From 0c02ba0a5b79bc8852f7d661af471f435a45f653 Mon Sep 17 00:00:00 2001
From: Marco Biasini <marco.biasini@unibas.ch>
Date: Thu, 4 Nov 2010 08:30:04 +0100
Subject: [PATCH] finalize and document new atom property interface
This finishes changes started in the mem-optimize branch to
remove the AtomProp class from the public interface.
---
examples/demos/the_hammer.py | 28 +++++++++++-------------
modules/mol/base/doc/editors.rst | 24 +++++++++++++++-----
modules/mol/base/doc/entity.rst | 25 +++++++++++----------
modules/mol/base/pymod/export_atom.cc | 11 ++++++++--
modules/mol/base/pymod/export_editors.cc | 5 ++---
modules/mol/base/pymod/wrap_mol.cc | 1 +
modules/mol/base/src/editor_base.cc | 10 +++++++--
modules/mol/base/src/editor_base.hh | 4 +++-
8 files changed, 68 insertions(+), 40 deletions(-)
diff --git a/examples/demos/the_hammer.py b/examples/demos/the_hammer.py
index f6c77ebca..48970cefb 100644
--- a/examples/demos/the_hammer.py
+++ b/examples/demos/the_hammer.py
@@ -12,7 +12,7 @@ class Anim(QtCore.QTimer):
self.b=b
self.angle=0.0
self.dir=0.01
- self.edi=self.a.view.handle.RequestXCSEditor(mol.EditMode.UNBUFFERED_EDIT)
+ self.edi=self.a.view.handle.EditXCS(mol.UNBUFFERED_EDIT)
QtCore.QObject.connect(self, QtCore.SIGNAL("timeout()"), self.OnTimer)
@@ -34,17 +34,15 @@ class Anim(QtCore.QTimer):
def Hammer(off=geom.Vec3()):
ent=mol.CreateEntity()
- edi=ent.RequestXCSEditor(mol.EditMode.BUFFERED_EDIT)
+ edi=ent.EditXCS(mol.BUFFERED_EDIT)
chain=edi.InsertChain("A")
res=edi.AppendResidue(chain, "QUAD")
- prop=mol.AtomProp()
- prop.radius=1.0
- a=edi.InsertAtom(res, "A", off+geom.Vec3(0.0, 0.0, 0.0), prop)
- b=edi.InsertAtom(res, "B", off+geom.Vec3(0.0, 4.0, 0.0), prop)
- c=edi.InsertAtom(res, "C", off+geom.Vec3(2.0, 4.0, 0.0), prop)
- d=edi.InsertAtom(res, "D", off+geom.Vec3(2.0, 5.0, 0.0), prop)
- e=edi.InsertAtom(res, "E", off+geom.Vec3(-2.0, 5.0, 0.0), prop)
- f=edi.InsertAtom(res, "F", off+geom.Vec3(-2.0, 4.0, 0.0), prop)
+ a=edi.InsertAtom(res, "A", off+geom.Vec3(0.0, 0.0, 0.0), "H")
+ b=edi.InsertAtom(res, "B", off+geom.Vec3(0.0, 4.0, 0.0), "H")
+ c=edi.InsertAtom(res, "C", off+geom.Vec3(2.0, 4.0, 0.0), "H")
+ d=edi.InsertAtom(res, "D", off+geom.Vec3(2.0, 5.0, 0.0), "H")
+ e=edi.InsertAtom(res, "E", off+geom.Vec3(-2.0, 5.0, 0.0), "H")
+ f=edi.InsertAtom(res, "F", off+geom.Vec3(-2.0, 4.0, 0.0), "H")
edi.Connect(a, b)
edi.Connect(b, c)
edi.Connect(c, d)
@@ -55,17 +53,17 @@ def Hammer(off=geom.Vec3()):
def TheWall():
ent=mol.CreateEntity()
- edi=ent.RequestXCSEditor(mol.EditMode.BUFFERED_EDIT)
+ edi=ent.EditXCS(mol.BUFFERED_EDIT)
chain=edi.InsertChain("A")
res=edi.AppendResidue(chain, "QUAD")
- prop=mol.AtomProp()
- prop.radius=0.25
index=0
for i in range(-10, 10):
for j in range(-10, 10):
index+=1
- edi.InsertAtom(res, "A%d" % index, geom.Vec3(4.0, -2.0, 0.0)+
- geom.Vec3(i, 0, j)*0.25, prop)
+ atom=edi.InsertAtom(res, "A%d" % index, geom.Vec3(4.0, -2.0, 0.0)+
+ geom.Vec3(i, 0, j)*0.25)
+ atom.radius=0.25
+
return ent
a=Hammer()
diff --git a/modules/mol/base/doc/editors.rst b/modules/mol/base/doc/editors.rst
index f224b2e1f..90fff6941 100644
--- a/modules/mol/base/doc/editors.rst
+++ b/modules/mol/base/doc/editors.rst
@@ -64,10 +64,14 @@ The basic functionality of editors is implemented in the EditorBase class.
