Class jalview.io.AnnotatedPDBFileInputTest
Tests
| Test |
Duration |
Result |
| checkAnnotationWiring |
0.001s |
passed |
| checkNoDuplicates |
0.001s |
passed |
| checkPDBSequenceFeatures |
0.001s |
passed |
| testJalviewProjectRelocationAnnotation |
0.579s |
passed |
Standard output
File format identified as PDB
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3 2018-01-29 21:09
java.vendor: Java: AdoptOpenJDK
java.version: Java 11.0.5
os.name: Linux
Access: ALL
memory: 165.1/359.7
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
OXIDOREDUCTASE/ELECTRON TRANSPORT 08-MAY-00 1GAQ
1GAQ
reading 690 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
690 atoms created
ModelSet: autobonding; use autobond=false to not generate bonds automatically
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@136d71f
Time for creating model: 4 ms
Attempting to connect with RNAalifoldWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@3726aea6
Attempting to connect with JronnWS...
Writing jar entry 1GAQ (1GAQ)
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@4ac1b042
Writing jar entry 1gaq.txt.xml
Attempting to connect with DisemblWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@2b8d829d
Attempting to connect with GlobPlotWS...
Writing jar entry 1454670300 Dataset for examples/1gaq.txt.xml
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@28e94c7a
Attempting to connect with IUPredWS...
File format identified as Jalview
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@19aded78
Standard error
Aug 13, 2020 12:06:39 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Aug 13, 2020 12:06:39 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Aug 13, 2020 12:06:39 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Aug 13, 2020 12:06:39 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Aug 13, 2020 12:06:39 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Aug 13, 2020 12:06:39 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
DEBUG - Created new dataset ds01 for alignment 913786150
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 29444879999701
DEBUG - Setting viewport's view id : 294448799.114947777199701
Warning - overwriting a sequenceSetId for a viewport!
PDB Entry 1GAQ /tmp/jalview_pdb7122480216333142186.txt
CalcId
CalcId jalview.ext.jmol.JmolParser
PDB Entry 1GAQ /tmp/jalview_pdb7122480216333142186.txt
CalcId
CalcId jalview.ext.jmol.JmolParser
PDB Entry 1GAQ /tmp/jalview_pdb7122480216333142186.txt
CalcId
CalcId jalview.ext.jmol.JmolParser