pyjess 0.5.0__tar.gz → 0.5.2__tar.gz

{pyjess-0.5.0 → pyjess-0.5.2}/.github/workflows/package.yml

@@ -89,7 +89,7 @@ jobs:
 
   wheel-win32-x86_64:
     name: Build Windows wheels (x86-64)
-    runs-on: windows-2019
+    runs-on: windows-latest
     steps:
     - uses: actions/checkout@v4
       with:

{pyjess-0.5.0 → pyjess-0.5.2}/CHANGELOG.md

@@ -6,7 +6,28 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 
 ## [Unreleased]
-[Unreleased]: https://github.com/althonos/pyjess/compare/v0.5.0...HEAD
+[Unreleased]: https://github.com/althonos/pyjess/compare/v0.5.2...HEAD
+
+
+## [v0.5.2] - 2025-08-26
+[v0.5.2]: https://github.com/althonos/pyjess/compare/v0.5.1...v0.5.2
+
+### Added
+- `pickle` protocol support to `Hit` objects.
+
+### Fixed
+- Improve performance of residue index using binary search on name queries.
+- Avoid copying atoms in `Hit.atoms` if no transformation is required.
+
+
+## [v0.5.1] - 2025-08-20
+[v0.5.1]: https://github.com/althonos/pyjess/compare/v0.5.0...v0.5.1
+
+### Fixed
+- Typo in `Hit.molecule` returning incorrect coordinates when transformation is required.
+
+### Changed
+- Implement an index to quickly access atoms by residue names in a `Molecule`, and accelerate initial candidate set creation for compatible match modes.
 
 
 ## [v0.5.0] - 2025-04-09

{pyjess-0.5.0 → pyjess-0.5.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: pyjess
-Version: 0.5.0
+Version: 0.5.2
 Summary: Cython bindings and Python interface to JESS, a 3D template matching software.
 Keywords: bioinformatics,structure,template,matching
 Author-Email: Martin Larralde <martin.larralde@embl.de>
@@ -76,7 +76,7 @@ Description-Content-Type: text/markdown
 [![Issues](https://img.shields.io/github/issues/althonos/pyjess.svg?style=flat-square&maxAge=600)](https://github.com/althonos/pyjess/issues)
 [![Docs](https://img.shields.io/readthedocs/pyjess/latest?style=flat-square&maxAge=600)](https://pyjess.readthedocs.io)
 [![Changelog](https://img.shields.io/badge/keep%20a-changelog-8A0707.svg?maxAge=2678400&style=flat-square)](https://github.com/althonos/pyjess/blob/main/CHANGELOG.md)
-[![Downloads](https://img.shields.io/pypi/dm/pyjess?style=flat-square&color=303f9f&maxAge=86400&label=downloads)](https://pepy.tech/project/pyjess)
+[![Downloads](https://img.shields.io/badge/dynamic/regex?url=https%3A%2F%2Fpepy.tech%2Fprojects%2Fpyjess&search=%5B0-9%5D%2B.%5B0-9%5D%2B(k%7CM)&style=flat-square&label=downloads&color=303f9f&cacheSeconds=86400)](https://pepy.tech/project/pyjess)
 
 
 ## 🗺️ Overview
@@ -184,7 +184,7 @@ If running Jess in parallel, make sure to use `v0.2.1` or later to use the code
 
 ### ⚠️ Issue Tracker
 
-Found a bug ? Have an enhancement request ? Head over to the [GitHub issue tracker](https://github.com/althonos/[pyjess]/issues)
+Found a bug ? Have an enhancement request ? Head over to the [GitHub issue tracker](https://github.com/althonos/pyjess/issues)
 if you need to report or ask something. If you are filing in on a bug,
 please include as much information as you can about the issue, and try to
 recreate the same bug in a simple, easily reproducible situation.

