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Commit 8061a6a1 authored by Pierre Gruet's avatar Pierre Gruet
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New upstream version 6.0.0

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.github/workflows/build.yml
+ 9
− 8
View file @ 8061a6a1
name: Build
name: SonarCloud
on:
push:
branches:
......@@ -7,24 +7,25 @@ on:
types: [opened, synchronize, reopened]
jobs:
build:
name: Build
name: Build and analyze
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
with:
fetch-depth: 0 # Shallow clones should be disabled for a better relevancy of analysis
- name: Set up JDK 11
uses: actions/setup-java@v1
- name: Set up JDK 17
uses: actions/setup-java@v3
with:
java-version: 11
java-version: 17
distribution: 'zulu' # Alternative distribution options are available.
- name: Cache SonarCloud packages
uses: actions/cache@v1
uses: actions/cache@v3
with:
path: ~/.sonar/cache
key: ${{ runner.os }}-sonar
restore-keys: ${{ runner.os }}-sonar
- name: Cache Maven packages
uses: actions/cache@v1
uses: actions/cache@v3
with:
path: ~/.m2
key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml') }}
......
CHANGELOG.md
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− 0
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......@@ -3,6 +3,19 @@ CIFTools Changelog
This project uses semantic versioning. Furthermore, this project provides code that was generated from schemata. Any schema change that introduces a breaking change in the generated code is considered as breaking for the whole project. Additional information is provided below when this occurs (named `Breaking schema changes`). Most of these occur in experimental categories and are unlikely to affect your code. `Breaking API changes` will be avoided starting with version 1.0.0.
ciftools-java 6.0.0 - March 2024
-------------
### Breaking schema changes
* cif-core:
* renaming of `atom_site` tensors
* `atom_type_scat_versus_stol_list` from float to String
* drops `citation_author_key`
* drops `citation_editor_id`
* `journal_index_id` from int to String
* `refln_f_complex_su` from float to String
* mmCIF/ihm-extension:
* drops `ihm_entry_collection_mapping.id`
ciftools-java 5.0.2 - October 2023
-------------
### Bug fixes
......
README.md
+ 1
− 1
View file @ 8061a6a1
......@@ -14,7 +14,7 @@ CIFTools is distributed by maven. To get started, append your `pom.xml` by:
<dependency>
<groupId>org.rcsb</groupId>
<artifactId>ciftools-java</artifactId>
<version>5.0.1</version>
<version>6.0.0</version>
</dependency>
```
......
pom.xml
+ 8
− 8
View file @ 8061a6a1
......@@ -3,7 +3,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>org.rcsb</groupId>
<artifactId>ciftools-java</artifactId>
<version>5.0.2</version>
<version>6.0.0</version>
<packaging>jar</packaging>
<description>
A Java library for handling text and binary CIF files.
......@@ -35,7 +35,7 @@
<connection>scm:git:git://github.com/rcsb/ciftools-java.git</connection>
<developerConnection>scm:git:git@github.com:rcsb/ciftools-java.git</developerConnection>
<url>https://github.com/rcsb/ciftools-java</url>
<tag>ciftools-java-5.0.2</tag>
<tag>ciftools-java-6.0.0</tag>
</scm>
<dependencies>
......@@ -50,7 +50,7 @@
<dependency>
<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
<version>2.10</version>
<version>2.10.1</version>
<scope>compile</scope>
</dependency>
......@@ -58,7 +58,7 @@
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-api</artifactId>
<version>5.9.0</version>
<version>5.10.2</version>
<scope>test</scope>
</dependency>
......@@ -76,7 +76,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.10.1</version>
<version>3.13.0</version>
<configuration>
<source>11</source>
<target>11</target>
......@@ -120,7 +120,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-gpg-plugin</artifactId>
<version>3.0.1</version>
<version>3.2.1</version>
<executions>
<execution>
<id>sign-artifacts</id>
......@@ -143,7 +143,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>3.2.1</version>
<version>3.3.0</version>
<executions>
<execution>
<id>attach-sources</id>
......@@ -158,7 +158,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>3.4.0</version>
<version>3.6.3</version>
<configuration>
<source>11</source>
</configuration>
......
pom.xml.releaseBackup 0 → 100644
+ 178
− 0
View file @ 8061a6a1
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>org.rcsb</groupId>
<artifactId>ciftools-java</artifactId>
<version>5.0.3-SNAPSHOT</version>
<packaging>jar</packaging>
<description>
A Java library for handling text and binary CIF files.
</description>
<name>ciftools-java</name>
<url>https://github.com/rcsb/ciftools-java</url>
<organization>
<name>RCSB PDB</name>
<url>https://www.rcsb.org/</url>
</organization>
<licenses>
<license>
<name>MIT License</name>
<url>https://www.opensource.org/licenses/mit-license.php</url>
</license>
</licenses>
<developers>
<developer>
<name>Sebastian Bittrich</name>
<email>sebastian.bittrich@rcsb.org</email>
<organization>RCSB PDB</organization>
<organizationUrl>https://www.rcsb.org</organizationUrl>
</developer>
</developers>
<scm>
<connection>scm:git:git://github.com/rcsb/ciftools-java.git</connection>
<developerConnection>scm:git:git@github.com:rcsb/ciftools-java.git</developerConnection>
<url>https://github.com/rcsb/ciftools-java</url>
<tag>HEAD</tag>
</scm>
<dependencies>
<!-- provides @Generated -->
<dependency>
<groupId>javax.annotation</groupId>
<artifactId>javax.annotation-api</artifactId>
<version>1.3.2</version>
</dependency>
<!-- optional functionality to read json configs -->
<dependency>
<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
<version>2.10.1</version>
<scope>compile</scope>
</dependency>
<!-- test dependencies -->
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-api</artifactId>
<version>5.10.2</version>
<scope>test</scope>
</dependency>
</dependencies>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.build.targetEncoding>UTF-8</project.build.targetEncoding>
<sonar.organization>rcsb</sonar.organization>
<sonar.host.url>https://sonarcloud.io</sonar.host.url>
</properties>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.13.0</version>
<configuration>
<source>11</source>
<target>11</target>
</configuration>
</plugin>
</plugins>
</build>
<!-- https://central.sonatype.org/pages/apache-maven.html -->
<!-- https://github.com/chhh/sonatype-ossrh-parent/blob/master/pom.xml -->
