Class jalview.io.AnnotatedPDBFileInputTest
Tests
| Test |
Duration |
Result |
| checkAnnotationWiring |
0.001s |
passed |
| checkNoDuplicates |
0.001s |
passed |
| checkPDBSequenceFeatures |
0.001s |
passed |
| testJalviewProjectRelocationAnnotation |
0.700s |
passed |
Standard output
File format identified as PDB
CIR resolver set to https://cactus.nci.nih.gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53 2021-02-10 09:12
java.vendor: Java: Oracle Corporation
java.version: Java 11.0.19
os.name: Linux
Access: ALL
memory: 160.0/293.6
processors available: 8
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
Time for creating model: 8 ms
Writing jar entry 1GAQ (1GAQ)
Writing jar entry 1gaq.txt.xml
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@2c0d7367
Writing jar entry 1133495646 Dataset for examples/1gaq.txt.xml
Attempting to connect with MuscleWS...
File format identified as Jalview
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@f02c5f7
Standard error
Rebuild WS Menu for service change
Rebuild WS Menu for service change
Jul 02, 2023 10:12:06 AM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
DEBUG - Scanning news items: newsnew=false and lastDate is Fri Jun 30 20:04:22 CEST 2023
DEBUG - Saved last read date as 30 Jun 2023, 20:04:22
DEBUG - Scanning news items: newsnew=false and lastDate is Fri Jun 30 20:04:22 CEST 2023
DEBUG - Saved last read date as 30 Jun 2023, 20:04:22
DEBUG - Scanning news items: newsnew=false and lastDate is Fri Jun 30 20:04:22 CEST 2023
DEBUG - Saved last read date as 30 Jun 2023, 20:04:22
DEBUG - BACKUPFILES using temp file /tmp/JalviewTest4948767848052774951.jvp11544955105775073043.tmp_newfile
DEBUG - Scanning news items: newsnew=false and lastDate is Fri Jun 30 20:04:22 CEST 2023
DEBUG - Saved last read date as 30 Jun 2023, 20:04:22
DEBUG - Scanning news items: newsnew=false and lastDate is Fri Jun 30 20:04:22 CEST 2023
DEBUG - Saved last read date as 30 Jun 2023, 20:04:22
DEBUG - Scanning news items: newsnew=false and lastDate is Fri Jun 30 20:04:22 CEST 2023
DEBUG - Saved last read date as 30 Jun 2023, 20:04:22
DEBUG - BACKUPFILES moving /tmp/JalviewTest4948767848052774951.jvp to /tmp/JalviewTest4948767848052774951.jvp_BACKUPFILESTESTTMP000001 was successful
Jul 02, 2023 10:12:07 AM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
DEBUG - Created new dataset ds01 for alignment 1885780198
Assuming project file with TEST is compatible with Jalview version 2.8.1
DEBUG - Setting viewport's sequence set id : 90635071227176
DEBUG - Setting viewport's view id : 906350712.121102632527176
Warning - overwriting a sequenceSetId for a viewport!
PDB Entry 1GAQ /tmp/jalview_pdb12025394066789216284.txt
CalcId mc_view.PDBChain
CalcId jalview.ext.jmol.JmolParser
PDB Entry 1GAQ /tmp/jalview_pdb12025394066789216284.txt
CalcId mc_view.PDBChain
CalcId jalview.ext.jmol.JmolParser
PDB Entry 1GAQ /tmp/jalview_pdb12025394066789216284.txt
CalcId mc_view.PDBChain
CalcId jalview.ext.jmol.JmolParser