Package schrodinger :: Package application :: Package desmond :: Module ffiostructure

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Module ffiostructure

Classes

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__metaclass__
type(object) -> the object's type type(name, bases, dict) -> a new type

_FFIOSubBlockProperty
A dictionary of ffio sub-block properties.

_FFIOSubBlockMeta
A meta-class to different ffio sub block type classses.

_FFIOSubBlock
A class to make access of ffio sub-block properties more pythonic.

_FFIOSite
A class to make access of mmffio site properties more pythonic.

_FFIOBond
A class to make access of mmffio bond properties more pythonic.

_FFIOAngle
A class to make access of mmffio angle properties more pythonic.

_FFIODihedral
A class to make access of mmffio dihedral properties more pythonic.

_FFIOExclusion
A class to make access of mmffio exclusion properties more pythonic.

_FFIOPair
A class to make access of mmffio pair properties more pythonic.

_FFIOVdwtype
A class to make access of mmffio vdwtype properties more pythonic.

_FFIOVdwtypescombined
A class to make access of mmffio vdwtype properties more pythonic.

_FFIORestraint
A class to make access of mmffio restraint properties more pythonic.

_FFIOVirtual
A class to make access of mmffio virtual properties more pythonic.

_FFIOPseudo
A class to make access of mmffio pseudo properties more pythonic.

_FFIOConstraint
A class to make access of mmffio constraint properties more pythonic.

_FFIOPosFBHW
A class to make access of mmffio position flat bottom properties more pythonic.

_FFIOAngleFBHW
A class to make access of mmffio angle flat bottom properties more pythonic.

_FFIOImproperFBHW
A class to make access of mmffio improper flat bottom properties more pythonic.

_FFIOStretchFBHW
A class to make access of mmffio stretch flat bottom properties more pythonic.

_FFIOSubBlockContainer

_FFIOSiteContainer

_FFIOBondContainer

_FFIOAngleContainer

_FFIODihedralContainer

_FFIOExclusionContainer

_FFIOPairContainer

_FFIOVdwtypeContainer

_FFIOVdwtypescombinedContainer

_FFIORestraintContainer

_FFIOVirtualContainer

_FFIOPseudoContainer

_FFIOConstraintContainer

_FFIOPosFBHWContainer

_FFIOAngleFBHWContainer

_FFIOImproperFBHWContainer

_FFIOStretchFBHWContainer

_ElementProperty
A dictionary of other_block element based properties.

_FFIOElementProperty
hash(x)

_Element

_FFIOElement
hash(x)

_OtherBlock

_FFIOOtherBlock
hash(x)

_OtherBlockContainer
The class to provide access to other block instances.

_FFIOOtherBlockContainer

_FFIOProperty
A dictionary of ffio properties, with all dict methods.

_FFIO
A class to make access of ffio block pythonic.

_FEPIOElementProperty
hash(x)

_FEPIOElement
hash(x)

_FEPIOOtherBlock
hash(x)

_FEPIOOtherBlockContainer

_FEPIOSubBlockProperty
A dictionary of fepio sub-block properties.

_FEPIOSubBlock
A class to make access of fepio sub-block properties more pythonic.

_FEPIOSubBlockMeta
A meta-class to different fepio sub block type classses.

_FEPIOAtomMap
hash(x)

_FEPIOBondMap
hash(x)

_FEPIOAngleMap
hash(x)

_FEPIODihedMap
hash(x)

_FEPIOExclMap
hash(x)

_FEPIOPairMap
hash(x)

_FEPIOSubBlockContainer

_FEPIOAtomMapContainer

_FEPIOBondMapContainer

_FEPIOAngleMapContainer

_FEPIODihedMapContainer

_FEPIOExclMapContainer

_FEPIOPairMapContainer

_FEPIOProperty
A dictionary of fepio properties, with all dict methods.

_FEPIO
A class to make access of fepio block pythonic.

FFIOStructure
Class to create python interface to force field data.

CMSReader
A class for reading structures from a CMS format file.

Functions

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make_property(getter, setter, doc)

get_ffio_sub_block_std_prop_short_name(block_type, prop_name)
Function to get short names of properties.

get_ffio_sub_block_std_prop_getter(block_type, prop_name)
Function to get mmffio getter method of properties.

get_ffio_sub_block_std_prop_setter(block_type, prop_name)
Function to get mmffio setter method of properties.

make_property_fepio(getter, setter, doc)

get_fepio_sub_block_std_prop_short_name(block_type, prop_name)
Function to get short names of properties.

get_fepio_sub_block_std_prop_getter(block_type, prop_name)
Function to get mmfepio getter method of properties.

get_fepio_sub_block_std_prop_setter(block_type, prop_name)
Function to get mmfepio setter method of properties.

write_cms(ct, filename, mode=mm.M2IO_WRITE, error_handler=None)
Write a CT to a Maestro format file.

write_cms_to_string(ct, error_handler=None)
Write a CT to a string.

merge_ct(ct0, ct1)
Returns a new ct which is the result of merging ct0 and ct1.

