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Re: [IMP-dev] pdb patch
To follow pdb conventions, a patch that renames the type attribute to name
attribute in both AtomDecerator and ResidueDecerator is attached.
On Feb 12, 2008, at 4:56 PM, Daniel Russel wrote:
<02.fix_atom_name_in_pdb>
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Index: kernel/include/IMP/decorators/AtomDecorator.h
===================================================================
--- kernel/include/IMP/decorators/AtomDecorator.h (revision 354)
+++ kernel/include/IMP/decorators/AtomDecorator.h (working copy)
@@ -15,7 +15,6 @@
#include "../Model.h"
#include "utility.h"
#include "XYZDecorator.h"
-
namespace IMP
{
@@ -31,15 +30,17 @@
class IMPDLLEXPORT AtomDecorator: public XYZDecorator
{
IMP_DECORATOR(AtomDecorator, XYZDecorator,
- return p->has_attribute(type_key_),
- { p->add_attribute(type_key_, AT_UNKNOWN.get_index()); });
+ return p->has_attribute(name_key_),
+ { p->add_attribute(name_key_, AT_UNKNOWN.get_index());
+ p->add_attribute(index_key_, -1);
+ });
protected:
static IntKey element_key_;
static FloatKey charge_key_;
//static FloatKey vdw_radius_key_;
static FloatKey mass_key_;
- static IntKey type_key_;
-
+ static IntKey name_key_;
+ static IntKey index_key_;
public:
//! The various elements currently supported
/**
@@ -216,11 +217,11 @@
static AtomType AT_H72;
static AtomType AT_H73;
- AtomType get_type() const {
- return AtomType(get_particle()->get_value(type_key_));
+ AtomType get_name() const {
+ return AtomType(get_particle()->get_value(name_key_));
}
- void set_type(AtomType t);
+ void set_name(AtomType t);
IMP_DECORATOR_GET_SET_OPT(charge, charge_key_,
Float, Float, 0);
@@ -230,6 +231,10 @@
IMP_DECORATOR_GET_SET_OPT(mass, mass_key_,
Float, Float, 0);
+ IMP_DECORATOR_GET_SET(index, index_key_,
+ Int, unsigned int);
+
+
};
IMP_OUTPUT_OPERATOR(AtomDecorator);
Index: kernel/include/IMP/decorators/ResidueDecorator.h
===================================================================
--- kernel/include/IMP/decorators/ResidueDecorator.h (revision 354)
+++ kernel/include/IMP/decorators/ResidueDecorator.h (working copy)
@@ -26,13 +26,13 @@
class IMPDLLEXPORT ResidueDecorator: public DecoratorBase
{
IMP_DECORATOR(ResidueDecorator, DecoratorBase,
- return p->has_attribute(type_key_)
+ return p->has_attribute(name_key_)
&& p->has_attribute(index_key_),
- { p->add_attribute(type_key_, -1);
+ { p->add_attribute(name_key_, -1);
p->add_attribute(index_key_, -1);
});
protected:
- static IntKey type_key_;
+ static IntKey name_key_;
static IntKey index_key_;
public:
@@ -70,12 +70,12 @@
static ResidueType GUA;
static ResidueType THY;
- ResidueType get_type() const {
- return ResidueType(get_particle()->get_value(type_key_));
+ ResidueType get_name() const {
+ return ResidueType(get_particle()->get_value(name_key_));
}
- void set_type(ResidueType t) {
- return get_particle()->set_value(type_key_, t.get_index());
+ void set_name(ResidueType t) {
+ return get_particle()->set_value(name_key_, t.get_index());
}
//! The residues index in the chain
Index: kernel/src/decorators/AtomDecorator.cpp
===================================================================
--- kernel/src/decorators/AtomDecorator.cpp (revision 354)
+++ kernel/src/decorators/AtomDecorator.cpp (working copy)
@@ -10,6 +10,10 @@
#include <limits>
#include "IMP/decorators/AtomDecorator.h"
+#include "IMP/decorators/ResidueDecorator.h"
+#include "IMP/decorators/MolecularHierarchyDecorator.h"
+#include "IMP/decorators/NameDecorator.h"
+
#include "IMP/log.h"
namespace IMP
@@ -27,7 +31,9 @@
IntKey AtomDecorator::element_key_;
FloatKey AtomDecorator::charge_key_;
FloatKey AtomDecorator::mass_key_;
-IntKey AtomDecorator::type_key_;
+IntKey AtomDecorator::name_key_;
+IntKey AtomDecorator::index_key_;
+
TYPE_DEF(N);
TYPE_DEF(H);
TYPE_DEF(1H);
@@ -199,16 +205,16 @@
void AtomDecorator::show(std::ostream &out, std::string prefix) const
{
//out <<prefix << "Element:"<< get_element() << std::endl;
- out << prefix<< "Type: "<< get_type() << std::endl;
+ out << prefix<< "Type: "<< get_name() << std::endl;
XYZDecorator::show(out, prefix);
}
-void AtomDecorator::set_type(AtomType t)
+void AtomDecorator::set_name(AtomType t)
{
// ultimate the secondary info should be set from a
// better source. But this is good enough for now.
- get_particle()->set_value(type_key_, t.get_index());
+ get_particle()->set_value(name_key_, t.get_index());
}
IMP_DECORATOR_INITIALIZE(AtomDecorator, XYZDecorator,
@@ -217,7 +223,8 @@
charge_key_= FloatKey("atom charge");
mass_key_= FloatKey("atom mass");
//vdw_radius_key_= FloatKey("atom vdw radius");
- type_key_ = IntKey("atom type");
+ name_key_ = IntKey("atom name");
+ index_key_= IntKey("residue index");
TYPE_INIT(N);
TYPE_INIT(H);
TYPE_INIT(1H);
Index: kernel/src/decorators/ResidueDecorator.cpp
===================================================================
--- kernel/src/decorators/ResidueDecorator.cpp (revision 354)
+++ kernel/src/decorators/ResidueDecorator.cpp (working copy)
@@ -17,7 +17,7 @@
-IntKey ResidueDecorator::type_key_;
+IntKey ResidueDecorator::name_key_;
IntKey ResidueDecorator::index_key_;
#define TYPE_INIT(STR) STR= ResidueType(#STR);
@@ -54,13 +54,13 @@
void ResidueDecorator::show(std::ostream &out, std::string pre) const
{
out << pre << "residue #" << get_index() << " of type "
- << get_type() << std::endl;
+ << get_name() << std::endl;
}
IMP_DECORATOR_INITIALIZE(ResidueDecorator, DecoratorBase,
- { type_key_= IntKey("residue type");
+ { name_key_= IntKey("residue name");
index_key_= IntKey("residue index");
TYPE_INIT(UNK);
TYPE_INIT(GLY);