pyjess 0.7.0a3__tar.gz → 0.7.0a5__tar.gz

{pyjess-0.7.0a3 → pyjess-0.7.0a5}/CHANGELOG.md

@@ -6,7 +6,21 @@ 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.3...HEAD
+[Unreleased]: https://github.com/althonos/pyjess/compare/v0.7.0-alpha.5...HEAD
+
+
+## [v0.7.0-alpha.5] - 2025-09-03
+[v0.7.0-alpha.5]: https://github.com/althonos/pyjess/compare/v0.7.0-alpha.5...v0.7.0-alpha.5
+
+### Fixed
+- Issue with new residue support introduced in `v0.7.0-alpha.4`.
+
+
+## [v0.7.0-alpha.4] - 2025-09-03
+[v0.7.0-alpha.4]: https://github.com/althonos/pyjess/compare/v0.7.0-alpha.3...v0.7.0-alpha.4
+
+### Added
+- Support for [Selenocysteine](https://en.wikipedia.org/wiki/Selenocysteine) and [Pyrrolysine](https://en.wikipedia.org/wiki/Pyrrolysine) residues in `TemplateAtom`.
 
 
 ## [v0.7.0-alpha.3] - 2025-09-03

{pyjess-0.7.0a3 → pyjess-0.7.0a5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: pyjess
-Version: 0.7.0a3
+Version: 0.7.0a5
 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>

{pyjess-0.7.0a3 → pyjess-0.7.0a5}/patches/Box.h.patch

@@ -1,9 +1,9 @@
 diff --git a/src/Box.h b/src/Box.h
 new file mode 100644
-index 0000000..ca8384d
+index 0000000..9d8693b
 --- /dev/null
 +++ b/src/Box.h
-@@ -0,0 +1,87 @@
+@@ -0,0 +1,80 @@
 +// ==================================================================
 +// Box.h
 +// Copyright (c) Martin Larralde, 2025
@@ -46,13 +46,6 @@ index 0000000..ca8384d
 +extern void Box_free(Box*);
 +
 +// ==================================================================
-+// Local "functions"
-+// ==================================================================
-+
-+#define min(x,y) (x<y ? x:y)
-+#define max(x,y) (x>y ? x:y)
-+
-+// ==================================================================
 +// Oracles
 +// ==================================================================
 +

{pyjess-0.7.0a3 → pyjess-0.7.0a5}/patches/TessAtom.c.patch

@@ -1,5 +1,5 @@
 diff --git a/src/TessAtom.c b/src/TessAtom.c
-index e1cce1a..9ba021e 100644
+index e1cce1a..3f06daa 100644
 --- a/src/TessAtom.c
 +++ b/src/TessAtom.c
 @@ -7,40 +7,13 @@
@@ -45,7 +45,39 @@ index e1cce1a..9ba021e 100644
  // ==================================================================
  // Methods of type TessAtom (ARGGH!!!)
  // ==================================================================
-@@ -91,7 +64,7 @@ TessAtom *TessAtom_create(const char *s)
+@@ -51,7 +24,7 @@ static const char *TessAtom_convertResidue(char p)
+ 
+ 	int k;
+ 	struct _dummy {char one; const char *three; };
+-	static const struct _dummy table[21] =
++	static const struct _dummy table[23] =
+ 	{
+ 		{ 'A',"ALA" },
+ 		{ 'C',"CYS" },
+@@ -66,18 +39,20 @@ static const char *TessAtom_convertResidue(char p)
+ 		{ 'M',"MET" },
+ 		{ 'N',"ASN" },
+ 		{ 'P',"PRO" },
++		{ 'O',"PYL" },
+ 		{ 'Q',"GLN" },
+ 		{ 'R',"ARG" },
+ 		{ 'S',"SER" },
+ 		{ 'T',"THR" },
++		{ 'U',"SEC" },
+ 		{ 'V',"VAL" },
+ 		{ 'W',"TRP" },
+ 		{ 'Y',"TYR" },
+ 		{ 'X',"XXX" }
+ 	};
+ 
+-	for(k=0; k<21 && p!=table[k].one; k++);
+-	return k<21 ? table[k].three:NULL;
++	for(k=0; k<23 && p!=table[k].one; k++);
++	return k<23 ? table[k].three:NULL;
+ }
+ 
+ TessAtom *TessAtom_create(const char *s)
+@@ -91,7 +66,7 @@ TessAtom *TessAtom_create(const char *s)
  	int rq;
  	const char *q;
  	const char *tmp;
@@ -54,7 +86,7 @@ index e1cce1a..9ba021e 100644
  
