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schwede
openstructure
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fb2e12f7
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fb2e12f7
authored
1 year ago
by
Xavier Robin
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doc: link to generic properties
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modules/mol/base/doc/entity.rst
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modules/mol/base/doc/entity.rst
modules/seq/base/doc/seq.rst
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modules/seq/base/doc/seq.rst
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modules/mol/base/doc/entity.rst
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@@ -8,6 +8,10 @@ This document describes the :class:`EntityHandle` and the related classes.
The Handle Classes
--------------------------------------------------------------------------------
:class:`Entity <EntityHandle>`, :class:`residue <ResidueHandle>`,
:class:`atom <AtomHandle>` and :class:`bond <BondHandle>` handles can store
arbitrary :doc:`generic properties <../../base/generic>`.
.. function:: CreateEntity()
Creates a new entity. The created entity is empty, that is, it does not
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@@ -30,6 +34,10 @@ Entity Handle
represent a ligand or a collection of water molecules - hence the rather
generic name.
.. attribute:: properties
All the :class:`generic properties <ost.GenericPropContainer>` are available.
.. attribute:: chains
List of all chains of this entity. The chains are in the same
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@@ -350,6 +358,10 @@ Chain Handle
A chain of one or more :class:`residues <ResidueHandle>`. Chains are always
part of an entity.
.. attribute:: properties
All the :class:`generic properties <ost.GenericPropContainer>` are available.
.. attribute:: atoms
Get list of all atoms of this chain. To access a single atom, use
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@@ -593,6 +605,10 @@ Residue Handle
more :class:`atoms <AtomHandle>`. Residues are always part of a
:class:`ChainHandle`, even if they are ligands or water molecules where the
concept of a chain does not apply.
.. attribute:: properties
All the :class:`generic properties <ost.GenericPropContainer>` are available.
.. attribute:: name
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@@ -1026,6 +1042,10 @@ Atom Handle
Represents an atom in a molecular structure. Atoms are always part of a
residue.
.. attribute:: properties
All the :class:`generic properties <ost.GenericPropContainer>` are available.
.. attribute:: name
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@@ -1269,6 +1289,10 @@ Bond Handle
Represents a chemical bond between two atoms (first and second).
.. attribute:: properties
All the :class:`generic properties <ost.GenericPropContainer>` are available.
.. attribute:: first
.. attribute:: second
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@@ -1367,6 +1391,10 @@ Bond Handle
The View Classes
--------------------------------------------------------------------------------
:class:`Entity <EntityView>`, :class:`residue <ResidueView>` and
:class:`atom <AtomView>` views can store arbitrary
:doc:`generic properties <../../base/generic>`.
Entity View
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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@@ -1377,6 +1405,10 @@ Entity View
:class:`BondHandle`\s.
For an introduction, see :doc:`../../intro-01`.
.. attribute:: properties
All the :class:`generic properties <ost.GenericPropContainer>` are available.
.. attribute:: handle
The underlying :class:`handle <EntityHandle>` of the entity view. Also
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@@ -1795,6 +1827,10 @@ Chain View
A view representation of a :class:`ChainHandle`. Mostly, the same
functionality is provided as for the handle.
.. attribute:: properties
All the :class:`generic properties <ost.GenericPropContainer>` are available.
.. attribute:: handle
The chain handle this view points to. Also available as :meth:`GetHandle`.
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@@ -2043,6 +2079,10 @@ Residue View
A view representation of a :class:`ResidueHandle`. Mostly, the same
functionality is provided as for the handle.
.. attribute:: properties
All the :class:`generic properties <ost.GenericPropContainer>` are available.
.. attribute:: handle
The residue handle this view points to. Also available as
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@@ -2229,6 +2269,10 @@ Atom View
A view representation of an :class:`AtomHandle`. Mostly, the same
functionality is provided as for the handle.
.. attribute:: properties
All the :class:`generic properties <ost.GenericPropContainer>` are available.
.. attribute:: handle
The underlying :class:`AtomHandle` of the atom view. Also available as
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modules/seq/base/doc/seq.rst
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@@ -83,6 +83,10 @@ The SequenceHandle
ConstSequenceHandle
Represents a sequence. New instances are created with :func:`CreateSequence`.
.. attribute:: properties
All the :class:`generic properties <ost.GenericPropContainer>` are available.
.. method:: GetPos(residue_index)
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