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2017-2 Schrodinger Python API
Package schrodinger :: Package application :: Package desmond :: Module ffiostructure :: Class _FFIO
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Class _FFIO

object --+
         |
        _FFIO

A class to make access of ffio block pythonic.

Instance Methods [hide private]
 
__init__(self, ffhandle)
x.__init__(...) initializes x; see help(type(x)) for signature
 
_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.
 
_proxy(...)
 
_createSiteContainer(self)
 
site(...)
A list of ffio sites, each of which is a _FFIOSite instance.
 
_createFFIOBondContainer(self)
 
bond(...)
A list of ffio bonds, each of which is a _FFIOBond instance.
 
_createFFIOAngleContainer(self)
 
angle(...)
A list of ffio angles, each of which is a _FFIOAngle instance.
 
_createFFIODihedralContainer(self)
 
dihedral(...)
A list of ffio dihedrals, each of which is a _FFIODihedral instance.
 
_createFFIOExclusionContainer(self)
 
exclusion(...)
A list of ffio exclusions, each of which is a _FFIOExclusion instance.
 
_createFFIOPairContainer(self)
 
pair(...)
A list of ffio pairs, each of which is a _FFIOPair instance.
 
_createFFIOVdwtypeContainer(self)
 
vdwtype(...)
A list of ffio vdwtypes, each of which is a _FFIOVdwtype instance.
 
_createFFIOVdwtypescombinedContainer(self)
 
vdwtypescombined(...)
A list of ffio restraints, each of which is a _FFIORestraint instance.
 
_createFFIORestraintContainer(self)
 
restraint(...)
A list of ffio vdwtypes in the vdwtypes_combined block, each of which is a _FFIOVdwcombined instance.
 
_createFFIOVirtualContainer(self)
 
virtual(...)
A list of ffio virtuals, each of which is a _FFIOVirtual instance.
 
_createFFIOPseudoContainer(self)
 
pseudo(...)
A list of ffio pseudos, each of which is a _FFIOPseudo instance.
 
_createFFIOConstraintContainer(self)
 
constraint(...)
A list of ffio constraints, each of which is a _FFIOConstraint instance.
 
_createFFIOPosFBHWContainer(self)
 
posfbhw(...)
A list of ffio position flat bottoms, each of which is a _FFIOPosFBHW instance.
 
_createFFIOAngleFBHWContainer(self)
 
anglefbhw(...)
A list of ffio angle flat bottoms, each of which is a _FFIOAngleFBHW instance.
 
_createFFIOImproperFBHWContainer(self)
 
improperfbhw(...)
A list of ffio improper flat bottoms, each of which is a _FFIOImproperFBHW instance.
 
_createFFIOStretchFBHWContainer(self)
 
stretchfbhw(...)
A list of ffio stretch flat bottoms, each of which is a _FFIOStretchFBHW instance.
 
_createFFIOOtherBlockContainer(self)
 
other_block(...)
A list of ffio other blocks, each of which is a _FFIOOtherBlock instance.
 
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.

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables [hide private]
  _doc = '\n A list of ffio other blocks, each of which is ...
Properties [hide private]
  name
ffio block name
  version
version
  combining_rule
combining rule
  property
A dictionary of ffio properties.

Inherited from object: __class__

Method Details [hide private]

__init__(self, ffhandle)
(Constructor)

 

x.__init__(...) initializes x; see help(type(x)) for signature

Overrides: object.__init__
(inherited documentation)

_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.

site(...)

 

A list of ffio sites, each of which is a _FFIOSite instance.

Example usage, where st is a FFIOStructure instance:

 # Access an site
 siteobj = st.ffio.site[n]

 # Delete an site 
 del st.ffio.site[n]

 # Find the number of sites
 len(st.ffio.site)

 # Iterate over all sites
 for site in st.ffio.site:
     take_some_action(site)

Note: As with many other collections, the contents of the site list should not be modified through additions or deletions while you are iterating over it.

bond(...)

 

A list of ffio bonds, each of which is a _FFIOBond instance.

Example usage, where st is a FFIOStructure instance:

 # Access an bond
 bondobj = st.ffio.bond[n]

 # Delete an bond 
 del st.ffio.bond[n]

 # Find the number of bonds
 len(st.ffio.bond)

 # Iterate over all bonds
 for bond in st.ffio.bond:
     take_some_action(bond)

Note: As with many other collections, the contents of the bond list should not be modified through additions or deletions while you are iterating over it.

angle(...)

