pyjess 0.7.0a1__tar.gz → 0.7.0a2__tar.gz

{pyjess-0.7.0a1 → pyjess-0.7.0a2}/CHANGELOG.md

@@ -6,7 +6,18 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 
 ## [Unreleased]
-[Unreleased]: https://github.com/althonos/pyjess/compare/v0.7.0-alpha.1...HEAD
+[Unreleased]: https://github.com/althonos/pyjess/compare/v0.7.0-alpha.2...HEAD
+
+
+## [v0.7.0-alpha.2] - 2025-09-02
+[v0.7.0-alpha.2]: https://github.com/althonos/pyjess/compare/v0.7.0-alpha.1...v0.7.0-alpha.2
+
+### Fixed
+- `max_candidates` causing `Query` to stop before reaching the actual number of maximum candidates.
+
+### Changed
+- **breaking**: Use string variants instead of `bool` to control the behaviour of `ignore_chain` argument.
+- Use unrolled string comparison to compare atom names instead of `strcasecmp` in Jess code.
 
 
 ## [v0.7.0-alpha.1] - 2025-09-02
@@ -14,6 +25,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### Fixed
 - **breaking**: Incorrect handling of `max_candidates` in `Jess.query`, causing PyJess to erroneously ignore some templates.
+- `Template.dimension` reporting incorrect numbers for identical residues across different residues.
 
 ### Changed
 - **breaking**: Set the `max_candidates` default value to `None` in `Jess.query`, disabling max candidates filtering by default.

{pyjess-0.7.0a1 → pyjess-0.7.0a2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: pyjess
-Version: 0.7.0a1
+Version: 0.7.0a2
 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>
@@ -193,7 +193,8 @@ structures to the $m=7607$ templates of
 | ``v0.5.0``  | 586.3       | 142.7                       | x1.05       |
 | ``v0.5.1``  | 365.6       | 228.9                       | x1.69       |
 | ``v0.5.2``  | 327.2       | 255.7                       | x1.88       |
-| ``v0.6.0``  | 54.5        | 1535.4                      | **x11.34**  |
+| ``v0.6.0``  | 54.5        | 1535.4                      | x11.34      |
+| ``v0.7.0``  | 52.4        | 1597.5                      | **x11.80**  |
 
 *Benchmarks were run on a quiet [i7-1255U](https://www.intel.com/content/www/us/en/products/sku/226259/intel-core-i71255u-processor-12m-cache-up-to-4-70-ghz/specifications.html) CPU running @4.70GHz with 10 physical cores / 12 logical
 cores.*

{pyjess-0.7.0a1 → pyjess-0.7.0a2}/README.md

@@ -133,7 +133,8 @@ structures to the $m=7607$ templates of
 | ``v0.5.0``  | 586.3       | 142.7                       | x1.05       |
 | ``v0.5.1``  | 365.6       | 228.9                       | x1.69       |
 | ``v0.5.2``  | 327.2       | 255.7                       | x1.88       |
-| ``v0.6.0``  | 54.5        | 1535.4                      | **x11.34**  |
+| ``v0.6.0``  | 54.5        | 1535.4                      | x11.34      |
+| ``v0.7.0``  | 52.4        | 1597.5                      | **x11.80**  |
 
 *Benchmarks were run on a quiet [i7-1255U](https://www.intel.com/content/www/us/en/products/sku/226259/intel-core-i71255u-processor-12m-cache-up-to-4-70-ghz/specifications.html) CPU running @4.70GHz with 10 physical cores / 12 logical
 cores.*

{pyjess-0.7.0a1 → pyjess-0.7.0a2}/include/jess/jess.pxd

@@ -1,7 +1,7 @@
 from .atom cimport Atom
 from .molecule cimport Molecule
 from .super cimport Superposition
-from .template cimport Template
+from .template cimport Template, IgnoreType
 
 
 cdef extern from "Jess.h" nogil:
@@ -21,7 +21,7 @@ cdef extern from "Jess.h" nogil:
     JessQuery* Jess_query(Jess*, Molecule*, double, double, bint)
 
     void JessQuery_free(JessQuery*)
-    int JessQuery_next(JessQuery*, int)
+    int JessQuery_next(JessQuery*, IgnoreType)
     int JessQuery_nextTemplate(JessQuery*)
     Template* JessQuery_template(JessQuery*)
     const Molecule* JessQuery_molecule(JessQuery*)

