among sites assigned to
the same atom, and that the special " " flag must occur only for unique
sites. Sites which violate the first check are flagged as "u", for
"unknown"; they are omitted from all ensemble definitions but are
nontheless retained in the coordinate list. Sites which violate the second
check are flagged "b" for "blank", and are included in an appropriately
named ensemble. The model type for pdb all models is 4.
Note that in the MMDB database models are stored in the ASN.1 stream in
order of increasing model type value. Since models occur as the last item
in a biostruc, parsers may avoid reading the entire stream if the desired
model is one of the simplified types, which occur first in the stream. This
can save considerable I/O time, particularly for large ensemble models from
NMR determinations.
-->
<!ELEMENT Biostruc-model (
Biostruc-model_id,
Biostruc-model_type,
Biostruc-model_descr?,
Biostruc-model_model-space?,
Biostruc-model_model-coordinates?)>
<!ELEMENT Biostruc-model_id (Model-id)>
<!ELEMENT Biostruc-model_type (Model-type)>
<!ELEMENT Biostruc-model_descr (Model-descr*)>
<!--
The model space defines measurement units and any external reference frame.
Coordinates refer to a right-handed orthogonal system defined on axes
tagged x, y and z in the coordinate and feature definitions of a biostruc.
Coordinates from PDB-derived structures are reported without change, in
angstrom units. The units of temperature and occupancy factors are not
defined explicitly in PDB, but are inferred from their value range.
-->
<!ELEMENT Biostruc-model_model-space (Model-space)>
<!ELEMENT Biostruc-model_model-coordinates (Model-coordinate-set*)>
<!ELEMENT Model-id (%INTEGER;)>
<!ELEMENT Model-type (%INTEGER;)>
<!ATTLIST Model-type value (
ncbi-vector |
ncbi-backbone |
ncbi-all-atom |
pdb-model |
other
) #IMPLIED >
<!ELEMENT Model-descr (
Model-descr_name |
Model-descr_pdb-reso |
Model-descr_pdb-method |
Model-descr_pdb-comment |
Model-descr_other-comment |
Model-descr_attribution)>
<!ELEMENT Model-descr_name (#PCDATA)>
<!ELEMENT Model-descr_pdb-reso (#PCDATA)>
<!ELEMENT Model-descr_pdb-method (#PCDATA)>
<!ELEMENT Model-descr_pdb-comment (#PCDATA)>
<!ELEMENT Model-descr_other-comment (#PCDATA)>
<!ELEMENT Model-descr_attribution (Pub)>
<!--
The model space defines measurement units and any external reference frame.
Coordinates refer to a right-handed orthogonal system defined on axes
tagged x, y and z in the coordinate and feature definitions of a biostruc.
Coordinates from PDB-derived structures are reported without change, in
angstrom units. The units of temperature and occupancy factors are not
defined explicitly in PDB, but are inferred from their value range.
-->
<!ELEMENT Model-space (
Model-space_coordinate-units,
Model-space_thermal-factor-units?,
Model-space_occupancy-factor-units?,
Model-space_density-units?,
Model-space_reference-frame?)>
<!ELEMENT Model-space_coordinate-units %ENUM;>
<!ATTLIST Model-space_coordinate-units value (
angstroms |
nanometers |
other |
unknown
) #REQUIRED >
<!ELEMENT Model-space_thermal-factor-units %ENUM;>
<!ATTLIST Model-space_thermal-factor-units value (
b |
u |
other |
unknown
) #REQUIRED >
<!ELEMENT Model-space_occupancy-factor-units %ENUM;>
<!ATTLIST Model-space_occupancy-factor-units value (
fractional |
electrons |
other |
unknown
) #REQUIRED >
<!ELEMENT Model-space_density-units %ENUM;>
<!ATTLIST Model-space_density-units value (
electrons-per-unit-volume |
arbitrary-scale |
other |
unknown
) #REQUIRED >
<!--
An external reference frame is a pointer to another biostruc, with an
optional operator to rotate and translate coordinates into its model space.
This item is intended for representation of homology-derived model
structures, and is not present for structures from PDB.
-->
<!ELEMENT Model-space_reference-frame (Reference-frame)>
<!--
An external reference frame is a pointer to another biostruc, with an
optional operator to rotate and translate coordinates into its model space.