:type residue_name: string
:returns: :class:`ResidueHandle`
- .. method:: InsertAtom(residue, atom_name, pos, [prop=mol.AtomProp()])
+ .. method:: InsertAtom(residue, atom_name, pos, element="", occupancy=1.0, b_factor=0.0, is_hetatm=False)
Insert new atom and add it to residue. For atoms with alternative atom
- locations use :meth:`InsertAltAtom`.
+ locations use :meth:`InsertAltAtom`. If the element parameter is a valid
+ element, the atom properties mass, charge, and radius are set to default
+ values for that element. If element is an empty string (or an invalid
+ element), the properties are set to rather meaningless default values. You
+ may later set any of the properties manually.
:param residue: is the parent residue and must be valid
:type residue: :class:`ResidueHandle`
@@ -79,10 +83,18 @@ The basic functionality of editors is implemented in the EditorBase class.
:type atom_name: string
:param pos: is the position of the atom in global coordinates
:type pos: :class:`geom.Vec3`
- :param prop: are the atom's properties such as element, van der Waals
- radius charge and so on. The default set of atom
- properties is rather meaningless.
- :type prop: class:`AtomProp`
+ :param element: is the atom's element. If set to a a valid element,
+ atom properties such as mass, charge, radius are set
+ based on default values for that element. If the element
+ string is empty, or unknown, the properties are filled
+ with rather meaningless default values.
+ :type element: class:`string`
+ :param occupancy: The occupancy of the atom. between 0 and 1
+ :type occupancy: float
+ :param b_factor: temperature factor.
+ :type b_factor: float
+ :param is_hetatm: whether the atom is an atom coming from a HETATM record.
+ :type is_hetatm: bool
:returns: :class:`AtomHandle`
Editor for the External Coordinate System
diff --git a/modules/mol/base/doc/entity.rst b/modules/mol/base/doc/entity.rst
index 6b8bff973..79df5fcf2 100644
--- a/modules/mol/base/doc/entity.rst
+++ b/modules/mol/base/doc/entity.rst
@@ -591,25 +591,32 @@ The Handle Classes
.. attribute:: radius
The van-der-Waals radius of the atom. Also available as :meth:`GetRadius`.
- Read-only.
+ Read/write.
:type: float
.. attribute:: occupancy
- The atom's occupancy in the range 0 to 1. Also available as
- :meth:`GetOccupancy`. Read-only.
-
+ The atom's occupancy in the range 0 to 1. Read/write. Also available as
+ meth:`GetOccupancy`, :meth:`SetOccupancy`.
:type: float
+
+ .. attribute:: b_factor
+
+ The atom's temperature factor. Read/write. Also available as
+ :meth:`GetBFactor`, :meth:`SetBFactor`.
+
+ :type: float
+
.. attribute:: charge
- The atom's charge
+ The atom's charge. Also available as :meth:`GetCharge`, :meth:`SetCharge`.
:type: float
.. attribute:: residue
- The residue this atom belongs to.
+ The residue this atom belongs to. Read-only.
:type: :class:`ResidueHandle`
@@ -634,11 +641,7 @@ The Handle Classes
:type other_atom: :class:`AtomHandle`
:rtype: :class:`BondHandle`
- .. method:: GetAtomProps()
-
- Get atom properties such as mass, charge, element and occupancy.