{pyjess-0.7.0a1 → pyjess-0.7.0a2}/include/jess/scanner.pxd

@@ -1,5 +1,5 @@
 from .molecule import Molecule
-from .template import Template
+from .template import Template, IgnoreType
 
 
 cdef extern from "Scanner.h" nogil:
@@ -10,6 +10,6 @@ cdef extern from "Scanner.h" nogil:
 
     Scanner* Scanner_create(Molecule*, Template*, double, double)
     void Scanner_free(Scanner*)
-    Atom** Scanner_next(Scanner*, int)
+    Atom** Scanner_next(Scanner*, IgnoreType)
     double Scanner_rmsd(Scanner*)
 

{pyjess-0.7.0a1 → pyjess-0.7.0a2}/include/jess/template.pxd

@@ -5,6 +5,12 @@ from .candidate_set cimport CandidateSet
 cdef extern from "Template.h" nogil:
 
     ctypedef _Template Template
+
+    ctypedef enum IgnoreType:
+        ignoreNone
+        ignoreResidues
+        ignoreAtoms
+
     cdef struct _Template:
         void (*free)(Template*) nogil
         int (*count)(const Template*) nogil

{pyjess-0.7.0a1 → pyjess-0.7.0a2}/patches/Jess.c.patch

@@ -1,5 +1,5 @@
 diff --git a/src/Jess.c b/src/Jess.c
-index e81bda0..44fa672 100644
+index e81bda0..a0929cd 100644
 --- a/src/Jess.c
 +++ b/src/Jess.c
 @@ -4,15 +4,18 @@
@@ -162,7 +162,8 @@ index e81bda0..44fa672 100644
 +	return (Q->node) ? 1 : 0;
  }
  
- int JessQuery_next(JessQuery *Q, int ignore_chain)
+-int JessQuery_next(JessQuery *Q, int ignore_chain)
++int JessQuery_next(JessQuery *Q, IgnoreType ignore_chain)
  {
  	Template *T;
  	Atom **A;

{pyjess-0.7.0a1 → pyjess-0.7.0a2}/patches/Jess.h.patch

@@ -1,5 +1,5 @@
 diff --git a/src/Jess.h b/src/Jess.h
-index c90abe6..704b5e8 100644
+index c90abe6..4361958 100644
 --- a/src/Jess.h
 +++ b/src/Jess.h
 @@ -8,6 +8,8 @@
@@ -27,14 +27,16 @@ index c90abe6..704b5e8 100644
  
  // ==================================================================
  // Methods of type JessQuery
-@@ -50,10 +52,11 @@ extern JessQuery *Jess_query(Jess*,Molecule*,double,double);
+@@ -49,11 +51,12 @@ extern JessQuery *Jess_query(Jess*,Molecule*,double,double);
+ // ==================================================================
  
  extern void JessQuery_free(JessQuery*);
- extern int JessQuery_next(JessQuery*, int);
+-extern int JessQuery_next(JessQuery*, int);
 -extern Template *JessQuery_template(JessQuery*);
 -extern const Molecule *JessQuery_molecule(JessQuery*);
 -extern Atom **JessQuery_atoms(JessQuery*);
 -extern Superposition *JessQuery_superposition(JessQuery*);
++extern int JessQuery_next(JessQuery*, IgnoreType);
 +extern int JessQuery_nextTemplate(JessQuery*);
 +extern Template *JessQuery_template(const JessQuery*);
 +extern const Molecule *JessQuery_molecule(const JessQuery*);

{pyjess-0.7.0a1 → pyjess-0.7.0a2}/patches/Main.c.patch

@@ -1,5 +1,5 @@
 diff --git a/src/Main.c b/src/Main.c
-index dff22b9..476cb01 100644
+index dff22b9..5baeb17 100644
 --- a/src/Main.c
 +++ b/src/Main.c
 @@ -14,6 +14,7 @@
@@ -10,12 +10,21 @@ index dff22b9..476cb01 100644
  
