Fix issue with matched atoms

3 files changed, 43 insertions, 4 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 14fb38fce1ea..ea068f952069 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,7 +1,7 @@
 pkgbase = python-pdb2pqr
 	pkgdesc = Automates many of the common tasks of preparing structures for continuum solvation calculations as well as many other types of biomolecular structure modeling, analysis, and simulation.
 	pkgver = 3.0.1
-	pkgrel = 2
+	pkgrel = 3
 	url = http://pypi.python.org/pypi/pdb2pqr
 	arch = any
 	license = BSD
@@ -13,8 +13,10 @@ pkgbase = python-pdb2pqr
 	options = !emptydirs
 	source = https://files.pythonhosted.org/packages/source/p/pdb2pqr/pdb2pqr-3.0.1.tar.gz
 	source = fix_entrypoint.patch
+	source = fix_matchedatoms.patch
 	sha256sums = 15ac0ce77dc17fb459092aca12cc7c2c070904f77914f1197282e28f418b6bd0
 	sha256sums = bb177e8fb9a31f2486e5682ae97139ebf87948fb4dc33dc892e90ff606df7211
+	sha256sums = 8708438980e5dda5036d2c4fa404d1817104ebbf0443f7798a2698b75a38fe9c
 
 pkgname = python-pdb2pqr
 
diff --git a/PKGBUILD b/PKGBUILD
index 237145672d6e..e91c130c296d 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -3,7 +3,7 @@
 pkgname=python-pdb2pqr
 _name=${pkgname#python-}
 pkgver=3.0.1
-pkgrel=2
+pkgrel=3
 pkgdesc="Automates many of the common tasks of preparing structures for continuum solvation calculations as well as many other types of biomolecular structure modeling, analysis, and simulation."
 arch=(any)
 url="http://pypi.python.org/pypi/${_name}"
@@ -11,14 +11,17 @@ license=(BSD)
 depends=('python>=3.5' 'python-propka>=3.2' 'python-pandas>=1.0' 'python-pytest>=5.4.1')
 makedepends=(patch)
 source=("https://files.pythonhosted.org/packages/source/${_name::1}/${_name}/${_name}-${pkgver}.tar.gz"
-        "fix_entrypoint.patch")
+        "fix_entrypoint.patch"
+        "fix_matchedatoms.patch")
 sha256sums=('15ac0ce77dc17fb459092aca12cc7c2c070904f77914f1197282e28f418b6bd0'
-            'bb177e8fb9a31f2486e5682ae97139ebf87948fb4dc33dc892e90ff606df7211')
+            'bb177e8fb9a31f2486e5682ae97139ebf87948fb4dc33dc892e90ff606df7211'
+            '8708438980e5dda5036d2c4fa404d1817104ebbf0443f7798a2698b75a38fe9c')
 options=(!emptydirs)
 
 prepare() {
     cd "${srcdir}/${_name}-${pkgver}"
     patch -Np0 -i "${srcdir}/fix_entrypoint.patch"
+    patch -Np0 -i "${srcdir}/fix_matchedatoms.patch"
 }
 
 build() {
diff --git a/fix_matchedatoms.patch b/fix_matchedatoms.patch
new file mode 100644
index 000000000000..ce1b64135cf0
--- /dev/null
+++ b/fix_matchedatoms.patch
@@ -0,0 +1,34 @@
+--- pdb2pqr/main.py	2020-08-25 20:53:35.000000000 +0300
++++ pdb2pqr/main.py	2020-08-25 21:15:39.017396736 +0300
+@@ -470,17 +470,16 @@
+             hydrogen_routines.optimize_hydrogens()

+         hydrogen_routines.cleanup()

+ 

+     _LOGGER.info("Applying force field to biomolecule states.")

+     protein.set_states()

+-    hitlist, misslist = protein.apply_force_field(forcefield_)

++    matched_atoms, missing_atoms = protein.apply_force_field(forcefield_)

+ 

+     if args.ligand is not None:

+         _LOGGER.info("Processing ligand.")

+         _LOGGER.warning("Using ZAP9 forcefield for ligand radii.")

+         ligand.assign_parameters()

+-        missing_atoms = []

+         lig_atoms = []

+         for residue in protein.residues:

+             tot_charge = 0

+             for pdb_atom in residue.atoms:

+                 # Only check residues with HETATM

+@@ -497,11 +496,11 @@
+                         "Can't find HETATM {r.name} {r.res_seq} {a.name} "

+                         "in MOL2 file").format(r=residue, a=pdb_atom)

+                     _LOGGER.warning(err)

+                     missing_atoms.append(pdb_atom)

+ 

+-    matched_atoms = hitlist + lig_atoms

++        matched_atoms += lig_atoms

+ 

+     for residue in protein.residues:

+         if not isclose(

+                 residue.charge, int(residue.charge), abs_tol=CHARGE_ERROR):

+             err = (