From 4566cd67f9a6a641ee87985cc768be9ef631399b Mon Sep 17 00:00:00 2001
From: Matvey Adzhigirey <matvey.adzhigirey@schrodinger.com>
Date: Tue, 4 Dec 2012 20:10:09 -0800
Subject: [PATCH] Fix a number of crashes and special conditions

- Fix an issue where non-existing interactions were analyzed.

  Bug fix in setIonDeterminants(): skip interactions if either
  titratable_group_interaction_atoms or the backbone_interaction_atoms
  is empty.

- Set center of COO_group to self.atom if no oxygens present in residue.

  COO_group: If self.atom.get_bonded_elements('O') returns an emtpy list
  (the residue has missing side-chain), simply set the center of the
  group to the <self.atom> atom, instead of the center of the
  (non-existing) oxygens.

- Raise more friendly exception in Group.set_center() if an empty atom
  set is passed in.

- Cterm_group: Fix crash if residue is missing a carbon.

  The previous code would crash if the C-termini residue group was
  missing the carbon atom.

- Fix a failure when a HIS residue has missing side-chain atoms.

- Added an entry for Iodine (I) to the valence electrons table.
---
 propka/determinants.py |  7 ++++++-
 propka/group.py        | 39 +++++++++++++++++++++++++++++----------
 propka/protonate.py    |  4 +++-
 3 files changed, 38 insertions(+), 12 deletions(-)

diff --git a/propka/determinants.py b/propka/determinants.py
index b3ed586..4299432 100644
--- a/propka/determinants.py
+++ b/propka/determinants.py
@@ -168,11 +168,16 @@ def setIonDeterminants(conformation_container, version):
 def setBackBoneDeterminants(titratable_groups, backbone_groups, version):
 
     for titratable_group in titratable_groups:
+        titratable_group_interaction_atoms = titratable_group.interaction_atoms_for_acids
+        if not titratable_group_interaction_atoms:
+            continue
+
         # find out which backbone groups this titratable is interacting with
         for backbone_group in backbone_groups:
             # find the interacting atoms
             backbone_interaction_atoms = backbone_group.get_interaction_atoms(titratable_group)
-            titratable_group_interaction_atoms = titratable_group.interaction_atoms_for_acids
+            if not backbone_interaction_atoms:
+                continue
 
             # find the smallest distance
             [backbone_atom, distance, titratable_atom] = propka.calculations.get_smallest_distance(backbone_interaction_atoms,
diff --git a/propka/group.py b/propka/group.py
index ac52d3e..b5c5a06 100644
--- a/propka/group.py
+++ b/propka/group.py
@@ -420,6 +420,9 @@ class Group:
             return self.interaction_atoms_for_acids #default is acid interaction atoms - cf. 3.0
 
     def set_center(self, atoms):
+        if not atoms:
+            raise ValueError("At least one atom must be specified")
+
         # reset center
         self.x = 0.0; self.y = 0.0; self.z = 0.0
 
@@ -614,8 +617,14 @@ class COO_group(Group):
         # Identify the two caroxyl oxygen atoms
         the_oxygens = self.atom.get_bonded_elements('O')
 
-        # set the center using the two oxygen carboxyl atoms
-        self.set_center(the_oxygens)
+        # set the center using the two oxygen carboxyl atoms (if present)
+        if the_oxygens:
+            self.set_center(the_oxygens)
+        else:
+            self.set_center([self.atom])
+            # FIXME perhaps it would be better to ignore this group completely
+            # if the oxygen is missing from this residue?
+
         self.set_interaction_atoms(the_oxygens, the_oxygens)
         return
 
@@ -636,7 +645,12 @@ class HIS_group(Group):
             my_protonator.protonate_atom(r)
 
         # set the center using the ring atoms
-        self.set_center(ring_atoms)
+        if ring_atoms:
+            self.set_center(ring_atoms)
+        else:
+            # Missing side-chain atoms
+            self.set_center([self.atom])
+            # FIXME perhaps it would be better to ignore this group completely?
 
         # find the hydrogens on the ring-nitrogens
         hydrogens = []
@@ -751,14 +765,19 @@ class Cterm_group(Group):
 
     def setup_atoms(self):
         # Identify the carbon and other oxygen carboxyl atoms
-        the_carbon = self.atom.get_bonded_elements('C')
-        the_other_oxygen = the_carbon[0].get_bonded_elements('O')
-        the_other_oxygen.remove(self.atom)
+        the_carbons = self.atom.get_bonded_elements('C')
+        if not the_carbons:
+            self.set_center([self.atom])
+            # FIXME perhaps it would be better to ignore this group completely
+            # if the carbon is missing from this residue?
+        else:
+            the_other_oxygen = the_carbons[0].get_bonded_elements('O')
+            the_other_oxygen.remove(self.atom)
 
-        # set the center and interaction atoms
-        the_oxygens = [self.atom]+ the_other_oxygen
-        self.set_center(the_oxygens)
-        self.set_interaction_atoms(the_oxygens, the_oxygens)
+            # set the center and interaction atoms
+            the_oxygens = [self.atom]+ the_other_oxygen
+            self.set_center(the_oxygens)
+            self.set_interaction_atoms(the_oxygens, the_oxygens)
 
 
         return
diff --git a/propka/protonate.py b/propka/protonate.py
index 396790b..34b8a01 100644
--- a/propka/protonate.py
+++ b/propka/protonate.py
@@ -47,7 +47,9 @@ class Protonate:
                                   'As':5,
                                   'Se':6,
                                   'Br':7,
-                                  'Kr':8}
+                                  'Kr':8,
+                                  'I':7,
+                                }