update schemata

src/main/java/org/rcsb/cif/schema/core/Atom.java

@@ -1,6 +1,7 @@
 package org.rcsb.cif.schema.core;
 
-import org.rcsb.cif.schema.DelegatingCategory;
+import org.rcsb.cif.model.*;
+import org.rcsb.cif.schema.*;
 
 import javax.annotation.Generated;
 

src/main/java/org/rcsb/cif/schema/core/ChemicalConnBond.java

@@ -22,6 +22,14 @@ public ChemicalConnBond(CifCoreBlock parentBlock) {
         super(NAME, parentBlock);
     }
 
+    /**
+     * Unique identifier for the bond.
+     * @return StrColumn
+     */
+    public StrColumn getId() {
+        return new DelegatingStrColumn(parentBlock.getColumn("chemical_conn_bond_id"));
+    }
+
     /**
      * Index id of first atom in a bond connecting two atom sites.
      * @return IntColumn

src/main/java/org/rcsb/cif/schema/core/CifCoreCategoryBuilder.java

@@ -2124,6 +2124,10 @@ public ChemicalConnBondBuilder(CifCoreBlockBuilder parent) {
             super(CATEGORY_NAME, parent);
         }
 
+        public StrColumnBuilder<ChemicalConnBondBuilder, CifCoreBlockBuilder, CifCoreFileBuilder> enterId() {
+            return new StrColumnBuilderImpl<>(CATEGORY_NAME, "id", this);
+        }
+
         public IntColumnBuilder<ChemicalConnBondBuilder, CifCoreBlockBuilder, CifCoreFileBuilder> enterAtom1() {
             return new IntColumnBuilderImpl<>(CATEGORY_NAME, "atom_1", this);
         }

src/main/java/org/rcsb/cif/schema/core/GeomAngle.java

@@ -26,9 +26,8 @@ public FloatColumn getDistances() {
     }
 
     /**
-     * Atom site labels and symmetry operators as pairs for each of the
-     * three atom sites which identify the angle. The second label-symop
-     * pair in the list identifies the site at the apex of the angle.
+     * An arbitrary, unique identifier for the angle formed by the
+     * three atoms.
      * @return StrColumn
      */
     public StrColumn getId() {

src/main/java/org/rcsb/cif/schema/core/GeomBond.java

@@ -18,8 +18,7 @@ public GeomBond(CifCoreBlock parentBlock) {
     }
 
     /**
-     * Identity of bond distance in terms of the atom site labels and
-     * symmetry operators as pairs for each of the two "bonded" atom sites.
+     * Unique identifier for the bond.
      * @return StrColumn
      */
     public StrColumn getId() {

src/main/java/org/rcsb/cif/schema/core/GeomContact.java

@@ -18,8 +18,7 @@ public GeomContact(CifCoreBlock parentBlock) {
     }
 
     /**
-     * Atom site labels and symmetry operators as pairs for each of the
-     * two atom sites which define the geom_contact bond.
+     * An identifier for the contact that is unique within the loop.
      * @return StrColumn
      */
     public StrColumn getId() {

src/main/java/org/rcsb/cif/schema/core/GeomHbond.java

@@ -27,9 +27,7 @@ public FloatColumn getAngleDHA() {
     }
 
     /**
-     * Atom site labels and symmetry operators as pairs for each of the
-     * three atom sites which define the hydrogen angle and distances.
-     * Site H is at the apex of the angle.
+     * An identifier for the hydrogen bond that is unique within the loop.
      * @return StrColumn
      */
     public StrColumn getId() {

src/main/java/org/rcsb/cif/schema/core/GeomTorsion.java

@@ -26,8 +26,7 @@ public FloatColumn getDistances() {
     }
 
     /**
-     * Atom site labels and symmetry operators as pairs for each of the
-     * four atom sites which define the torsion angle.
+     * An identifier for the torsion angle that is unique within its loop.
      * @return StrColumn
      */
     public StrColumn getId() {

src/main/java/org/rcsb/cif/schema/core/ModelSite.java

@@ -68,8 +68,7 @@ public FloatColumn getFractXyz() {
     }
 
     /**
-     * Identifier of model site in terms of the atom site label and
-     * symmetry operator.
+     * An identifier for the model site that is unique within its loop.
      * @return StrColumn
      */
     public StrColumn getId() {

src/main/java/org/rcsb/cif/schema/mm/EmSingleParticleEntity.java

@@ -43,10 +43,10 @@ public StrColumn getEntryId() {
 
     /**
      * Unique category label.
-     * @return StrColumn
+     * @return IntColumn
      */
-    public StrColumn getId() {
-        return delegate.getColumn("id", DelegatingStrColumn::new);
+    public IntColumn getId() {
+        return delegate.getColumn("id", DelegatingIntColumn::new);
     }
 
