Dev

.gitignore

@@ -4,3 +4,4 @@ examples/*
 .vscode/*
 .pytest_cache/*
 .mypy_cache
+arpeggio.egg-info

README.md

@@ -35,15 +35,15 @@ Arpeggio is written in Python and currently has the following dependencies:
 * Python (v3.6)
 * Numpy
 * BioPython (>= v1.60)
-* OpenBabel (with Python bindings)
+* OpenBabel (>=3.0)
 * PDBeCIF
 
 If you need to use Arpeggio programmatically or to run for many structures:
 
 The easiest way to set up with Arpeggio is using [Conda](https://docs.conda.io/en/latest/). In your conda environment run the two following commands:
 
 ```bash
-conda install -c openbabel openbabel
+conda install -c conda-forge openbabel
 pip install git+https://github.com/PDBeurope/arpeggio.git@master#egg=arpeggio
 ```
 
@@ -63,7 +63,7 @@ conda activate arpeggio-env
 
 `arpeggio 1tqn_h.cif [options]`
 
-e.g. 
+e.g.
 
 `arpeggio -s /A/508/ -o out/ 1tqn_h.cif`
 

arpeggio/core/interactions.py

@@ -6,7 +6,7 @@
 from functools import reduce
 
 import numpy as np
-import openbabel as ob
+from openbabel import openbabel as ob
 from Bio.PDB import NeighborSearch
 from Bio.PDB.Atom import DisorderedAtom
 from Bio.PDB.PDBParser import PDBParser
@@ -226,7 +226,7 @@ def minimize_hydrogens(self, minimisation_forcefield, minimisation_method, minim
 
         for ob_atom in ob.OBMolAtomIter(self.ob_mol):
 
-            if not ob_atom.IsHydrogen():
+            if not ob_atom.GetAtomicNum() == ob.Hydrogen:
                 constraints.AddAtomConstraint(ob_atom.GetIdx())
 
         logging.debug('Constrained non-hydrogen atoms.')
@@ -1226,9 +1226,6 @@ def __calculate_group_group_contacts(self):
                 if amide_key == amide_key2:
                     continue
 
-                if amide_key == 441 and amide2 == 442:
-                    print('foo')
-
                 # CHECK RING IS INVOLVED WITH THE SELECTION OR BINDING SITE
                 if amide_key2 not in self.selection_plus_amide_ids:
                     continue
@@ -1493,14 +1490,14 @@ def _add_atomic_radii(self):
         # ADD VDW RADII TO ENTITY ATOMS
         # USING OPENBABEL VDW RADII
         for atom in self.s_atoms:
-            atom.vdw_radius = ob.etab.GetVdwRad(self.ob_mol.GetAtomById(self.bio_to_ob[atom]).GetAtomicNum())
+            atom.vdw_radius = ob.GetVdwRad(self.ob_mol.GetAtomById(self.bio_to_ob[atom]).GetAtomicNum())
 
         logging.debug('Added VdW radii.')
 
         # ADD COVALENT RADII TO ENTITY ATOMS
         # USING OPENBABEL VDW RADII
         for atom in self.s_atoms:
-            atom.cov_radius = ob.etab.GetCovalentRad(self.ob_mol.GetAtomById(self.bio_to_ob[atom]).GetAtomicNum())
+            atom.cov_radius = ob.GetCovalentRad(self.ob_mol.GetAtomById(self.bio_to_ob[atom]).GetAtomicNum())
 
         logging.debug('Added covalent radii.')
 
@@ -1516,7 +1513,7 @@ def _add_hydrogens_to_biopython(self):
 
                 # GET THE BONDED ATOMS OF THE OBATOM
                 for atom_neighbour in ob.OBAtomAtomIter(atom):
-                    if atom_neighbour.IsHydrogen():
+                    if atom_neighbour.GetAtomicNum() == ob.Hydrogen:
 
                         # APPEND THE HYDROGEN COORDINATES TO THE BIOPYTHON ATOM 'h_coords' ATTRIBUTE
                         biopython_atom.h_coords.append(np.array([atom_neighbour.GetX(), atom_neighbour.GetY(), atom_neighbour.GetZ()]))
@@ -1877,21 +1874,23 @@ def _initialize_residue_sift(self):
 
     def _handle_hydrogens(self):
         """Determine atom valences and explicit hydrogen counts.
+        Methods renamed according to the: https://open-babel.readthedocs.io/en/latest/UseTheLibrary/migration.html
+
         """
         for ob_atom in ob.OBMolAtomIter(self.ob_mol):
             if not self.input_has_hydrogens:
-                if ob_atom.IsHydrogen():
+                if ob_atom.GetAtomicNum() == ob.Hydrogen:
                     continue
 
             # `http://openbabel.org/api/2.3/classOpenBabel_1_1OBAtom.shtml`
             # CURRENT NUMBER OF EXPLICIT CONNECTIONS
-            valence = ob_atom.GetValence()
+            valence = ob_atom.GetExplicitDegree()
 
             # MAXIMUM NUMBER OF CONNECTIONS EXPECTED
-            implicit_valence = ob_atom.GetImplicitValence()
+            implicit_valence = ob_atom.GetImplicitHCount()
 
             # BOND ORDER
-            bond_order = ob_atom.BOSum()
+            bond_order = ob_atom.GetExplicitValence()
 
             # NUMBER OF BOUND HYDROGENS
             num_hydrogens = ob_atom.ExplicitHydrogenCount()