This item is intended for representation of homology-derived model
structures, and is not present for structures from PDB.
-->
<!ELEMENT Reference-frame (
Reference-frame_biostruc-id,
Reference-frame_rotation-translation?)>
<!ELEMENT Reference-frame_biostruc-id (Biostruc-id)>
<!ELEMENT Reference-frame_rotation-translation (Transform)>
<!--
Atomic coordinates may be assigned literally or by reference to another
biostruc. The reference coordinate type is used to represent homology-
derived model structures. PDB-derived structures have literal coordinates.
Referenced coordinates identify another biostruc, any transformation to be
applied to coordinates from that biostruc, and a mapping of the chemical
graph of the present biostruc onto that of the referenced biostruc. They
give an "alignment" of atoms in the current biostruc with those in another,
from which the coordinates of matched atoms may be retrieved. For non-
atomic models "alignment" may also be represented by molecule and residue
equivalence lists. Referenced coordinates are a data item inteded for
representation of homology models, with an explicit pointer to their source
information. They do not occur in PDB-derived models.
-->
<!ELEMENT Model-coordinate-set (
Model-coordinate-set_id?,
Model-coordinate-set_descr?,
Model-coordinate-set_coordinates)>
<!ELEMENT Model-coordinate-set_id (Model-coordinate-set-id)>
<!ELEMENT Model-coordinate-set_descr (Model-descr*)>
<!ELEMENT Model-coordinate-set_coordinates (
Model-coordinate-set_coordinates_literal |
Model-coordinate-set_coordinates_reference)>
<!--
Literal coordinates map chemical components into the model space. Three
mapping types are allowed, atomic coordinate models, density-grid models,
and surface models. A model consists of a sequence of such coordinate sets,
and may thus combine coordinate subsets which have a different source.
PDB-derived models contain a single atomic coordinate set, as they by
definition represent information from a single source.
-->
<!ELEMENT Model-coordinate-set_coordinates_literal (Coordinates)>
<!ELEMENT Model-coordinate-set_coordinates_reference (Chem-graph-alignment)>
<!ELEMENT Model-coordinate-set-id (%INTEGER;)>
<!--
Literal coordinates map chemical components into the model space. Three
mapping types are allowed, atomic coordinate models, density-grid models,
and surface models. A model consists of a sequence of such coordinate sets,
and may thus combine coordinate subsets which have a different source.
PDB-derived models contain a single atomic coordinate set, as they by
definition represent information from a single source.
-->
<!ELEMENT Coordinates (
Coordinates_atomic |
Coordinates_surface |
Coordinates_density)>
<!--
Literal atomic coordinate values give location, occupancy and order
parameters, and a pointer to a specific atom defined in the biostruc graph.
Temperature and occupancy factors have their conventional crystallographic
definitions, with units defined in the model space declaration. Atoms,
sites, temperature-factors, occupancies and alternate-conformation-ids
are parallel arrays, i.e. the have the same number of values as given by
number-of-points. Conformation ensembles represent distinct correlated-
disorder subsets of the coordinates. They will be present only for certain
"views" of PDB structures, as described above. Their derivation from PDB-
supplied "alternate-conformation" ids is described below.
-->
<!ELEMENT Coordinates_atomic (Atomic-coordinates)>
<!--
Literal surface coordinates define the chemical components whose structure
is described by a surface, and the surface itself. The surface may be
either a regular geometric solid or a triangle-mesh of arbitrary shape.
-->
<!ELEMENT Coordinates_surface (Surface-coordinates)>
<!--
Literal density coordinates define the chemical components whose structure
is described by a density grid, parameters of this grid, and density values.
-->
<!ELEMENT Coordinates_density (Density-coordinates)>
<!--
Literal atomic coordinate values give location, occupancy and order
parameters, and a pointer to a specific atom defined in the biostruc graph.
Temperature and occupancy factors have their conventional crystallographic
definitions, with units defined in the model space declaration. Atoms,
sites, temperature-factors, occupancies and alternate-conformation-ids
are parallel arrays, i.e. the have the same number of values as given by
number-of-points. Conformation ensembles represent distinct correlated-
disorder subsets of the coordinates. They will be present only for certain
"views" of PDB structures, as described above. Their derivation from PDB-
supplied "alternate-conformation" ids is described below.