  
  	// 0. Parse the record as a standard PDB atom. We must
-@@ -157,8 +130,8 @@ TessAtom *TessAtom_create(const char *s)
+@@ -157,8 +132,8 @@ TessAtom *TessAtom_create(const char *s)
  	// Set up all the pointers to the
  	// residue name and atom name fields
  
@@ -65,7 +97,7 @@ index e1cce1a..9ba021e 100644
  	p+=sizeof(char*)*ac;
  	for(m=0; m<ac; m++)
  	{
-@@ -166,7 +139,7 @@ TessAtom *TessAtom_create(const char *s)
+@@ -166,7 +141,7 @@ TessAtom *TessAtom_create(const char *s)
  		p+=5;
  	}
  
@@ -74,7 +106,7 @@ index e1cce1a..9ba021e 100644
  	p+=sizeof(char*)*rc;
  	for(m=0; m<rc; m++)
  	{
-@@ -259,41 +232,7 @@ TessAtom *TessAtom_create(const char *s)
+@@ -259,41 +234,7 @@ TessAtom *TessAtom_create(const char *s)
  }
  
  //Riziotis edit
@@ -116,7 +148,7 @@ index e1cce1a..9ba021e 100644
  static int TessAtom_isCarbon(const Atom *A)
  {
  	return A->name[0]=='_' && A->name[1]=='C' ? 1:0;
-@@ -327,9 +266,9 @@ static int TessAtom_isInSamePosition(const TessAtom *T, const Atom *A)
+@@ -327,9 +268,9 @@ static int TessAtom_isInSamePosition(const TessAtom *T, const Atom *A)
  
  static int TessAtom_isMainChain(const Atom *A)
  {
@@ -129,7 +161,7 @@ index e1cce1a..9ba021e 100644
  
  	return 0;
  }
-@@ -340,7 +279,7 @@ static int TessAtom_matchName(const TessAtom *T, const Atom *A)
+@@ -340,7 +281,7 @@ static int TessAtom_matchName(const TessAtom *T, const Atom *A)
  
  	for(k=0; k<T->nameCount; k++)
  	{
@@ -138,7 +170,7 @@ index e1cce1a..9ba021e 100644
  	}
  
  	return 0;
-@@ -352,7 +291,7 @@ static int TessAtom_matchResName(const TessAtom *T, const Atom *A)
+@@ -352,7 +293,7 @@ static int TessAtom_matchResName(const TessAtom *T, const Atom *A)
  
  	for(k=0; k<T->resNameCount; k++)
  	{
@@ -147,7 +179,7 @@ index e1cce1a..9ba021e 100644
  	}
  
  	return 0;
-@@ -507,5 +446,65 @@ int TessAtom_match(const TessAtom *T, const Atom *A)
+@@ -507,5 +448,65 @@ int TessAtom_match(const TessAtom *T, const Atom *A)
  	}
  }
  

{pyjess-0.7.0a3 → pyjess-0.7.0a5}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "scikit_build_core.build"
 
 [project]
 name = "pyjess"
-version = "0.7.0-alpha.3"
+version = "0.7.0-alpha.5"
 description = "Cython bindings and Python interface to JESS, a 3D template matching software."
 readme = "README.md"
 requires-python = ">=3.7"