  // ==================================================================
  // Global constants
-@@ -116,11 +117,11 @@ static void output(
+@@ -21,6 +22,8 @@
+ // atomFormat			The format of a PDB ATOM record (for printf)
+ // ==================================================================
+ 
++#define MAX_CANDIDATES -1
++
+ static const char *atomFormat =
+ 	"ATOM  %5i%5s%c%-3s%c%c%4i%-4c%8.3f%8.3f%8.3f%6.2f%6.2f\n"; //Riziotis edit
+ 	//"ATOM  %5i%5s%c%-3s%c%c%4i%-4c%8.3f%8.3f%8.3f\n"; //Riziotis edit
+@@ -116,11 +119,11 @@ static void output(
  		A->charge
  		);
  }
 -static void search(const char *filename,Jess *J,double tRmsd,double tDistance,double max_total_threshold,int no_transform,int ignore_chain,int write_filename,int ignore_endmdl, float conservation_cutoff)
-+static void search(const char *filename,Jess *J,double tRmsd,double tDistance,double max_total_threshold,int no_transform,int ignore_chain,int write_filename,int ignore_endmdl, float conservation_cutoff, bool fastScan)
++static void search(const char *filename,Jess *J,double tRmsd,double tDistance,double max_total_threshold,int no_transform,IgnoreType ignore_chain,int write_filename,int ignore_endmdl, float conservation_cutoff, bool fastScan)
  {
  	Molecule *M;
  	Superposition *sup;
@@ -24,7 +33,16 @@ index dff22b9..476cb01 100644
  	Atom **A;
  	FILE *file;
  	JessQuery *Q;
-@@ -145,11 +146,21 @@ static void search(const char *filename,Jess *J,double tRmsd,double tDistance,do
+@@ -128,7 +131,7 @@ static void search(const char *filename,Jess *J,double tRmsd,double tDistance,do
+ 	const double *P,*c[2];
+ 	double det;
+ 	double logE;
+-	int killswitch = 0;
++	int candidates = 0;
+ 
+ 	if(!(file=fopen(filename,"r")))
+ 	{
+@@ -145,11 +148,21 @@ static void search(const char *filename,Jess *J,double tRmsd,double tDistance,do
  		return;
  	}
  
@@ -39,8 +57,8 @@ index dff22b9..476cb01 100644
  		T=JessQuery_template(Q);
 +		// printf("current template: %s\n", T->name(T));
 +
-+		killswitch = (T!=Tprev) ? 0 : killswitch + 1;
-+		if(killswitch == 1000)
++		candidates = (T!=Tprev) ? 0 : candidates + 1;
++		if(candidates == MAX_CANDIDATES)
 +		{
 +			JessQuery_nextTemplate(Q);
 +			continue;
@@ -48,7 +66,7 @@ index dff22b9..476cb01 100644
  
  		count=T->count(T);
  		sup = JessQuery_superposition(Q);
-@@ -193,7 +204,8 @@ static void search(const char *filename,Jess *J,double tRmsd,double tDistance,do
+@@ -193,7 +206,8 @@ static void search(const char *filename,Jess *J,double tRmsd,double tDistance,do
  
  			printf("ENDMDL\n\n");
  		}
@@ -58,23 +76,32 @@ index dff22b9..476cb01 100644
  	}
  
  	JessQuery_free(Q);
-@@ -339,6 +351,7 @@ int main(int argc, char **argv)
- 	int ignore_chain=0;
+@@ -336,9 +350,10 @@ int main(int argc, char **argv)
+ 	int count;
+ 	//Riziotis edit
+ 	int no_transform=0;
+-	int ignore_chain=0;
++	IgnoreType ignore_chain=ignoreNone;
  	int write_filename=0;
  	int ignore_endmdl=0;
 +	int fastScan=0;
  
  	if(argc<7 || argc>8) help();
  
