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schwede
openstructure
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18dcd749
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18dcd749
authored
6 years ago
by
Rafal Gumienny
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docs: SCHWED-3121 Update ReadStereoChemicalPropsFile documentation
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modules/io/doc/io.rst
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@@ -351,37 +351,23 @@ before computing the lDDT scores it is required to pass parameter file based on
Engh and Huber parameters, and on the atomic radii as defined in the Cambridge
Structural Database. OpenStructure ships with default file called
`stereo_chemical_props.txt` located in `$OST_ROOT/share/openstructure`
directory. A
class :class
:`~ost.io.StereoChemicalP
aramsReader
` is used to
read
this file.
directory. A
function :function
:`~ost.io.
Read
StereoChemicalP
ropsFile
` is used to
read
this file.
.. class:: StereoChemicalParamsReader(filename="")
Object that holds and reads stereochemical parameters.
:param filename: Sets :attr:`filename`.
.. function:: ReadStereoChemicalPropsFile(filename="", check=True)
.. attribute:: bond_table
Read stereochemical parameters - if not provided a local version will be used.
The table containing bond information of type :class:`~ost.mol.alg.StereoChemicalParams`.
:param filename: The path to the parameter file that will be used. If set
to "", it reads the default file shipped with OpenStructure.
:type filename: :class:`str`
:param check: Raise an error when any of the resulting tables are empty.
:type check: :class:`bool`
:return: Object containing stereochemical parameters
:rtype: :class:`~ost.mol.alg.StereoChemicalProps`
..
attribute:: angle_table
..
function:: GetStereoChemicalPropsFile()
The table containing angle information of type :class:`~ost.mol.alg.StereoChemicalParams`.
.. attribute:: nonbonded_table
The table containing clashes of type :class:`~ost.mol.alg.ClashingDistances`.
.. attribute:: filename
The path to the parameter file that will be used. If set to "", it reads the
default file shipped with OpenStructure.
:type: :class:`str`
.. method:: Read(check=False)
Read the file.
:param check: Raise an error when any of the resulting tables are empty.
:type check: :class:`bool`
Get the default path to the stereochemical paramteres file.
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