First release

3 files changed, 132 insertions, 0 deletions

diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..904b95d39749
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,23 @@
+pkgbase = pdb2pqr
+	pkgdesc = Electrostatic and solvation properties for complex molecules
+	pkgver = 2.1.1
+	pkgrel = 1
+	url = http://www.poissonboltzmann.org/
+	arch = x86_64
+	arch = i686
+	license = MIT
+	makedepends = pyinstaller2
+	makedepends = git
+	makedepends = gcc
+	depends = swig
+	depends = python2
+	depends = python2-networkx
+	depends = python2-numpy
+	depends = apbs
+	source = git+https://github.com/Electrostatics/apbs-pdb2pqr.git#commit=044f531f8fb944f7b14c9f34ff33833357b0fea4
+	source = pdb2pqr.patch
+	md5sums = SKIP
+	md5sums = 19cb8e794d49e4d2bc04df54a895f3ad
+
+pkgname = pdb2pqr
+
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..8d923286f849
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,35 @@
+# Maintainer: Viktor Drobot (aka dviktor) linux776 [at] gmail [dot] com
+pkgname=pdb2pqr
+pkgver=2.1.1
+pkgrel=1
+pkgdesc="Electrostatic and solvation properties for complex molecules"
+arch=(x86_64 i686)
+url="http://www.poissonboltzmann.org/"
+license=('MIT')
+depends=('swig' 'python2' 'python2-networkx' 'python2-numpy' 'apbs')
+makedepends=('pyinstaller2' 'git' 'gcc')
+source=("git+https://github.com/Electrostatics/apbs-pdb2pqr.git#commit=044f531f8fb944f7b14c9f34ff33833357b0fea4"
+        "pdb2pqr.patch")
+md5sums=('SKIP'
+         '19cb8e794d49e4d2bc04df54a895f3ad')
+
+prepare() {
+    cd ${srcdir}/apbs-pdb2pqr/pdb2pqr
+
+    patch -Np0 -i "${srcdir}/pdb2pqr.patch"
+}
+
+build() {
+	cd ${srcdir}/apbs-pdb2pqr/pdb2pqr
+
+    python2 scons/scons.py
+}
+
+package() {
+	cd ${srcdir}/apbs-pdb2pqr/pdb2pqr
+
+    pyinstaller2 pdb2pqr.spec
+
+    mkdir -p ${pkgdir}/opt
+    cp -ar dist/pdb2pqr ${pkgdir}/opt/pdb2pqr
+}
diff --git a/pdb2pqr.patch b/pdb2pqr.patch
new file mode 100644
index 000000000000..977c0f285e22
--- /dev/null
+++ b/pdb2pqr.patch
@@ -0,0 +1,74 @@
+--- build_config.py	2018-12-05 19:05:52.848580011 +0300
++++ build_config.py	2018-12-05 19:04:58.499308161 +0300
+@@ -9,7 +9,7 @@
+ #Sets the install location of pdb2pqr.

+ #This defaults to ~/pdb2pqr

+ 

+-#PREFIX="~/pdb2pqr"

++PREFIX="/opt/pdb2pqr"

+ 

+ 

+ #Website URL

+@@ -17,28 +17,28 @@
+ #This defaults to http://<COMPUTER NAME>/pdb2pqr/

+ # where <COMPUTER NAME> is the network name of the computer.

+ 

+-#URL="http://<COMPUTER NAME>/pdb2pqr/"

++URL="http://nbcr-222.ucsd.edu/pdb2pqr_2.1.1/"

+ 

+ 

+ #APBS binary

+ #Change this to specify the location of the APBS binary if installed.

+ #This is used for the web interface to pdb2pqr. Provide an absolute path. Relative paths and ~ usually will not work correctly.

+ 

+-#APBS=""

++APBS="/usr/bin/apbs"

+ 

+ 

+ #OPAL service URL

+ #Set this value to use an opal service for processing

+ # pdb2pqr jobs for the web front end.

+ 

+-#OPAL="http://nbcr-222.ucsd.edu/opal2/services/pdb2pqr_1.8"

++OPAL="http://nbcr-222.ucsd.edu/opal2/services/pdb2pqr_2.1.1"

+ 

+ 

+ #APBS_OPAL service URL

+ #Set this value to use an opal service for processing

+ # apbs jobs for the web front end.

+ 

+-#APBS_OPAL="http://nbcr-222.ucsd.edu/opal2/services/apbs_1.3"

++APBS_OPAL="http://nbcr-222.ucsd.edu/opal2/services/apbs_1.4.2.1"

+ 

+ 

+ #MAX_ATOMS

+@@ -52,19 +52,19 @@
+ #Set to False to skip building ligand and pdb2pka support. Requires numpy.

+ # Defaults to True

+ 

+-#BUILD_PDB2PKA=False

++BUILD_PDB2PKA=True

+ 

+ #DEBUG

+ #Set to True to build compiled extentions with debug headers.

+ #Defaults to False

+ 

+-#DEBUG=True

++DEBUG=False

+ 

+ #CXXFLAGS

+ #Set to add extra CXX flags to the build.

+ #Defaults to ""

+ 

+-#EXTRA_CXXFLAGS="-fPIC"

++EXTRA_CXXFLAGS="-fPIC"

+ 

+ #EXTRA_LINKFLAGS

+ #Set to add extra CXX flags to the build.

+@@ -78,4 +78,4 @@
+ # Requires swig on the the user path.

+ # Defaults to False

+ 

+-#REBUILD_SWIG=True
+\ В конце файла нет новой строки
++REBUILD_SWIG=True