{pyjess-0.5.0 → pyjess-0.5.2}/README.md

@@ -16,7 +16,7 @@
 [![Issues](https://img.shields.io/github/issues/althonos/pyjess.svg?style=flat-square&maxAge=600)](https://github.com/althonos/pyjess/issues)
 [![Docs](https://img.shields.io/readthedocs/pyjess/latest?style=flat-square&maxAge=600)](https://pyjess.readthedocs.io)
 [![Changelog](https://img.shields.io/badge/keep%20a-changelog-8A0707.svg?maxAge=2678400&style=flat-square)](https://github.com/althonos/pyjess/blob/main/CHANGELOG.md)
-[![Downloads](https://img.shields.io/pypi/dm/pyjess?style=flat-square&color=303f9f&maxAge=86400&label=downloads)](https://pepy.tech/project/pyjess)
+[![Downloads](https://img.shields.io/badge/dynamic/regex?url=https%3A%2F%2Fpepy.tech%2Fprojects%2Fpyjess&search=%5B0-9%5D%2B.%5B0-9%5D%2B(k%7CM)&style=flat-square&label=downloads&color=303f9f&cacheSeconds=86400)](https://pepy.tech/project/pyjess)
 
 
 ## 🗺️ Overview
@@ -124,7 +124,7 @@ If running Jess in parallel, make sure to use `v0.2.1` or later to use the code
 
 ### ⚠️ Issue Tracker
 
-Found a bug ? Have an enhancement request ? Head over to the [GitHub issue tracker](https://github.com/althonos/[pyjess]/issues)
+Found a bug ? Have an enhancement request ? Head over to the [GitHub issue tracker](https://github.com/althonos/pyjess/issues)
 if you need to report or ask something. If you are filing in on a bug,
 please include as much information as you can about the issue, and try to
 recreate the same bug in a simple, easily reproducible situation.

{pyjess-0.5.0 → pyjess-0.5.2}/docs/_static/json/switcher.json

@@ -1,6 +1,11 @@
 [
     {
-        "name": "v0.4 (latest)",
+        "name": "v0.5 (latest)",
+        "version": "0.5.2",
+        "url": "https://pyjess.readthedocs.io/en/v0.5.2/"
+    },
+    {
+        "name": "v0.4",
         "version": "0.4.1",
         "url": "https://pyjess.readthedocs.io/en/v0.4.1/"
     },

{pyjess-0.5.0 → pyjess-0.5.2}/docs/index.rst

@@ -65,7 +65,7 @@ PyJess |Stars|
    :target: https://github.com/althonos/pyjess/blob/main/CHANGELOG.md
    :class: dark-light
 
-.. |Downloads| image:: https://img.shields.io/pypi/dm/pyjess?style=flat-square&color=303f9f&maxAge=3600&label=downloads
+.. |Downloads| image:: https://img.shields.io/badge/dynamic/regex?url=https%3A%2F%2Fpepy.tech%2Fprojects%2Fpyjess&search=%5B0-9%5D%2B.%5B0-9%5D%2B(k%7CM)&style=flat-square&label=downloads&color=303f9f&cacheSeconds=86400
    :target: https://pepy.tech/project/pyjess
    :class: dark-light
 

pyjess-0.5.2/include/jess/candidate_set.pxd

@@ -0,0 +1,15 @@
+from .atom cimport Atom
+from .molecule cimport Molecule
+
+
+cdef extern from "CandidateSet.h" nogil:
+
+    struct _CandidateSet:
+        int count
+        Atom **atom
+        double **coord
+
+    ctypedef _CandidateSet CandidateSet
+
+    CandidateSet *CandidateSet_create(const Molecule *M)
+    void CandidateSet_free(CandidateSet*)

{pyjess-0.5.0 → pyjess-0.5.2}/include/jess/molecule.pxd

@@ -1,6 +1,7 @@
 from libc.stdio cimport FILE
 
 from .atom cimport Atom
+from .res_index cimport ResIndex
 
 
 cdef extern from "Molecule.h" nogil:
@@ -8,6 +9,7 @@ cdef extern from "Molecule.h" nogil:
     cdef struct _Molecule:
         int count
         char[5] id
+        ResIndex* index
         Atom** atom
 
     ctypedef _Molecule Molecule
@@ -15,5 +17,5 @@ cdef extern from "Molecule.h" nogil:
     Molecule* Molecule_create(FILE*, int, double)
     void Molecule_free(Molecule*) 
     int Molecule_count(const Molecule*)
-    Atom* Molecule_atom(const Molecule*, int)
+    const Atom* Molecule_atom(const Molecule*, int)
     const char* Molecule_id(const Molecule*)

pyjess-0.5.2/include/jess/res_index.pxd

@@ -0,0 +1,15 @@
+from .atom cimport Atom
+
+
+cdef extern from "ResIndex.h" nogil:
+
+    struct _ResIndex:
+        int count
+        Atom **atom
+        double **coord
+
+    ctypedef _ResIndex ResIndex
+
+    extern ResIndex* ResIndex_create(Atom**, int)
+    extern Atom** ResIndex_get(ResIndex*, const char[4])
+    extern void ResIndex_free(ResIndex*)

