OpenMM
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Topology stores the topological information about a system. More...
Public Member Functions | |
def | __init__ |
Create a new Topology object. | |
def | addChain |
Create a new Chain and add it to the Topology. | |
def | addResidue |
Create a new Residue and add it to the Topology. | |
def | addAtom |
Create a new Atom and add it to the Topology. | |
def | addBond |
Create a new bond and add it to the Topology. | |
def | chains |
Iterate over all Chains in the Topology. | |
def | residues |
Iterate over all Residues in the Topology. | |
def | atoms |
Iterate over all Atoms in the Topology. | |
def | bonds |
Iterate over all bonds (each represented as a tuple of two Atoms) in the Topology. | |
def | getUnitCellDimensions |
Get the dimensions of the crystallographic unit cell. | |
def | setUnitCellDimensions |
Set the dimensions of the crystallographic unit cell. | |
def | createStandardBonds |
Create bonds based on the atom and residue names for all standard residue types. | |
def | createDisulfideBonds |
Identify disulfide bonds based on proximity and add them to the Topology. | |
Topology stores the topological information about a system.
The structure of a Topology object is similar to that of a PDB file. It consists of a set of Chains (often but not always corresponding to polymer chains). Each Chain contains a set of Residues, and each Residue contains a set of Atoms. In addition, the Topology stores a list of which atom pairs are bonded to each other, and the dimensions of the crystallographic unit cell.
Atom and residue names should follow the PDB 3.0 nomenclature for all molecules for which one exists.
def __init__ | ( | self | ) |
Create a new Topology object.
def addAtom | ( | self, | |
name, | |||
element, | |||
residue | |||
) |
def addBond | ( | self, | |
atom1, | |||
atom2 | |||
) |
def addResidue | ( | self, | |
name, | |||
chain | |||
) |
def atoms | ( | self | ) |
Iterate over all Atoms in the Topology.
def bonds | ( | self | ) |
Iterate over all bonds (each represented as a tuple of two Atoms) in the Topology.
def chains | ( | self | ) |
Iterate over all Chains in the Topology.
def createDisulfideBonds | ( | self, | |
positions | |||
) |
Identify disulfide bonds based on proximity and add them to the Topology.
positions | (list) The list of atomic positions based on which to identify bonded atoms |
def createStandardBonds | ( | self | ) |
Create bonds based on the atom and residue names for all standard residue types.
def getUnitCellDimensions | ( | self | ) |
Get the dimensions of the crystallographic unit cell.
The return value may be None if this Topology does not represent a periodic structure.
def residues | ( | self | ) |
Iterate over all Residues in the Topology.
def setUnitCellDimensions | ( | self, | |
dimensions | |||
) |
Set the dimensions of the crystallographic unit cell.