<distributionManagement>
<snapshotRepository>
<id>ossrh</id>
<url>https://oss.sonatype.org/content/repositories/snapshots</url>
</snapshotRepository>
<repository>
<id>ossrh</id>
<url>https://oss.sonatype.org/service/local/staging/deploy/maven2/</url>
</repository>
</distributionManagement>
<profiles>
<profile>
<id>release</id>
<build>
<plugins>
<!-- handles propagating the build to the staging repository -->
<plugin>
<groupId>org.sonatype.plugins</groupId>
<artifactId>nexus-staging-maven-plugin</artifactId>
<version>1.6.13</version>
<extensions>true</extensions>
<configuration>
<serverId>ossrh</serverId>
<nexusUrl>https://oss.sonatype.org/</nexusUrl>
<autoReleaseAfterClose>true</autoReleaseAfterClose>
</configuration>
</plugin>
<!-- signing of content to be published -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-gpg-plugin</artifactId>
<version>3.2.1</version>
<executions>
<execution>
<id>sign-artifacts</id>
<phase>verify</phase>
<goals>
<goal>sign</goal>
</goals>
<configuration>
<!-- This is necessary for gpg to not try to use the pinentry programs -->
<gpgArguments>
<arg>--pinentry-mode</arg>
<arg>loopback</arg>
</gpgArguments>
</configuration>
</execution>
</executions>
</plugin>
<!-- create source -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>3.3.0</version>
<executions>
<execution>
<id>attach-sources</id>
<goals>
<goal>jar-no-fork</goal>
</goals>
</execution>
</executions>
</plugin>
<!-- create javadoc -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>3.6.3</version>
<configuration>
<source>11</source>
</configuration>
<executions>
<execution>
<id>attach-javadocs</id>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
</profiles>
</project>
\ No newline at end of file
release.properties 0 → 100644
+ 27
− 0
View file @ 8061a6a1
#release configuration
#Tue Mar 19 12:10:16 PDT 2024
completedPhase=generate-release-poms
exec.activateProfiles=nexus,release
exec.pomFileName=pom.xml
exec.snapshotReleasePluginAllowed=false
pinExternals=false
preparationGoals=clean verify
project.dev.org.rcsb\:ciftools-java=6.0.1-SNAPSHOT
project.rel.org.rcsb\:ciftools-java=6.0.0
project.scm.org.rcsb\:ciftools-java.connection=scm\:git\:git\://github.com/rcsb/ciftools-java.git
project.scm.org.rcsb\:ciftools-java.developerConnection=scm\:git\:git@github.com\:rcsb/ciftools-java.git
project.scm.org.rcsb\:ciftools-java.tag=HEAD
project.scm.org.rcsb\:ciftools-java.url=https\://github.com/rcsb/ciftools-java
projectVersionPolicyConfig=<projectVersionPolicyConfig>${projectVersionPolicyConfig}</projectVersionPolicyConfig>\n
projectVersionPolicyId=default
pushChanges=true
releaseStrategyId=default
remoteTagging=true
scm.branchCommitComment=@{prefix} prepare branch @{releaseLabel}
scm.commentPrefix=[maven-release-plugin]
scm.developmentCommitComment=@{prefix} prepare for next development iteration
scm.releaseCommitComment=@{prefix} prepare release @{releaseLabel}
scm.rollbackCommitComment=@{prefix} rollback the release of @{releaseLabel}
scm.tag=ciftools-java-6.0.0
scm.tagNameFormat=@{project.artifactId}-@{project.version}
scm.url=scm\:git\:git@github.com\:rcsb/ciftools-java.git
src/main/java/org/rcsb/cif/schema/core/AtomAnalyticalMassLoss.java
+ 2
− 2
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......@@ -47,7 +47,7 @@ public class AtomAnalyticalMassLoss extends DelegatingCategory.DelegatingCifCore
* is represented by a negative value.
*
* This data name would be used to record mass loss on drying, or mass
* loss on ignitition, during, for example, fusion bead preparation for
* loss on ignition, during, for example, fusion bead preparation for
* XRF analysis.
* @return FloatColumn
*/
......@@ -77,7 +77,7 @@ public class AtomAnalyticalMassLoss extends DelegatingCategory.DelegatingCifCore
* The temperature, in kelvin, at which the mass loss was recorded
* as given by _atom_analytical_mass_loss.percent.
*
* This would be used to record the temperature of drying or ignitition,
* This would be used to record the temperature of drying or ignition,
* during, for example, fusion bead preparation for XRF analysis.
* @return FloatColumn
*/
......
src/main/java/org/rcsb/cif/schema/core/AtomScatVersusStol.java 0 → 100644
+ 57
− 0
View file @ 8061a6a1
package org.rcsb.cif.schema.core;
import org.rcsb.cif.model.*;
import org.rcsb.cif.schema.*;
import javax.annotation.Generated;
/**
* The CATEGORY of data items used to list atomic scattering factor values for
* use in crystallographic structure studies.
*/
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class AtomScatVersusStol extends DelegatingCategory.DelegatingCifCoreCategory {
private static final String NAME = "atom_scat_versus_stol";
public AtomScatVersusStol(CifCoreBlock parentBlock) {
super(NAME, parentBlock);
}
/**
* The identity of the atom specie(s) representing this atom type.
* See _atom_type.symbol for further details.
* @return StrColumn
*/
public StrColumn getAtomType() {
return new DelegatingStrColumn(parentBlock.getColumn("atom_scat_versus_stol_atom_type"));
}
/**
* The value of the scattering factor of a particular atom type at a particular
* stol value.
* @return FloatColumn
*/
public FloatColumn getScatValue() {
return new DelegatingFloatColumn(parentBlock.getColumn("atom_scat_versus_stol_scat_value"));
}
/**
* Standard uncertainty of _atom_scat_versus_stol.scat_value.
* @return FloatColumn
*/
public FloatColumn getScatValueSu() {
return new DelegatingFloatColumn(parentBlock.getColumn("atom_scat_versus_stol_scat_value_su"));
}
/**
* The value of sin(θ)/λ (sin theta over lambda, stol) to which the
* accompanying atom symbol and scattering factor value correspond to.
*
* A regularly spaced grid is strongly recommended.
* @return FloatColumn
*/
public FloatColumn getStolValue() {
return new DelegatingFloatColumn(parentBlock.getColumn("atom_scat_versus_stol_stol_value"));
}
}
\ No newline at end of file
src/main/java/org/rcsb/cif/schema/core/AtomSite.java
+ 442
− 255
View file @ 8061a6a1
This diff is collapsed.
src/main/java/org/rcsb/cif/schema/core/AtomSiteAniso.java
+ 434
− 126
View file @ 8061a6a1
This diff is collapsed.
src/main/java/org/rcsb/cif/schema/core/AtomSites.java
+ 3
− 3
View file @ 8061a6a1
......@@ -25,7 +25,7 @@ public class AtomSites extends DelegatingCategory.DelegatingCifCoreCategory {
* *_hydrogens code identifies how the hydrogen sites were located.