{pyjess-0.5.0 → pyjess-0.5.2}/include/jess/template.pxd

@@ -1,5 +1,6 @@
 from .atom cimport Atom
-
+from .molecule cimport Molecule
+from .candidate_set cimport CandidateSet
 
 cdef extern from "Template.h" nogil:
 
@@ -10,6 +11,7 @@ cdef extern from "Template.h" nogil:
         int (*match)(const Template*, int, const Atom*) nogil
         int (*range)(const Template*, int, int, double*, double*) nogil
         int (*check)(const Template*, Atom**, int, int) nogil
+        CandidateSet* (*candidates)(const Template*, const Molecule*, int);
         const double* (*position)(const Template*, int) nogil
         const char* (*name)(const Template*) nogil
         double (*logE)(const Template*, double, int) nogil

{pyjess-0.5.0 → pyjess-0.5.2}/include/jess/tess_template.pxd

@@ -3,6 +3,8 @@ from libc.stdio cimport FILE
 from .atom cimport Atom
 from .tess_atom cimport TessAtom
 from .template cimport Template
+from .molecule cimport Molecule
+from .candidate_set cimport CandidateSet
 
 
 cdef extern from "TessTemplate.h" nogil:
@@ -22,6 +24,7 @@ cdef extern from "TessTemplate.h" nogil:
     const double *TessTemplate_position(const Template *T, int k)
     double TessTemplate_distWeight(const Template *T, int k)
     int TessTemplate_check(const Template *T, Atom **A, int k, int ignore_chain)
+    CandidateSet* TessTemplate_candidates(const Template *T, const Molecule *M, int k)
     const char *TessTemplate_name(const Template *T)
     double TessTemplate_logE(const Template *T,double rmsd, int n)
     void TessTemplate_free(Template *T)

pyjess-0.5.2/patches/CMakeLists.txt.patch

@@ -0,0 +1,35 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+new file mode 100644
+index 0000000..b34b6e7
+--- /dev/null
++++ b/CMakeLists.txt
+@@ -0,0 +1,29 @@
++cmake_minimum_required(VERSION 3.10)
++project(Jess)
++
++include(CheckSymbolExists)
++check_symbol_exists(alloca "alloca.h" HAVE_ALLOCA)
++
++add_library(jess)
++target_sources(jess PRIVATE
++	src/Annulus.c
++	src/Join.c
++	src/Molecule.c
++	src/Super.c
++	src/Atom.c
++	src/KdTree.c
++	src/Region.c
++	src/TessAtom.c
++	src/Jess.c
++	src/Scanner.c
++	src/TessTemplate.c
++	src/CandidateSet.c
++	src/ResIndex.c)
++if(HAVE_ALLOCA)
++	target_compile_definitions(jess PUBLIC -DHAVE_ALLOCA)
++endif()
++
++add_executable(jess_bin)
++target_sources(jess_bin PRIVATE src/Main.c)
++target_link_libraries(jess_bin jess m)
++set_property(TARGET jess_bin PROPERTY OUTPUT_NAME jess)

