Towards solving issue eppic-team#37, not working well yet: crashes on…

… 4hhb
josemduarte · Nov 23, 2016 · 5dd35d6 · 5dd35d6
1 parent 846c07b
commit 5dd35d6
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Showing 6 changed files with 90 additions and 7 deletions.
diff --git a/eppic-cli/pom.xml b/eppic-cli/pom.xml
@@ -9,7 +9,7 @@
  <artifactId>eppic-cli</artifactId>
 
  <properties>
- <biojava.version>4.2.4</biojava.version>
+ <biojava.version>4.2.5-SNAPSHOT</biojava.version>
  </properties>
 
  <repositories>

diff --git a/eppic-cli/src/main/java/eppic/DataModelAdaptor.java b/eppic-cli/src/main/java/eppic/DataModelAdaptor.java
@@ -145,7 +145,12 @@ public void setPdbMetadata(Structure pdb) {
  }
  pdbInfo.setExpMethod(exp);
 
- pdbInfo.setNcsOpsPresent(pdb.getCrystallographicInfo().getNcsOperators()!=null);
+ if (pdbXtallographicInfo!=null) {
+ pdbInfo.setNcsOpsPresent(pdbXtallographicInfo.getNcsOperators()!=null);
+
+ pdbInfo.setNonStandardSg(pdbXtallographicInfo.isNonStandardSg());
+ pdbInfo.setNonStandardCoordFrameConvention(pdbXtallographicInfo.isNonStandardCoordFrameConvention());
+ }
 
  CrystalCell cc = (pdbXtallographicInfo==null?null:pdbXtallographicInfo.getCrystalCell());
  if (cc!=null) {

diff --git a/eppic-cli/src/main/java/eppic/TextOutputWriter.java b/eppic-cli/src/main/java/eppic/TextOutputWriter.java
@@ -5,8 +5,8 @@
 import java.util.ArrayList;
 import java.util.List;
 
-//import org.slf4j.Logger;
-//import org.slf4j.LoggerFactory;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import eppic.model.AssemblyContentDB;
 import eppic.model.AssemblyDB;
@@ -24,14 +24,17 @@
 
 public class TextOutputWriter {
 
- //private static final Logger LOGGER = LoggerFactory.getLogger(TextOutputWriter.class);
+ private static final Logger LOGGER = LoggerFactory.getLogger(TextOutputWriter.class);
 
  private PdbInfoDB pdbInfo;
  private EppicParams params;
 
  public TextOutputWriter (PdbInfoDB pdbInfo, EppicParams params) {
  this.pdbInfo = pdbInfo;
  this.params = params;
+
+ LOGGER.debug("Is non-standard SG: {}", pdbInfo.isNonStandardSg());
+ LOGGER.debug("Is non-standard coord frame convention: {}", pdbInfo.isNonStandardCoordFrameConvention());
  }
 
 

diff --git a/eppic-model/src/main/java/ch/systemsx/sybit/crkwebui/shared/model/PdbInfo.java b/eppic-model/src/main/java/ch/systemsx/sybit/crkwebui/shared/model/PdbInfo.java
@@ -22,15 +22,15 @@
 import eppic.model.PdbInfoDB;
 
 /**
- * DTO class for PDBScore item.
+ * DTO class for PDBInfo.
  * @author AS
  */
 
 @XmlRootElement(name = "eppicAnalysis")
 @XmlType(propOrder = { "pdbCode", "title", "releaseDate", "expMethod",
  "spaceGroup", "resolution", "rfreeValue", "numChainClusters",
  "cellA","cellB","cellC","cellAlpha","cellBeta","cellGamma",
- "crystalFormId",
+ "crystalFormId", "ncsOpsPresent", "nonStandardSg", "nonStandardCoordFrameConvention",
  "chainClusters", "interfaceClusters", "assemblies",
 "runParameters"})
 @XmlAccessorType(XmlAccessType.FIELD)
@@ -69,6 +69,11 @@ public class PdbInfo implements Serializable, ProcessingData
  private double cellGamma;
 
  private int crystalFormId;
+
+ private boolean ncsOpsPresent;
+
+ private boolean nonStandardSg;
+ private boolean nonStandardCoordFrameConvention;
 
  private RunParameters runParameters;
 