 

A list of ffio angles, each of which is a _FFIOAngle instance.

Example usage, where st is a FFIOStructure instance:

 # Access an angle
 angleobj = st.ffio.angle[n]

 # Delete an angle 
 del st.ffio.angle[n]

 # Find the number of angles
 len(st.ffio.angle)

 # Iterate over all angles
 for angle in st.ffio.angle:
     take_some_action(angle)

Note: As with many other collections, the contents of the angle list should not be modified through additions or deletions while you are iterating over it.

dihedral(...)

 

A list of ffio dihedrals, each of which is a _FFIODihedral instance.

Example usage, where st is a FFIOStructure instance:

 # Access an dihedral
 dihedralobj = st.ffio.dihedral[n]

 # Delete an dihedral 
 del st.ffio.dihedral[n]

 # Find the number of dihedrals
 len(st.ffio.dihedral)

 # Iterate over all dihedrals
 for dihedral in st.ffio.dihedral:
     take_some_action(dihedral)

Note: As with many other collections, the contents of the dihedral list should not be modified through additions or deletions while you are iterating over it.

exclusion(...)

 

A list of ffio exclusions, each of which is a _FFIOExclusion instance.

Example usage, where st is a FFIOStructure instance:

 # Access an exclusion
 exclusionobj = st.ffio.exclusion[n]

 # Delete an exclusion 
 del st.ffio.exclusion[n]

 # Find the number of exclusions
 len(st.ffio.exclusion)

 # Iterate over all exclusions
 for exclusion in st.ffio.exclusion:
     take_some_action(exclusion)

Note: As with many other collections, the contents of the exclusion list should not be modified through additions or deletions while you are iterating over it.

pair(...)

 

A list of ffio pairs, each of which is a _FFIOPair instance.

Example usage, where st is a FFIOStructure instance:

 # Access an pair
 pairobj = st.ffio.pair[n]

 # Delete an pair 
 del st.ffio.pair[n]

 # Find the number of pairs
 len(st.ffio.pair)

 # Iterate over all pairs
 for pair in st.ffio.pair:
     take_some_action(pair)

Note: As with many other collections, the contents of the site list should not be modified through additions or deletions while you are iterating over it.

vdwtype(...)

 

A list of ffio vdwtypes, each of which is a _FFIOVdwtype instance.

Example usage, where st is a FFIOStructure instance:

 # Access an vdwtype
 vdwtypeobj = st.ffio.vdwtype[n]

 # Delete an vdwtype 
 del st.ffio.vdwtype[n]

 # Find the number of vdwtypes
 len(st.ffio.vdwtype)

 # Iterate over all vdwtypes
 for vdwtype in st.ffio.vdwtype:
     take_some_action(vdwtype)

Note: As with many other collections, the contents of the vdwtype list should not be modified through additions or deletions while you are iterating over it.

vdwtypescombined(...)

 

A list of ffio restraints, each of which is a _FFIORestraint instance.

Example usage, where st is a FFIOStructure instance:

 # Access an restraint
 restraintobj = st.ffio.restraint[n]

 # Delete an restraint 
 del st.ffio.restraint[n]

 # Find the number of restraints
 len(st.ffio.restraint)

 # Iterate over all restraints
 for restraint in st.ffio.restraint:
     take_some_action(restraint)

Note: As with many other collections, the contents of the restraint list should not be modified through additions or deletions while you are iterating over it.

virtual(...)

 

A list of ffio virtuals, each of which is a _FFIOVirtual instance.

Example usage, where st is a FFIOStructure instance:

 # Access an virtual
 virtualobj = st.ffio.virtual[n]

 # Delete an virtual 
 del st.ffio.virtual[n]

 # Find the number of virtuals
 len(st.ffio.virtual)

 # Iterate over all virtuals
 for virtual in st.ffio.virtual:
     take_some_action(virtual)

Note: As with many other collections, the contents of the virtual list should not be modified through additions or deletions while you are iterating over it.

pseudo(...)

 

A list of ffio pseudos, each of which is a _FFIOPseudo instance.