-->
<!ELEMENT Atomic-coordinates (
Atomic-coordinates_number-of-points,
Atomic-coordinates_atoms,
Atomic-coordinates_sites,
Atomic-coordinates_temperature-factors?,
Atomic-coordinates_occupancies?,
Atomic-coordinates_alternate-conf-ids?,
Atomic-coordinates_conf-ensembles?)>
<!ELEMENT Atomic-coordinates_number-of-points (%INTEGER;)>
<!ELEMENT Atomic-coordinates_atoms (Atom-pntrs)>
<!--
The atoms whose location is described by each coordinate are identified
via a hierarchical pointer to the chemical graph of the biomolecular
assembly. Coordinates may be matched with atoms in the chemical structure
by the values of the molecule, residue and atom id's given here, which
match exactly the items of the same type defined in Biostruc-graph.
Coordinates are given as integer values, with a scale factor to convert
to real values for each x, y or z, in the units indicated in model-space.
Integer values must be divided by the the scale factor. This use of integer
values reduces the ASN.1 stream size. The scale factors for temperature
factors and occupancies are given separately, but must be used in the same
fashion to produce properly scaled real values.
-->
<!ELEMENT Atomic-coordinates_sites (Model-space-points)>
<!ELEMENT Atomic-coordinates_temperature-factors (Atomic-temperature-factors)>
<!ELEMENT Atomic-coordinates_occupancies (Atomic-occupancies)>
<!--
An alternate conformation id is optionally associated with each coordinate.
Aside from corrections due to the validation checks described above, the
contents of MMDB Alternate-conformation-ids are identical to the PDB
"alternate conformation" field.
-->
<!ELEMENT Atomic-coordinates_alternate-conf-ids (Alternate-conformation-ids)>
<!ELEMENT Atomic-coordinates_conf-ensembles (Conformation-ensemble*)>
<!--
The atoms whose location is described by each coordinate are identified
via a hierarchical pointer to the chemical graph of the biomolecular
assembly. Coordinates may be matched with atoms in the chemical structure
by the values of the molecule, residue and atom id's given here, which
match exactly the items of the same type defined in Biostruc-graph.
Coordinates are given as integer values, with a scale factor to convert
to real values for each x, y or z, in the units indicated in model-space.
Integer values must be divided by the the scale factor. This use of integer
values reduces the ASN.1 stream size. The scale factors for temperature
factors and occupancies are given separately, but must be used in the same
fashion to produce properly scaled real values.
-->
<!ELEMENT Model-space-points (
Model-space-points_scale-factor,
Model-space-points_x,
Model-space-points_y,
Model-space-points_z)>
<!ELEMENT Model-space-points_scale-factor (%INTEGER;)>
<!ELEMENT Model-space-points_x (Model-space-points_x_E*)>
<!ELEMENT Model-space-points_x_E (%INTEGER;)>
<!ELEMENT Model-space-points_y (Model-space-points_y_E*)>
<!ELEMENT Model-space-points_y_E (%INTEGER;)>
<!ELEMENT Model-space-points_z (Model-space-points_z_E*)>
<!ELEMENT Model-space-points_z_E (%INTEGER;)>
<!ELEMENT Atomic-temperature-factors (
Atomic-temperature-factors_isotropic |
Atomic-temperature-factors_anisotropic)>
<!ELEMENT Atomic-temperature-factors_isotropic (Isotropic-temperature-factors)>
<!ELEMENT Atomic-temperature-factors_anisotropic (Anisotropic-temperature-factors)>
<!ELEMENT Isotropic-temperature-factors (
Isotropic-temperature-factors_scale-factor,
Isotropic-temperature-factors_b)>
<!ELEMENT Isotropic-temperature-factors_scale-factor (%INTEGER;)>
<!ELEMENT Isotropic-temperature-factors_b (Isotropic-temperature-factors_b_E*)>
<!ELEMENT Isotropic-temperature-factors_b_E (%INTEGER;)>
<!ELEMENT Anisotropic-temperature-factors (