*
* Ref: Sheldrick, G. M., Hauptman, H. A., Weeks, C. M.,
* Miller, R. and Us\'on, I. (2001). Ab initio phasing.
* Miller, R. and Usón, I. (2001). Ab initio phasing.
* In International Tables for Crystallography,
* Vol. F. Crystallography of biological macromolecules,
* edited by M. G. Rossmann and E. Arnold, ch. 16.1.
......@@ -44,7 +44,7 @@ public class AtomSites extends DelegatingCategory.DelegatingCifCoreCategory {
* *_hydrogens code identifies how the hydrogen sites were located.
*
* Ref: Sheldrick, G. M., Hauptman, H. A., Weeks, C. M.,
* Miller, R. and Us\'on, I. (2001). Ab initio phasing.
* Miller, R. and Usón, I. (2001). Ab initio phasing.
* In International Tables for Crystallography,
* Vol. F. Crystallography of biological macromolecules,
* edited by M. G. Rossmann and E. Arnold, ch. 16.1.
......@@ -63,7 +63,7 @@ public class AtomSites extends DelegatingCategory.DelegatingCifCoreCategory {
* *_hydrogens code identifies how the hydrogen sites were located.
*
* Ref: Sheldrick, G. M., Hauptman, H. A., Weeks, C. M.,
* Miller, R. and Us\'on, I. (2001). Ab initio phasing.
* Miller, R. and Usón, I. (2001). Ab initio phasing.
* In International Tables for Crystallography,
* Vol. F. Crystallography of biological macromolecules,
* edited by M. G. Rossmann and E. Arnold, ch. 16.1.
......
src/main/java/org/rcsb/cif/schema/core/AtomType.java
+ 138
− 31
View file @ 8061a6a1
......@@ -54,7 +54,7 @@ public class AtomType extends DelegatingCategory.DelegatingCifCoreCategory {
/**
* The display colour assigned to this atom type. Note that the
* possible colours are enumerated in the display_colour list
* possible colours are enumerated in the DISPLAY_COLOUR list
* category of items.
* @return StrColumn
*/
......@@ -89,6 +89,17 @@ public class AtomType extends DelegatingCategory.DelegatingCifCoreCategory {
return new DelegatingStrColumn(parentBlock.getColumn("atom_type_key"));
}
/**
* Mass number of this atom type.
*
* Used to denote a specific isotope. Special value '.' indicates
* that the element is present in natural isotopic abundance.
* @return IntColumn
*/
public IntColumn getMassNumber() {
return new DelegatingIntColumn(parentBlock.getColumn("atom_type_mass_number"));
}
/**
* Total number of atoms of this atom type in the unit cell.
* @return FloatColumn
......@@ -151,7 +162,12 @@ public class AtomType extends DelegatingCategory.DelegatingCifCoreCategory {
/**
* The set of data items used to define Cromer-Mann coefficients
* for generation of X-ray scattering factors.
* for generation of (0.0 &lt; s &lt; 2.0 Å^-1^) X-ray scattering factors.
*
* f(s) = c + Sum(a~i~ * exp(-b~i~ * s^2^), i=1:4)
*
* where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
* of the incident radiation in angstroms.
*
* Ref: International Tables for X-ray Crystallography, Vol. IV
* (1974) Table 2.2B
......@@ -165,7 +181,12 @@ public class AtomType extends DelegatingCategory.DelegatingCifCoreCategory {
/**
* The set of data items used to define Cromer-Mann coefficients
* for generation of X-ray scattering factors.
* for generation of (0.0 &lt; s &lt; 2.0 Å^-1^) X-ray scattering factors.
*
* f(s) = c + Sum(a~i~ * exp(-b~i~ * s^2^), i=1:4)
*
* where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
* of the incident radiation in angstroms.
*
* Ref: International Tables for X-ray Crystallography, Vol. IV
* (1974) Table 2.2B
......@@ -179,7 +200,12 @@ public class AtomType extends DelegatingCategory.DelegatingCifCoreCategory {
/**
* The set of data items used to define Cromer-Mann coefficients
* for generation of X-ray scattering factors.
* for generation of (0.0 &lt; s &lt; 2.0 Å^-1^) X-ray scattering factors.
*
* f(s) = c + Sum(a~i~ * exp(-b~i~ * s^2^), i=1:4)
*
* where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
* of the incident radiation in angstroms.
*
* Ref: International Tables for X-ray Crystallography, Vol. IV
* (1974) Table 2.2B
......@@ -193,7 +219,12 @@ public class AtomType extends DelegatingCategory.DelegatingCifCoreCategory {
/**
* The set of data items used to define Cromer-Mann coefficients
* for generation of X-ray scattering factors.
* for generation of (0.0 &lt; s &lt; 2.0 Å^-1^) X-ray scattering factors.
*
* f(s) = c + Sum(a~i~ * exp(-b~i~ * s^2^), i=1:4)
*
* where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
* of the incident radiation in angstroms.
*
* Ref: International Tables for X-ray Crystallography, Vol. IV
* (1974) Table 2.2B
......@@ -207,7 +238,12 @@ public class AtomType extends DelegatingCategory.DelegatingCifCoreCategory {
/**
* The set of data items used to define Cromer-Mann coefficients
* for generation of X-ray scattering factors.
* for generation of (0.0 &lt; s &lt; 2.0 Å^-1^) X-ray scattering factors.
*
* f(s) = c + Sum(a~i~ * exp(-b~i~ * s^2^), i=1:4)
*
* where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
* of the incident radiation in angstroms.
*
* Ref: International Tables for X-ray Crystallography, Vol. IV
* (1974) Table 2.2B
......@@ -221,7 +257,12 @@ public class AtomType extends DelegatingCategory.DelegatingCifCoreCategory {
/**
* The set of data items used to define Cromer-Mann coefficients
* for generation of X-ray scattering factors.
* for generation of (0.0 &lt; s &lt; 2.0 Å^-1^) X-ray scattering factors.
*
* f(s) = c + Sum(a~i~ * exp(-b~i~ * s^2^), i=1:4)
*
* where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
* of the incident radiation in angstroms.
*
* Ref: International Tables for X-ray Crystallography, Vol. IV
* (1974) Table 2.2B
......@@ -235,7 +276,12 @@ public class AtomType extends DelegatingCategory.DelegatingCifCoreCategory {
/**
* The set of data items used to define Cromer-Mann coefficients
* for generation of X-ray scattering factors.