-
- :rtype: :class:`AtomProp`
+
.. method:: GetBondCount()
diff --git a/modules/mol/base/pymod/export_atom.cc b/modules/mol/base/pymod/export_atom.cc
index fe12a2f64..23828236e 100644
--- a/modules/mol/base/pymod/export_atom.cc
+++ b/modules/mol/base/pymod/export_atom.cc
@@ -50,18 +50,25 @@ void export_Atom()
make_function(&AtomBase::GetName,
return_value_policy<copy_const_reference>()),
&AtomBase::SetName)
- .add_property("index",&AtomBase::GetIndex)
+ .add_property("index", &AtomBase::GetIndex)
.def("GetRadius", &AtomBase::GetRadius)
.def("GetElement", &AtomBase::GetElement,
return_value_policy<copy_const_reference>())
.def("SetElement", &AtomBase::SetElement)
.def("GetCharge", &AtomBase::GetCharge)
+ .def("GetBFactor", &AtomBase::GetBFactor)
+ .def("SetBFactor", &AtomBase::SetBFactor)
+ .def("SetOccupancy", &AtomBase::SetOccupancy)
+ .def("GetOccupancy", &AtomBase::GetOccupancy)
.def("GetMass", &AtomBase::GetMass)
.def("IsHetAtom", &AtomBase::IsHetAtom)
.def("SetMass", &AtomBase::SetMass)
+ .add_property("b_factor", &AtomBase::GetBFactor, &AtomBase::SetBFactor)
+ .add_property("occupancy", &AtomBase::GetOccupancy,
+ &AtomBase::SetOccupancy)
.def("SetCharge", &AtomBase::SetCharge)
- .add_property("radius", &AtomBase::GetRadius)
+ .add_property("radius", &AtomBase::GetRadius, &AtomBase::SetRadius)
.add_property("element", make_function(&AtomBase::GetElement,
return_value_policy<copy_const_reference>()),
&AtomBase::SetElement)
diff --git a/modules/mol/base/pymod/export_editors.cc b/modules/mol/base/pymod/export_editors.cc
index 8c485cb7f..4b8d4123e 100644
--- a/modules/mol/base/pymod/export_editors.cc
+++ b/modules/mol/base/pymod/export_editors.cc
@@ -54,8 +54,6 @@ void (ICSEditor::*rotate_torsion_b)(const AtomHandle&, const AtomHandle&,
const AtomHandle&, const AtomHandle&,
Real)=&ICSEditor::RotateTorsionAngle;
-BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(X_insert_atom_overloads,
- EditorBase::InsertAtom, 3, 4)
}
void export_Editors()
@@ -63,7 +61,8 @@ void export_Editors()
class_<EditorBase>("EditorBase", no_init)
.def("InsertChain", &EditorBase::InsertChain)
.def("InsertAtom", &EditorBase::InsertAtom,
- X_insert_atom_overloads())
+ (arg("residue"), arg("name"), arg("pos"), arg("element")="",
+ arg("occupancy")=1.0, arg("b_factor")=0.0, arg("is_hetatm")=false))
.def("InsertAltAtom", &EditorBase::InsertAltAtom)
.def("DeleteResidue", &EditorBase::DeleteResidue)
.def("DeleteChain", &EditorBase::DeleteChain)
diff --git a/modules/mol/base/pymod/wrap_mol.cc b/modules/mol/base/pymod/wrap_mol.cc
index 800af3a1c..16db0ed59 100644
--- a/modules/mol/base/pymod/wrap_mol.cc
+++ b/modules/mol/base/pymod/wrap_mol.cc
@@ -48,6 +48,7 @@ BOOST_PYTHON_MODULE(_mol)
enum_<EditMode>("EditMode")
.value("BUFFERED_EDIT", BUFFERED_EDIT)
.value("UNBUFFERED_EDIT", UNBUFFERED_EDIT)
+ .export_values()
;
export_Entity();
export_Surface();
diff --git a/modules/mol/base/src/editor_base.cc b/modules/mol/base/src/editor_base.cc
index 4ed9b6a4b..29b5d1911 100644
--- a/modules/mol/base/src/editor_base.cc
+++ b/modules/mol/base/src/editor_base.cc
@@ -78,11 +78,17 @@ void EditorBase::RenameChain(ChainHandle chain, const String& new_name)
AtomHandle EditorBase::InsertAtom(ResidueHandle res, const String& name,
- const geom::Vec3& pos, const String& ele)
+ const geom::Vec3& pos, const String& ele,
+ Real occupancy, Real b_factor,
+ bool is_hetatm)
{
CheckHandleValidity(res);
ent_.Impl()->MarkTraceDirty();
- return AtomHandle(res.Impl()->InsertAtom(name, pos, ele));
+ AtomHandle atom(res.Impl()->InsertAtom(name, pos, ele));
+ atom.SetBFactor(b_factor);
+ atom.SetHetAtom(is_hetatm);
+ atom.SetOccupancy(occupancy);
+ return atom;
}
AtomHandle EditorBase::InsertAltAtom(ResidueHandle res, const String& name,
diff --git a/modules/mol/base/src/editor_base.hh b/modules/mol/base/src/editor_base.hh
index c0ee91350..964f2fdba 100644
--- a/modules/mol/base/src/editor_base.hh
+++ b/modules/mol/base/src/editor_base.hh
@@ -116,7 +116,9 @@ public:
/// naming.
/// \param pos is the position of the atom in global coordinates
AtomHandle InsertAtom(ResidueHandle residue, const String& name,
- const geom::Vec3& pos, const String& ele="");
+ const geom::Vec3& pos, const String& ele="",
+ Real occupancy=1.0, Real b_factor=0.0,
+ bool is_hetatm=false);
/// \brief Insert new atom with alternative position indicator
/// \sa EditorBase::AddAltAtomPos(), ResidueHandle
--
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