pyjess-0.5.2/patches/CandidateSet.c.patch

@@ -0,0 +1,71 @@
+diff --git a/src/CandidateSet.c b/src/CandidateSet.c
+new file mode 100644
+index 0000000..a67e878
+--- /dev/null
++++ b/src/CandidateSet.c
+@@ -0,0 +1,65 @@
++// ==================================================================
++// CandidateSet.h
++// Copyright (c) Jonathan Barker, 2002
++// Copyright (c) Martin Larralde, 2025
++// ==================================================================
++// Implementation of type CandidateSet.
++// ==================================================================
++
++#include <stdlib.h>
++
++#include "CandidateSet.h"
++#include "Atom.h"
++#include "Molecule.h"
++#include "Template.h"
++
++// ==================================================================
++// Methods of local type CandidateSet
++// ==================================================================
++
++CandidateSet *CandidateSet_create(const Molecule *M)
++{
++	CandidateSet *S;
++	Atom *A;
++	int n = Molecule_count(M);
++	int m;
++
++	S = (CandidateSet*)calloc(1,sizeof(CandidateSet));
++    if(!S) return NULL;
++
++	S->atom=(Atom**)calloc(n,sizeof(Atom*));
++	S->coord = NULL;
++	S->count = 0;
++    
++    return S;
++}
++
++void CandidateSet_addAtom(CandidateSet *S, Atom *A)
++{
++	S->atom[S->count]=A;
++	S->count++;
++}
++
++void CandidateSet_recordCoordinates(CandidateSet *S)
++{
++	int m;
++	
++	S->atom=(Atom**)realloc(S->atom,sizeof(Atom*)*S->count);
++	S->coord=(double**)calloc(S->count,sizeof(double*));
++
++	for(m=0; m<S->count; m++)
++		S->coord[m]=S->atom[m]->x;
++}
++
++
++void CandidateSet_free(CandidateSet *S)
++{
++	if(S)
++	{
++		if(S->atom) free(S->atom);
++		if(S->coord) free(S->coord);
++		free(S);
++	}
++}
++
++// ==================================================================

pyjess-0.5.2/patches/CandidateSet.h.patch

@@ -0,0 +1,51 @@
+diff --git a/src/CandidateSet.h b/src/CandidateSet.h
+new file mode 100644
+index 0000000..9b12e6e
+--- /dev/null
++++ b/src/CandidateSet.h
+@@ -0,0 +1,44 @@
++// ==================================================================
++// CandidateSet.h
++// Copyright (c) Jonathan Barker, 2002
++// Copyright (c) Martin Larralde, 2025
++// ==================================================================
++// Declaration of type CandidateSet.
++// ==================================================================
++
++#ifndef CANDIDATESET_H
++#define CANDIDATESET_H
++
++#include "Atom.h"
++#include "Molecule.h"
++
++// ==================================================================
++// Local type CandidateSet
++// ==================================================================
++// count				Number of atoms in the set
++// atom[k]				Points to ATOM record for kth candidate
++// coord[k]				Points to coordinates for kth candidate
++// ==================================================================
++
++struct _CandidateSet
++{
++	int count;
++	Atom **atom;
++	double **coord;
++};
++
++typedef struct _CandidateSet CandidateSet;
++
++// ==================================================================
++// Declaration of methods of local type CandidateSet
++// ==================================================================
++// create(M,T,k)		Create from molecule M, atom k of T
++// free(S)				Free candidate set
++// ==================================================================
++
++CandidateSet *CandidateSet_create(const Molecule*);
++void CandidateSet_addAtom(CandidateSet*, Atom*);
++void CandidateSet_recordCoordinates(CandidateSet*);
++void CandidateSet_free(CandidateSet*);
++
++#endif
+

{pyjess-0.5.0 → pyjess-0.5.2}/patches/Jess.c.patch

@@ -1,8 +1,30 @@
 diff --git a/src/Jess.c b/src/Jess.c
-index e81bda0..6d44558 100644
+index e81bda0..c4e581b 100644
 --- a/src/Jess.c
 +++ b/src/Jess.c
-@@ -91,8 +91,10 @@ void Jess_free(Jess *J)
+@@ -4,15 +4,17 @@
+ // Implementation of types Jess and JessQuery.
+ // ==================================================================
+ 
++#include <stdio.h>
++#include <stdlib.h>
++#include <math.h>
++#include <string.h>
++
+ #include "Jess.h"
+ #include "Molecule.h"
+ #include "Scanner.h"
+ #include "TessTemplate.h"
+ #include "Super.h"
+-#include <stdio.h>
+-#include <stdlib.h>
+-#include <math.h>
+-#include <string.h>
++
+ 
+ // ==================================================================
+ // Forward declarations of local types
+@@ -91,8 +93,10 @@ void Jess_free(Jess *J)
  			n=J->head->next;
  			T=J->head->template;
  			if(T) T->free(T);
@@ -13,13 +35,13 @@ index e81bda0..6d44558 100644
  	}
  }
  
-@@ -157,26 +159,26 @@ Superposition *JessQuery_superposition(JessQuery *Q)
+@@ -156,27 +160,25 @@ Superposition *JessQuery_superposition(JessQuery *Q)
+ 	int count;
  	Template *T;
  	Atom **A;
- 
+-
 -	if(Q->super) return Q->super;
 +	Superposition* super;
-+	// if(Q->super) return Q->super;
  
