import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import org.slf4j.Logger;
{
if (decimal > 0)
{
- subModelNumber = Integer.parseInt(inputLine.substring(decimal
- + hash + 2, space));
+ subModelNumber = Integer
+ .parseInt(inputLine.substring(decimal + hash + 2, space));
space = decimal + hash + 1;
}
modelNumber = Integer.parseInt(inputLine.substring(hash + 1, space));
{
if (decimal > 0)
{
- subModelNumber = Integer.parseInt(inputLine.substring(decimal
- + hash + 2, space));
+ subModelNumber = Integer
+ .parseInt(inputLine.substring(decimal + hash + 2, space));
space = decimal + hash + 1;
}
modelNumber = Integer.parseInt(inputLine.substring(hash + 1, space));
String resType = "";
if (split.length == 2)
{
- resType = split[0].trim().toUpperCase();
+ resType = split[0].trim().toUpperCase(Locale.ROOT);
}
else if (split.length == 3)
{
- resType = split[1].trim().toUpperCase();
+ resType = split[1].trim().toUpperCase(Locale.ROOT);
}
if (resType.equalsIgnoreCase("HOH") || resType.equalsIgnoreCase("WAT"))
{
{
try
{
- chimeraModel = chimeraManager.getChimeraModel(
- Integer.valueOf(model), 0);
+ chimeraModel = chimeraManager
+ .getChimeraModel(Integer.valueOf(model), 0);
} catch (NumberFormatException ex)
{
// ignore
if (modelIDNoResChain[0] != null)
{
String modelID = modelIDNoResChain[0];
- List<ChimeraModel> models = chimeraManager.getChimeraModels(
- modelID, ModelType.PDB_MODEL);
+ List<ChimeraModel> models = chimeraManager.getChimeraModels(modelID,
+ ModelType.PDB_MODEL);
if (models.size() == 1)
{ // usual case with only one model
chimeraModel = models.get(0);
// TODO: [Optional] What is this doing?
try
{
- chimeraModel = chimeraManager.getChimeraModel(
- Integer.valueOf(modelID), 0);
+ chimeraModel = chimeraManager
+ .getChimeraModel(Integer.valueOf(modelID), 0);
} catch (NumberFormatException ex)
{
// ignore
}
else if (chimeraModel.getChainCount() == 1)
{
- chimeraResidue = chimeraModel.getResidue(chimeraModel
- .getChainNames().iterator().next(), residue);
+ chimeraResidue = chimeraModel.getResidue(
+ chimeraModel.getChainNames().iterator().next(), residue);
}
// System.out.println("ChimeraResidue = " + chimeraResidue);
}
aaNames.put("LYS", "K Lys Lysine N[C@](CCCCN)([H])C(O)=O");
aaNames.put("DLY", "K Dly D-Lysine NCCCC[C@@H](N)C(O)=O");
aaNames.put("MET", "M Met Methionine N[C@](CCSC)([H])C(O)=O");
- aaNames.put("PHE", "F Phe Phenylalanine N[C@](CC1=CC=CC=C1)([H])C(O)=O");
+ aaNames.put("PHE",
+ "F Phe Phenylalanine N[C@](CC1=CC=CC=C1)([H])C(O)=O");
aaNames.put("PRO", "P Pro Proline OC([C@@]1([H])NCCC1)=O");
aaNames.put("SER", "S Ser Serine OC[C@](C(O)=O)([H])N");
aaNames.put("THR", "T Thr Threonine O[C@H](C)[C@](C(O)=O)([H])N");