java.lang.Object
- org.rcsb.cif.model.BaseCategory
- - org.rcsb.cif.model.generated.AtomSites

All Implemented Interfaces:

Category
```
@Generated("org.rcsb.cif.generator.SchemaGenerator")
public class AtomSites
extends BaseCategory
```
Data items in the ATOM_SITES category record details about the crystallographic cell and cell transformations, which are common to all atom sites.

Field Summary
- Fields inherited from class org.rcsb.cif.model.BaseCategory
  isText, textFields

Constructor Summary

Constructors
Constructor	Description
`AtomSites(String name)`
`AtomSites(String name, int rowCount, Object[] encodedColumns)`
`AtomSites(String name, Map<String,Column> columns)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`FloatColumn`	`getCartnTransfMatrix11()`	The elements of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category.
`FloatColumn`	`getCartnTransfMatrix12()`	The elements of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category.
`FloatColumn`	`getCartnTransfMatrix13()`	The elements of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category.
`FloatColumn`	`getCartnTransfMatrix21()`	The elements of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category.
`FloatColumn`	`getCartnTransfMatrix22()`	The elements of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category.
`FloatColumn`	`getCartnTransfMatrix23()`	The elements of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category.
`FloatColumn`	`getCartnTransfMatrix31()`	The elements of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category.
`FloatColumn`	`getCartnTransfMatrix32()`	The elements of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category.
`FloatColumn`	`getCartnTransfMatrix33()`	The elements of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category.
`StrColumn`	`getCartnTransformAxes()`	A description of the relative alignment of the crystal cell axes to the Cartesian orthogonal axes as applied in the transformation matrix _atom_sites.Cartn_transf_matrix[][].
`FloatColumn`	`getCartnTransfVector1()`	The elements of the three-element vector used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category.
`FloatColumn`	`getCartnTransfVector2()`	The elements of the three-element vector used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category.
`FloatColumn`	`getCartnTransfVector3()`	The elements of the three-element vector used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category.
`StrColumn`	`getEntryId()`	This data item is a pointer to _entry.id in the ENTRY category.
`FloatColumn`	`getFractTransfMatrix11()`	The elements of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category.
`FloatColumn`	`getFractTransfMatrix12()`	The elements of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category.
`FloatColumn`	`getFractTransfMatrix13()`	The elements of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category.
`FloatColumn`	`getFractTransfMatrix21()`	The elements of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category.
`FloatColumn`	`getFractTransfMatrix22()`	The elements of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category.
`FloatColumn`	`getFractTransfMatrix23()`	The elements of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category.
`FloatColumn`	`getFractTransfMatrix31()`	The elements of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category.
`FloatColumn`	`getFractTransfMatrix32()`	The elements of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category.
`FloatColumn`	`getFractTransfMatrix33()`	The elements of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category.
`FloatColumn`	`getFractTransfVector1()`	The elements of the three-element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category.
`FloatColumn`	`getFractTransfVector2()`	The elements of the three-element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category.
`FloatColumn`	`getFractTransfVector3()`	The elements of the three-element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category.
`StrColumn`	`getSolutionHydrogens()`	This code identifies the method used to locate the hydrogen atoms.
`StrColumn`	`getSolutionPrimary()`	This code identifies the method used to locate the initial atom sites.
`StrColumn`	`getSolutionSecondary()`	This code identifies the method used to locate the non-hydrogen-atom sites not found by _atom_sites.solution_primary.
`StrColumn`	`getSpecialDetails()`	Additional information about the atomic coordinates not coded elsewhere in the CIF.

Methods inherited from class org.rcsb.cif.model.BaseCategory
getBinaryColumn, getCategoryName, getColumn, getColumnNames, getRowCount, isDefined

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.rcsb.cif.model.Category
columnNames, columns, get

- Constructor Detail
  - AtomSites
```
public AtomSites(String name,
                 Map<String,Column> columns)
```
  - AtomSites
```
public AtomSites(String name,
                 int rowCount,
                 Object[] encodedColumns)
```
  - AtomSites
```
public AtomSites(String name)
```
- Method Detail
  - getEntryId
```
public StrColumn getEntryId()
```
    This data item is a pointer to _entry.id in the ENTRY category.
    
    Returns:
    
    StrColumn
  - getCartnTransfMatrix11
```
public FloatColumn getCartnTransfMatrix11()
```
    The elements of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|
    
    Returns:
    
    FloatColumn
  - getCartnTransfMatrix12
```
public FloatColumn getCartnTransfMatrix12()
```
    The elements of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|
    
    Returns:
    
    FloatColumn
  - getCartnTransfMatrix13
```
public FloatColumn getCartnTransfMatrix13()
```
    The elements of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|
    
    Returns:
    
    FloatColumn
  - getCartnTransfMatrix21
```
public FloatColumn getCartnTransfMatrix21()
```
    The elements of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|
    
    Returns:
    
    FloatColumn
  - getCartnTransfMatrix22
```
public FloatColumn getCartnTransfMatrix22()
```
    The elements of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|
    
    Returns:
    
    FloatColumn
  - getCartnTransfMatrix23
```
public FloatColumn getCartnTransfMatrix23()
```
    The elements of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|
    
    Returns:
    
    FloatColumn
  - getCartnTransfMatrix31
```
public FloatColumn getCartnTransfMatrix31()
```
    The elements of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|
    
    Returns:
    
    FloatColumn
  - getCartnTransfMatrix32
```
public FloatColumn getCartnTransfMatrix32()
```
    The elements of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|
    
