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104 lines (79 loc) · 2.86 KB
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package org.biojava.nbio.structure;
import java.util.ArrayList;
import java.util.List;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* An internal utility class for StructureImpl to make it easier to manage poly and nonpoly chains.
* Not to exposed to users through API.
*
* Created by andreas on 5/3/16.
* @author Andreas Prlic
* @since 5.0
*/
public class Model {
private static final Logger logger = LoggerFactory.getLogger(Model.class);
private List<Chain> polyChains;
private List<Chain> nonPolyChains;
private List<Chain> waterChains;
public Model(){
polyChains = new ArrayList<>();
nonPolyChains = new ArrayList<>();
waterChains = new ArrayList<>();
}
public List<Chain> getPolyChains() {
return polyChains;
}
public List<Chain> getNonPolyChains() {
return nonPolyChains;
}
public List<Chain> getWaterChains() {
return waterChains;
}
/**
* Get all chains: polymeric, non-polymeric and water
* @return
*/
public List<Chain> getChains(){
ArrayList<Chain> chains = new ArrayList<>();
chains.addAll(polyChains);
chains.addAll(nonPolyChains);
chains.addAll(waterChains);
chains.trimToSize();
return chains;
}
public void setChains(List<Chain> modelChains) {
polyChains.clear();
nonPolyChains.clear();
waterChains.clear();
for (Chain c : modelChains){
addChain(c);
}
}
public void addChain(Chain c) {
EntityInfo info = c.getEntityInfo();
if ( info == null || info.getType() == null) {
logger.warn("No entity info could be found while adding chain with asym id {} (author id {}). Will consider it a polymer chain.", c.getId(), c.getName());
polyChains.add(c);
} else if ( info.getType() == EntityType.POLYMER) {
polyChains.add(c);
} else if (info.getType() == EntityType.NONPOLYMER) {
nonPolyChains.add(c);
} else if (info.getType() == EntityType.WATER) {
waterChains.add(c);
} else if (info.getType() == EntityType.MACROLIDE) {
logger.warn("Chain with asym id {} (author id {}) has entity type 'macrolide', considering it non-polymeric", c.getId(), c.getName());
nonPolyChains.add(c);
} else {
logger.warn("Chain with asym id {} (author id {}) has unsupported entity type '{}'. Will not add it to the Structure.", c.getId(), c.getName(), info.getType().toString());
// ignore it
}
}
/**
* Returns the total number of chains in this model: polymeric, non-polymeric and water
* @return
*/
public int size() {
return polyChains.size() + nonPolyChains.size() + waterChains.size();
}
}