@@ -109,6 +114,9 @@ public PdbInfo(int uid,
  double cellBeta,
  double cellGamma,
  int crystalFormId,
+ boolean ncsOpsPresent,
+ boolean nonStandardSg,
+ boolean nonStandardCoordFrameConvention,
  RunParameters runParameters) 
  {
  this.interfaceClusters = new ArrayList<InterfaceCluster>();
@@ -129,6 +137,9 @@ public PdbInfo(int uid,
  this.cellBeta = cellBeta;
  this.cellGamma = cellGamma;
  this.crystalFormId = crystalFormId;
+ this.ncsOpsPresent = ncsOpsPresent;
+ this.nonStandardSg = nonStandardSg;
+ this.nonStandardCoordFrameConvention = nonStandardCoordFrameConvention;
  this.runParameters = runParameters;
  }
 
@@ -283,6 +294,30 @@ public int getCrystalFormId() {
  public void setCrystalFormId(int crystalFormId) {
  this.crystalFormId = crystalFormId;
  }
+
+ public boolean isNcsOpsPresent() {
+ return ncsOpsPresent;
+ }
+
+ public void setNcsOpsPresent(boolean ncsOpsPresent) {
+ this.ncsOpsPresent = ncsOpsPresent;
+ }
+
+ public boolean isNonStandardSg() {
+ return nonStandardSg;
+ }
+
+ public void setNonStandardSg(boolean nonStandardSg) {
+ this.nonStandardSg = nonStandardSg;
+ }
+
+ public boolean isNonStandardCoordFrameConvention() {
+ return nonStandardCoordFrameConvention;
+ }
+
+ public void setNonStandardCoordFrameConvention(boolean nonStandardCoordFrameConvention) {
+ this.nonStandardCoordFrameConvention = nonStandardCoordFrameConvention;
+ }
 
  public void setRunParameters(RunParameters runParameters) {
  this.runParameters = runParameters;
@@ -432,6 +467,10 @@ public static PdbInfo create(PdbInfoDB pdbInfoDB)
  pdbInfo.setCellBeta(pdbInfoDB.getCellBeta());
  pdbInfo.setCellGamma(pdbInfoDB.getCellGamma());
  pdbInfo.setCrystalFormId(pdbInfo.getCrystalFormId());
+ pdbInfo.setNcsOpsPresent(pdbInfoDB.isNcsOpsPresent());
+ pdbInfo.setNonStandardSg(pdbInfoDB.isNonStandardSg());
+ pdbInfo.setNonStandardCoordFrameConvention(pdbInfoDB.isNonStandardCoordFrameConvention());
+
  return pdbInfo;
  }
 

diff --git a/eppic-model/src/main/java/eppic/model/PdbInfoDB.java b/eppic-model/src/main/java/eppic/model/PdbInfoDB.java
@@ -37,6 +37,23 @@ public class PdbInfoDB implements Serializable {
 
  private int crystalFormId;
 
+ /**
+ * Whether this structure is a PDB structure in a non-standard space group 
+ */
+ private boolean nonStandardSg;
+
+ /**
+ * Whether this structure is a PDB structure in a 
+ * non-standard frame (for which our scale matrix calculation and thus the crystal reconstruction
+ * will be incorrect).
+ * There's ~ 200 old structures in the PDB affected by the non-standard frame problem, hopefully they will
+ * be remediated in the future.
+ * For more info see:
+ * https://github.com/eppic-team/eppic/issues/37 and
+ * https://github.com/eppic-team/owl/issues/4
+ */
+ private boolean nonStandardCoordFrameConvention;
+
  private RunParametersDB runParameters;
 
  private List<ChainClusterDB> chainClusters;
@@ -257,6 +274,22 @@ public void setNcsOpsPresent(boolean ncsOpsPresent) {
  this.ncsOpsPresent = ncsOpsPresent;
  }
 
+ public boolean isNonStandardSg() {
+ return nonStandardSg;
+ }
+
+ public void setNonStandardSg(boolean nonStandardSg) {
+ this.nonStandardSg = nonStandardSg;
+ }
+
+ public boolean isNonStandardCoordFrameConvention() {
+ return nonStandardCoordFrameConvention;
+ }
+
+ public void setNonStandardCoordFrameConvention(boolean nonStandardCoordFrameConvention) {
+ this.nonStandardCoordFrameConvention = nonStandardCoordFrameConvention;
+ }
+
  public double getCellA() {
  return cellA;
  }

diff --git a/eppic-model/src/main/resources/META-INF/orm.xml b/eppic-model/src/main/resources/META-INF/orm.xml
@@ -92,6 +92,9 @@
 
  <basic name="ncsOpsPresent"></basic>
 
+ <basic name="nonStandardSg"></basic>
+ <basic name="nonStandardCoordFrameConvention"></basic>
+
  <basic name="crystalFormId"></basic>
 
  <basic name="numChainClusters"></basic>