Graph/Tree Structure Modification Functions


Classes

class  phoenix::MOL
 MOL Class Class MOL can be used to copy molecules. More...

Functions

ChainKey phoenix::cCreate (string n)
 Create a new chain.
void phoenix::cDelete (ChainKey c)
 Delete a chain.
void phoenix::clDelete (const ChainList &cl)
 Delete several chains.
ResidueKey phoenix::rCreate (ChainKey p, RT rt)
 Create a new residue.
void phoenix::rDelete (ResidueKey r)
 Delete a residue.
void phoenix::rlDelete (const ResidueList &rl)
 Delete several residues.
AtomKey phoenix::aCreate (ResidueKey p, ELE e, Vec3_t c, GEO g)
 Create a new atom.
void phoenix::aDelete (AtomKey a)
 Delete an atom.
void phoenix::alDelete (const AtomList &al)
 Delete several atoms.
BondKey phoenix::bCreate (AtomKey a1, AtomKey a2, BT bt)
 Create a new bond.
void phoenix::bDelete (BondKey b)
 Delete a bond.
void phoenix::blDelete (const BondList &bl)
 Delete several bonds.

Detailed Description

These functions can be used to modify the hierarchical tree and the molecular graph.

Function Documentation

ChainKey phoenix::cCreate ( string  n  ) 

Create a new chain.

Create a new chain with name n and return the new ChainKey.

void phoenix::cDelete ( ChainKey  c  ) 

Delete a chain.

Delete chain c and all of its children.

void phoenix::clDelete ( const ChainList &  cl  ) 

Delete several chains.

Delete all chains in ChainList c and all of its children.

ResidueKey phoenix::rCreate ( ChainKey  p,
RT  rt 
)

Create a new residue.

Create a new residue of type rt at the end of chain p and return the new ResidueKey.

void phoenix::rDelete ( ResidueKey  r  ) 

Delete a residue.

Delete residue r and all of its children.

void phoenix::rlDelete ( const ResidueList &  rl  ) 

Delete several residues.

Delete all residues in ResidueList rl and all of its children.

AtomKey phoenix::aCreate ( ResidueKey  p,
ELE  e,
Vec3_t  c,
GEO  g 
)

Create a new atom.

Create a new atom with element e, coordinates c and geometrie g at the end of residue p and return the new AtomKey.

void phoenix::aDelete ( AtomKey  a  ) 

Delete an atom.

Delete atom a and all of its bonds.

void phoenix::alDelete ( const AtomList &  al  ) 

Delete several atoms.

Delete all atoms in AtomList al and all of its bonds.

BondKey phoenix::bCreate ( AtomKey  a1,
AtomKey  a2,
BT  bt 
)

Create a new bond.

Create a new bond with bond type bt from atom a1 to atom a2 and return the new BondKey. If a bond between this atoms already exists it will be overwriten.

void phoenix::bDelete ( BondKey  b  ) 

Delete a bond.

Delete bond b.

void phoenix::blDelete ( const BondList &  bl  ) 

Delete several bonds.

Delete all bonds in BondList bl.


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