Package schrodinger :: Package trajectory :: Module ffstructure :: Class FFStructure

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Class FFStructure

A class containing force field information.

Instance Methods

[hide private]

__init__(self, parent_st, ff_handle)

parent_structure(self)

ffangle(self)
Returns iterator for all angle force filed items

ffbond(self)
Returns iterator for all bond force filed items

ffconstraint(self)
Returns iterator for all constraints

ffdihedral(self)
Returns iterator for all dihedrals

ffexclusion(self)
Returns iterator for all exclusion pairs

ffpair(self)
Returns iterator for all pairs

ffpseudo(self)

ffrestraint(self)
Returns iterator for all restraints

ffsite(self)
Returns iterator for all sites

ffvdwtype(self)
Returns iterator for all Van der Waals types

ffvirtual(self)
Returns iterator for all virtual sites

_processFF(self)
Reading force field information from an ffio block.

_getCharge(self)

_getMass(self)

_getTotalMass(self)

_getTotalPseudo(self)

_getPseudoMass(self)

_getPseudoCharge(self)

_getAtomTotal(self)

_getMolTotal(self)

_getFfioMolTotal(self)

__copy__(self)
Copy the structure.

__del__(self)
Delete mmffio handle

Class Variables

[hide private]

charge = property(_getCharge, doc= 'charges of individual atom...

mass = property(_getMass, doc= 'mass of individual atoms in th...

total_mass = property(_getTotalMass, doc= 'mass of all atoms i...

total_pseudo = property(_getTotalPseudo, doc= 'total number of...

pseudo_mass = property(_getPseudoMass, doc= 'mass of individua...

pseudo_charge = property(_getPseudoCharge, doc= 'charge of ind...

atom_total = property(_getAtomTotal, doc= "total number of ato...

mol_total = property(_getMolTotal, doc= "total number of ct mo...

ffio_mol_total = property(_getMolTotal, doc= "total number of ...

Method Details

[hide private]

parent_structure(self)

Decorators:

@property

ffangle(self)

Returns iterator for all angle force filed items

Decorators:

@property

ffbond(self)

Returns iterator for all bond force filed items

Decorators:

@property

ffconstraint(self)

Returns iterator for all constraints

Decorators:

@property

ffdihedral(self)

Returns iterator for all dihedrals

Decorators:

@property

ffexclusion(self)

Returns iterator for all exclusion pairs

Decorators:

@property

ffpair(self)

Returns iterator for all pairs

Decorators:

@property

ffpseudo(self)

Decorators:

@property

ffrestraint(self)

Returns iterator for all restraints

Decorators:

@property

ffsite(self)

Returns iterator for all sites

Decorators:

@property

ffvdwtype(self)

Returns iterator for all Van der Waals types

Decorators:

@property

ffvirtual(self)

Returns iterator for all virtual sites

Decorators:

@property

copy(self)

Copy the structure. This method is invoked by copy.copy.

Class Variable Details

[hide private]

charge

Value:

property(_getCharge, doc= 'charges of individual atoms in the structur
e')

mass

Value:

property(_getMass, doc= 'mass of individual atoms in this structure')

total_mass

Value:

property(_getTotalMass, doc= 'mass of all atoms in this structure')

total_pseudo

Value:

property(_getTotalPseudo, doc= 'total number of pseudo atoms in this s
tructure')

pseudo_mass

Value:

property(_getPseudoMass, doc= 'mass of individual pseudo atoms in this
 structure ' '(will always be zero) .')

pseudo_charge

Value:

property(_getPseudoCharge, doc= 'charge of individual pseudo atoms in 
this structure')

atom_total

Value:

property(_getAtomTotal, doc= "total number of atoms in the structure")

mol_total

Value:

property(_getMolTotal, doc= "total number of ct molecules in the struc
ture")

ffio_mol_total

Value:

property(_getMolTotal, doc= "total number of ffio molecules in the str
ucture")