Class mc_view.PDBfileTest

all > mc_view > PDBfileTest

tests

failures

ignored

1.143s

duration

100%

successful

Tests
Standard output
Standard error

Tests

Test	Duration	Result
testIsRna	0.001s	passed
testParse	0.016s	passed
testParse_withAnnotations_noSS	0.017s	passed
testParse_withJmolAddAlignmentAnnotations	0.556s	passed
testParse_withJmol_noAnnotations	0.553s	passed

Standard output

Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@26e7cfb0
Attempting to connect with GLprobsWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@77e8de71
Attempting to connect with AAConWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@606479a8
Attempting to connect with RNAalifoldWS...
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: 214.7/359.7
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
ELECTRON TRANSPORT                      06-FEB-13   3W5V
CROSS-LINKED COMPLEX BETWEEN FERREDOXIN AND FERREDOXIN-NADP+ R
found biomolecule 1: A, D
biomolecule 1: number of transforms: 1
found biomolecule 2: C, B
biomolecule 2: number of transforms: 1
FAD = FLAVIN-ADENINE DINUCLEOTIDE
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 1 21 1
3W5V
reading 6290 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@7939db62
Default Van der Waals type for model set to Jmol
6290 atoms created
Attempting to connect with JronnWS...
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 22 ms
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@3be3a99b
Attempting to connect with DisemblWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@74bd294f
Attempting to connect with GlobPlotWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@286638a1
Attempting to connect with IUPredWS...
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@1f9e9a7
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: 132.6/359.7
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
ELECTRON TRANSPORT                      06-FEB-13   3W5V
CROSS-LINKED COMPLEX BETWEEN FERREDOXIN AND FERREDOXIN-NADP+ R
found biomolecule 1: A, D
biomolecule 1: number of transforms: 1
found biomolecule 2: C, B
biomolecule 2: number of transforms: 1
FAD = FLAVIN-ADENINE DINUCLEOTIDE
FES = FE2/S2 (INORGANIC) CLUSTER
Setting space group name to P 1 21 1
3W5V
reading 6290 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
6290 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 24 ms