Anisotropic-temperature-factors_scale-factor,
Anisotropic-temperature-factors_b-11,
Anisotropic-temperature-factors_b-12,
Anisotropic-temperature-factors_b-13,
Anisotropic-temperature-factors_b-22,
Anisotropic-temperature-factors_b-23,
Anisotropic-temperature-factors_b-33)>
<!ELEMENT Anisotropic-temperature-factors_scale-factor (%INTEGER;)>
<!ELEMENT Anisotropic-temperature-factors_b-11 (Anisotropic-temperature-factors_b-11_E*)>
<!ELEMENT Anisotropic-temperature-factors_b-11_E (%INTEGER;)>
<!ELEMENT Anisotropic-temperature-factors_b-12 (Anisotropic-temperature-factors_b-12_E*)>
<!ELEMENT Anisotropic-temperature-factors_b-12_E (%INTEGER;)>
<!ELEMENT Anisotropic-temperature-factors_b-13 (Anisotropic-temperature-factors_b-13_E*)>
<!ELEMENT Anisotropic-temperature-factors_b-13_E (%INTEGER;)>
<!ELEMENT Anisotropic-temperature-factors_b-22 (Anisotropic-temperature-factors_b-22_E*)>
<!ELEMENT Anisotropic-temperature-factors_b-22_E (%INTEGER;)>
<!ELEMENT Anisotropic-temperature-factors_b-23 (Anisotropic-temperature-factors_b-23_E*)>
<!ELEMENT Anisotropic-temperature-factors_b-23_E (%INTEGER;)>
<!ELEMENT Anisotropic-temperature-factors_b-33 (Anisotropic-temperature-factors_b-33_E*)>
<!ELEMENT Anisotropic-temperature-factors_b-33_E (%INTEGER;)>
<!ELEMENT Atomic-occupancies (
Atomic-occupancies_scale-factor,
Atomic-occupancies_o)>
<!ELEMENT Atomic-occupancies_scale-factor (%INTEGER;)>
<!ELEMENT Atomic-occupancies_o (Atomic-occupancies_o_E*)>
<!ELEMENT Atomic-occupancies_o_E (%INTEGER;)>
<!--
An alternate conformation id is optionally associated with each coordinate.
Aside from corrections due to the validation checks described above, the
contents of MMDB Alternate-conformation-ids are identical to the PDB
"alternate conformation" field.
-->
<!ELEMENT Alternate-conformation-ids (Alternate-conformation-id*)>
<!ELEMENT Alternate-conformation-id (#PCDATA)>
<!--
Correlated disorder ensemble is defined by a set of alternate conformation
id's which identify coordinates relevant to that ensemble. These are
defined from the validated and corrected contents of the PDB "alternate
conformation" field as described above. A given ensemble, for example, may
consist of atom sites flagged by " " and "A" Alternate-conformation-ids.
Names for ensembles are constructed from these flags. This example would be
named, in its description, "PDB Ensemble blank plus A".
Note that this interpretation is consistent with common PDB usage of the
"alternate conformation" field, but that PDB specifications do not formally
distinguish between correlated and uncorrelated disorder in crystallographic
models. Ensembles identified in MMDB thus may not correspond to the meaning
intended by PDB or the depositor. No information is lost, however, and
if the intended meaning is known alternative ensemble descriptions may be
reconstructed directly from the Alternate-conformation-ids.
Note that correlated disorder as defined here is allowed within an atomic
coordinate set but not between the multiple sets which may define a model.
Multiple sets within the same model are intended as a means to represent
assemblies modeled from different experimentally determined structures,
where correlated disorder between coordinate sets is not relevant.
-->
<!ELEMENT Conformation-ensemble (
Conformation-ensemble_name,
Conformation-ensemble_alt-conf-ids)>
<!ELEMENT Conformation-ensemble_name (#PCDATA)>
<!ELEMENT Conformation-ensemble_alt-conf-ids (Alternate-conformation-id*)>
<!--
Literal surface coordinates define the chemical components whose structure
is described by a surface, and the surface itself. The surface may be
either a regular geometric solid or a triangle-mesh of arbitrary shape.