Example usage, where st is a FFIOStructure instance:

 # Access an pseudo
 pseudoobj = st.ffio.pseudo[n]

 # Delete an pseudo 
 del st.ffio.pseudo[n]

 # Find the number of pseudos
 len(st.ffio.pseudo)

 # Iterate over all pseudos
 for pseudo in st.ffio.pseudo:
     take_some_action(pseudo)

Note: As with many other collections, the contents of the pseudo list should not be modified through additions or deletions while you are iterating over it.

constraint(...)

 

A list of ffio constraints, each of which is a _FFIOConstraint instance.

Example usage, where st is a FFIOStructure instance:

 # Access an constraint
 constraintobj = st.ffio.constraint[n]

 # Delete an constraint 
 del st.ffio.constraint[n]

 # Find the number of constraints
 len(st.ffio.constraint)

 # Iterate over all constraints
 for constraint in st.ffio.constraint:
     take_some_action(constraint)

Note: As with many other collections, the contents of the constraint list should not be modified through additions or deletions while you are iterating over it.

posfbhw(...)

 

A list of ffio position flat bottoms, each of which is a _FFIOPosFBHW instance.

Example usage, where st is a FFIOStructure instance:

 # Access an position flat bottom
 posfbhwobj = st.ffio.posfbhw[n]

 # Delete an position flat bottom
 del st.ffio.posfbhw[n]

 # Find the number of position flat bottoms
 len(st.ffio.posfbhw)

 # Iterate over all position flat bottoms
 for posfbhw in st.ffio.posfbhw:
     take_some_action(posfbhw)

anglefbhw(...)

 

A list of ffio angle flat bottoms, each of which is a _FFIOAngleFBHW instance.

Example usage, where st is a FFIOStructure instance:

 # Access an angle flat bottom
 anglefbhwobj = st.ffio.anglefbhw[n]

 # Delete an angle flat bottom
 del st.ffio.anglefbhw[n]

 # Find the number of angle flat bottoms
 len(st.ffio.anglefbhw)

 # Iterate over all angle flat bottoms
 for anglefbhw in st.ffio.anglefbhw:
     take_some_action(anglefbhw)

improperfbhw(...)

 

A list of ffio improper flat bottoms, each of which is a _FFIOImproperFBHW instance.

Example usage, where st is a FFIOStructure instance:

 # Access an improper flat bottom
 improperfbhwobj = st.ffio.improperfbhw[n]

 # Delete an improper flat bottom
 del st.ffio.improperfbhw[n]

 # Find the number of improper flat bottoms
 len(st.ffio.improperfbhw)

 # Iterate over all improper flat bottoms
 for improperfbhw in st.ffio.improperfbhw:
     take_some_action(improperfbhw)

stretchfbhw(...)

 

A list of ffio stretch flat bottoms, each of which is a _FFIOStretchFBHW instance.

Example usage, where st is a FFIOStructure instance:

 # Access an stretch flat bottom
 stretchfbhwobj = st.ffio.stretchfbhw[n]

 # Delete an stretch flat bottom
 del st.ffio.stretchfbhw[n]

 # Find the number of stretch flat bottoms
 len(st.ffio.stretchfbhw)

 # Iterate over all stretch flat bottoms
 for stretchfbhw in st.ffio.stretchfbhw:
     take_some_action(stretchfbhw)

other_block(...)

 

A list of ffio other blocks, each of which is a _FFIOOtherBlock instance.

Example usage, where st is a FFIOStructure instance:

 # Access an other block
 other_block = st.ffio.other_block[n]

 # Delete an other block
 del st.ffio.other_block[n]

 # Find the number of other blocks
 len(st.ffio.other_block)

 # Iterate over all other_blocks
 for other_block in st.ffio.other_block:
     take_some_action(other_block)

Note: As with many other collections, the contents of the other block list should not be modified through additions or deletions while you are iterating over it.

_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 [hide private]

_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
...

Property Details [hide private]

name

ffio block name

Get Method:
_getName(self) - Get the name for this ffio block
Set Method:
_setName(self, name) - Set the name for this ffio block

version

version

Get Method:
_getVersion(self) - Get the version
Set Method:
_setVersion(self, version) - Set the version

combining_rule

combining rule

Get Method:
_getCombiningRule(self) - Get the combining_rule
Set Method:
_setCombiningRule(self, combining_rule) - Set the combining_rule

property

A dictionary of ffio properties. Keys are strings of the form type_family_name as described in the PropertyName documentation and found in .cms files.

Get Method:
_getFFIOProperty(self)

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2017-2 Schrodinger Python API
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