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

Module ffiostructure

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

FFIOStructure is a pythonic, object oriented wrapper for the mmffio library that provides access to sites, bonds, angles, dihedrals, exclusions, pairs, vdwtypes, restraints, virtuals, pseudos, constraints and their properties. It inherits from Structure and hence provides access to atoms, bonds and their properties.

The default error handler for the ffiostructure module is set to mm.error_handler. If no error handler is specified for error_handler arguments, its value is what will be used.

Classes

[hide private]

_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

[hide private]

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=2, 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

[hide private]

__doc__ = ...

ffio_sub_block_prop_links = {'angle': {'i_ffio_ai': [], 'i_ffi...

ffio_block_names = {'angle': 'angle', 'anglefbhw': 'anglefbhw'...

prop_type_names = {'b': 'boolean', 'i': 'int', 'r': 'real', 's...

fepio_sub_block_prop_links = {'anglemap': {'i_fepio_ai': [], '...

fname = "md_test.cms"

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

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

__package__ = 'schrodinger.application.desmond'

Function Details

[hide private]

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:

{'angle': {'i_ffio_ai': [],
           'i_ffio_aj': [],
           'i_ffio_ak': [],
           'r_ffio_c1': [],
           'r_ffio_c2': [],
           's_ffio_funct': []},
 'anglefbhw': {'i_ffio_ai': [],
               'i_ffio_aj': [],
...

ffio_block_names

Value:

{'angle': 'angle',
 'anglefbhw': 'anglefbhw',
 'bond': 'bond',
 'constraint': 'constraint',
 'dihedral': 'dihed',
 'exclusion': 'excl',
 'improperfbhw': 'improperfbhw',
 'pair': 'pair',
...

prop_type_names

Value:

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

fepio_sub_block_prop_links

Value:

{'anglemap': {'i_fepio_ai': [],
              'i_fepio_aj': [],
              'i_fepio_ak': [],
              'i_fepio_ti': [],
              'i_fepio_tj': []},
 'atommap': {'i_fepio_ai': ['ai',
                            <schrodinger.infra.mmcheck._Wrapper instan
ce at 0x7f596902a050>,
...