Package schrodinger :: Package application :: Package desmond :: Module ffiostructure :: Class _FFIO

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Class _FFIO

A class to make access of ffio block pythonic.

Instance Methods

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__init__(self, ffhandle)

_setName(self, name)
Set the name for this ffio block

_getName(self)
Get the name for this ffio block

_setVersion(self, version)
Set the version

_getVersion(self)
Get the version

_setCombiningRule(self, combining_rule)
Set the combining_rule

_getCombiningRule(self)
Get the combining_rule

_createProxy(self)
A method to create a proxy to be passed to subobjects that need to hold a reference to the parent FFIO object.

_createSiteContainer(self)

_createFFIOBondContainer(self)

_createFFIOAngleContainer(self)

_createFFIODihedralContainer(self)

_createFFIOExclusionContainer(self)

_createFFIOPairContainer(self)

_createFFIOVdwtypeContainer(self)

_createFFIOVdwtypescombinedContainer(self)

_createFFIORestraintContainer(self)

_createFFIOVirtualContainer(self)

_createFFIOPseudoContainer(self)

_createFFIOConstraintContainer(self)

_createFFIOPosFBHWContainer(self)

_createFFIOAngleFBHWContainer(self)

_createFFIOImproperFBHWContainer(self)

_createFFIOStretchFBHWContainer(self)

_createFFIOOtherBlockContainer(self)

getOtherBlockNames(self)

_getFFIOProperty(self)

addSite(self)
Add a new site to this ffio block, and return its Site object.

addBond(self)
Add a new bond to this ffio block, and return its Bond object.

addAngle(self)
Add a new angle to this ffio block, and return its Angle object.

addDihedral(self)
Add a new dihedral to this ffio block, and return its Dihedral object.

addExclusion(self)
Add a new exclusion to this ffio block, and return its Exclusion object.

addPair(self)
Add a new pair to this ffio block, and return its Pair object.

addVdwtype(self)
Add a new vdwtype to this ffio block, and return its Vdwtype object.

addVdwtypescombined(self)
Add a new vdwtypescombined item to this ffio block, and return its Vdwtypescombined object.

addRestraint(self)
Add a new restraint to this ffio block, and return its Restraint object.

addVirtual(self)
Add a new virtual to this ffio block, and return its Virtual object.

addPseudo(self)
Add a new pseudo to this ffio block, and return its Pseudo object.

addConstraint(self)
Add a new constraint to this ffio block, and return its Constraint object.

addPosfbhw(self)

addAnglefbhw(self)

addImproperfbhw(self)

addStretchfbhw(self)

addOtherBlock(self, name)
Add a new other block to this ffio block, and return it.

addSites(self, num_sites)
Add the specified number of sites to this ffio block.

addBonds(self, num_bonds)
Add the specified number of bonds to this ffio block.

addAngles(self, num_angles)
Add the specified number of angles to this ffio block.

addDihedrals(self, num_dihedrals)
Add the specified number of dihedrals to this ffio block.

addExclusions(self, num_exclusions)
Add the specified number of exclusions to this ffio block.

addPairs(self, num_pairs)
Add the specified number of pairs to this ffio block.

addVdwtypes(self, num_vdwtypes)
Add the specified number of vdwtypes to this ffio block.

addVdwtypescombineds(self, num_vdwtypes)
Add the specified number of vdwtypes to this ffio block.

addRestraints(self, num_restraints)
Add the specified number of restraints to this ffio block.

addVirtuals(self, num_virtuals)
Add the specified number of virtuals to this ffio block.

addPseudos(self, num_pseudos)
Add the specified number of pseudos to this ffio block.

addConstraints(self, num_constraints)
Add the specified number of constraints to this ffio block.

addPosfbhws(self, num_posfbhws)

addAnglefbhws(self, num_anglefbhws)

addImproperfbhws(self, num_improperfbhws)

addStretchfbhws(self, num_stretchfbhws)

_deleteItems(self, indices, delete_method)
Delete multiple item from ffio sub-block.

deleteSites(self, indices)

deleteBonds(self, indices)

deleteAngles(self, indices)

deleteDihedrals(self, indices)

deleteExclusions(self, indices)

deletePairs(self, indices)

deleteVdwtypes(self, indices)

deleteVdwtypescombined(self, indices)

deleteRestraints(self, indices)

deleteVirtuals(self, indices)

deletePseudos(self, indices)

deleteConstraints(self, indices)

deletePosfbhws(self, indices)

deleteAnglefbhws(self, indices)

deleteImproperfbhws(self, indices)

deleteStretchfbhws(self, indices)

deleteOtherBlocks(self, indices)
Delete multiple other blocks from the ffio block.