* for generation of (0.0 &lt; s &lt; 2.0 Å^-1^) X-ray scattering factors.
*
* f(s) = c + Sum(a~i~ * exp(-b~i~ * s^2^), i=1:4)
*
* where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
* of the incident radiation in angstroms.
*
* Ref: International Tables for X-ray Crystallography, Vol. IV
* (1974) Table 2.2B
......@@ -249,7 +295,12 @@ public class AtomType extends DelegatingCategory.DelegatingCifCoreCategory {
/**
* The set of data items used to define Cromer-Mann coefficients
* for generation of X-ray scattering factors.
* for generation of (0.0 &lt; s &lt; 2.0 Å^-1^) X-ray scattering factors.
*
* f(s) = c + Sum(a~i~ * exp(-b~i~ * s^2^), i=1:4)
*
* where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
* of the incident radiation in angstroms.
*
* Ref: International Tables for X-ray Crystallography, Vol. IV
* (1974) Table 2.2B
......@@ -263,7 +314,12 @@ public class AtomType extends DelegatingCategory.DelegatingCifCoreCategory {
/**
* The set of data items used to define Cromer-Mann coefficients
* for generation of X-ray scattering factors.
* for generation of (0.0 &lt; s &lt; 2.0 Å^-1^) X-ray scattering factors.
*
* f(s) = c + Sum(a~i~ * exp(-b~i~ * s^2^), i=1:4)
*
* where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
* of the incident radiation in angstroms.
*
* Ref: International Tables for X-ray Crystallography, Vol. IV
* (1974) Table 2.2B
......@@ -277,7 +333,12 @@ public class AtomType extends DelegatingCategory.DelegatingCifCoreCategory {
/**
* The set of data items used to define Cromer-Mann coefficients
* for generation of X-ray scattering factors.
* for generation of (0.0 &lt; s &lt; 2.0 Å^-1^) X-ray scattering factors.
*
* f(s) = c + Sum(a~i~ * exp(-b~i~ * s^2^), i=1:4)
*
* where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
* of the incident radiation in angstroms.
*
* Ref: International Tables for X-ray Crystallography, Vol. IV
* (1974) Table 2.2B
......@@ -291,7 +352,12 @@ public class AtomType extends DelegatingCategory.DelegatingCifCoreCategory {
/**
* The set of data items used to define Cromer-Mann coefficients
* for generation of X-ray scattering factors.
* for generation of (0.0 &lt; s &lt; 2.0 Å^-1^) X-ray scattering factors.
*
* f(s) = c + Sum(a~i~ * exp(-b~i~ * s^2^), i=1:4)
*
* where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
* of the incident radiation in angstroms.
*
* Ref: International Tables for X-ray Crystallography, Vol. IV
* (1974) Table 2.2B
......@@ -305,7 +371,12 @@ public class AtomType extends DelegatingCategory.DelegatingCifCoreCategory {
/**
* The set of data items used to define Cromer-Mann coefficients
* for generation of X-ray scattering factors.
* for generation of (0.0 &lt; s &lt; 2.0 Å^-1^) X-ray scattering factors.
*
* f(s) = c + Sum(a~i~ * exp(-b~i~ * s^2^), i=1:4)
*
* where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
* of the incident radiation in angstroms.
*
* Ref: International Tables for X-ray Crystallography, Vol. IV
* (1974) Table 2.2B
......@@ -319,7 +390,12 @@ public class AtomType extends DelegatingCategory.DelegatingCifCoreCategory {
/**
* The set of data items used to define Cromer-Mann coefficients
* for generation of X-ray scattering factors.
* for generation of (0.0 &lt; s &lt; 2.0 Å^-1^) X-ray scattering factors.
*
* f(s) = c + Sum(a~i~ * exp(-b~i~ * s^2^), i=1:4)
*
* where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
* of the incident radiation in angstroms.
*
* Ref: International Tables for X-ray Crystallography, Vol. IV
* (1974) Table 2.2B
......@@ -333,7 +409,12 @@ public class AtomType extends DelegatingCategory.DelegatingCifCoreCategory {
/**
* The set of data items used to define Cromer-Mann coefficients
* for generation of X-ray scattering factors.
* for generation of (0.0 &lt; s &lt; 2.0 Å^-1^) X-ray scattering factors.
*
* f(s) = c + Sum(a~i~ * exp(-b~i~ * s^2^), i=1:4)
*
* where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
* of the incident radiation in angstroms.
*
* Ref: International Tables for X-ray Crystallography, Vol. IV
* (1974) Table 2.2B
......@@ -347,7 +428,12 @@ public class AtomType extends DelegatingCategory.DelegatingCifCoreCategory {
/**
* The set of data items used to define Cromer-Mann coefficients
* for generation of X-ray scattering factors.
* for generation of (0.0 &lt; s &lt; 2.0 Å^-1^) X-ray scattering factors.
*
* f(s) = c + Sum(a~i~ * exp(-b~i~ * s^2^), i=1:4)
*
* where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
* of the incident radiation in angstroms.
*
* Ref: International Tables for X-ray Crystallography, Vol. IV
* (1974) Table 2.2B
......@@ -361,7 +447,12 @@ public class AtomType extends DelegatingCategory.DelegatingCifCoreCategory {
/**
* The set of data items used to define Cromer-Mann coefficients
* for generation of X-ray scattering factors.
* for generation of (0.0 &lt; s &lt; 2.0 Å^-1^) X-ray scattering factors.
*
* f(s) = c + Sum(a~i~ * exp(-b~i~ * s^2^), i=1:4)
*
* where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
* of the incident radiation in angstroms.
*
* Ref: International Tables for X-ray Crystallography, Vol. IV
* (1974) Table 2.2B
......@@ -375,7 +466,12 @@ public class AtomType extends DelegatingCategory.DelegatingCifCoreCategory {
/**
* The set of data items used to define Cromer-Mann coefficients
* for generation of X-ray scattering factors.
* for generation of (0.0 &lt; s &lt; 2.0 Å^-1^) X-ray scattering factors.
*
* f(s) = c + Sum(a~i~ * exp(-b~i~ * s^2^), i=1:4)
*
* where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
* of the incident radiation in angstroms.
*
* Ref: International Tables for X-ray Crystallography, Vol. IV
* (1974) Table 2.2B
......@@ -389,7 +485,12 @@ public class AtomType extends DelegatingCategory.DelegatingCifCoreCategory {
/**
* The set of data items used to define Cromer-Mann coefficients
* for generation of X-ray scattering factors.
* for generation of (0.0 &lt; s &lt; 2.0 Å^-1^) X-ray scattering factors.