Variables

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__doc__ = ...

ffio_sub_block_prop_links = {'site': {'s_ffio_type': ['type', ...

ffio_block_names = {'site': 'site', 'bond': 'bond', 'angle': '...

prop_type_names = {"s": "string", "i": "int", "r": "real", "b"...

fepio_sub_block_prop_links = {'atommap': {'i_fepio_ai': ['ai',...

fname = "md_test.cms"

struc = [e for e in CMSReader(fname)]

ct = merge_ct(struc [2], struc [3])

Function Details

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get_ffio_sub_block_std_prop_short_name(block_type, prop_name)

Function to get short names of properties. It is picked from the ffio_sub_block_prop_links dict if avaiable, else deduced from property name

get_ffio_sub_block_std_prop_getter(block_type, prop_name)

Function to get mmffio getter method of properties. It is picked from the ffio_sub_block_prop_links dict if avaiable, else deduced from property name

get_ffio_sub_block_std_prop_setter(block_type, prop_name)

Function to get mmffio setter method of properties. It is picked from the ffio_sub_block_prop_links dict if avaiable, else deduced from property name

get_fepio_sub_block_std_prop_short_name(block_type, prop_name)

Function to get short names of properties. It is picked from the fepio_sub_block_prop_links dict if avaiable, else deduced from property name

get_fepio_sub_block_std_prop_getter(block_type, prop_name)

Function to get mmfepio getter method of properties. It is picked from the fepio_sub_block_prop_links dict if avaiable, else deduced from property name

get_fepio_sub_block_std_prop_setter(block_type, prop_name)

Function to get mmfepio setter method of properties. It is picked from the fepio_sub_block_prop_links dict if avaiable, else deduced from property name

Variables Details

[hide private]

doc

Value:

"""
The central interface for reading and editing Maestro format chemical
sructures with force field data.

L{FFIOStructure} is a pythonic, object oriented wrapper for the mmffio
 library
that provides access to sites, bonds, angles, dihedrals, exclusions, p
airs,
...

ffio_sub_block_prop_links

Value:

{'site': {'s_ffio_type': ['type', mm.mmffio_site_get_type, mm.mmffio_s
ite_set_type], 's_ffio_site': ['site', mm.mmffio_site_get_site_name, m
m.mmffio_site_set_site_name], 'r_ffio_charge': ['charge', mm.mmffio_si
te_get_charge, mm.mmffio_site_set_charge], 'r_ffio_mass': ['mass', mm.
mmffio_site_get_mass, mm.mmffio_site_set_mass], 's_ffio_vdwtype': ['vd
wtype', mm.mmffio_site_get_vdwtype, mm.mmffio_site_set_vdwtype], 'r_ff
io_c1': ['c1', mm.mmffio_site_get_c1, mm.mmffio_site_set_c1], 'r_ffio_
c2': ['c2', mm.mmffio_site_get_c2, mm.mmffio_site_set_c2]}, 'bond': {'
...

ffio_block_names

Value:

{'site': 'site', 'bond': 'bond', 'angle': 'angle', 'dihedral': 'dihed'
, 'exclusion': 'excl', 'pair': 'pair', 'vdwtype': 'vdwtype', 'restrain
t': 'restraint', 'virtual': 'virtual', 'pseudo': 'pseudo', 'constraint
': 'constraint', 'posfbhw': 'posfbhw', 'anglefbhw': 'anglefbhw', 'impr
operfbhw': 'improperfbhw', 'stretchfbhw': 'stretchfbhw', 'vdwtypescomb
ined': 'vdwtypescombined',}

prop_type_names

Value:

{"s": "string", "i": "int", "r": "real", "b": "boolean",}

fepio_sub_block_prop_links

Value:

{'atommap': {'i_fepio_ai': ['ai', mm.mmfepio_atommap_get_ai, mm.mmfepi
o_atommap_set_ai], 'i_fepio_aj': ['aj', mm.mmfepio_atommap_get_aj, mm.
mmfepio_atommap_set_aj]}, 'bondmap': {'i_fepio_ai': [], 'i_fepio_aj': 
[], 'i_fepio_ti': [], 'i_fepio_tj': []}, 'anglemap': {'i_fepio_ai': []
, 'i_fepio_aj': [], 'i_fepio_ak': [], 'i_fepio_ti': [], 'i_fepio_tj': 
[]}, 'dihedmap': {'i_fepio_ai': [], 'i_fepio_aj': [], 'i_fepio_ak': []
, 'i_fepio_al': [], 'i_fepio_ti': [], 'i_fepio_tj': []}, 'exclmap': {'
i_fepio_ai': [], 'i_fepio_aj': [], 'i_fepio_ti': [], 'i_fepio_tj': []}
...