Networks / Pajek | |
Package for Large Network Analysis |
To get the last version of Mage for Windows look at Duke-BioChem FTP and for other information about Mage to Mage Home Page.
To use PDB files with Pajek you should transform them into MAC (preserves also colors) or BS (Ball and Stick) format. This can be done using program Babel ( ZIP for DOS). To transform graph.pdb into graph.mac or graph.bs request
babel -ipdb graph.pdb -omacmol graph.macThere exists also an interface for Windows ( ZIP) - you will need also Babel for DOS.
babel -ipdb graph.pdb -obs graph.bs
After you read the BS file in Pajek you can try to draw it Draw/ Draw. To see it you should select Options/ Transform/ Fit Area and to control it activate scrollbars with Options/ ScrollBar On/Off.
File name | #vert | #arcs | #edgs | values | time | lines | source |
---|---|---|---|---|---|---|---|
H2O.bs | 3 | 0 | 2 | 00:00 | 4 | BS; PDB | |
Butane.bs | 14 | 0 | 13 | 00:00 | 15 | BS; PDB | |
C6H12.bs | 18 | 0 | 24 | 00:00 | 19 | BS; PDB | |
Ethanol.bs | 9 | 0 | 8 | 00:00 | 10 | BS; PDB | |
Hexane.bs | 20 | 0 | 19 | 00:00 | 21 | BS; PDB | |
pdb101d.bs | 556 | 0 | 579 | 00:00 | 557 | BS; PDB | |
pdb201d.bs | 0 | 00:00 | BS; PDB | ||||
pdb201l.bs | 2763 | 0 | 2686 | 00:00 | 2764 | BS; PDB | |
pdb301d.bs | 878 | 0 | 960 | 00:00 | 879 | BS; PDB | |
1atn.bs | 5020 | 0 | 5128 | 00:00 | 5021 | BS; PDB | |
1crn.bs | 327 | 0 | 337 | 00:00 | 328 | BS; PDB | |
3cro.bs | 1881 | 0 | 1966 | 00:00 | 1882 | BS; PDB | |
Arb003.bs | 221 | 0 | 226 | 00:00 | 222 | BS; PDB |