*
* f(s) = c + Sum(a~i~ * exp(-b~i~ * s^2^), i=1:4)
*
* where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
* of the incident radiation in angstroms.
*
* Ref: International Tables for X-ray Crystallography, Vol. IV
* (1974) Table 2.2B
......@@ -490,23 +591,29 @@ public class AtomType extends DelegatingCategory.DelegatingCifCoreCategory {
}
/**
* List of scattering factors as a function of sin theta on lambda.
* List has the form [[&lt;stol value 1&gt; &lt;scatfac 1&gt;] [&lt;stol value 2&gt; &lt;scatfac
* 2&gt;] ....] in increments of 0.01, increasing from 0.0.
* @return FloatColumn
* Deprecated. Data items from the ATOM_SCAT_VERSUS_STOL category should be
* used instead of this item.
*
* A table of scattering factors as a function of sin(θ)/λ (sin theta over
* lambda, stol). This table should be well-commented to indicate the items
* present. Regularly formatted lists are strongly recommended.
* @return StrColumn
*/
public FloatColumn getScatVersusStolList() {
return new DelegatingFloatColumn(parentBlock.getColumn("atom_type_scat_versus_stol_list"));
public StrColumn getScatVersusStolList() {
return new DelegatingStrColumn(parentBlock.getColumn("atom_type_scat_versus_stol_list"));
}
/**
* List of scattering factors as a function of sin theta on lambda.
* List has the form [[&lt;stol value 1&gt; &lt;scatfac 1&gt;] [&lt;stol value 2&gt; &lt;scatfac
* 2&gt;] ....] in increments of 0.01, increasing from 0.0.
* @return FloatColumn
* Deprecated. Data items from the ATOM_SCAT_VERSUS_STOL category should be
* used instead of this item.
*
* A table of scattering factors as a function of sin(θ)/λ (sin theta over
* lambda, stol). This table should be well-commented to indicate the items
* present. Regularly formatted lists are strongly recommended.
* @return StrColumn
*/
public FloatColumn getVersusStolList() {
return new DelegatingFloatColumn(parentBlock.getColumn("atom_type_scat_versus_stol_list"));
public StrColumn getVersusStolList() {
return new DelegatingStrColumn(parentBlock.getColumn("atom_type_scat_versus_stol_list"));
}
}
\ No newline at end of file
src/main/java/org/rcsb/cif/schema/core/AtomTypeScat.java
+ 231
− 28
View file @ 8061a6a1
......@@ -19,7 +19,7 @@ public class AtomTypeScat extends DelegatingCategory.DelegatingCifCoreCategory {
/**
* The set of Cromer-Mann coefficients for generating X-ray scattering
* factors. [ a1, b1, a2, b2, a3, b3, a4, b4, c]
* factors. [ c, a1, b1, a2, b2, a3, b3, a4, b4 ]
* Ref: International Tables for Crystallography, Vol. C
* (1991) Table 6.1.1.4
* @return FloatColumn
......@@ -39,7 +39,7 @@ public class AtomTypeScat extends DelegatingCategory.DelegatingCifCoreCategory {
/**
* The imaginary component of the anomalous dispersion scattering factors
* for this atom type and Cu K alpha radiation
* for this atom type and Cu Kα radiation.
* @return FloatColumn
*/
public FloatColumn getDispersionImagCu() {
......@@ -48,7 +48,7 @@ public class AtomTypeScat extends DelegatingCategory.DelegatingCifCoreCategory {
/**
* The imaginary component of the anomalous dispersion scattering factors
* for this atom type and Mo K alpha radiation
* for this atom type and Mo Kα radiation.
* @return FloatColumn
*/
public FloatColumn getDispersionImagMo() {
......@@ -57,7 +57,7 @@ public class AtomTypeScat extends DelegatingCategory.DelegatingCifCoreCategory {
/**
* The real component of the anomalous dispersion scattering factors
* for this atom type and Cu K alpha radiation
* for this atom type and Cu Kα radiation.
* @return FloatColumn
*/
public FloatColumn getDispersionRealCu() {
......@@ -66,7 +66,7 @@ public class AtomTypeScat extends DelegatingCategory.DelegatingCifCoreCategory {
/**
* The real component of the anomalous dispersion scattering factors
* for this atom type and Mo K alpha radiation
* for this atom type and Mo Kα radiation.
* @return FloatColumn
*/
public FloatColumn getDispersionRealMo() {
......@@ -74,8 +74,101 @@ public class AtomTypeScat extends DelegatingCategory.DelegatingCifCoreCategory {
}
/**
* The set of data items used to define Fox et al. coefficients
* for generation of high angle (s &gt;2.0) X-ray scattering factors.
* The set of polynomial coefficients for generating X-ray scattering factors:
* [ a_0, a_1, ... , a_N ].
*
* f(s; Z) = exp(Sum(a~i~ * s^i^), i=0:N)
*
* where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
* of the incident radiation in angstroms.
* @return FloatColumn
*/
public FloatColumn getExponentialPolynomialCoefs() {
return new DelegatingFloatColumn(parentBlock.getColumn("atom_type_scat_exponential_polynomial_coefs"));
}
/**
* Standard uncertainty of _atom_type_scat.exponential_polynomial_coefs.
* @return FloatColumn
*/
public FloatColumn getExponentialPolynomialCoefsSu() {
return new DelegatingFloatColumn(parentBlock.getColumn("atom_type_scat_exponential_polynomial_coefs_su"));
}
/**
* The inclusive lower limit of s for which the corresponding exponential
* polynomial coefficients are valid.
*
* See _atom_type_scat.exponential_polynomial_coefs.
* @return FloatColumn
*/
public FloatColumn getExponentialPolynomialLowerLimit() {
return new DelegatingFloatColumn(parentBlock.getColumn("atom_type_scat_exponential_polynomial_lower_limit"));
}
/**
* The exclusive upper limit of s for which the corresponding exponential
* polynomial coefficients are valid.
*
* See _atom_type_scat.exponential_polynomial_coefs.
* @return FloatColumn
*/
public FloatColumn getExponentialPolynomialUpperLimit() {
return new DelegatingFloatColumn(parentBlock.getColumn("atom_type_scat_exponential_polynomial_upper_limit"));
}
/**
* The set of Gaussian coefficients for generating X-ray scattering factors:
* [ c, a_1, b_1, a_2, b_2, ... , a_N, b_N ].
*
* f(s; Z) = c + Sum(a~i~ * exp(-b~i~ * s^2^), i=1:N)
*
* where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
* of the incident radiation in angstroms.