Standard error

Aug 13, 2020 12:06:21 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Aug 13, 2020 12:06:21 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Aug 13, 2020 12:06:21 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
DEBUG - Not enabling Google Tracking.
Aug 13, 2020 12:06:21 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Aug 13, 2020 12:06:21 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Aug 13, 2020 12:06:21 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Aug 13, 2020 12:06:21 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Aug 13, 2020 12:06:21 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@f9c8af3, jalview.ws.jws2.jabaws2.Jws2Instance@26e7cfb0, jalview.ws.jws2.jabaws2.Jws2Instance@77e8de71, jalview.ws.jws2.jabaws2.Jws2Instance@40f1acb, jalview.ws.jws2.jabaws2.Jws2Instance@7c00d4ea, jalview.ws.jws2.jabaws2.Jws2Instance@64e0000f, jalview.ws.jws2.jabaws2.Jws2Instance@21346caa, jalview.ws.jws2.jabaws2.Jws2Instance@4e6f3783, jalview.ws.jws2.jabaws2.Jws2Instance@606479a8, jalview.ws.jws2.jabaws2.Jws2Instance@74bd294f, jalview.ws.jws2.jabaws2.Jws2Instance@286638a1, jalview.ws.jws2.jabaws2.Jws2Instance@1f9e9a7, jalview.ws.jws2.jabaws2.Jws2Instance@3be3a99b, jalview.ws.jws2.jabaws2.Jws2Instance@7939db62]
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@f9c8af3, jalview.ws.jws2.jabaws2.Jws2Instance@26e7cfb0, jalview.ws.jws2.jabaws2.Jws2Instance@77e8de71, jalview.ws.jws2.jabaws2.Jws2Instance@40f1acb, jalview.ws.jws2.jabaws2.Jws2Instance@7c00d4ea, jalview.ws.jws2.jabaws2.Jws2Instance@64e0000f, jalview.ws.jws2.jabaws2.Jws2Instance@21346caa, jalview.ws.jws2.jabaws2.Jws2Instance@4e6f3783, jalview.ws.jws2.jabaws2.Jws2Instance@606479a8, jalview.ws.jws2.jabaws2.Jws2Instance@74bd294f, jalview.ws.jws2.jabaws2.Jws2Instance@286638a1, jalview.ws.jws2.jabaws2.Jws2Instance@1f9e9a7, jalview.ws.jws2.jabaws2.Jws2Instance@3be3a99b, jalview.ws.jws2.jabaws2.Jws2Instance@7939db62]
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@f9c8af3, jalview.ws.jws2.jabaws2.Jws2Instance@26e7cfb0, jalview.ws.jws2.jabaws2.Jws2Instance@77e8de71, jalview.ws.jws2.jabaws2.Jws2Instance@40f1acb, jalview.ws.jws2.jabaws2.Jws2Instance@7c00d4ea, jalview.ws.jws2.jabaws2.Jws2Instance@64e0000f, jalview.ws.jws2.jabaws2.Jws2Instance@21346caa, jalview.ws.jws2.jabaws2.Jws2Instance@4e6f3783, jalview.ws.jws2.jabaws2.Jws2Instance@606479a8, jalview.ws.jws2.jabaws2.Jws2Instance@74bd294f, jalview.ws.jws2.jabaws2.Jws2Instance@286638a1, jalview.ws.jws2.jabaws2.Jws2Instance@1f9e9a7, jalview.ws.jws2.jabaws2.Jws2Instance@3be3a99b, jalview.ws.jws2.jabaws2.Jws2Instance@7939db62]
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@f9c8af3, jalview.ws.jws2.jabaws2.Jws2Instance@26e7cfb0, jalview.ws.jws2.jabaws2.Jws2Instance@77e8de71, jalview.ws.jws2.jabaws2.Jws2Instance@40f1acb, jalview.ws.jws2.jabaws2.Jws2Instance@7c00d4ea, jalview.ws.jws2.jabaws2.Jws2Instance@64e0000f, jalview.ws.jws2.jabaws2.Jws2Instance@21346caa, jalview.ws.jws2.jabaws2.Jws2Instance@4e6f3783, jalview.ws.jws2.jabaws2.Jws2Instance@606479a8, jalview.ws.jws2.jabaws2.Jws2Instance@74bd294f, jalview.ws.jws2.jabaws2.Jws2Instance@286638a1, jalview.ws.jws2.jabaws2.Jws2Instance@1f9e9a7, jalview.ws.jws2.jabaws2.Jws2Instance@3be3a99b, jalview.ws.jws2.jabaws2.Jws2Instance@7939db62]
