mda_openbabel_converter.OpenBabelParser

OpenBabel topology parser — mda_openbabel_converter.OpenBabel

Converts an OpenBabel openbabel.openbabel.OBMol into a MDAnalysis.core.Topology.

See also

mda_openbabel_converter.OpenBabel

Classes

class mda_openbabel_converter.OpenBabelParser.OpenBabelParser(filename)[source]

For OpenBabel structure

Inherits from TopologyReaderBase and converts an OpenBabel OBMol to a MDAnalysis Topology or adds it to a pre-existing Topology. This parser does not work in the reverse direction.

For use examples, please see mda_openbabel_converter.OpenBabel

Creates the following Attributes:

  • Atomids

  • Atomtypes

  • Aromaticities

  • Elements

  • Masses

  • Bonds

  • Resids

  • Resnums

  • Segids

Depending on OpenBabel’s input, the following Attributes might be present:

  • Charges

  • Resnames

  • ICodes

Guesses the following:

  • Atomnames

Missing Attributes unable to be retrieved from OpenBabel:

  • Chiralities

  • RSChirality

  • Occupancies

  • Tempfactors

  • ChainIDs

  • AltLocs

Attributes table:

OpenBabel attribute

MDAnalysis equivalent

altLocs

atom.IsAromatic()

aromaticities

chainIDs

atom.GetPartialCharge()

charges

GetSymbol(atom.GetAtomicNum())

elements

atom.GetResidue().GetInsertionCode()

icodes

atom.GetIdx()

indices

atom.GetExactMass()

masses

“%s%d” % (GetSymbol(atom.GetAtomicNum()), atom.GetIdx())

names

chiralities

occupancies

atom.GetResidue().GetName()

resnames

atom.GetResidue().GetNum()

resnums

tempfactors

atom.GetType()

types
Raises:

ValueError – If only some of the atoms have ResidueInfo, from resid.GetNum(), available

close()

Close the trajectory file.

convert_forces_from_native(force, inplace=True)

Conversion of forces array force from native to base units

Parameters:

  • force (array_like) – Forces to transform

  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input force is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

Added in version 0.7.7.

convert_forces_to_native(force, inplace=True)

Conversion of force array force from base to native units.

Parameters:

  • force (array_like) – Forces to transform

  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input force is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

Added in version 0.7.7.

convert_pos_from_native(x, inplace=True)

Conversion of coordinate array x from native units to base units.

Parameters:

  • x (array_like) – Positions to transform

  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input x is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

convert_pos_to_native(x, inplace=True)

Conversion of coordinate array x from base units to native units.

Parameters:

  • x (array_like) – Positions to transform

  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input x is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

convert_time_from_native(t, inplace=True)

Convert time t from native units to base units.

Parameters:

  • t (array_like) – Time values to transform

  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input t is modified in place and also returned (although note that scalar values t are passed by value in Python and hence an in-place modification has no effect on the caller.) In-place operations improve performance because allocating new arrays is avoided.

Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

convert_time_to_native(t, inplace=True)

Convert time t from base units to native units.

Parameters:

  • t (array_like) – Time values to transform

  • inplace (bool, optional) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input t is modified in place and also returned. (Also note that scalar values t are passed by value in Python and hence an in-place modification has no effect on the caller.)

Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

convert_velocities_from_native(v, inplace=True)

Conversion of velocities array v from native to base units

Parameters:

  • v (array_like) – Velocities to transform

  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input v is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

Added in version 0.7.5.

convert_velocities_to_native(v, inplace=True)

Conversion of coordinate array v from base to native units

Parameters:

  • v (array_like) – Velocities to transform

  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input v is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

Added in version 0.7.5.

parse(**kwargs)[source]

Accepts an OpenBabel OBMol and returns a MDAnalysis Topology. Will need to extract the number of atoms, number of residues, number of segments, atom_residue index, residue_segment index and all of the atom’s relevant attributes from the OBMol to initialise a new Topology.

units = {'length': None, 'time': None, 'velocity': None}

dict with units of of time and length (and velocity, force, … for formats that support it)

Classes

OpenBabelParser(filename)

For OpenBabel structure