* @return FloatColumn
*/
public FloatColumn getGaussianCoefs() {
return new DelegatingFloatColumn(parentBlock.getColumn("atom_type_scat_gaussian_coefs"));
}
/**
* Standard uncertainty of _atom_type_scat.Gaussian_coefs.
* @return FloatColumn
*/
public FloatColumn getGaussianCoefsSu() {
return new DelegatingFloatColumn(parentBlock.getColumn("atom_type_scat_gaussian_coefs_su"));
}
/**
* The inclusive lower limit of s for which the corresponding Gaussian
* coefficients are valid.
*
* See _atom_type_scat.Gaussian_coefs.
* @return FloatColumn
*/
public FloatColumn getGaussianLowerLimit() {
return new DelegatingFloatColumn(parentBlock.getColumn("atom_type_scat_gaussian_lower_limit"));
}
/**
* The exclusive upper limit of s for which the corresponding Gaussian
* coefficients are valid.
*
* See _atom_type_scat.Gaussian_coefs.
* @return FloatColumn
*/
public FloatColumn getGaussianUpperLimit() {
return new DelegatingFloatColumn(parentBlock.getColumn("atom_type_scat_gaussian_upper_limit"));
}
/**
* The set of data items used to define Fox et al. coefficients
* for generation of high angle (2.0 &lt; s &lt; 6.0 Å^-1^) X-ray scattering factors.
*
* f(s) = exp(Sum(c~i~ * s^i^, i=0:3))
*
* where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
* of the incident radiation in angstroms.
*
* Ref: International Tables for Crystallography, Vol. C
* (1991) Table 6.1.1.5
......@@ -86,8 +179,13 @@ public class AtomTypeScat extends DelegatingCategory.DelegatingCifCoreCategory {
}
/**
* The set of data items used to define Fox et al. coefficients
* for generation of high angle (s &gt;2.0) X-ray scattering factors.
* The set of data items used to define Fox et al. coefficients
* for generation of high angle (2.0 &lt; s &lt; 6.0 Å^-1^) X-ray scattering factors.
*
* f(s) = exp(Sum(c~i~ * s^i^, i=0:3))
*
* where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
* of the incident radiation in angstroms.
*
* Ref: International Tables for Crystallography, Vol. C
* (1991) Table 6.1.1.5
......@@ -98,8 +196,13 @@ public class AtomTypeScat extends DelegatingCategory.DelegatingCifCoreCategory {
}
/**
* The set of data items used to define Fox et al. coefficients
* for generation of high angle (s &gt;2.0) X-ray scattering factors.
* The set of data items used to define Fox et al. coefficients
* for generation of high angle (2.0 &lt; s &lt; 6.0 Å^-1^) X-ray scattering factors.
*
* f(s) = exp(Sum(c~i~ * s^i^, i=0:3))
*
* where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
* of the incident radiation in angstroms.
*
* Ref: International Tables for Crystallography, Vol. C
* (1991) Table 6.1.1.5
......@@ -110,8 +213,13 @@ public class AtomTypeScat extends DelegatingCategory.DelegatingCifCoreCategory {
}
/**
* The set of data items used to define Fox et al. coefficients
* for generation of high angle (s &gt;2.0) X-ray scattering factors.
* The set of data items used to define Fox et al. coefficients
* for generation of high angle (2.0 &lt; s &lt; 6.0 Å^-1^) X-ray scattering factors.
*
* f(s) = exp(Sum(c~i~ * s^i^, i=0:3))
*
* where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
* of the incident radiation in angstroms.
*
* Ref: International Tables for Crystallography, Vol. C
* (1991) Table 6.1.1.5
......@@ -132,6 +240,53 @@ public class AtomTypeScat extends DelegatingCategory.DelegatingCifCoreCategory {
return new DelegatingFloatColumn(parentBlock.getColumn("atom_type_scat_hi_ang_fox_coeffs"));
}
/**
* The set of Gaussian coefficients for use in the inverse Mott-Bethe
* relationship for generating X-ray scattering factors:
* [ e, c_1, d_1, c_2, d_2, ... , c_N, d_N ].
*
* f(s; Z) =
* Z - 8π * a~0~ * s^2^ * (e + Sum( c~i~ * exp(-d~i~ * s^2^), i=1:N))
*
* where s = sin(θ)/λ, a~0~ is the Bohr radius, and Z is the atomic number.
* θ is the diffraction angle and λ is the wavelength of the incident
* radiation in angstroms.
* @return FloatColumn
*/
public FloatColumn getInvMottBetheCoefs() {
return new DelegatingFloatColumn(parentBlock.getColumn("atom_type_scat_inv_mott_bethe_coefs"));
}
/**
* Standard uncertainty of _atom_type_scat.inv_Mott_Bethe_coefs.
* @return FloatColumn
*/
public FloatColumn getInvMottBetheCoefsSu() {
return new DelegatingFloatColumn(parentBlock.getColumn("atom_type_scat_inv_mott_bethe_coefs_su"));
}
/**
* The inclusive lower limit of s for which the corresponding Gaussian
* coefficients are valid.
*
* See _atom_type_scat.inv_Mott_Bethe_coefs.
* @return FloatColumn
*/
public FloatColumn getInvMottBetheLowerLimit() {
return new DelegatingFloatColumn(parentBlock.getColumn("atom_type_scat_inv_mott_bethe_lower_limit"));
}
/**
* The exclusive upper limit of s for which the corresponding Gaussian
* coefficients are valid.
*
* See _atom_type_scat.inv_Mott_Bethe_coefs.
* @return FloatColumn
*/
public FloatColumn getInvMottBetheUpperLimit() {
return new DelegatingFloatColumn(parentBlock.getColumn("atom_type_scat_inv_mott_bethe_upper_limit"));
}
/**
* The identity of the atom specie(s) representing this atom type.
* See _atom_type.symbol for further details.
......@@ -143,7 +298,12 @@ public class AtomTypeScat extends DelegatingCategory.DelegatingCifCoreCategory {
/**
* The set of data items used to define Cromer-Mann coefficients
* for generation of X-ray scattering factors.
* for generation of (0.0 &lt; s &lt; 2.0 Å^-1^) X-ray scattering factors.
*
* f(s) = c + Sum(a~i~ * exp(-b~i~ * s^2^), i=1:4)
*
* where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
* of the incident radiation in angstroms.
*
* Ref: International Tables for X-ray Crystallography, Vol. IV
* (1974) Table 2.2B
......@@ -157,7 +317,12 @@ public class AtomTypeScat extends DelegatingCategory.DelegatingCifCoreCategory {
/**
* The set of data items used to define Cromer-Mann coefficients
* for generation of X-ray scattering factors.