-@@ -354,6 +367,7 @@ int main(int argc, char **argv)
- 			else if(*s=='i') ignore_chain=1;
+@@ -351,9 +366,11 @@ int main(int argc, char **argv)
+ 			if(*s=='f') feedbackQ=1;
+ 			//Riziotis edit
+ 			else if(*s=='n') no_transform=1;
+-			else if(*s=='i') ignore_chain=1;
++			else if(*s=='i') ignore_chain=ignoreAtoms;
++			else if(*s=='I') ignore_chain=ignoreResidues;
  			else if(*s=='q') write_filename=1;
  			else if(*s=='e') ignore_endmdl=1;
 +			else if(*s=='s') fastScan=1;
  			else help();
  		}
  	}
-@@ -388,10 +402,11 @@ int main(int argc, char **argv)
+@@ -388,10 +405,11 @@ int main(int argc, char **argv)
  		if(strlen(s)==0) continue;
  
  		if(feedbackQ) fprintf(stderr,"%s\n",s);

{pyjess-0.7.0a1 → pyjess-0.7.0a2}/patches/ResIndex.c.patch

@@ -1,9 +1,9 @@
 diff --git a/src/ResIndex.c b/src/ResIndex.c
 new file mode 100644
-index 0000000..0010445
+index 0000000..ed907f4
 --- /dev/null
 +++ b/src/ResIndex.c
-@@ -0,0 +1,167 @@
+@@ -0,0 +1,163 @@
 +// ==================================================================
 +// HashMap.h
 +// Copyright (c) Martin Larralde, 2025
@@ -18,18 +18,14 @@ index 0000000..0010445
 +#include <stdio.h>
 +
 +#include "Atom.h"
++#include "TessAtom.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);
++    int result = TessAtom_compareName(&a->resName[0], &b->resName[0]);
 +    if (result != 0)
 +        return result;
 +    return a->serial - b->serial;
@@ -75,7 +71,7 @@ index 0000000..0010445
 +
 +    numRes = 1;
 +    for (i = 1; i < n; i++) 
-+        numRes += (strncasecmp((*tmp[i-1])->resName, (*tmp[i])->resName, 4) != 0);
++        numRes += (TessAtom_compareName((*tmp[i-1])->resName, (*tmp[i])->resName) != 0);
 +    
 +    // Allocate data for residues
 +
@@ -100,7 +96,7 @@ index 0000000..0010445
 +
 +    for (i = 1, j = 4, k = 1; i < n; i++) {
 +
-+        if (strncasecmp((*tmp[i-1])->resName, (*tmp[i])->resName, 4) != 0) {
++        if (TessAtom_compareName((*tmp[i-1])->resName, (*tmp[i])->resName) != 0) {
 +            memcpy(names, (*tmp[i])->resName, 4*sizeof(char));
 +            names += 4;
 +
@@ -133,7 +129,7 @@ index 0000000..0010445
 +
 +    while (start < end) {
 +        mid = (start + end) / 2;
-+        cmp = strncasecmp(&I->names[4*mid], resName, 4);
++        cmp = TessAtom_compareName(&I->names[4*mid], resName);
 +        if(cmp < 0) {
 +            start = (mid == start) ? mid + 1 : mid;
 +        } else if (cmp > 0) {

{pyjess-0.7.0a1 → pyjess-0.7.0a2}/patches/Scanner.c.patch

@@ -1,5 +1,5 @@
 diff --git a/src/Scanner.c b/src/Scanner.c
-index 19a35a7..d796132 100644
+index 19a35a7..2d0e528 100644
 --- a/src/Scanner.c
 +++ b/src/Scanner.c
 @@ -5,41 +5,37 @@
@@ -201,7 +201,7 @@ index 19a35a7..d796132 100644
  	}
  
  	return S;
-@@ -119,26 +184,8 @@ Scanner *Scanner_create(Molecule *M, Template *T,double r, double s)
+@@ -119,36 +184,16 @@ Scanner *Scanner_create(Molecule *M, Template *T,double r, double s)
  
  void Scanner_free(Scanner *S)
  {
@@ -228,7 +228,9 @@ index 19a35a7..d796132 100644
  		free(S);
  	}
  }
-@@ -147,8 +194,6 @@ Atom **Scanner_next(Scanner *S, int ignore_chain)
+ 
+-Atom **Scanner_next(Scanner *S, int ignore_chain)
++Atom **Scanner_next(Scanner *S, IgnoreType ignore_chain)
  {
  	int j,k;
  	double min,max;

