Package schrodinger :: Package utils :: Module cgxutils

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Module cgxutils

Classes

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SerializationError

FragmentLibrary
Encapsulates access to CGX fragment library (SQLite3 file).

Functions

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numpy.ndarray

serialize_conformations(conformations)
Converts conformations into numpy.ndarray instance.

list((float, numpy.ndarray))

deserialize_conformations(data)
Does the opposite of serialize_conformations: converts array of floats (buffer) into a list of conformations.

_order(i, j)

tuple(dict, dict)

_get_stereo(st, logger)
Extracts and parses mmstereo properties (s_st_).

recompute_stereo(st)

has_undefined_stereo(st, logger)
Extracts and parses mmstereo properties (s_st_), return True if there is an undefined (labelled as '?') chirality or cis/trans.

_discard_stereo(st)
Deletes mmstereo properties.

_compute_stereo(st)

_parity(*x)
Returns parity of the permutation (O(N^2)).

_set_stereo(origin_cc, origin_sb, st, logger, i_f3d_origin)
Set fragment's s_st_ properties from the origin's data in origin_cc and origin_sb.

list(schrodinger.Structure)

chop(engine, st, logger=None, i_f3d_origin='i_f3d_origin')
Chops structure into ConfGenX fragments (side effect: modifies atom properties of the input structure).

is_builtin_fragment(smiles)
Checks whether the smiles is for one of the "built-in" fragments.

uniquesmiler()
Returns unique SMILES generator.

read_structures_as_conformations(source, energy_property, logger=None, engine=None)
Gets structures from file/generator, chops them into fragments.

default_custom_fraglib()
Path to the custom fragments library that is to be used by default.

Variables

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_LOGGER_NAME = 'cgxutils'

__package__ = 'schrodinger.utils'

Function Details

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serialize_conformations(conformations)

Converts conformations into numpy.ndarray instance.

Parameters:

conformations (Iterable of iterables.) - Iterable over conformations. Each conformation must be an iterable with two elements (energy, coordinates). The "energy" must be convertible to float and "coordinates" must be a numpy.ndarray of shape (natoms, 3). Number of the "coordinates" must be the same for all "conformations".

Returns: numpy.ndarray

Serialized conformations.

deserialize_conformations(data)

Does the opposite of serialize_conformations: converts array of floats (buffer) into a list of conformations.

Parameters:

data (buffer) - Serialized conformations.

Returns: list((float, numpy.ndarray))

List of conformations.

_get_stereo(st, logger)

Extracts and parses mmstereo properties (s_st_).

Parameters:

st (schrodinger.Structure) - Structure.

Returns: tuple(dict, dict)

Dictionaries for chiral atoms and stereo bonds. The chirality dictionary maps chiral atom indices to 4- or 5-tuples

(X, 
          a1, a2, a3, a4)

(4-tuples lack a4) where X denotes the "chirality" (R, S, ANR or ANS), and a1, a2, a3, a4 are bonded atom indices in the appropriate order. The stereo dictionary maps bonds (as ordered 2-tuples of atom indices) to the tuples like

(X, a1, a2, 
          a3, a4)

where X is E, Z, P or M and the remaining members are indices of the atoms involved.

has_undefined_stereo(st, logger)

Extracts and parses mmstereo properties (s_st_), return True if there is an undefined (labelled as '?') chirality or cis/trans.

Parameters:

st (schrodinger.Structure) - Structure.

_set_stereo(origin_cc, origin_sb, st, logger, i_f3d_origin)

Set fragment's s_st_ properties from the origin's data in origin_cc and origin_sb.

Parameters:

origin_cc (dict) - Chiral centers dictionary returned by _get_stereo() for the origin (parent) structure.
origin_sb (dict) - EZPM dictionary returned by _get_stereo() for the origin (parent) structure.

chop(engine, st, logger=None, i_f3d_origin=`'i_f3d_origin'`)

Chops structure into ConfGenX fragments (side effect: modifies atom properties of the input structure).

Parameters:

engine (schrodinger.infra.fast3d.Engine) - Fast3D engine.
st (schrodinger.Structure) - Structure (may include several molecules).
i_f3d_origin (str) - Name of the atom property to keep track of the original atom indices.

Returns: list(schrodinger.Structure)

List of fragments.

read_structures_as_conformations(source, energy_property, logger=None, engine=None)

Gets structures from file/generator, chops them into fragments. Skips the ones that have more than one fragment. Gathers conformations of the "elementary" (indivisible) fragments into a dictionary keyed by unique SMILES.

Parameters:

source (str or generator) - Structure file name or generator of structures.
energy_property (str) - Name of the "energy" CT-level property (required).
logger (log.Logger) - Logger (can be None).
engine (schrodinger.infra.fast3d.Engine) - Fast3D engine (can be None).

Module cgxutils

serialize_conformations(conformations)

deserialize_conformations(data)

_get_stereo(st, logger)

has_undefined_stereo(st, logger)

_set_stereo(origin_cc, origin_sb, st, logger, i_f3d_origin)

chop(engine, st, logger=None, i_f3d_origin='i_f3d_origin')

read_structures_as_conformations(source, energy_property, logger=None, engine=None)

chop(engine, st, logger=None, i_f3d_origin=`'i_f3d_origin'`)