* for generation of (0.0 &lt; s &lt; 2.0 Å^-1^) X-ray scattering factors.
*
* f(s) = c + Sum(a~i~ * exp(-b~i~ * s^2^), i=1:4)
*
* where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
* of the incident radiation in angstroms.
*
* Ref: International Tables for X-ray Crystallography, Vol. IV
* (1974) Table 2.2B
......@@ -171,7 +336,12 @@ public class AtomTypeScat extends DelegatingCategory.DelegatingCifCoreCategory {
/**
* The set of data items used to define Cromer-Mann coefficients
* for generation of X-ray scattering factors.
* for generation of (0.0 &lt; s &lt; 2.0 Å^-1^) X-ray scattering factors.
*
* f(s) = c + Sum(a~i~ * exp(-b~i~ * s^2^), i=1:4)
*
* where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
* of the incident radiation in angstroms.
*
* Ref: International Tables for X-ray Crystallography, Vol. IV
* (1974) Table 2.2B
......@@ -185,7 +355,12 @@ public class AtomTypeScat extends DelegatingCategory.DelegatingCifCoreCategory {
/**
* The set of data items used to define Cromer-Mann coefficients
* for generation of X-ray scattering factors.
* for generation of (0.0 &lt; s &lt; 2.0 Å^-1^) X-ray scattering factors.
*
* f(s) = c + Sum(a~i~ * exp(-b~i~ * s^2^), i=1:4)
*
* where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
* of the incident radiation in angstroms.
*
* Ref: International Tables for X-ray Crystallography, Vol. IV
* (1974) Table 2.2B
......@@ -199,7 +374,12 @@ public class AtomTypeScat extends DelegatingCategory.DelegatingCifCoreCategory {
/**
* The set of data items used to define Cromer-Mann coefficients
* for generation of X-ray scattering factors.
* for generation of (0.0 &lt; s &lt; 2.0 Å^-1^) X-ray scattering factors.
*
* f(s) = c + Sum(a~i~ * exp(-b~i~ * s^2^), i=1:4)
*
* where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
* of the incident radiation in angstroms.
*
* Ref: International Tables for X-ray Crystallography, Vol. IV
* (1974) Table 2.2B
......@@ -213,7 +393,12 @@ public class AtomTypeScat extends DelegatingCategory.DelegatingCifCoreCategory {
/**
* The set of data items used to define Cromer-Mann coefficients
* for generation of X-ray scattering factors.
* for generation of (0.0 &lt; s &lt; 2.0 Å^-1^) X-ray scattering factors.
*
* f(s) = c + Sum(a~i~ * exp(-b~i~ * s^2^), i=1:4)
*
* where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
* of the incident radiation in angstroms.
*
* Ref: International Tables for X-ray Crystallography, Vol. IV
* (1974) Table 2.2B
......@@ -227,7 +412,12 @@ public class AtomTypeScat extends DelegatingCategory.DelegatingCifCoreCategory {
/**
* The set of data items used to define Cromer-Mann coefficients
* for generation of X-ray scattering factors.
* for generation of (0.0 &lt; s &lt; 2.0 Å^-1^) X-ray scattering factors.
*
* f(s) = c + Sum(a~i~ * exp(-b~i~ * s^2^), i=1:4)
*
* where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
* of the incident radiation in angstroms.
*
* Ref: International Tables for X-ray Crystallography, Vol. IV
* (1974) Table 2.2B
......@@ -241,7 +431,12 @@ public class AtomTypeScat extends DelegatingCategory.DelegatingCifCoreCategory {
/**
* The set of data items used to define Cromer-Mann coefficients
* for generation of X-ray scattering factors.
* for generation of (0.0 &lt; s &lt; 2.0 Å^-1^) X-ray scattering factors.
*
* f(s) = c + Sum(a~i~ * exp(-b~i~ * s^2^), i=1:4)
*
* where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
* of the incident radiation in angstroms.
*
* Ref: International Tables for X-ray Crystallography, Vol. IV
* (1974) Table 2.2B
......@@ -255,7 +450,12 @@ public class AtomTypeScat extends DelegatingCategory.DelegatingCifCoreCategory {
/**
* The set of data items used to define Cromer-Mann coefficients
* for generation of X-ray scattering factors.
* for generation of (0.0 &lt; s &lt; 2.0 Å^-1^) X-ray scattering factors.
*
* f(s) = c + Sum(a~i~ * exp(-b~i~ * s^2^), i=1:4)
*
* where s = sin(θ)/λ and θ is the diffraction angle and λ is the wavelength
* of the incident radiation in angstroms.
*
* Ref: International Tables for X-ray Crystallography, Vol. IV
* (1974) Table 2.2B
......@@ -312,13 +512,16 @@ public class AtomTypeScat extends DelegatingCategory.DelegatingCifCoreCategory {
}
/**
* List of scattering factors as a function of sin theta on lambda.
* List has the form [[&lt;stol value 1&gt; &lt;scatfac 1&gt;] [&lt;stol value 2&gt; &lt;scatfac
* 2&gt;] ....] in increments of 0.01, increasing from 0.0.
* @return FloatColumn
* Deprecated. Data items from the ATOM_SCAT_VERSUS_STOL category should be
* used instead of this item.
*
* A table of scattering factors as a function of sin(θ)/λ (sin theta over
* lambda, stol). This table should be well-commented to indicate the items
* present. Regularly formatted lists are strongly recommended.
* @return StrColumn
*/
public FloatColumn getVersusStolList() {
return new DelegatingFloatColumn(parentBlock.getColumn("atom_type_scat_versus_stol_list"));
public StrColumn getVersusStolList() {
return new DelegatingStrColumn(parentBlock.getColumn("atom_type_scat_versus_stol_list"));
}
}
\ No newline at end of file
src/main/java/org/rcsb/cif/schema/core/Audit.java
+ 1
− 1
View file @ 8061a6a1
......@@ -35,7 +35,7 @@ public class Audit extends DelegatingCategory.DelegatingCifCoreCategory {
* of the Internet concepts of Uniform Resource Name and
* Universal Resource Locator managed according to the
* specifications of the International DOI Foundation
* (see http://www.doi.org).
* (see https://www.doi.org/).
* @return StrColumn
*/
public StrColumn getBlockDoi() {
......
src/main/java/org/rcsb/cif/schema/core/AuditAuthor.java
+ 38
− 2
View file @ 8061a6a1
......@@ -27,7 +27,30 @@ public class AuditAuthor extends DelegatingCategory.DelegatingCifCoreCategory {
}
/**
* Arbitrary identifier for this author
* The electronic mail address of an author of the data block, in a form
* recognizable to international networks. The format of e-mail addresses is
* given in Section 3.4, Address Specification, of Internet Message Format,
* RFC 2822, P. Resnick (Editor), Network Standards Group, April 2001.
