Perl modules for molecular chemistry

WWW:	http://search.cpan.org/dist/PerlMol/

PR:		ports/145143
Submitted by:	Steve Wills <steve at mouf.net>

6 files changed, 116 insertions, 0 deletions

diff --git a/science/Makefile b/science/Makefile
index 3c80f50a905b..4ac63bed6de9 100644
--- a/science/Makefile
+++ b/science/Makefile
@@ -126,6 +126,7 @@
     SUBDIR += p5-Chemistry-Ring
     SUBDIR += p5-Geo-ReadGRIB
     SUBDIR += p5-Geo-WebService-Elevation-USGS
+    SUBDIR += p5-PerlMol
     SUBDIR += paje
     SUBDIR += paraview
     SUBDIR += pcp
diff --git a/science/p5-PerlMol/Makefile b/science/p5-PerlMol/Makefile
new file mode 100644
index 000000000000..1e5216b366b6
--- /dev/null
+++ b/science/p5-PerlMol/Makefile
@@ -0,0 +1,69 @@
+# New ports collection makefile for:	p5-PerlMol
+# Date created:		2010-03-04
+# Whom:			Steve Wills <steve@mouf.net>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	PerlMol
+PORTVERSION=	0.3500
+CATEGORIES=	science perl5
+MASTER_SITES=	CPAN
+MASTER_SITE_SUBDIR=	../../authors/id/I/IT/ITUB
+PKGNAMEPREFIX=	p5-
+
+MAINTAINER=	steve@mouf.net
+COMMENT=	Perl modules for molecular chemistry
+
+BUILD_DEPENDS=	${SITE_PERL}/Chemistry/Mol.pm:${PORTSDIR}/science/p5-Chemistry-Mol \
+		${SITE_PERL}/Chemistry/MacroMol.pm:${PORTSDIR}/science/p5-Chemistry-MacroMol \
+		${SITE_PERL}/Parse/Yapp/Parse.pm:${PORTSDIR}/devel/p5-Parse-Yapp \
+		${SITE_PERL}/Chemistry/File/SMILES.pm:${PORTSDIR}/science/p5-Chemistry-File-SMILES \
+		${SITE_PERL}/Chemistry/File/SMARTS.pm:${PORTSDIR}/science/p5-Chemistry-File-SMARTS \
+		${SITE_PERL}/Chemistry/InternalCoords.pm:${PORTSDIR}/science/p5-Chemistry-InternalCoords \
+		${SITE_PERL}/Chemistry/Pattern.pm:${PORTSDIR}/science/p5-Chemistry-Pattern \
+		${SITE_PERL}/Chemistry/Ring.pm:${PORTSDIR}/science/p5-Chemistry-Ring \
+		${SITE_PERL}/Chemistry/Isotope.pm:${PORTSDIR}/science/p5-Chemistry-Isotope \
+		${SITE_PERL}/Chemistry/3DBuilder.pm:${PORTSDIR}/science/p5-Chemistry-3DBuilder \
+		${SITE_PERL}/Chemistry/Bond/Find.pm:${PORTSDIR}/science/p5-Chemistry-Bond-Find \
+		${SITE_PERL}/Chemistry/Canonicalize.pm:${PORTSDIR}/science/p5-Chemistry-Canonicalize \
+		${SITE_PERL}/Chemistry/File/PDB.pm:${PORTSDIR}/science/p5-Chemistry-File-PDB \
+		${SITE_PERL}/Chemistry/File/XYZ.pm:${PORTSDIR}/science/p5-Chemistry-File-XYZ \
+		${SITE_PERL}/Chemistry/File/VRML.pm:${PORTSDIR}/science/p5-Chemistry-File-VRML \
+		${SITE_PERL}/Chemistry/File/SLN.pm:${PORTSDIR}/science/p5-Chemistry-File-SLN \
+		${SITE_PERL}/Chemistry/File/Mopac.pm:${PORTSDIR}/science/p5-Chemistry-File-Mopac \
+		${SITE_PERL}/Chemistry/File/MDLMol.pm:${PORTSDIR}/science/p5-Chemistry-File-MDLMol \
+		${SITE_PERL}/Chemistry/Reaction.pm:${PORTSDIR}/science/p5-Chemistry-Reaction \
+		${SITE_PERL}/Chemistry/FormulaPattern.pm:${PORTSDIR}/science/p5-Chemistry-FormulaPattern \
+		${SITE_PERL}/Chemistry/MidasPattern.pm:${PORTSDIR}/science/p5-Chemistry-MidasPattern \
+		${SITE_PERL}/Chemistry/Mok.pm:${PORTSDIR}/science/p5-Chemistry-Mok \
+		${SITE_PERL}/Statistics/Regression.pm:${PORTSDIR}/math/p5-Statistics-Regression
+BUILD_DEPENDS=	${SITE_PERL}/Chemistry/Mol.pm:${PORTSDIR}/science/p5-Chemistry-Mol \
+		${SITE_PERL}/Chemistry/MacroMol.pm:${PORTSDIR}/science/p5-Chemistry-MacroMol \
+		${SITE_PERL}/Parse/Yapp/Parse.pm:${PORTSDIR}/devel/p5-Parse-Yapp \
+		${SITE_PERL}/Chemistry/File/SMILES.pm:${PORTSDIR}/science/p5-Chemistry-File-SMILES \
+		${SITE_PERL}/Chemistry/File/SMARTS.pm:${PORTSDIR}/science/p5-Chemistry-File-SMARTS \
+		${SITE_PERL}/Chemistry/InternalCoords.pm:${PORTSDIR}/science/p5-Chemistry-InternalCoords \
+		${SITE_PERL}/Chemistry/Pattern.pm:${PORTSDIR}/science/p5-Chemistry-Pattern \
+		${SITE_PERL}/Chemistry/Ring.pm:${PORTSDIR}/science/p5-Chemistry-Ring \
+		${SITE_PERL}/Chemistry/Isotope.pm:${PORTSDIR}/science/p5-Chemistry-Isotope \