     /**

src/main/java/org/rcsb/cif/schema/mm/EntityNameCom.java

@@ -49,7 +49,7 @@ public StrColumn getName() {
     }
 
     /**
-     * Provides the provenance of the name in the _entity_name_com.name field/
+     * Provides the provenance of the name in the _entity_name_com.name field
      * @return StrColumn
      */
     public StrColumn getPdbxProvenance() {

src/main/java/org/rcsb/cif/schema/mm/IhmDataTransformation.java

@@ -0,0 +1,157 @@
+package org.rcsb.cif.schema.mm;
+
+import org.rcsb.cif.model.*;
+import org.rcsb.cif.schema.*;
+
+import javax.annotation.Generated;
+
+/**
+ * Data items in the IHM_DATA_TRANSFORMATION category records the
+ * details of the rotation matrix and translation vector that can be
+ * applied to transform the data.
+ */
+@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
+public class IhmDataTransformation extends DelegatingCategory {
+    public IhmDataTransformation(Category delegate) {
+        super(delegate);
+    }
+
+    @Override
+    protected Column createDelegate(String columnName, Column column) {
+        switch (columnName) {
+            case "id":
+                return getId();
+            case "rot_matrix[1][1]":
+                return getRotMatrix11();
+            case "rot_matrix[2][1]":
+                return getRotMatrix21();
+            case "rot_matrix[3][1]":
+                return getRotMatrix31();
+            case "rot_matrix[1][2]":
+                return getRotMatrix12();
+            case "rot_matrix[2][2]":
+                return getRotMatrix22();
+            case "rot_matrix[3][2]":
+                return getRotMatrix32();
+            case "rot_matrix[1][3]":
+                return getRotMatrix13();
+            case "rot_matrix[2][3]":
+                return getRotMatrix23();
+            case "rot_matrix[3][3]":
+                return getRotMatrix33();
+            case "tr_vector[1]":
+                return getTrVector1();
+            case "tr_vector[2]":
+                return getTrVector2();
+            case "tr_vector[3]":
+                return getTrVector3();
+            default:
+                return new DelegatingColumn(column);
+        }
+    }
+
+    /**
+     * A unique identifier for the transformation.
+     * @return IntColumn
+     */
+    public IntColumn getId() {
+        return delegate.getColumn("id", DelegatingIntColumn::new);
+    }
+
+    /**
+     * Data item  of the rotation matrix used in the transformation.
+     * @return FloatColumn
+     */
+    public FloatColumn getRotMatrix11() {
+        return delegate.getColumn("rot_matrix[1][1]", DelegatingFloatColumn::new);
+    }
+
+    /**
+     * Data item  of the rotation matrix used in the transformation.
+     * @return FloatColumn
+     */
+    public FloatColumn getRotMatrix21() {
+        return delegate.getColumn("rot_matrix[2][1]", DelegatingFloatColumn::new);
+    }
+
+    /**
+     * Data item  of the rotation matrix used in the transformation.
+     * @return FloatColumn
+     */
+    public FloatColumn getRotMatrix31() {
+        return delegate.getColumn("rot_matrix[3][1]", DelegatingFloatColumn::new);
+    }
+
+    /**
+     * Data item  of the rotation matrix used in the transformation.
+     * @return FloatColumn
+     */
+    public FloatColumn getRotMatrix12() {
+        return delegate.getColumn("rot_matrix[1][2]", DelegatingFloatColumn::new);
+    }
+
+    /**
+     * Data item  of the rotation matrix used in the transformation.
+     * @return FloatColumn
+     */
+    public FloatColumn getRotMatrix22() {
+        return delegate.getColumn("rot_matrix[2][2]", DelegatingFloatColumn::new);
+    }
+
+    /**
+     * Data item  of the rotation matrix used in the transformation.
+     * @return FloatColumn
+     */
+    public FloatColumn getRotMatrix32() {
+        return delegate.getColumn("rot_matrix[3][2]", DelegatingFloatColumn::new);
+    }
+
+    /**
+     * Data item  of the rotation matrix used in the transformation.
+     * @return FloatColumn
+     */
+    public FloatColumn getRotMatrix13() {
+        return delegate.getColumn("rot_matrix[1][3]", DelegatingFloatColumn::new);
+    }
+
+    /**
+     * Data item  of the rotation matrix used in the transformation.
+     * @return FloatColumn
+     */
+    public FloatColumn getRotMatrix23() {
+        return delegate.getColumn("rot_matrix[2][3]", DelegatingFloatColumn::new);
+    }
+
+    /**
+     * Data item  of the rotation matrix used in the transformation.
+     * @return FloatColumn
+     */
+    public FloatColumn getRotMatrix33() {
+        return delegate.getColumn("rot_matrix[3][3]", DelegatingFloatColumn::new);
+    }
+
+    /**
+     * Data item  of the translation vector used in the transformation.
+     * @return FloatColumn
+     */
+    public FloatColumn getTrVector1() {
+        return delegate.getColumn("tr_vector[1]", DelegatingFloatColumn::new);
+    }
+
+    /**
+     * Data item  of the translation vector used in the transformation.
+     * @return FloatColumn
+     */
+    public FloatColumn getTrVector2() {
+        return delegate.getColumn("tr_vector[2]", DelegatingFloatColumn::new);
+    }
+
+    /**
+     * Data item  of the translation vector used in the transformation.
+     * @return FloatColumn
+     */
+    public FloatColumn getTrVector3() {
+        return delegate.getColumn("tr_vector[3]", DelegatingFloatColumn::new);
+    }
+
+}