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CIF parsing: entity type should be case insensitive #1109

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Merged
josemduarte merged 2 commits into from
Mar 18, 2025
+8 −15
Merged

CIF parsing: entity type should be case insensitive #1109

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501a09e
Make entity type case insensitive. Also improved docs
josemduarte Mar 17, 2025
aa0d576
Update biojava-structure/src/main/java/org/biojava/nbio/structure/Ent…
josemduarte Mar 18, 2025
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23 changes: 8 additions & 15 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/EntityType.java
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Original file line number Diff line number Diff line change
Expand Up @@ -21,8 +21,7 @@
package org.biojava.nbio.structure;

/**
*
* The type of entity (polymer, non-polymer, water, macrolide)
* The type of entity (polymer, non-polymer, water, macrolide, branched)
* as defined in the mmCIF dictionary: <a href="http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_entity.type.html"></a>
* <p>
* Entities are of four types: polymer, non-polymer, macrolide and water.
Expand Down Expand Up @@ -76,10 +75,8 @@ public enum EntityType {
/**
* @param entType the type of the Entity
*/
private EntityType(String entType) {

EntityType(String entType) {
this.setEntityType(entType);

}

/**
Expand All @@ -101,19 +98,15 @@ private void setEntityType(String entityType) {
* Returns null if entityType is null or not one of the supported
* standard types.
*
* @param entityType String value , should be one of "polymer","non-polymer","water","macrolide"
* @return an EntityType object
* @param entityType should be one of "polymer", "non-polymer", "water", "macrolide", "branched" (case insensitive)
* @return an EntityType object or null if the input string doesn't correspond to a known entity
*/
public static EntityType entityTypeFromString(String entityType)
{

if ( entityType == null)
public static EntityType entityTypeFromString(String entityType) {
if (entityType == null)
return null;

for(EntityType et : EntityType.values())
{
if(entityType.equals(et.entityType))
{
for(EntityType et : EntityType.values()) {
if (entityType.equalsIgnoreCase(et.entityType)) {
return et;
}
}
Expand Down
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