{pyjess-0.7.0a1 → pyjess-0.7.0a2}/patches/Scanner.h.patch

@@ -1,5 +1,5 @@
 diff --git a/src/Scanner.h b/src/Scanner.h
-index d775ce7..e049f40 100644
+index d775ce7..8a83fbc 100644
 --- a/src/Scanner.h
 +++ b/src/Scanner.h
 @@ -11,27 +11,43 @@
@@ -31,7 +31,8 @@ index d775ce7..e049f40 100644
 +extern Scanner *Scanner_create(Molecule*,Template*,ScannerData*,double,double,bool);
 +extern Scanner *Scanner_reuse(Scanner*,Molecule*,Template*,ScannerData*,double,double,bool);
  extern void Scanner_free(Scanner*);
- extern Atom **Scanner_next(Scanner*, int);
+-extern Atom **Scanner_next(Scanner*, int);
++extern Atom **Scanner_next(Scanner*, IgnoreType);
  extern double Scanner_rmsd(Scanner*);
  
 +// ==================================================================

{pyjess-0.7.0a1 → pyjess-0.7.0a2}/patches/Template.h.patch

@@ -1,8 +1,8 @@
 diff --git a/src/Template.h b/src/Template.h
-index 13f68f1..21e12c8 100644
+index 13f68f1..8cb0ee7 100644
 --- a/src/Template.h
 +++ b/src/Template.h
-@@ -9,6 +9,7 @@
+@@ -9,14 +9,17 @@
  #define TEMPLATE_H
  
  #include "Atom.h"
@@ -10,7 +10,17 @@ index 13f68f1..21e12c8 100644
  
  // ==================================================================
  // Forward declarations
-@@ -26,6 +27,7 @@ typedef struct _Template Template;
+ // ==================================================================
+ // Template				The template interface
++// IgnoreChainType		The type of ignore_chain in check
+ // ==================================================================
+ 
+ typedef struct _Template Template;
++typedef enum { ignoreNone,ignoreResidues,ignoreAtoms } IgnoreType;
+ 
+ // ==================================================================
+ // type Template
+@@ -26,6 +29,7 @@ typedef struct _Template Template;
  // match(T,k,A)			True if A matches atom k of T
  // range(T,i,j,a,b)		[*a,*b] <- range of |atom i - atom j|
  // check(T,A,k,ignore_chain)	Check n-ary rules on atom k-1 and 0,...,k-2
@@ -18,12 +28,12 @@ index 13f68f1..21e12c8 100644
  // position(T,i)		Position of atom i (example position)
  // name(T)			Returns the symbolic name for the template
  // logE(T,x,n)			Provide an estimate of logE for a hit
-@@ -37,11 +39,13 @@ struct _Template
+@@ -37,11 +41,13 @@ struct _Template
  	int (*count)(const Template*);
  	int (*match)(const Template*,int,const Atom*);
  	int (*range)(const Template*,int,int,double*,double*);
 -	int (*check)(const Template*,Atom**,int,int);
-+	int (*check)(const Template*,Atom**,int*,int,int);
++	int (*check)(const Template*,Atom**,int*,int,IgnoreType);
 +	void (*candidates)(const Template*, const Molecule*, int, CandidateSet**);
  	const double *(*position)(const Template*,int);
  	const char *(*name)(const Template*);

{pyjess-0.7.0a1 → pyjess-0.7.0a2}/patches/TessAtom.c.patch

@@ -1,8 +1,8 @@
 diff --git a/src/TessAtom.c b/src/TessAtom.c
-index e1cce1a..324347d 100644
+index e1cce1a..9ba021e 100644
 --- a/src/TessAtom.c
 +++ b/src/TessAtom.c
-@@ -7,39 +7,17 @@
+@@ -7,40 +7,13 @@
  