  	A = Q->atoms;
  	T = Q->node->template;

pyjess-0.5.2/patches/Molecule.c.patch

@@ -0,0 +1,54 @@
+diff --git a/src/Molecule.c b/src/Molecule.c
+index d6c327e..7a293ff 100644
+--- a/src/Molecule.c
++++ b/src/Molecule.c
+@@ -25,21 +25,6 @@ struct _Node
+ 	Atom *atom;
+ };
+ 
+-// ==================================================================
+-// type Molecule
+-// ==================================================================
+-// count				Number of atoms in the molecule
+-// id					The molecule PDB code (if found)
+-// atom[k]				Pointer to kth atom in the molecule
+-// ==================================================================
+-
+-struct _Molecule
+-{
+-	int count;
+-	char id[5];
+-	Atom *atom[0];
+-};
+-
+ // ==================================================================
+ // Methods of type Molecule;
+ // ==================================================================
+@@ -113,6 +98,7 @@ Molecule *Molecule_create(FILE *file, int ignore_endmdl, float conservation_cuto
+ 	// Create the molecule...
+ 
+ 	M = (Molecule*)calloc(1,sizeof(Molecule)+count*sizeof(Atom*));
++	M->index = NULL;
+ 	M->count=count;
+ 	strcpy(M->id,pdb);
+ 
+@@ -127,6 +113,10 @@ Molecule *Molecule_create(FILE *file, int ignore_endmdl, float conservation_cuto
+ 		head=N;
+ 	}
+ 
++	// Create an index to access atoms by residue name
++
++	M->index = ResIndex_create(M->atom, M->count);
++
+ 	// Check memory leaks??
+ 
+ 	return M;
+@@ -138,6 +128,8 @@ void Molecule_free(Molecule *M)
+ 
+ 	if(M)
+ 	{
++		if(M->index) ResIndex_free(M->index);
++
+ 		for(k=0; k<M->count; k++)
+ 		{
+ 			if(M->atom[k]) free(M->atom[k]);

pyjess-0.5.2/patches/Molecule.h.patch

@@ -0,0 +1,35 @@
+diff --git a/src/Molecule.h b/src/Molecule.h
+index d838488..c44bf6f 100644
+--- a/src/Molecule.h
++++ b/src/Molecule.h
+@@ -8,15 +8,27 @@
+ #ifndef MOLECULE_H
+ #define MOLECULE_H
+ 
+-#include "Atom.h"
+ #include <stdio.h>
+ 
++#include "Atom.h"
++#include "ResIndex.h"
++
+ // ==================================================================
+-// Forward declarations
++// type Molecule
+ // ==================================================================
+-// Molecule					A complete molecule
++// count				Number of atoms in the molecule
++// id					The molecule PDB code (if found)
++// atom[k]				Pointer to kth atom in the molecule
+ // ==================================================================
+ 
++struct _Molecule
++{
++	int count;
++	char id[5];
++    ResIndex *index;
++	Atom *atom[0];
++};
++
+ typedef struct _Molecule Molecule;
+ 
+ // ==================================================================

