Package org.rcsb.cif.model.generated

Class PhasingMIR

java.lang.Object

org.rcsb.cif.model.BaseCategory

org.rcsb.cif.model.generated.PhasingMIR

All Implemented Interfaces:

Category

@Generated("org.rcsb.cif.generator.SchemaGenerator")
public class PhasingMIR
extends BaseCategory

Data items in the PHASING_MIR category record details about the phasing of the structure where methods involving isomorphous replacement are involved. All isomorphous-replacement-based techniques are covered by this category, including single isomorphous replacement (SIR), multiple isomorphous replacement (MIR) and single or multiple isomorphous replacement plus anomalous scattering (SIRAS, MIRAS).

Field Summary

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

isText, textFields

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
StrColumn	getDetails()	A description of special aspects of the isomorphous-replacement phasing.
FloatColumn	getDResHigh()	The lowest value in angstroms for the interplanar spacings for the reflection data used for the native data set.
FloatColumn	getDResLow()	The highest value in angstroms for the interplanar spacings for the reflection data used for the native data set.
StrColumn	getEntryId()	This data item is a pointer to _entry.id in the ENTRY category.
FloatColumn	getFOM()	The mean value of the figure of merit m for all reflections phased in the native data set.
FloatColumn	getFOMAcentric()	The mean value of the figure of merit m for the acentric reflections phased in the native data set.
FloatColumn	getFOMCentric()	The mean value of the figure of merit m for the centric reflections phased in the native data set.
StrColumn	getMethod()	A description of the MIR phasing method applied to phase this structure.
IntColumn	getPdbxNumberDerivatives()	The number of derivatives used in this phasing experiment.
IntColumn	getReflns()	The total number of reflections phased in the native data set.
IntColumn	getReflnsAcentric()	The number of acentric reflections phased in the native data set.
IntColumn	getReflnsCentric()	The number of centric reflections phased in the native data set.
StrColumn	getReflnsCriterion()	Criterion used to limit the reflections used in the phasing calculations.

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

PhasingMIR

public PhasingMIR(String name,
                  Map<String,Column> columns)

PhasingMIR

public PhasingMIR(String name,
                  int rowCount,
                  Object[] encodedColumns)

PhasingMIR

public PhasingMIR(String name)

Method Detail

getDetails

public StrColumn getDetails()

A description of special aspects of the isomorphous-replacement phasing.

Returns:

StrColumn

getDResHigh

public FloatColumn getDResHigh()

The lowest value in angstroms for the interplanar spacings for the reflection data used for the native data set. This is called the highest resolution.

Returns:

FloatColumn

getDResLow

public FloatColumn getDResLow()

The highest value in angstroms for the interplanar spacings for the reflection data used for the native data set. This is called the lowest resolution.

Returns:

FloatColumn

getEntryId

public StrColumn getEntryId()

This data item is a pointer to _entry.id in the ENTRY category.

Returns:

StrColumn

getFOM

public FloatColumn getFOM()

The mean value of the figure of merit m for all reflections phased in the native data set. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that the phase angle a is correct the integral is taken over the range alpha = 0 to 2 pi.

Returns:

FloatColumn

getFOMAcentric

public FloatColumn getFOMAcentric()

The mean value of the figure of merit m for the acentric reflections phased in the native data set. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that the phase angle a is correct the integral is taken over the range alpha = 0 to 2 pi.

Returns:

FloatColumn

getFOMCentric

public FloatColumn getFOMCentric()

The mean value of the figure of merit m for the centric reflections phased in the native data set. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that the phase angle a is correct the integral is taken over the range alpha = 0 to 2 pi.

Returns:

FloatColumn

getMethod

public StrColumn getMethod()

A description of the MIR phasing method applied to phase this structure. Note that this is not the computer program used, which is described in the SOFTWARE category, but rather the method itself. This data item should be used to describe significant methodological options used within the MIR phasing program.

Returns:

StrColumn

getReflns

public IntColumn getReflns()

The total number of reflections phased in the native data set.

Returns:

IntColumn

getReflnsAcentric

public IntColumn getReflnsAcentric()

The number of acentric reflections phased in the native data set.

Returns:

IntColumn

getReflnsCentric

public IntColumn getReflnsCentric()

The number of centric reflections phased in the native data set.

Returns:

IntColumn

getReflnsCriterion

public StrColumn getReflnsCriterion()

Criterion used to limit the reflections used in the phasing calculations.

Returns:

StrColumn

getPdbxNumberDerivatives

public IntColumn getPdbxNumberDerivatives()

The number of derivatives used in this phasing experiment.

Returns:

IntColumn