  #include "TessAtom.h"
  #include "Atom.h"
@@ -41,14 +41,11 @@ index e1cce1a..324347d 100644
 -	double pos[3];
 -	double distWeight;
 -};
-+#ifdef _MSC_VER
-+#define strncasecmp _strnicmp
-+#define strcasecmp _stricmp
-+#endif
- 
+-
  // ==================================================================
  // Methods of type TessAtom (ARGGH!!!)
-@@ -91,7 +69,7 @@ TessAtom *TessAtom_create(const char *s)
+ // ==================================================================
+@@ -91,7 +64,7 @@ TessAtom *TessAtom_create(const char *s)
  	int rq;
  	const char *q;
  	const char *tmp;
@@ -57,7 +54,7 @@ index e1cce1a..324347d 100644
  
  
  	// 0. Parse the record as a standard PDB atom. We must
-@@ -157,8 +135,8 @@ TessAtom *TessAtom_create(const char *s)
+@@ -157,8 +130,8 @@ TessAtom *TessAtom_create(const char *s)
  	// Set up all the pointers to the
  	// residue name and atom name fields
  
@@ -68,7 +65,7 @@ index e1cce1a..324347d 100644
  	p+=sizeof(char*)*ac;
  	for(m=0; m<ac; m++)
  	{
-@@ -166,7 +144,7 @@ TessAtom *TessAtom_create(const char *s)
+@@ -166,7 +139,7 @@ TessAtom *TessAtom_create(const char *s)
  		p+=5;
  	}
  
@@ -77,7 +74,7 @@ index e1cce1a..324347d 100644
  	p+=sizeof(char*)*rc;
  	for(m=0; m<rc; m++)
  	{
-@@ -259,41 +237,7 @@ TessAtom *TessAtom_create(const char *s)
+@@ -259,41 +232,7 @@ TessAtom *TessAtom_create(const char *s)
  }
  
  //Riziotis edit
@@ -119,7 +116,38 @@ index e1cce1a..324347d 100644
  static int TessAtom_isCarbon(const Atom *A)
  {
  	return A->name[0]=='_' && A->name[1]=='C' ? 1:0;
-@@ -507,5 +451,65 @@ int TessAtom_match(const TessAtom *T, const Atom *A)
+@@ -327,9 +266,9 @@ static int TessAtom_isInSamePosition(const TessAtom *T, const Atom *A)
+ 
+ static int TessAtom_isMainChain(const Atom *A)
+ {
+-	if(strcasecmp(A->name,"_CA_")==0) return 1;
+-	if(strcasecmp(A->name,"_N__")==0) return 1;
+-	if(strcasecmp(A->name,"_O__")==0) return 1;
++	if(TessAtom_compareName(A->name,"_CA_")==0) return 1;
++	if(TessAtom_compareName(A->name,"_N__")==0) return 1;
++	if(TessAtom_compareName(A->name,"_O__")==0) return 1;
+ 
+ 	return 0;
+ }
+@@ -340,7 +279,7 @@ static int TessAtom_matchName(const TessAtom *T, const Atom *A)
+ 
+ 	for(k=0; k<T->nameCount; k++)
+ 	{
+-		if(strcasecmp(A->name,T->name[k])==0) return 1;
++		if(TessAtom_compareName(A->name,T->name[k])==0) return 1;
+ 	}
+ 
+ 	return 0;
+@@ -352,7 +291,7 @@ static int TessAtom_matchResName(const TessAtom *T, const Atom *A)
+ 
+ 	for(k=0; k<T->resNameCount; k++)
+ 	{
+-		if(strcasecmp(A->resName,T->resName[k])==0) return 1;
++		if(TessAtom_compareName(A->resName,T->resName[k])==0) return 1;
+ 	}
+ 
+ 	return 0;
+@@ -507,5 +446,65 @@ int TessAtom_match(const TessAtom *T, const Atom *A)
  	}
  }
  

