Class jalview.ext.jmol.JmolParserTest

6

tests

0

failures

0

ignored

2.561s

duration

100%

successful

Test Duration Result
testAlignmentLoader 1.426s passed
testFileParser 0.685s passed
testLocalPDBId 0.159s passed
testParse_alternativeResidues 0.142s passed
testParse_missingResidues 0.149s passed
testSetSecondaryStructure 0s passed
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: Eclipse Adoptium
java.version: Java 11.0.25
os.name: Linux
Access: ALL
memory: 130.7/180.4
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
Time for creating model: 35 ms
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: Eclipse Adoptium
java.version: Java 11.0.25
os.name: Linux
Access: ALL
memory: 64.7/175.1
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
GLYCOSYLTRANSFERASE                     07-JUN-95   1XYZ
A COMMON PROTEIN FOLD AND SIMILAR ACTIVE SITE IN TWO
DISTINCT FAMILIES OF BETA-GLYCANASES
found biomolecule 1: A
biomolecule 1: number of transforms: 1
found biomolecule 2: B
biomolecule 2: number of transforms: 1
Setting space group name to P 1
1XYZ
reading 5621 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
5621 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 52 ms
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: Eclipse Adoptium
java.version: Java 11.0.25
os.name: Linux
Access: ALL
memory: 65.3/175.1
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
TYROSINE KINASE                         04-MAY-99   1QCF
CRYSTAL STRUCTURE OF HCK IN COMPLEX WITH A SRC FAMILY-
SELECTIVE TYROSINE KINASE INHIBITOR
found biomolecule 1: A
biomolecule 1: number of transforms: 1
PTR = O-PHOSPHOTYROSINE
PP1 = 1-TER-BUTYL-3-P-TOLYL-1H-PYRAZOLO[3,4-D]PYRIMIDIN-4-
PP1 = 1-TER-BUTYL-3-P-TOLYL-1H-PYRAZOLO[3,4-D]PYRIMIDIN-4-YLAMINE
Setting space group name to P 21 21 21
1QCF
reading 3959 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
3959 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 24 ms
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: Eclipse Adoptium
java.version: Java 11.0.25
os.name: Linux
Access: ALL
memory: 65.8/175.1
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
Time for creating model: 7 ms
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: Eclipse Adoptium
java.version: Java 11.0.25
os.name: Linux
Access: ALL
memory: 60.0/175.1
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
GLYCOSYLTRANSFERASE                     07-JUN-95   1XYZ
A COMMON PROTEIN FOLD AND SIMILAR ACTIVE SITE IN TWO
DISTINCT FAMILIES OF BETA-GLYCANASES
found biomolecule 1: A
biomolecule 1: number of transforms: 1
found biomolecule 2: B
biomolecule 2: number of transforms: 1
Setting space group name to P 1
1XYZ
reading 5621 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
5621 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 31 ms
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: Eclipse Adoptium
java.version: Java 11.0.25
os.name: Linux
Access: ALL
memory: 60.2/175.1
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
TYROSINE KINASE                         04-MAY-99   1QCF
CRYSTAL STRUCTURE OF HCK IN COMPLEX WITH A SRC FAMILY-
SELECTIVE TYROSINE KINASE INHIBITOR
found biomolecule 1: A
biomolecule 1: number of transforms: 1
PTR = O-PHOSPHOTYROSINE
PP1 = 1-TER-BUTYL-3-P-TOLYL-1H-PYRAZOLO[3,4-D]PYRIMIDIN-4-
PP1 = 1-TER-BUTYL-3-P-TOLYL-1H-PYRAZOLO[3,4-D]PYRIMIDIN-4-YLAMINE
Setting space group name to P 21 21 21
1QCF
reading 3959 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
3959 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 21 ms
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: Eclipse Adoptium
java.version: Java 11.0.25
os.name: Linux
Access: ALL
memory: 58.5/175.1
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
reading 51 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
51 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Jmol 15.1.3  2018-01-29 21:09 DSSP analysis for model 1.1 - null

W. Kabsch and C. Sander, Biopolymers, vol 22, 1983, pp 2577-2637

We thank Wolfgang Kabsch and Chris Sander for writing the DSSP software,
and we thank the CMBI for maintaining it to the extent that it was easy to
re-engineer in Java for our purposes. 

Second generation DSSP 2.0 is used in this analysis. See Int. J. Mol. Sci. 2014, 15, 7841-7864; doi:10.3390/ijms15057841.

All bioshapes have been deleted and must be regenerated.

Time for creating model: 3 ms
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: Eclipse Adoptium
java.version: Java 11.0.25
os.name: Linux
Access: ALL
memory: 56.1/175.1
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
TRANSPORT PROTEIN                       08-APR-15   1EJG
1EJG
reading 4 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
model 1.1 alternative locations: AB
Default Van der Waals type for model set to Jmol
4 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 0 ms
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.3  2018-01-29 21:09
java.vendor: Java: Eclipse Adoptium
java.version: Java 11.0.25
os.name: Linux
Access: ALL
memory: 56.1/175.1
processors available: 4
useCommandThread: false
The Resolver thinks Pdb
TRANSPORT PROTEIN                       08-APR-15   4UJ4
4UJ4
reading 6 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
6 atoms created
ModelSet: autobonding; use  autobond=false  to not generate bonds automatically
Time for creating model: 1 ms
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4
INFO - Rebuiling WS menu
INFO - Building web service menu for slivka
INFO - Building web services menu for jobs dispatcher
INFO - Building web services menu for jpred4