From 8835ca8dbf04f84f078b1857ab26e18476ef03e0 Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Mon, 31 Oct 2016 15:01:05 +0100
Subject: [PATCH] Fixed doc for editors.
---
modules/mol/base/doc/editors.rst | 108 +++++--------------------------
1 file changed, 17 insertions(+), 91 deletions(-)
diff --git a/modules/mol/base/doc/editors.rst b/modules/mol/base/doc/editors.rst
index 4d272dd56..497cff0fd 100644
--- a/modules/mol/base/doc/editors.rst
+++ b/modules/mol/base/doc/editors.rst
@@ -358,12 +358,7 @@ The basic functionality of editors is implemented in the EditorBase class.
:type atom2: :class:`AtomHandle`
:param bond_order: bond order (e.g. 1=single, 2=double, 3=triple)
:type bond_order: :class:`int`
-
-BondHandle (EditorBase::*connect_b)(const AtomHandle&, const AtomHandle&,
- Real, Real, Real)=&EditorBase::Connect;
-BondHandle (EditorBase::*connect_d)(const AtomHandle&, const AtomHandle&,
- Real, Real, Real,
- unsigned char)=&EditorBase::Connect;
+
Editor for the External Coordinate System
--------------------------------------------------------------------------------
@@ -419,107 +414,38 @@ Euclidian space.
Force spatial organizer and ICS update workaround for delayed editor call from Python garbage collection
.. method:: SetAtomPos(atom, pos)
+ SetAtomPos(atom_list, pos_list)
+ SetAtomTransformedPos(atom, pos)
+ SetAtomTransformedPos(atom_list, pos_list)
- Set the (transformed) position of atom. This method will also update the
+ Set the transformed position of atoms. This method will also update the
original position of the atom by applying the inverse of the entity
transform.
- :param atom: must be a valid atom handle
+ :param atom: A valid atom handle
:type atom: :class:`ost.mol.AtomHandle`
+ :param atom_list: A valid atom handle
+ :type atom_list: :class:`ost.mol.AtomHandleList`
:param pos: The new position
:type pos: :class:`~ost.geom.Vec3`
-
- .. method:: SetAtomPos(atom, pos)
-
- Set the (transformed) position of atom. This method will also update the
- original position of the atom by applying the inverse of the entity
- transform.
-
- :param atom_list: must be a valid atom handle list
- :type atom_list: :class:`ost.mol.AtomHandleList`
- :param pos_list: a numpy array of floats having a length of 3*atom_list.size()
- :type pos_list: numpy array
-
- .. method:: SetAtomPos(atom, pos)
-
- Set the (transformed) position of atom. This method will also update the
- original position of the atom by applying the inverse of the entity
- transform.
-
- :param atom_list: must be a valid atom handle list
- :type atom_list: :class:`ost.mol.AtomHandleList`
- :param pos_list: a list of double having a length of 3*atom_list.size()
- :type pos_list: list
+ :param pos_list: An array or a list of 3*atom_list.size() floats
+ :type pos_list: :class:`numpy.array` or :class:`list` of :class:`float`
.. method:: SetAtomOriginalPos(atom, pos)
+ SetAtomOriginalPos(atom_list, pos_list)
- Set the original (untransformed) position of the atom. This method will
+ Set the original (untransformed) position of atoms. This method will
also update the transformed position by applying the entity transform to
the original pos.
- :param atom: must be a valid atom handle
+ :param atom: A valid atom handle
:type atom: :class:`ost.mol.AtomHandle`
- :param pos: The new untransformed position
- :type pos: :class:`~ost.geom.Vec3`
-
-
- .. method:: SetAtomOriginalPos(atom_list, pos_list)
-
- Set the original (untransformed) position of the atoms in the given list. This method will
- also update the transformed position by applying the entity transform to
- the original pos.
-
- :param atom_list: must be a valid atom handle list
+ :param atom_list: A valid atom handle
:type atom_list: :class:`ost.mol.AtomHandleList`
- :param pos_list: a list of double having a length of 3*atom_list.size()
- :type pos_list: list
-
- .. method:: SetAtomOriginalPos(atom_list, pos_list)
-
- Set the original (untransformed) position of the atoms in the given list. This method will
- also update the transformed position by applying the entity transform to
- the original pos.
-
- :param atom_list: must be a valid atom handle list
- :type atom_list: :class:`ost.mol.AtomHandleList`
- :param pos_list: a numpy array of floats having a length of 3*atom_list.size()
- :type pos_list: numpy array
-
-
- .. method:: SetAtomTransformedPos(atom, pos)
-
- Set the (transformed) position of atom. This method will also update the
- original position of the atom by applying the inverse of the entity
- transform.
-
- :param atom: must be a valid atom handle
- :type atom: :class:`ost.mol.AtomHandle`
- :param pos: The new position
+ :param pos: The new untransformed position
:type pos: :class:`~ost.geom.Vec3`
-
- .. method:: SetAtomTransformedPos(atom_list, pos_list)
-
- Set the (transformed) position of atom. This method will also update the
- original position of the atom by applying the inverse of the entity
- transform.
-
- :param atom_list: must be a valid atom handle list
- :type atom_list: :class:`ost.mol.AtomHandleList`
- :param pos_list: a numpy array of floats having a length of 3*atom_list.size()
- :type pos_list: numpy array
-
- .. method:: SetAtomTransformedPos(atom_list, pos_list)
-
- Set the (transformed) position of atom. This method will also update the
- original position of the atom by applying the inverse of the entity
- transform.
-
- :param atom_list: must be a valid atom handle list
- :type atom_list: :class:`ost.mol.AtomHandleList`
- :param pos_list: a list of double having a length of 3*atom_list.size()
- :type pos_list: list
-
-
+ :param pos_list: An array or a list of 3*atom_list.size() floats
+ :type pos_list: :class:`numpy.array` or :class:`list` of :class:`float`
Editor for the Internal Coordinate System
--
GitLab