{pyjess-0.7.0a1 → pyjess-0.7.0a2}/patches/TessAtom.h.patch

@@ -1,5 +1,5 @@
 diff --git a/src/TessAtom.h b/src/TessAtom.h
-index 6480d8b..648f55f 100644
+index 6480d8b..8ec3618 100644
 --- a/src/TessAtom.h
 +++ b/src/TessAtom.h
 @@ -9,6 +9,7 @@
@@ -46,12 +46,16 @@ index 6480d8b..648f55f 100644
  // ==================================================================
  // Methods of type TessAtom
  // ==================================================================
-@@ -30,16 +60,62 @@ typedef struct _TessAtom TessAtom;
+@@ -30,16 +60,79 @@ typedef struct _TessAtom TessAtom;
  // ==================================================================
  
  extern TessAtom *TessAtom_create(const char*);
 -extern void TessAtom_free(TessAtom*);
 -extern const double *TessAtom_position(const TessAtom*);
++extern TessAtom* TessAtom_copy(const TessAtom*);
+ extern int TessAtom_match(const TessAtom*,const Atom*);
+-extern int TessAtom_resSeq(const TessAtom*);
++extern double TessAtom_distance(const TessAtom*, const TessAtom*);
 +
 +static inline void TessAtom_free(TessAtom *A)
 +{
@@ -63,8 +67,22 @@ index 6480d8b..648f55f 100644
 +	return A->pos;
 +}
 +
- extern int TessAtom_match(const TessAtom*,const Atom*);
--extern int TessAtom_resSeq(const TessAtom*);
++#ifndef TessAtom_toupper
++#define TessAtom_toupper(c) ((( c >= 'a' ) && (c <= 'z')) ? c & (~0x20) : c);
++#endif
++
++static int TessAtom_compareName(const char* restrict a, const char* restrict b)
++{
++	for(int i=0; i<4;i++)
++	{
++		char ca = TessAtom_toupper(a[i]);
++		char cb = TessAtom_toupper(b[i]);
++		int cmp = ca - cb;
++		if(cmp != 0) return cmp;
++	}
++	return 0;
++}
++
 +
 +static inline int TessAtom_resSeq(const TessAtom *A)
 +{
@@ -109,8 +127,7 @@ index 6480d8b..648f55f 100644
 +	return A->code;
 +}
 +
-+extern TessAtom* TessAtom_copy(const TessAtom*);
-+extern double TessAtom_distance(const TessAtom*, const TessAtom*);
++
 +
  // ==================================================================
  

{pyjess-0.7.0a1 → pyjess-0.7.0a2}/patches/TessTemplate.c.patch

@@ -1,5 +1,5 @@
 diff --git a/src/TessTemplate.c b/src/TessTemplate.c
-index 1eb6914..27539c8 100644
+index 1eb6914..eb635cf 100644
 --- a/src/TessTemplate.c
 +++ b/src/TessTemplate.c
 @@ -5,13 +5,21 @@
@@ -99,11 +99,11 @@ index 1eb6914..27539c8 100644
  }
  
 -static int TessTemplate_check(const Template *T, Atom **A, int k, int ignore_chain)
-+int TessTemplate_check(const Template *T, Atom **A, int *order, int k, int ignore_chain)
++int TessTemplate_check(const Template *T, Atom **A, int *order, int k, IgnoreType ignore_chain)
  {
  	const TessTemplate *J = (const TessTemplate*)&T[1];
  	int i;
-@@ -98,8 +86,8 @@ static int TessTemplate_check(const Template *T, Atom **A, int k, int ignore_cha
+@@ -98,44 +86,45 @@ static int TessTemplate_check(const Template *T, Atom **A, int k, int ignore_cha
  		// Compare chain ids
  
  		//Riziotis edit
@@ -114,7 +114,26 @@ index 1eb6914..27539c8 100644
  		//c = A[i]->chainID-A[k-1]->chainID;
  		//d = TessAtom_chainID(J->atom[i])-TessAtom_chainID(J->atom[k-1]);
  
