Package org.jmol.adapter.readers.cif
Class TopoCifParser.TopoLink
- java.lang.Object
-
- org.jmol.adapter.readers.cif.TopoCifParser.TopoLink
-
- Enclosing class:
- TopoCifParser
private class TopoCifParser.TopoLink extends Object
A class to hold the _topol block information and transform it as needed. A key field is the primitives array of TopoPrimitives. These structures allow us to create a set of "primitive" operation results that operate specifically on the links themselves. Rather than showing those links (as with the Jmol script commented at the end of this class), we choose to first create the standard Jmol atom set using, for example, load hcb.cif PACKED or load xxx.cif {1 1 1} or load xxx.cif {444 666 1}, etc. Then we match those atoms with link edges by unitizing the atom back to its unit cell 555 site and then comparing with the primitive associated with a given operator.
-
-
Field Summary
Fields Modifier and Type Field Description (package private) Atom
a1
(package private) Atom
a2
(package private) double
d
(package private) javajs.util.P3
dt
(package private) int
op1
(package private) int
op2
(package private) int
order
(package private) javajs.util.P3
p1f
(package private) javajs.util.P3
p2f
(package private) TopoCifParser.TopoPrimitive[]
primitives
(package private) String
type
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description (package private) void
setPrimitives(SymmetryInterface sym, javajs.util.M4[] operations)
Primitives are set by doing the operations and adding dt to the second point's position only.String
toString()
-
-
-
Field Detail
-
a1
Atom a1
-
a2
Atom a2
-
op1
int op1
-
op2
int op2
-
type
String type
-
p1f
javajs.util.P3 p1f
-
p2f
javajs.util.P3 p2f
-
d
double d
-
dt
javajs.util.P3 dt
-
order
int order
-
primitives
TopoCifParser.TopoPrimitive[] primitives
-
-
Method Detail
-
setPrimitives
void setPrimitives(SymmetryInterface sym, javajs.util.M4[] operations)
Primitives are set by doing the operations and adding dt to the second point's position only. This works because we are going to unitize this anyway, so only the relative final lattice translation for point 1 and point 2 is needed.- Parameters:
sym
-nOps
-
-
-