Home | Trees | Indices | Help |
|
---|
|
ViewerFramework.VFCommand.Command --+ | mvCommand.MVCommand --+ | AddHydrogensCommand
This command adds hydrogen atoms to all atoms in all molecules that have at least one member (i.e atom, residue, chain, base-pair etc..) specified in the first argument. Package:Pmv Module :editCommands Class:AddHydrogensCommand Command:add_h Synopsis: AtomSet<---add_h(nodes, polarOnly=0, method='noBondOrder, renumber=1,**kw) Required Arguments: nodes --- TreeNodeSet holding the current selection polarOnly --- default is 0 method --- Hydrogen atoms can be added using 2 different methods, ex: method='withBondOrder', default is 'noBondOrder' renumber --- default is 1 Returns an atomSet containing the created H atoms NOTE: This command adds hydrogens to all atoms in the molecule specified using the nodes argument. The hydrogen atoms added to each molecule are also saved as a set called mol.name + '_addedH' This class uses the AddHydrogens class from the PyBabel package. Before this AddHydrogens object can be used, atoms must have been assigned a type see (AtomHybridization in types.py). Hydrogen atoms can be added using 2 different methods. The first one requires bondOrders to have been calculated previousely. example: >>> atype = AtomHybridization() >>> atype.assignHybridization(atoms) >>> addh = AddHydrogens() >>> hat = addh.addHydrogens(atoms) atoms has to be a list of atom objects Atom: a .coords : 3-sequence of floats a .bonds : list of Bond objects babel_type: string babel_atomic_number: int Bond: b .atom1 : instance of Atom b .atom2 : instance of Atom or >>> addh = AddHydrogens() >>> hat = addh.addHydrogens(atoms, method='withBondOrder') atoms has to be a list of atom objects as above and Bond: b .atom1 : instance of Atom b .atom2 : instance of Atom b .bondOrder : integer these calls return a list 'hat' containing a tuple for each Hydrogen atom to be added. This tuple provides: coordsH : 3-float coordinates of the H atom atom : the atom to which the H atom is to be connected atomic_number : the babel_atomic_number of the H atom type : tyhe b:wabel_type of the H atom reimplementation of Babel1.6 in Python by Michel Sanner April 2000 Original code by W. Patrick Walters and Matthew T. Stahl
|
|||
| __init__(self, func=None) | ||
|
onAddCmdToViewer(self) method called when an instance of this command is added to the viewer. |
||
|
__call__(self,
nodes,
polarOnly=False,
method='noBondOrder',
renumber=True,
**kw) AtomSet <- add_h(nodes, polarOnly=0, method='noBondOrder, renumber=1,**kw) nodes --- TreeNodeSet holding the current selection polarOnly --- default is False method --- Hydrogen atoms can be added using 2 different methods, ex --- method='withBondOrder', default is 'noBondOrder' renumber --- default is True Returns an atomSet containing the created H atoms NOTE: This command adds hydrogens to all atoms in the molecule specified using the nodes argument. |
||
|
doit(self,
nodes,
polarOnly=False,
method='noBondOrder',
renumber=True) None <- add_h(nodes, polarOnly=False, method='noBondOrder', renumber=True) |
||
Inherited from Inherited from Inherited from |
|
|||
Inherited from |
|
|
|
AtomSet <- add_h(nodes, polarOnly=0, method='noBondOrder, renumber=1,**kw) nodes --- TreeNodeSet holding the current selection polarOnly --- default is False method --- Hydrogen atoms can be added using 2 different methods, ex --- method='withBondOrder', default is 'noBondOrder' renumber --- default is True Returns an atomSet containing the created H atoms NOTE: This command adds hydrogens to all atoms in the molecule specified using the nodes argument. The hydrogen atoms added to each molecule are also saved as a set called mol.name + '_addedH'
|
|
Home | Trees | Indices | Help |
|
---|
Generated by Epydoc 3.0alpha3 on Fri Nov 2 14:14:30 2007 | http://epydoc.sourceforge.net |