-@@ -119,8 +107,8 @@ static int TessTemplate_check(const Template *T, Atom **A, int k, int ignore_cha
+-		if(ignore_chain==1)
+-		{
+-			c=0;
+-			d=0;
+-		}
+-
+-		if(c==0 && d!=0) return 0;
+-		if(c!=0 && d==0) return 0;
+-
+-		if(c!=0)
++		if(ignore_chain==ignoreNone)
+ 		{
+-			continue;
++			if(c==0 && d!=0) return 0;
++			if(c!=0 && d==0) return 0;
++			if(c!=0)
++			{
++				continue;
++			}
+ 		}
  
  		// Compare residue sequence numbers
  
@@ -125,7 +144,13 @@ index 1eb6914..27539c8 100644
  
  		if(a==0 && b!=0) return 0;
  		if(a!=0 && b==0) return 0;
-@@ -129,13 +117,13 @@ static int TessTemplate_check(const Template *T, Atom **A, int k, int ignore_cha
++
++		if(ignore_chain!=ignoreAtoms)
++		{
++			if(a==0 && c!=0) return 0;
++		}
+ 	}
+ 
  	return 1;
  }
  
@@ -141,7 +166,7 @@ index 1eb6914..27539c8 100644
  {
  	const TessTemplate *J = (const TessTemplate*)&T[1];
  	const double logA = -8.5;
-@@ -149,11 +137,73 @@ static double TessTemplate_logE(const Template *T,double rmsd, int n)
+@@ -149,11 +138,73 @@ static double TessTemplate_logE(const Template *T,double rmsd, int n)
  	return logA + alpha*rmsd + beta*(double)J->dim + log((double)n);
  }
  
@@ -216,7 +241,7 @@ index 1eb6914..27539c8 100644
  {
  	TessTemplate *J;
  	int i;
-@@ -224,7 +274,7 @@ Template *TessTemplate_create(FILE *file,const char *sym)
+@@ -224,7 +275,7 @@ Template *TessTemplate_create(FILE *file,const char *sym)
  			// No errors thus far - add the atom template
  			// to the list we're creating...
  
@@ -225,7 +250,7 @@ index 1eb6914..27539c8 100644
  			n->succ=head;
  			head=n;
  			n->atom=A;
-@@ -269,6 +319,7 @@ Template *TessTemplate_create(FILE *file,const char *sym)
+@@ -269,6 +320,7 @@ Template *TessTemplate_create(FILE *file,const char *sym)
  	T->name=TessTemplate_name;
  	T->logE=TessTemplate_logE;
  	T->distWeight=TessTemplate_distWeight;
@@ -233,7 +258,7 @@ index 1eb6914..27539c8 100644
  
  	// Set up the data fields
  
-@@ -333,4 +384,78 @@ Template *TessTemplate_create(FILE *file,const char *sym)
+@@ -333,4 +385,78 @@ Template *TessTemplate_create(FILE *file,const char *sym)
  	return T;
  }
  

{pyjess-0.7.0a1 → pyjess-0.7.0a2}/patches/TessTemplate.h.patch

@@ -1,5 +1,5 @@
 diff --git a/src/TessTemplate.h b/src/TessTemplate.h
-index 1e597f2..8dd8f06 100644
+index 1e597f2..eb7c2ec 100644
 --- a/src/TessTemplate.h
 +++ b/src/TessTemplate.h
 @@ -9,8 +9,57 @@
@@ -46,7 +46,7 @@ index 1e597f2..8dd8f06 100644
 +extern int TessTemplate_range(const Template *T,int i,int j,double *a,double *b);
 +extern const double *TessTemplate_position(const Template *T, int k);
 +extern double TessTemplate_distWeight(const Template *T, int k);
-+extern int TessTemplate_check(const Template *T, Atom **A, int *order, int k, int ignore_chain);
++extern int TessTemplate_check(const Template *T, Atom **A, int *order, int k, IgnoreType ignore_chain);
 +extern void TessTemplate_candidates(const Template *T, const Molecule *M, int k, CandidateSet** S);
 +extern const char *TessTemplate_name(const Template *T);
 +extern double TessTemplate_logE(const Template *T,double rmsd, int n);