Class Variables

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name = property(_getName, _setName, doc= "ffio block name")

version = property(_getVersion, _setVersion, doc= "version")

combining_rule = property(_getCombiningRule, _setCombiningRule...

_proxy = CreateWhenNeeded(_createProxy, "_proxy")

site = CreateWhenNeeded(_createSiteContainer, "site", _doc)

bond = CreateWhenNeeded(_createFFIOBondContainer, "bond", _doc)

angle = CreateWhenNeeded(_createFFIOAngleContainer, "angle", _...

dihedral = CreateWhenNeeded(_createFFIODihedralContainer, "dih...

exclusion = CreateWhenNeeded(_createFFIOExclusionContainer, "e...

pair = CreateWhenNeeded(_createFFIOPairContainer, "pair", _doc)

vdwtype = CreateWhenNeeded(_createFFIOVdwtypeContainer, "vdwty...

vdwtypescombined = CreateWhenNeeded(_createFFIOVdwtypescombine...

restraint = CreateWhenNeeded(_createFFIORestraintContainer, "r...

virtual = CreateWhenNeeded(_createFFIOVirtualContainer, "virtu...

pseudo = CreateWhenNeeded(_createFFIOPseudoContainer, "pseudo"...

constraint = CreateWhenNeeded(_createFFIOConstraintContainer, ...

posfbhw = CreateWhenNeeded(_createFFIOPosFBHWContainer, "posfb...

anglefbhw = CreateWhenNeeded(_createFFIOAngleFBHWContainer, "a...

improperfbhw = CreateWhenNeeded(_createFFIOImproperFBHWContain...

stretchfbhw = CreateWhenNeeded(_createFFIOStretchFBHWContainer...

_doc = ...

other_block = CreateWhenNeeded(_createFFIOOtherBlockContainer,...

property = property(_getFFIOProperty, doc= "A dictionary of ff...

Method Details

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_createProxy(self)

A method to create a proxy to be passed to subobjects that need to hold a reference to the parent FFIO object. This prevents cyclic references and therefore allows FFIO instances to be deallocated by reference counting rather than waiting for a garbage collection sweep.

_deleteItems(self, indices, delete_method)

Delete multiple item from ffio sub-block. The argument indices must be a sequence or an iterable, and able to be interpreted as ints.

After deletion, indices are renumbered from 1 to len(<sub-block>). Pre-existing references to items will not be correct, as they store index values.

deleteOtherBlocks(self, indices)

Delete multiple other blocks from the ffio block. The argument indices must be a sequence or an iterable, and able to be interpreted as ints.

After deletion, indices are renumbered from 0 to len(other_block) - 1.

Class Variable Details

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combining_rule

Value:

property(_getCombiningRule, _setCombiningRule, doc= "combining rule")

angle

Value:

CreateWhenNeeded(_createFFIOAngleContainer, "angle", _doc)

dihedral

Value:

CreateWhenNeeded(_createFFIODihedralContainer, "dihedral", _doc)

exclusion

Value:

CreateWhenNeeded(_createFFIOExclusionContainer, "exclusion", _doc)

vdwtype

Value:

CreateWhenNeeded(_createFFIOVdwtypeContainer, "vdwtype", _doc)

vdwtypescombined

Value:

CreateWhenNeeded(_createFFIOVdwtypescombinedContainer, "vdwtypescombin
ed", _doc)

restraint

Value:

CreateWhenNeeded(_createFFIORestraintContainer, "restraint", _doc)

virtual

Value:

CreateWhenNeeded(_createFFIOVirtualContainer, "virtual", _doc)

pseudo

Value:

CreateWhenNeeded(_createFFIOPseudoContainer, "pseudo", _doc)

constraint

Value:

CreateWhenNeeded(_createFFIOConstraintContainer, "constraint", _doc)

posfbhw

Value:

CreateWhenNeeded(_createFFIOPosFBHWContainer, "posfbhw", _doc)

anglefbhw

Value:

CreateWhenNeeded(_createFFIOAngleFBHWContainer, "anglefbhw", _doc)

improperfbhw

Value:

CreateWhenNeeded(_createFFIOImproperFBHWContainer, "improperfbhw", _do
c)

stretchfbhw

Value:

CreateWhenNeeded(_createFFIOStretchFBHWContainer, "stretchfbhw", _doc)

_doc

Value:

"""
      A list of ffio other blocks, each of which is a L{_FFIOOtherBloc
k}
      instance. 
    
      Example usage, where C{st} is a FFIOStructure instance::

        # Access an other block
...

other_block

Value:

CreateWhenNeeded(_createFFIOOtherBlockContainer, "other_block", _doc)

property

Value:

property(_getFFIOProperty, doc= "A dictionary of ffio properties. Keys
 are strings of " "the form C{type_family_name} as described in the " 
"L{PropertyName} documentation and found in C{.cms} files.")