sci-chemistry/ccp4-apps -- Fix for 301762, thanks Johan Hattne for the patch

(Portage version: 2.2_rc62/git/Linux x86_64)
 (Signed Manifest commit)

4 files changed, 86 insertions, 5 deletions

diff --git a/sci-chemistry/ccp4-apps/ChangeLog b/sci-chemistry/ccp4-apps/ChangeLog
index c7e1f2900..3946ea389 100644
--- a/sci-chemistry/ccp4-apps/ChangeLog
+++ b/sci-chemistry/ccp4-apps/ChangeLog
@@ -2,6 +2,13 @@
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*ccp4-apps-6.1.3-r2 (30 Jan 2010)
+
+  30 Jan 2010; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +files/6.1.3-clipper-template.patch, -ccp4-apps-6.1.3-r1.ebuild,
+  +ccp4-apps-6.1.3-r2.ebuild:
+  Fix for 301762, thanks Johan Hattne for the patch
+
 *ccp4-apps-6.1.3-r1 (30 Jan 2010)
 
   30 Jan 2010; Justin Lecher (jlec) <jlec@j-schmitz.net>
diff --git a/sci-chemistry/ccp4-apps/Manifest b/sci-chemistry/ccp4-apps/Manifest
index 7b16b62d7..16b63aaf2 100644
--- a/sci-chemistry/ccp4-apps/Manifest
+++ b/sci-chemistry/ccp4-apps/Manifest
@@ -18,6 +18,7 @@ AUX 6.1.2-rename-rapper.patch 2856 RMD160 37504bed3cb4e1858d88331305deef6564616b
 AUX 6.1.2-rename-truncate.patch 1515 RMD160 eff332faa67a1732e0f99cc6cdcb846932eadc87 SHA1 b504542cf710e1b54a684b0fa0e8d73d967c96ac SHA256 50a59a1856867daa3de1f8f53e92bcfe74dea3a6d3c4ba238a9ea83dbcdfbf07
 AUX 6.1.2-setup.patch 12338 RMD160 2107d599dfe477863710d6b8098b3ca43b8cd22d SHA1 38b3d6ef1e40bf505f4227646d9afce1fe828395 SHA256 c9843cf27af9809ecf96a700521972aa434970a7fdaaf571c36b05fd4be516eb
 AUX 6.1.3-clipper-mmdbold-ggc-4.3.patch 656 RMD160 6b302779b48217a14f5ac9110bc307db3a3b51eb SHA1 f5813d6769fa9dc11605425cdbda85691d3016bc SHA256 982eff0336a6dfaf4e280d51a59cf722fc063ca89d15ca0af46ce83727fb9a8a
+AUX 6.1.3-clipper-template.patch 2619 RMD160 a3a4998365c4e516325cf95472e8493729ee4b46 SHA1 f3d92469ac5ec4483818abbf50c32ac9b05a622c SHA256 a185a93f76c23ce06256866cfaf0e9854a5702b95a1e49e4d3a5f732e0d1e2a3
 AUX 6.1.3-dont-build-double-and-make-bindir.patch 688 RMD160 f5f93cbec122ce81a1ddb1cf57a852d51fa5e5d6 SHA1 4c924554c5c1991ed691fe3474eeffbd108493a9 SHA256 037a3d9042c784c895083fe5348ed3bde74620c1b6b3b2cd4eea53bdbfe77d53
 AUX 6.1.3-dont-build-imosflm.patch 365 RMD160 3f8d5354a2469cc38ef16e98d726eeea7be08ef9 SHA1 47d52b554c594b00ea8e6f84768548879b02a36e SHA256 d57b800c78a1624c665771add717b8b94169d5a5432c5201efa7d9a2cfa62277
 AUX 6.1.3-dont-build-libs.patch 1266 RMD160 95d2960fbd2f3d8661187ea9ed7ffc5f2f30e61f SHA1 7b5fa26432f57a11c8bedff79209f687b6bd95cb SHA256 329d29c58e18403105ed06fdd6b012a481b7c2b43af53b86395204b2acea51ed
@@ -40,13 +41,13 @@ EBUILD ccp4-apps-6.1.2-r5.ebuild 11481 RMD160 3415982bdc5dd1d1c9cda7244a54304aea
 EBUILD ccp4-apps-6.1.2-r6.ebuild 11562 RMD160 28b884fc0ea91f80aef7380f711c32870a03e44c SHA1 b15e25be05064c4f6d6fa9207c431526321b6485 SHA256 ebe12c47a2fb3378b74d62f10ff55a78120e1407865eaa4b8e0f3c41ad795403
 EBUILD ccp4-apps-6.1.2-r7.ebuild 11696 RMD160 c13e71584504c65d3b72697b3affd01020793b10 SHA1 515b4657655e0c0319c87f937bee74409de7c362 SHA256 93d4b4096c5320cb28f033f8ebcbd154b1188fbe8b62b5916c11955d78177fbd
 EBUILD ccp4-apps-6.1.2-r9.ebuild 11882 RMD160 b1b1e7b3cef0b748193800d535bb1d00163bb646 SHA1 eb025e81b10991cd9d50c887b44146c69f4ae5df SHA256 9334070574d24366fd95c0d8a51875d2844eede94453f1d090f938841a11a012
-EBUILD ccp4-apps-6.1.3-r1.ebuild 11736 RMD160 1611434fdf055a351a553a97b8ba2e38e2680f1b SHA1 73ea4b31eab72aae0d75d0a7c1fbf435d10f41be SHA256 3bba7ea84ec4b2bdd776303f17c80741f19b7b502de0fa0b6b5db03fdc6df937
-MISC ChangeLog 8779 RMD160 5975fa3037e74d3ac92b4cff57ebdf5b689b7607 SHA1 5c067690c05f72ae1422235393f0606eedfa47c9 SHA256 7d9e489c37f7719ef9f71e139d89b8755d4831f10a4cfebf3b144bf2ca8cd51d
+EBUILD ccp4-apps-6.1.3-r2.ebuild 11821 RMD160 00c5406263773398444530aa49422e6483816738 SHA1 2a59730876db61e940eaf1abe12f89a37d6945db SHA256 ee28b241a56f52856fb3a756c89c83b38ecd970a8145e28e9e093b7b14326597
+MISC ChangeLog 9021 RMD160 9dacafc60da862f53548ae19c75b6f8d27d1d6c6 SHA1 7b4066677f51cd962d6038eec88f4c212a1e7f00 SHA256 d83529584d70b162c8ca345dfb3b62e3f1d9584148556034b4bc60192052467c
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
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diff --git a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r1.ebuild b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r2.ebuild
index 3dc6e0a9b..00ceef6ad 100644
--- a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r1.ebuild
+++ b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r2.ebuild
@@ -158,6 +158,9 @@ src_prepare() {
 	# Set python paths correctly
 	ccp_patch "${FILESDIR}"/${PV}-pisa.patch
 
