A Node with two out-going bonds. More...
#include <TrigonalGroup.hh>
Inheritance diagram for prf::TrigonalGroup:
Public Member Functions | |
| void | Initialize () |
| Initialize the node, possibly pre-calculate anything that can be. | |
| void | SetTheta (double x0, double x1) |
| Set the two available theta angles. | |
| void | SetBondLengths (double x0, double x1, double x2) |
| Set bond lengths. | |
| void | Create () |
| Assign coordinates to atoms attached to outgoing bonds. | |
 Public Member Functions inherited from prf::Node | |
| void | ReCreate () |
| Recursive Create. Self followed by subnodes. | |
| virtual void | AssignPhi (double) |
| assign to the dof of the Node. | |
| double | Phi () |
| retrieve the torsional angle | |
| void | LockPhi (double xx) |
| Lock the torsional dof of the Node to value xx. | |
| int | Locked () const |
| if it is really a dof | |
| Atom & | ATOM (int i) |
| Reference to i'th atom. | |
| Atom & | atom (int i) |
| Reference to i'th atom. | |
| void | AddSubnode (Node *nd) |
| Make another node a subnode. | |
| void | AtomOffset (int i) |
| void | RevertPhi (double) |
| Revert the torsional angle to a given value. | |
| virtual void | ExportConnections (ConnectionsMatrix &aa) |
| Export connection information to an external ConnectionsMatrix. | |
| virtual void | LocPairs (std::deque< std::pair< int, int > > &lcp) |
| List pairs of member atoms which are connected by 3 covalent bonds. | |
| virtual void | BuildConnections () |
| Assign proper Bases to subnodes and call BuildConnections on them. | |
| virtual void | SetBase (Atom &ap) |
| Set a new atom as one Base. | |
| void | SetBase (Atom &, Atom &, Atom &) |
| be careful: This actually means set Base, Root and Junction | |
| void | set_bases (Atom &b1, Atom &b2, Atom &b3) |
| And this means set all bases. | |
| void | MobileAtoms (int &r1, int &r2) |
| Atoms that move when the node turns. | |
| void | SetMobileAtoms (int i, int j) |
| Set what range should be returned as the mobile atoms. | |
| virtual void | AssignAtoms (Atom &a0, Atom &a1, Atom &a2, std::vector< Atom > &att, int st) |
| virtual void | AssignAtoms (Atom &a0, Atom &a1, Atom &a2, Atom &a3) |
| virtual void | AssignAtoms (Atom &a0, Atom &a1, Atom &a2, Atom &a3, Atom &a4) |
| virtual void | AssignAtoms (Atom &a0, Atom &a1, Atom &a2, Atom &a3, Atom &a4, Atom &a5) |
| virtual void | SetRelPhi (double, double) |
| Public Member Functions inherited from prf::Named | |
| Named () | |
| Create an object with name "unnamed". | |
| Named (const char *st) | |
| Create an object with name st given as a C string. | |
| Named (std::string st) | |
| Create an object with a name given as a string. | |
| std::string | Name () const |
| Retrive the name of an object. | |
| void | Name (std::string gnm) |
| Assign a new name to an object. | |
Detailed Description
This group is planar, unlike the ATriGroup, which also has two out-going bonds. By planar, we mean, Root, Junction, Branch1 and Branch2 lie in one plane. This is meant to represent groups like CO2, NH2 etc, where the outgoing atoms are identical. The Root-Junction-Branch_i angle is adjustible.
Member Function Documentation
|
virtual |
*Using the position of Base, Root and Junction, and the state of the degree of freedom associated with the node, find the coordinates of all other atoms in the node.
Reimplemented from prf::Node.
The documentation for this class was generated from the following files:
- model/Elements/TrigonalGroup.hh
- model/Elements/TrigonalGroup.cc