-->
<!ELEMENT Surface-coordinates (
Surface-coordinates_contents,
Surface-coordinates_surface)>
<!ELEMENT Surface-coordinates_contents (Chem-graph-pntrs)>
<!ELEMENT Surface-coordinates_surface (
Surface-coordinates_surface_sphere |
Surface-coordinates_surface_cone |
Surface-coordinates_surface_cylinder |
Surface-coordinates_surface_brick |
Surface-coordinates_surface_tmesh |
Surface-coordinates_surface_triangles)>
<!ELEMENT Surface-coordinates_surface_sphere (Sphere)>
<!ELEMENT Surface-coordinates_surface_cone (Cone)>
<!ELEMENT Surface-coordinates_surface_cylinder (Cylinder)>
<!ELEMENT Surface-coordinates_surface_brick (Brick)>
<!ELEMENT Surface-coordinates_surface_tmesh (T-mesh)>
<!ELEMENT Surface-coordinates_surface_triangles (Triangles)>
<!ELEMENT T-mesh (
T-mesh_number-of-points,
T-mesh_scale-factor,
T-mesh_swap,
T-mesh_x,
T-mesh_y,
T-mesh_z)>
<!ELEMENT T-mesh_number-of-points (%INTEGER;)>
<!ELEMENT T-mesh_scale-factor (%INTEGER;)>
<!ELEMENT T-mesh_swap (T-mesh_swap_E*)>
<!ELEMENT T-mesh_swap_E EMPTY>
<!ATTLIST T-mesh_swap_E value ( true | false ) #REQUIRED >
<!ELEMENT T-mesh_x (T-mesh_x_E*)>
<!ELEMENT T-mesh_x_E (%INTEGER;)>
<!ELEMENT T-mesh_y (T-mesh_y_E*)>
<!ELEMENT T-mesh_y_E (%INTEGER;)>
<!ELEMENT T-mesh_z (T-mesh_z_E*)>
<!ELEMENT T-mesh_z_E (%INTEGER;)>
<!ELEMENT Triangles (
Triangles_number-of-points,
Triangles_scale-factor,
Triangles_x,
Triangles_y,
Triangles_z,
Triangles_number-of-triangles,
Triangles_v1,
Triangles_v2,
Triangles_v3)>
<!ELEMENT Triangles_number-of-points (%INTEGER;)>
<!ELEMENT Triangles_scale-factor (%INTEGER;)>
<!ELEMENT Triangles_x (Triangles_x_E*)>
<!ELEMENT Triangles_x_E (%INTEGER;)>
<!ELEMENT Triangles_y (Triangles_y_E*)>
<!ELEMENT Triangles_y_E (%INTEGER;)>
<!ELEMENT Triangles_z (Triangles_z_E*)>
<!ELEMENT Triangles_z_E (%INTEGER;)>
<!ELEMENT Triangles_number-of-triangles (%INTEGER;)>
<!ELEMENT Triangles_v1 (Triangles_v1_E*)>
<!ELEMENT Triangles_v1_E (%INTEGER;)>
<!ELEMENT Triangles_v2 (Triangles_v2_E*)>
<!ELEMENT Triangles_v2_E (%INTEGER;)>
<!ELEMENT Triangles_v3 (Triangles_v3_E*)>
<!ELEMENT Triangles_v3_E (%INTEGER;)>
<!--
Literal density coordinates define the chemical components whose structure
is described by a density grid, parameters of this grid, and density values.
-->
<!ELEMENT Density-coordinates (
Density-coordinates_contents,
Density-coordinates_grid-corners,
Density-coordinates_grid-steps-x,
Density-coordinates_grid-steps-y,
Density-coordinates_grid-steps-z,
Density-coordinates_fastest-varying,
Density-coordinates_slowest-varying,
Density-coordinates_scale-factor,
Density-coordinates_density)>
<!ELEMENT Density-coordinates_contents (Chem-graph-pntrs)>
<!ELEMENT Density-coordinates_grid-corners (Brick)>
<!ELEMENT Density-coordinates_grid-steps-x (%INTEGER;)>
<!ELEMENT Density-coordinates_grid-steps-y (%INTEGER;)>
<!ELEMENT Density-coordinates_grid-steps-z (%INTEGER;)>
<!ELEMENT Density-coordinates_fastest-varying %ENUM;>
<!ATTLIST Density-coordinates_fastest-varying value (
x |
y |
z
) #REQUIRED >
<!ELEMENT Density-coordinates_slowest-varying %ENUM;>
<!ATTLIST Density-coordinates_slowest-varying value (
x |
y |
z
) #REQUIRED >
<!ELEMENT Density-coordinates_scale-factor (%INTEGER;)>
<!ELEMENT Density-coordinates_density (Density-coordinates_density_E*)>
<!ELEMENT Density-coordinates_density_E (%INTEGER;)>
|