+	# Set python paths correctly
+	ccp_patch "${FILESDIR}"/${PV}-clipper-template.patch
+
 	# Update things for oasis 4 usage
 	epatch "${WORKDIR}"/${PV}-oasis4.0.patch
 	sed 's: oasis : :g' -i src/Makefile.in || die
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch b/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch
new file mode 100644
index 000000000..433a78dbd
--- /dev/null
+++ b/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch
@@ -0,0 +1,70 @@
+--- src/clipper_progs/src/intensity_target.h.orig	2010-01-21 11:27:13.236795886 -0600
++++ src/clipper_progs/src/intensity_target.h	2010-01-21 11:31:33.450686927 -0600
+@@ -70,9 +70,31 @@
+   {
+   public:
+     //! constructor: takes the datalist against which to calc target
+-    TargetFn_scaleLogI1I2( const HKL_data<T1>& hkl_data1_, const HKL_data<T2>& hkl_data2_ );
++    TargetFn_scaleLogI1I2( const HKL_data<T1>& hkl_data1_, const HKL_data<T2>& hkl_data2_ )
++    {
++      hkl_data1 = &hkl_data1_;
++      hkl_data2 = &hkl_data2_;
++    }
+     //! return the value and derivatives of the target function
+-    Rderiv rderiv( const HKL_info::HKL_reference_index& ih, const ftype& intensityh ) const;
++    Rderiv rderiv( const HKL_info::HKL_reference_index& ih, const ftype& intensityh ) const
++    {
++      Rderiv result;
++      result.r = result.dr = result.dr2 = 0.0;
++      const T1& it1 = (*hkl_data1)[ih];
++      const T2& it2 = (*hkl_data2)[ih];
++      if ( !it1.missing() && !it2.missing() )
++        if ( it1.I() > 1.0e-6 && it2.I() > 1.0e-6 ) {
++          const ftype eps = ih.hkl_class().epsilon();
++          const ftype i1 = it1.I() / eps;
++          const ftype i2 = it2.I() / eps;
++          const ftype w = sqrt( i1 * i2 );    
++          const ftype d = intensityh + log(i1) - log(i2);
++          result.r   =       w * d * d;
++          result.dr  = 2.0 * w * d;
++          result.dr2 = 2.0 * w;
++      }
++      return result;
++    }
+     //! the type of the function: optionally used to improve convergence
+     FNtype type() const { return QUADRATIC; }
+   private:
+@@ -109,33 +131,4 @@
+     return result;
+   }
+ 
+-  // Log I1-I2 scaling
+-
+-  template<class T1, class T2> TargetFn_scaleLogI1I2<T1,T2>::TargetFn_scaleLogI1I2( const HKL_data<T1>& hkl_data1_, const HKL_data<T2>& hkl_data2_ )
+-  {
+-    hkl_data1 = &hkl_data1_;
+-    hkl_data2 = &hkl_data2_;
+-  }
+-
+-  template<class T1, class T2> TargetFn_base::Rderiv TargetFn_scaleLogI1I2<T1,T2>::rderiv( const HKL_info::HKL_reference_index& ih, const ftype& intensityh ) const
+-  {
+-    Rderiv result;
+-    result.r = result.dr = result.dr2 = 0.0;
+-    const T1& it1 = (*hkl_data1)[ih];
+-    const T2& it2 = (*hkl_data2)[ih];
+-    if ( !it1.missing() && !it2.missing() )
+-      if ( it1.I() > 1.0e-6 && it2.I() > 1.0e-6 ) {
+-	const ftype eps = ih.hkl_class().epsilon();
+-	const ftype i1 = it1.I() / eps;
+-	const ftype i2 = it2.I() / eps;
+-	const ftype w = sqrt( i1 * i2 );    
+-	const ftype d = intensityh + log(i1) - log(i2);
+-	result.r   =       w * d * d;
+-	result.dr  = 2.0 * w * d;
+-	result.dr2 = 2.0 * w;
+-    }
+-    return result;
+-  }
+-
+-
+ #endif