    Returns:
    
    FloatColumn
  - getCartnTransfMatrix33
```
public FloatColumn getCartnTransfMatrix33()
```
    The elements of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|
    
    Returns:
    
    FloatColumn
  - getCartnTransfVector1
```
public FloatColumn getCartnTransfVector1()
```
    The elements of the three-element vector used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The rotation matrix is defined in _atom_sites.Cartn_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|
    
    Returns:
    
    FloatColumn
  - getCartnTransfVector2
```
public FloatColumn getCartnTransfVector2()
```
    The elements of the three-element vector used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The rotation matrix is defined in _atom_sites.Cartn_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|
    
    Returns:
    
    FloatColumn
  - getCartnTransfVector3
```
public FloatColumn getCartnTransfVector3()
```
    The elements of the three-element vector used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The rotation matrix is defined in _atom_sites.Cartn_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3|
    
    Returns:
    
    FloatColumn
  - getCartnTransformAxes
```
public StrColumn getCartnTransformAxes()
```
    A description of the relative alignment of the crystal cell axes to the Cartesian orthogonal axes as applied in the transformation matrix _atom_sites.Cartn_transf_matrix[][].
    
    Returns:
    
    StrColumn
  - getFractTransfMatrix11
```
public FloatColumn getFractTransfMatrix11()
```
    The elements of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|
    
    Returns:
    
    FloatColumn
  - getFractTransfMatrix12
```
public FloatColumn getFractTransfMatrix12()
```
    The elements of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|
    
    Returns:
    
    FloatColumn
  - getFractTransfMatrix13
```
public FloatColumn getFractTransfMatrix13()
```
    The elements of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|
    
    Returns:
    
    FloatColumn
  - getFractTransfMatrix21
```
public FloatColumn getFractTransfMatrix21()
```
    The elements of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|
    
    Returns:
    
    FloatColumn
  - getFractTransfMatrix22
```
public FloatColumn getFractTransfMatrix22()
```
    The elements of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|
    
    Returns:
    
    FloatColumn
  - getFractTransfMatrix23
```
public FloatColumn getFractTransfMatrix23()
```
    The elements of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|
    
    Returns:
    
    FloatColumn
  - getFractTransfMatrix31
```
public FloatColumn getFractTransfMatrix31()
```
    The elements of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|
    
    Returns:
    
    FloatColumn
  - getFractTransfMatrix32
```
public FloatColumn getFractTransfMatrix32()
```
    The elements of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|
    
    Returns:
    
    FloatColumn
  - getFractTransfMatrix33
```
public FloatColumn getFractTransfMatrix33()
```
    The elements of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|
    
    Returns:
    
    FloatColumn
  - getFractTransfVector1
```
public FloatColumn getFractTransfVector1()
```
    The elements of the three-element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x3 rotation is defined in _atom_sites.fract_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|
    
    Returns:
    
    FloatColumn
  - getFractTransfVector2
```
public FloatColumn getFractTransfVector2()
```
    The elements of the three-element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x3 rotation is defined in _atom_sites.fract_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|
    
    Returns:
    
    FloatColumn
  - getFractTransfVector3
```
public FloatColumn getFractTransfVector3()
```
    The elements of the three-element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x3 rotation is defined in _atom_sites.fract_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3|
    
    Returns:
    
    FloatColumn
  - getSolutionPrimary
```
public StrColumn getSolutionPrimary()
```
    This code identifies the method used to locate the initial atom sites. *** This data item would not in general be used in a macromolecular data block. ***
    
    Returns:
    
    StrColumn
  - getSolutionSecondary
```
public StrColumn getSolutionSecondary()
```
    This code identifies the method used to locate the non-hydrogen-atom sites not found by _atom_sites.solution_primary. *** This data item would not in general be used in a macromolecular data block. ***
    
    Returns:
    
    StrColumn
  - getSolutionHydrogens
```
public StrColumn getSolutionHydrogens()
```
    This code identifies the method used to locate the hydrogen atoms. *** This data item would not in general be used in a macromolecular data block. ***
    
    Returns:
    
    StrColumn
  - getSpecialDetails
```
public StrColumn getSpecialDetails()
```
    Additional information about the atomic coordinates not coded elsewhere in the CIF.
    
    Returns:
    
    StrColumn

Class AtomSites

Field Summary

Fields inherited from class org.rcsb.cif.model.BaseCategory

Constructor Summary

Method Summary

Methods inherited from class org.rcsb.cif.model.BaseCategory

Methods inherited from class java.lang.Object

Methods inherited from interface org.rcsb.cif.model.Category

Constructor Detail

AtomSites

AtomSites

AtomSites

Method Detail

getEntryId

getCartnTransfMatrix11

getCartnTransfMatrix12

getCartnTransfMatrix13

getCartnTransfMatrix21

getCartnTransfMatrix22

getCartnTransfMatrix23

getCartnTransfMatrix31

getCartnTransfMatrix32

getCartnTransfMatrix33

getCartnTransfVector1

getCartnTransfVector2

getCartnTransfVector3

getCartnTransformAxes

getFractTransfMatrix11

getFractTransfMatrix12

getFractTransfMatrix13

getFractTransfMatrix21

getFractTransfMatrix22

getFractTransfMatrix23

getFractTransfMatrix31

getFractTransfMatrix32

getFractTransfMatrix33

getFractTransfVector1

getFractTransfVector2

getFractTransfVector3

getSolutionPrimary

getSolutionSecondary

getSolutionHydrogens

getSpecialDetails