pyjess-0.5.2/patches/ResIndex.c.patch

@@ -0,0 +1,181 @@
+diff --git a/src/ResIndex.c b/src/ResIndex.c
+new file mode 100644
+index 0000000..e88790e
+--- /dev/null
++++ b/src/ResIndex.c
+@@ -0,0 +1,175 @@
++// ==================================================================
++// HashMap.h
++// Copyright (c) Martin Larralde, 2025
++// ==================================================================
++// Implementation of type ResIndex.
++// ==================================================================
++
++#include <assert.h>
++#include <stddef.h>
++#include <stdlib.h>
++#include <string.h>
++#include <stdio.h>
++
++#include "Atom.h"
++#include "ResIndex.h"
++
++#ifdef _MSC_VER
++#define strncasecmp _strnicmp
++#define strcasecmp _stricmp
++#endif
++
++static int ResNames_compare(const void *pa, const void *pb)
++{
++	const Atom *a = **((const Atom***)pa);
++	const Atom *b = **((const Atom***)pb);
++    int result = strncasecmp(&a->resName[0], &b->resName[0], 4);
++    if (result != 0)
++        return result;
++    return a->serial - b->serial;
++}
++
++extern ResIndex* ResIndex_create(Atom** atoms, int n)
++{
++    int i;
++    int j;
++    int k;
++    int numRes;
++    Atom*** tmp;
++    ResIndex* I;
++
++    // Allocate struct
++
++    I = calloc(1, sizeof(ResIndex));
++    if(!I) {
++        return NULL;
++    }
++
++    // Initialize fields
++    I->n = 0;
++    I->names = NULL;
++    I->offset = NULL;
++    I->atoms = NULL;
++
++    // Handle empty case
++    if(n==0) {
++        I->offset = calloc(2, sizeof(size_t));
++        I->atoms = (Atom**) calloc(1, sizeof(Atom*));
++        I->offset[0] = I->offset[1] = 0;
++        I->atoms[0] = NULL;
++        return I;
++    }
++
++    // Allocate auxilliary data to sort names
++
++    tmp = (Atom***) calloc(n, sizeof(Atom**));
++    if(!tmp) {
++        ResIndex_free(I);
++        return NULL;
++    }
++
++    // Sort residue names found in molecule
++
++    for (i = 0; i < n; i++) tmp[i] = (Atom**) &atoms[i];
++    qsort(tmp,n, sizeof(Atom**),ResNames_compare);
++
++    // Count number of distinct residue names in molecule
++
++    numRes = 1;
++    for (i = 1; i < n; i++) 
++        numRes += (strncasecmp((*tmp[i-1])->resName, (*tmp[i])->resName, 4) != 0);
++    
++    // Allocate data for residues
++
++    I->names = (char*) calloc(numRes, 4*sizeof(char));
++    I->offset = (size_t*) calloc(numRes+1, sizeof(size_t));
++    I->atoms = (Atom**) calloc(n + numRes, sizeof(Atom*));
++    if ((I->names == NULL) || (I->atoms == NULL) || (I->offset == NULL)) {
++        free(tmp);
++        ResIndex_free(I);
++        return NULL;
++    }
++
++    // Record data in index
++
++    memcpy(&I->names[0], (*tmp[0])->resName, 4*sizeof(char));
++    I->n = numRes;
++    I->offset[0] = 0;
++    I->atoms[0] = *tmp[0];
++
++    char* names = &I->names[4];
++    size_t* offset = &I->offset[1];
++
++    for (i = 1, j = 4, k = 1; i < n; i++) {
++
++        if (strncasecmp((*tmp[i-1])->resName, (*tmp[i])->resName, 4) != 0) {
++            memcpy(names, (*tmp[i])->resName, 4*sizeof(char));
++            names += 4;
++
++            I->atoms[k] = NULL;
++            k += 1;
++
++            (*offset) = k;
++            offset++;
++        }
++
++        I->atoms[k] = *tmp[i];
++        k += 1;
++    }
++
++    (*offset) = k;
++
++    free(tmp);
++    
++    return I;
++}
++
++extern int ResIndex_find(ResIndex* I, const char resName[4]) {
++    //NB: As the names have been sorted with `qsort`, we can use a binary search
++    
++    int cmp;
++    size_t mid;
++    size_t start = 0;
++    size_t end = I->n;
++    size_t n = 0;
++
++    while (start < end) {
++        mid = (start + end) / 2;
++        cmp = strncasecmp(&I->names[4*mid], resName, 4);
++        if(cmp < 0) {
++            start = (mid == start) ? mid + 1 : mid;
++        } else if (cmp > 0) {
++            end = (mid == end) ? mid - 1 : mid;
++        } else {
++            return mid;
++        }
++
++        n++;
++        assert(n < I->n);
++    }
++
++    return -1;
++}
++
++extern Atom** ResIndex_get(ResIndex* I, const char resName[4])
++{
++    int i = ResIndex_find(I, resName);
++    return ResIndex_values(I, i);
++}
++
++extern Atom** ResIndex_values(ResIndex* I, int i)
++{
++    if(i > I->n)
++        return &I->atoms[I->offset[1] - 1];
++    return &I->atoms[I->offset[i]];
++}
++
++extern void ResIndex_free(ResIndex* I)
++{
++    if(I) {
++        if (I->names) free(I->names);
++        if (I->atoms) free(I->atoms);
++        if (I->offset) free(I->offset);
++        free(I);
++    }
++}