Package schrodinger :: Package structutils :: Module rmsd :: Class _ConformerRmsdBase

Class _ConformerRmsdBase

object --+
         |
        _ConformerRmsdBase

Known Subclasses:

Instance Methods

[hide private]

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

_encodeOriginalAtomNumbers(self, st)

populatePatternDict(self, st)
Populates the self._mol_pattern_dict based on the molecules in the given structure.

_getRenumberedStructure(self, st)
Returns: a new structure with a normalized atom order, based on unique SMILEs.

_getReducedStructure(self, st)
Returns: a Structure that is a simplified copy of the input: a neutral, single bond connected, heavy atom only frame.

string

getRmsdDataname(self)
Returns: m2io property dataname string.

writeStructures(self, file_name='rmsd.mae', mode='w')
Writes the reference and test structures to file.

writeCommand(self, file_name='rmsd.cmd')
Writes a Maestro command file and structures with the pair wise atom mapping in command file mode.

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

Class Variables

[hide private]

orig_index_prop = 'i_confrmsd_original_index'

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self)
(Constructor)

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

Overrides: object.__init__: (inherited documentation)

_encodeOriginalAtomNumbers(self, st)

Parameters:

st (structure.Structure) - Structure to store original atom indexes as atom-level properties.

_getRenumberedStructure(self, st)

Parameters:

st (structure.Structure) - The structure to renumber.

Returns:

a new structure with a normalized atom order, based on unique SMILEs.

_getReducedStructure(self, st)

Parameters:

st (structure.Structure) - Structure to reduce.

Returns:

a Structure that is a simplified copy of the input: a neutral, single bond connected, heavy atom only frame. The returned structure is handy for making RMSD comparisons between pseudo conformers that differ by ionization state or tautomerism.

getRmsdDataname(self)

Returns: string: m2io property dataname string. The property name indicates the reference structure, the title, the ASL used to identify comparison atoms and if the structure is in-place or mobile.

writeStructures(self, file_name=`'rmsd.mae'`, mode=`'w'`)

Writes the reference and test structures to file.

Parameters:

file_name (string) - Path of the structure file to write.
mode (string) - 'w' => write, clobber as needed 'a' => append

writeCommand(self, file_name=`'rmsd.cmd'`)

Writes a Maestro command file and structures with the pair wise atom mapping in command file mode. The Maestro file has the same basename as the command file. Clobbers existing files.

Parameters:

file_name (string) - Path to the maestro command file with the atom pairings.

Class _ConformerRmsdBase

__init__(self) (Constructor)

_encodeOriginalAtomNumbers(self, st)

_getRenumberedStructure(self, st)

_getReducedStructure(self, st)

getRmsdDataname(self)

writeStructures(self, file_name='rmsd.mae', mode='w')

writeCommand(self, file_name='rmsd.cmd')

init(self)
(Constructor)

writeStructures(self, file_name=`'rmsd.mae'`, mode=`'w'`)

writeCommand(self, file_name=`'rmsd.cmd'`)