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- Forcefield
- ForcefieldAtom
- ForcefieldResidue
class Forcefield |
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Forcefield class
The forcefield class contains definitions for a given forcefield.
Each forcefield object contains a dictionary of residues, with each
residue containing a dictionary of atoms. Dictionaries are used
instead of lists as the ordering is not important. The forcefield
definition files are unedited, directly from the forcefield - all
transformations are done within.
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Methods defined here:
- __init__(self, ff)
- Initialize the class by parsing the definition file
Parameters
ff: The name of the forcefield (string)
- getAmberParams(self, residue, name)
- Get the forcefield definitions from the Amber database
Parameters
residue: The residue (residue)
name: The atom name (string)
Returns
resname: The name of the amber residue
atomname: The name of the amber atom
- getCharmmParams(self, residue, name)
- Get the forcefield definitions from the Charmm database
Parameters
residue: The residue (residue)
name: The atom name (string)
Returns
resname: The name of the Charmm residue
atomname: The name of the Charmm atom
- getParams(self, residue, name)
- Get the parameters associated with the input fields.
The residue itself is needed instead of simply its name
because the forcefield may use a different residue name
than the standard amino acid name.
Parameters
residue: The residue (residue)
name: The atom name (string)
Returns
charge: The charge on the atom (float)
radius: The radius of the atom (float)
- getParseParams(self, residue, name)
- Get the forcefield definitions from the Parse database
Parameters
residue: The residue (residue)
name: The atom name (string)
Returns
resname: The name of the amber residue
atomname: The name of the amber atom
- getResidue(self, resname)
- Return the residue object with the given resname
Parameters
resname: The name of the residue (string)
Returns
residue: The residue object (ForcefieldResidue)
Data and non-method functions defined here:
- __doc__ = '\n Forcefield class\n\n The forcefiel...ll\n transformations are done within.\n\n '
- __module__ = 'forcefield'
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class ForcefieldAtom |
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ForcefieldAtom class
The ForcefieldAtom object contains fields that are related to the
forcefield at the atom level
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Methods defined here:
- __init__(self, name, charge, radius)
- Initialize the object
Parameters
name: The atom name (string)
charge: The charge on the atom (float)
radius: The radius of the atom (float)
- get(self, name)
- Get a member of the ForcefieldAtom class
Parameters
name: The name of the member (string)
Possible Values
name: The atom name (string)
charge: The charge on the atom (float)
radius: The radius of the atom (float)
epsilon: The epsilon assocaited with the atom (float)
Returns
item: The value of the member
Data and non-method functions defined here:
- __doc__ = '\n ForcefieldAtom class\n\n The Force... to the\n forcefield at the atom level\n '
- __module__ = 'forcefield'
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class ForcefieldResidue |
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ForcefieldResidue class
The ForceFieldResidue class contains a mapping of all atoms within
the residue for easy searching.
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Methods defined here:
- __init__(self, name)
- Initialize the ForceFieldResidue object
Parameters
name: The name of the residue (string)
- addAtom(self, atom)
- Add an atom to the ForcefieldResidue
Parameters
atom: The atom to be added (atom)
- getAtom(self, atomname)
- Return the atom object with the given atomname
Parameters
resname: The name of the atom (string)
Returns
residue: The atom object (ForcefieldAtom)
Data and non-method functions defined here:
- __doc__ = '\n ForcefieldResidue class\n\n The Fo...thin\n the residue for easy searching.\n '
- __module__ = 'forcefield'
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