org.rcsb.cif.schema.mm.PdbxConstruct Maven / Gradle / Ivy
package org.rcsb.cif.schema.mm;
import org.rcsb.cif.model.*;
import org.rcsb.cif.schema.*;
import javax.annotation.Generated;
/**
* Data items in the PDBX_CONSTRUCT category specify a sequence of
* nucleic acids or amino acids. It is a catch-all that may be used to
* provide details of sequences known to be relevant to the project as well
* as primers, plasmids, proteins and such like that are either used or
* produced during the protein production process. Molecules described
* here are not necessarily complete, so for instance it would be
* possible to include either a complete plasmid or just its insert.
* This category may be considered as an abbreviated form of _entity where
* the molecules described are not required to appear in the final co-ordinates.
*
* Note that the details provided here all pertain to a single entry as defined
* at deposition. It is anticipated that _pdbx_construct.id would also be
* composed of a sequence that is unique within a given site prefixed by a code
* that identifies that site and would, therefore, be GLOBALLY unique. Thus
* this category could also be used locally to store details about the different
* constructs used during protein production without reference to the entry_id
* (which only becomes a meaningful concept during deposition).
*/
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class PdbxConstruct extends DelegatingCategory {
public PdbxConstruct(Category delegate) {
super(delegate);
}
@Override
protected Column createDelegate(String columnName, Column column) {
switch (columnName) {
case "entry_id":
return getEntryId();
case "id":
return getId();
case "name":
return getName();
case "organisation":
return getOrganisation();
case "entity_id":
return getEntityId();
case "robot_id":
return getRobotId();
case "date":
return getDate();
case "details":
return getDetails();
case "class":
return getClazz();
case "type":
return getType();
case "seq":
return getSeq();
default:
return new DelegatingColumn(column);
}
}
/**
* The value of _pdbx_construct.entry_id uniquely identifies
* a sample consisting of one or more proteins whose structure is
* to be determined. This is a pointer to _entry.id. This item may
* be a site dependent bar code.
* @return StrColumn
*/
public StrColumn getEntryId() {
return delegate.getColumn("entry_id", DelegatingStrColumn::new);
}
/**
* The value of _pdbx_construct.id must uniquely identify a record
* in the PDBX_CONSTRUCT list and should be arranged so that it is
* composed of a site-speicific prefix combined with a value that is
* unique within a given site.Note that this item need not be a
* number; it can be any unique identifier.
* @return StrColumn
*/
public StrColumn getId() {
return delegate.getColumn("id", DelegatingStrColumn::new);
}
/**
* _pdbx_construct.name provides a placeholder for the local name
* of the construct, for example the plasmid name if this category
* is used to list plasmids.
* @return StrColumn
*/
public StrColumn getName() {
return delegate.getColumn("name", DelegatingStrColumn::new);
}
/**
* _pdbx_construct.organisation describes the organisation in which
* the _pdbx_construct.id is unique. This will normally be the lab
* in which the constrcut originated. It is envisaged that this item
* will permit a globally unique identifier to be constructed in cases
* where this is not possible from the _pdbx_construct.id alone.
* @return StrColumn
*/
public StrColumn getOrganisation() {
return delegate.getColumn("organisation", DelegatingStrColumn::new);
}
/**
* In cases where the construct IS found in the co-ordinates then this
* item provides a pointer to _entity.id in the ENTITY category for
* the corresponding molecule.
* @return StrColumn
*/
public StrColumn getEntityId() {
return delegate.getColumn("entity_id", DelegatingStrColumn::new);
}
/**
* In cases where the sequence has been determined by a robot this
* data item provides a pointer to pdbx_robot_system.id in the
* PDBX_ROBOT_SYSTEM category for the robot responsible
* @return StrColumn
*/
public StrColumn getRobotId() {
return delegate.getColumn("robot_id", DelegatingStrColumn::new);
}
/**
* The date that the sequence was determined.
* @return StrColumn
*/
public StrColumn getDate() {
return delegate.getColumn("date", DelegatingStrColumn::new);
}
/**
* Additional details about the construct that cannot be
* represented in the category _pdbx_construct_feature.
* @return StrColumn
*/
public StrColumn getDetails() {
return delegate.getColumn("details", DelegatingStrColumn::new);
}
/**
* The primary function of the construct. This should be considered
* as a guideline only.
* @return StrColumn
*/
public StrColumn getClazz() {
return delegate.getColumn("class", DelegatingStrColumn::new);
}
/**
* The type of nucleic acid sequence in the construct. Note that
* to find all the DNA molecules it is necessary to search for
* DNA + cDNA and for RNA, RNA + mRNA + tRNA.
* @return StrColumn
*/
public StrColumn getType() {
return delegate.getColumn("type", DelegatingStrColumn::new);
}
/**
* sequence expressed as string of one-letter base codes or one
* letter amino acid codes. Unusual residues may be represented
* either using the appropriate one letter code wild cards or
* by the three letter code in parentheses.
* @return StrColumn
*/
public StrColumn getSeq() {
return delegate.getColumn("seq", DelegatingStrColumn::new);
}
}