* @return StrColumn
*/
public StrColumn getEmail() {
return new DelegatingStrColumn(parentBlock.getColumn("audit_author_email"));
}
/**
* Facsimile telephone number of an author of the data block.
* The recommended style is the international dialing prefix, followed
* by the area code in parentheses, followed by the local number with
* no spaces. The earlier convention of including the international
* dialing prefix in parentheses is no longer recommended.
* @return StrColumn
*/
public StrColumn getFax() {
return new DelegatingStrColumn(parentBlock.getColumn("audit_author_fax"));
}
/**
* Arbitrary identifier for this author.
* @return StrColumn
*/
public StrColumn getId() {
......@@ -38,7 +61,7 @@ public class AuditAuthor extends DelegatingCategory.DelegatingCifCoreCategory {
* Identifier in the ORCID Registry of a publication
* author. ORCID is an open, non-profit, community-driven
* service to provide a registry of unique researcher
* identifiers (http://orcid.org).
* identifiers (https://orcid.org/).
* @return StrColumn
*/
public StrColumn getIdOrcid() {
......@@ -58,4 +81,17 @@ public class AuditAuthor extends DelegatingCategory.DelegatingCifCoreCategory {
return new DelegatingStrColumn(parentBlock.getColumn("audit_author_name"));
}
/**
* Telephone number of an author of the data block.
* The recommended style is the international dialing prefix,
* followed by the area code in parentheses, followed by the
* local number and any extension number prefixed by 'x', with
* no spaces. The earlier convention of including the international
* dialing prefix in parentheses is no longer recommended.
* @return StrColumn
*/
public StrColumn getPhone() {
return new DelegatingStrColumn(parentBlock.getColumn("audit_author_phone"));
}
}
\ No newline at end of file
src/main/java/org/rcsb/cif/schema/core/AuditAuthorRole.java
+ 1
− 1
View file @ 8061a6a1
......@@ -21,7 +21,7 @@ public class AuditAuthorRole extends DelegatingCategory.DelegatingCifCoreCategor
* Unique identifier for the author for whom a role is identified.
* This may be repeated where an author took on multiple roles.
* The identifier for the author is drawn from the list of authors
* given in the audit_author category.
* given in the AUDIT_AUTHOR category.
* @return StrColumn
*/
public StrColumn getId() {
......
src/main/java/org/rcsb/cif/schema/core/AuditContactAuthor.java
+ 1
− 1
View file @ 8061a6a1
......@@ -52,7 +52,7 @@ public class AuditContactAuthor extends DelegatingCategory.DelegatingCifCoreCate
}
/**
* Arbitrary identifier for this author
* Arbitrary identifier for this author.
* @return StrColumn
*/
public StrColumn getId() {
......
src/main/java/org/rcsb/cif/schema/core/AuditSupport.java
+ 2
− 2
View file @ 8061a6a1
......@@ -45,8 +45,8 @@ public class AuditSupport extends DelegatingCategory.DelegatingCifCoreCategory {
/**
* The name of the organization providing funding support for
* the data collected and analysed in the data block. The
* recommended source for such names is the Open Funder
* Registry (https://github.com/CrossRef/open-funder-registry)
* recommended source for such names is the Open Funder Registry
* (https://gitlab.com/crossref/open_funder_registry).
* @return StrColumn
*/
public StrColumn getFundingOrganization() {
......
src/main/java/org/rcsb/cif/schema/core/Cell.java
+ 22
− 9
View file @ 8061a6a1
......@@ -7,7 +7,7 @@ import javax.annotation.Generated;
/**
* The CATEGORY of data items used to describe the parameters of
* the crystal unit cell and their measurement.
* the crystal unit cell.
*/
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class Cell extends DelegatingCategory.DelegatingCifCoreCategory {
......@@ -56,13 +56,13 @@ public class Cell extends DelegatingCategory.DelegatingCifCoreCategory {
* atomic displacement parameters to a dimensionless beta(IJ) matrix.
* The ADP factor in a structure factor expression:
*
* t = exp -2pi**2 ( U11 h h a* a* + ...... 2 U23 k l b* c* )
* t = exp - 0.25 ( B11 h h a* a* + ...... 2 B23 k l b* c* )
* = exp - ( beta11 h h + ............ 2 beta23 k l )
* t = exp - 2π^2^ ( U11 h h a* a* + ...... 2 U23 k l b* c* )
* t = exp - 0.25 ( B11 h h a* a* + ...... 2 B23 k l b* c* )
* = exp - ( β11 h h + ............ 2 β23 k l )
*
* The conversion of the U or B matrices to the beta matrix
* The conversion of the U or B matrices to the β matrix
*
* beta = C U C = C B C /8pi**2
* β = C U C = C B C /8π^2^
*
* where C is conversion matrix defined here.
* @return FloatColumn
......@@ -83,9 +83,9 @@ public class Cell extends DelegatingCategory.DelegatingCifCoreCategory {
* The reciprocal space matrix for converting the isotropic Uiso
* atomic displacement parameter to the anisotropic matrix Uij.
*
* | 1 cos(gamma*) cos(beta*) |
* U[i,j] = Uiso * | cos(gamma*) 1 cos(alpha*) |
* | cos(beta*) cos(alpha*) 1 |
* | 1 cos(γ*) cos(β*) |
* U[i,j] = Uiso * | cos(γ*) 1 cos(α*) |
* | cos(β*) cos(α*) 1 |
* @return FloatColumn
*/
public FloatColumn getConvertUisoToUij() {
......@@ -100,6 +100,19 @@ public class Cell extends DelegatingCategory.DelegatingCifCoreCategory {
return new DelegatingFloatColumn(parentBlock.getColumn("cell_convert_uiso_to_uij_su"));
}
/**
* A pointer to the diffraction conditions to which this cell has been applied,
* for example, to locate and extract diffraction peaks. These will normally be
* the same conditions as those under which the cell was measured, but some
* legacy data sets may have used a cell measured under differing conditions,
* in which case those conditions should be indicated using the
* _cell_measurement.condition_id data item.
* @return StrColumn
*/
public StrColumn getDiffrnId() {
return new DelegatingStrColumn(parentBlock.getColumn("cell_diffrn_id"));
}
/**
* The number of the formula units in the unit cell as specified
* by _chemical_formula.structural, _chemical_formula.moiety or
......
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