+		${SITE_PERL}/Chemistry/3DBuilder.pm:${PORTSDIR}/science/p5-Chemistry-3DBuilder \
+		${SITE_PERL}/Chemistry/Bond/Find.pm:${PORTSDIR}/science/p5-Chemistry-Bond-Find \
+		${SITE_PERL}/Chemistry/Canonicalize.pm:${PORTSDIR}/science/p5-Chemistry-Canonicalize \
+		${SITE_PERL}/Chemistry/File/PDB.pm:${PORTSDIR}/science/p5-Chemistry-File-PDB \
+		${SITE_PERL}/Chemistry/File/XYZ.pm:${PORTSDIR}/science/p5-Chemistry-File-XYZ \
+		${SITE_PERL}/Chemistry/File/VRML.pm:${PORTSDIR}/science/p5-Chemistry-File-VRML \
+		${SITE_PERL}/Chemistry/File/SLN.pm:${PORTSDIR}/science/p5-Chemistry-File-SLN \
+		${SITE_PERL}/Chemistry/File/Mopac.pm:${PORTSDIR}/science/p5-Chemistry-File-Mopac \
+		${SITE_PERL}/Chemistry/File/MDLMol.pm:${PORTSDIR}/science/p5-Chemistry-File-MDLMol \
+		${SITE_PERL}/Chemistry/Reaction.pm:${PORTSDIR}/science/p5-Chemistry-Reaction \
+		${SITE_PERL}/Chemistry/FormulaPattern.pm:${PORTSDIR}/science/p5-Chemistry-FormulaPattern \
+		${SITE_PERL}/Chemistry/MidasPattern.pm:${PORTSDIR}/science/p5-Chemistry-MidasPattern \
+		${SITE_PERL}/Chemistry/Mok.pm:${PORTSDIR}/science/p5-Chemistry-Mok \
+		${SITE_PERL}/Statistics/Regression.pm:${PORTSDIR}/math/p5-Statistics-Regression
+
+PERL_CONFIGURE=	yes
+
+MAN3=	PerlMol.3
+
+.include <bsd.port.mk>
diff --git a/science/p5-PerlMol/distinfo b/science/p5-PerlMol/distinfo
new file mode 100644
index 000000000000..8dfcf3720933
--- /dev/null
+++ b/science/p5-PerlMol/distinfo
@@ -0,0 +1,3 @@
+MD5 (PerlMol-0.3500.tar.gz) = 0af1b556c09245772446577f4e6308ed
+SHA256 (PerlMol-0.3500.tar.gz) = a0795bc7f1ea30dff1559b03b74671910fbbce02601e8dda8ebee32186bd91a5
+SIZE (PerlMol-0.3500.tar.gz) = 337781
diff --git a/science/p5-PerlMol/files/patch-Makefile.PL b/science/p5-PerlMol/files/patch-Makefile.PL
new file mode 100644
index 000000000000..7bd72c04b2f5
--- /dev/null
+++ b/science/p5-PerlMol/files/patch-Makefile.PL
@@ -0,0 +1,37 @@
+--- Makefile.PL.orig	2010-03-11 02:51:47.000000000 -0500
++++ Makefile.PL	2010-03-11 02:52:00.000000000 -0500
+@@ -17,34 +17,6 @@
+     Text::Balanced      1.89
+ ));
+ 
+-bundle(qw(
+-    Chemistry::File::VRML           0.10
+-    Chemistry::3DBuilder            0.10
+-    Chemistry::Mol                  0.35
+-    Chemistry::Mok                  0.25
+-    Chemistry::File::SMILES         0.44
+-    Chemistry::File::SMARTS         0.22
+-    Chemistry::File::PDB            0.21
+-    Chemistry::Pattern              0.26
+-    Chemistry::MidasPattern         0.11
+-    Chemistry::File::MDLMol         0.20
+-    Chemistry::InternalCoords       0.18
+-    Chemistry::MacroMol             0.06
+-    Chemistry::Ring                 0.18
+-    Chemistry::Canonicalize         0.10
+-    Chemistry::Bond::Find           0.21
+-    Chemistry::File::SLN            0.10
+-    Chemistry::FormulaPattern       0.10
+-    Chemistry::File::Mopac          0.15
+-    Chemistry::File::XYZ            0.11
+-    Chemistry::Isotope              0.11
+-    Chemistry::Reaction             0.02
+-    Math::VectorReal                1.00
+-    Statistics::Regression          0.15
+-    Parse::Yapp::Driver             1.05
+-
+-));
+-
+ check_nmake();
+ 
+ &WriteAll();
diff --git a/science/p5-PerlMol/pkg-descr b/science/p5-PerlMol/pkg-descr
new file mode 100644
index 000000000000..c80ab5453065
--- /dev/null
+++ b/science/p5-PerlMol/pkg-descr
@@ -0,0 +1,3 @@
+Perl modules for molecular chemistry
+
+WWW:	http://search.cpan.org/dist/PerlMol/
diff --git a/science/p5-PerlMol/pkg-plist b/science/p5-PerlMol/pkg-plist
new file mode 100644
index 000000000000..28ab912610e4
--- /dev/null
+++ b/science/p5-PerlMol/pkg-plist
@@ -0,0 +1,3 @@
+%%SITE_PERL%%/mach/auto/PerlMol/.packlist
+%%SITE_PERL%%/PerlMol.pm
+@dirrmtry %%SITE_PERL%%/mach/auto/PerlMol