Re: [IMP-dev] pdb patch

[Keren Lasker <>]

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>
> > > >
> > > > _______________________________________________
> > > > IMP-dev mailing list
> > > >
> > > > https://salilab.org/mailman/listinfo/imp-dev
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);