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@f9c8af3, jalview.ws.jws2.jabaws2.Jws2Instance@26e7cfb0, jalview.ws.jws2.jabaws2.Jws2Instance@77e8de71, jalview.ws.jws2.jabaws2.Jws2Instance@40f1acb, jalview.ws.jws2.jabaws2.Jws2Instance@7c00d4ea, jalview.ws.jws2.jabaws2.Jws2Instance@64e0000f, jalview.ws.jws2.jabaws2.Jws2Instance@21346caa, jalview.ws.jws2.jabaws2.Jws2Instance@4e6f3783, jalview.ws.jws2.jabaws2.Jws2Instance@606479a8, jalview.ws.jws2.jabaws2.Jws2Instance@74bd294f, jalview.ws.jws2.jabaws2.Jws2Instance@286638a1, jalview.ws.jws2.jabaws2.Jws2Instance@1f9e9a7, jalview.ws.jws2.jabaws2.Jws2Instance@3be3a99b, jalview.ws.jws2.jabaws2.Jws2Instance@7939db62]
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@f9c8af3, jalview.ws.jws2.jabaws2.Jws2Instance@26e7cfb0, jalview.ws.jws2.jabaws2.Jws2Instance@77e8de71, jalview.ws.jws2.jabaws2.Jws2Instance@40f1acb, jalview.ws.jws2.jabaws2.Jws2Instance@7c00d4ea, jalview.ws.jws2.jabaws2.Jws2Instance@64e0000f, jalview.ws.jws2.jabaws2.Jws2Instance@21346caa, jalview.ws.jws2.jabaws2.Jws2Instance@4e6f3783, jalview.ws.jws2.jabaws2.Jws2Instance@606479a8, jalview.ws.jws2.jabaws2.Jws2Instance@74bd294f, jalview.ws.jws2.jabaws2.Jws2Instance@286638a1, jalview.ws.jws2.jabaws2.Jws2Instance@1f9e9a7, jalview.ws.jws2.jabaws2.Jws2Instance@3be3a99b, jalview.ws.jws2.jabaws2.Jws2Instance@7939db62]
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@f9c8af3, jalview.ws.jws2.jabaws2.Jws2Instance@26e7cfb0, jalview.ws.jws2.jabaws2.Jws2Instance@77e8de71, jalview.ws.jws2.jabaws2.Jws2Instance@40f1acb, jalview.ws.jws2.jabaws2.Jws2Instance@7c00d4ea, jalview.ws.jws2.jabaws2.Jws2Instance@64e0000f, jalview.ws.jws2.jabaws2.Jws2Instance@21346caa, jalview.ws.jws2.jabaws2.Jws2Instance@4e6f3783, jalview.ws.jws2.jabaws2.Jws2Instance@606479a8, jalview.ws.jws2.jabaws2.Jws2Instance@74bd294f, jalview.ws.jws2.jabaws2.Jws2Instance@286638a1, jalview.ws.jws2.jabaws2.Jws2Instance@1f9e9a7, jalview.ws.jws2.jabaws2.Jws2Instance@3be3a99b, jalview.ws.jws2.jabaws2.Jws2Instance@7939db62]
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@f9c8af3, jalview.ws.jws2.jabaws2.Jws2Instance@26e7cfb0, jalview.ws.jws2.jabaws2.Jws2Instance@77e8de71, jalview.ws.jws2.jabaws2.Jws2Instance@40f1acb, jalview.ws.jws2.jabaws2.Jws2Instance@7c00d4ea, jalview.ws.jws2.jabaws2.Jws2Instance@64e0000f, jalview.ws.jws2.jabaws2.Jws2Instance@21346caa, jalview.ws.jws2.jabaws2.Jws2Instance@4e6f3783, jalview.ws.jws2.jabaws2.Jws2Instance@606479a8, jalview.ws.jws2.jabaws2.Jws2Instance@74bd294f, jalview.ws.jws2.jabaws2.Jws2Instance@286638a1, jalview.ws.jws2.jabaws2.Jws2Instance@1f9e9a7, jalview.ws.jws2.jabaws2.Jws2Instance@3be3a99b, jalview.ws.jws2.jabaws2.Jws2Instance@7939db62]
DEBUG - Firing service changed event for [jalview.ws.jws2.jabaws2.Jws2Instance@f9c8af3, jalview.ws.jws2.jabaws2.Jws2Instance@26e7cfb0, jalview.ws.jws2.jabaws2.Jws2Instance@77e8de71, jalview.ws.jws2.jabaws2.Jws2Instance@40f1acb, jalview.ws.jws2.jabaws2.Jws2Instance@7c00d4ea, jalview.ws.jws2.jabaws2.Jws2Instance@64e0000f, jalview.ws.jws2.jabaws2.Jws2Instance@21346caa, jalview.ws.jws2.jabaws2.Jws2Instance@4e6f3783, jalview.ws.jws2.jabaws2.Jws2Instance@606479a8, jalview.ws.jws2.jabaws2.Jws2Instance@74bd294f, jalview.ws.jws2.jabaws2.Jws2Instance@286638a1, jalview.ws.jws2.jabaws2.Jws2Instance@1f9e9a7, jalview.ws.jws2.jabaws2.Jws2Instance@3be3a99b, jalview.ws.jws2.jabaws2.Jws2Instance@7939db62]
Rebuild WS Menu for service change
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