Merge pull request #27 from alexandrefassio/master

Latest version

Author: alexandrefassio

luna/MyBio/PDB/Residue.py

@@ -218,6 +218,24 @@ def get_atom(self):
     def set_as_target(self, is_target=True):
         self._is_target = is_target
 
+    def as_json(self):
+
+        if self.is_water():
+            comp_repr = "sphere"
+        elif self.is_hetatm():
+            if len(self.child_list) == 1 or len([atm for atm in self.child_list if atm.element != "H"]) == 1:
+                comp_repr = "sphere"
+            else:
+                comp_repr = "stick"
+        else:
+            comp_repr = "stick"
+
+        return {"chain": self.parent.id,
+                "name": self.resname,
+                "number": self.id[1],
+                "icode": self.id[2].strip(),
+                "repr": comp_repr}
+
 
 class DisorderedResidue(DisorderedEntityWrapper):
     """DisorderedResidue is a wrapper around two or more Residue objects.

luna/mol/atom.py

@@ -128,6 +128,16 @@ def get_neighbor_info(self, atom):
     def is_neighbor(self, atom):
         return atom.serial_number in [i.serial_number for i in self._nb_info]
 
+    def as_json(self):
+        full_id = self.get_full_id()
+
+        return {"pdb_id": full_id[0],
+                "model": full_id[1],
+                "chain": full_id[2],
+                "res_name": self.parent.resname,
+                "res_id": [full_id[3][1], full_id[2].strip()],
+                "name": [full_id[4][0], full_id[4][1].strip()]}
+
     def __getattr__(self, attr):
         if hasattr(self._atom, attr):
             return getattr(self._atom, attr)

luna/mol/entry.py

@@ -199,7 +199,7 @@ def from_string(cls, entry_str, sep=ENTRY_SEPARATOR):
 
     @property
     def full_id(self):
-        return (self.pdb_id, self.mol_id)
+        return (self.pdb_id, self.chain_id)
 
 
 class CompoundEntry(Entry):

luna/mol/groups.py

@@ -407,6 +407,18 @@ def has_target(self):
         """Return 1 if at least one compound is the target."""
         return any([a.parent.is_target() for a in self.atoms])
 
+    def as_json(self):
+        grp_obj = {}
+
+        grp_obj["atoms"] = [atm.as_json() for atm in self.atoms]
+
+        grp_obj["compounds"] = [comp.as_json() for comp in self.compounds]
+
+        grp_obj["features"] = [feat.name for feat in self.features if feat.name != "Atom"]
+        grp_obj["classes"] = [comps.get_class() for comps in self.compounds]
+
+        return grp_obj
+
     def clear_refs(self):
         if self._recursive:
             for atm in self.atoms:

luna/mol/interaction/calc.py

@@ -2,6 +2,7 @@
 from operator import le, ge
 from itertools import combinations, product
 from collections import defaultdict
+import json
 
 import luna.mol.interaction.math as im
 from luna.mol.interaction.conf import DefaultInteractionConf, InteractionConf
@@ -100,6 +101,11 @@ def to_csv(self, output_file):
             # Sort lines before writing to always keep the same order.
             OUT.write("\n".join([",".join(k) for k in sorted(interactions_set)]))
 
+    def to_json(self, output_file=None, indent=None):
+        with open(output_file, 'w') as OUT:
+            inter_objs = [inter.as_json() for inter in self.interactions]
+            json.dump(inter_objs, OUT, indent=indent)
+
     def save(self, output_file, compressed=True):
         pickle_data(self, output_file, compressed)
 

luna/mol/interaction/type.py

@@ -1,6 +1,18 @@
 import numpy as np
 
 from luna.mol.interaction.math import atom_coordinates, centroid
+from luna.util.default_values import PYMOL_INTERACTION_COLOR_AS_RGB
+from luna.util import rgb2hex
+
+
+NUCLEOPHILE_INTERS = ["Orthogonal multipolar", "Parallel multipolar", "Antiparallel multipolar", "Tilted multipolar", "Multipolar",
+                      "Cation-nucleophile", "Unfavorable anion-nucleophile", "Unfavorable nucleophile-nucleophile"]
+
+ELECTROPHILE_INTERS = ["Orthogonal multipolar", "Parallel multipolar", "Antiparallel multipolar", "Tilted multipolar", "Multipolar",
+                       "Anion-electrophile", "Unfavorable cation-electrophile", "Unfavorable electrophile-electrophile"]
+
+UNFAVORABLE_INTERS = ["Repulsive", "Unfavorable anion-nucleophile", "Unfavorable cation-electrophile",
+                      "Unfavorable nucleophile-nucleophile", "Unfavorable electrophile-electrophile"]
 
 
 class InteractionType():
@@ -66,7 +78,21 @@ def src_centroid(self):
             if self._src_interacting_atms:
                 self._src_centroid = centroid(atom_coordinates(self._src_interacting_atms))
             else:
-                self._src_centroid = self._src_grp.centroid
+                src_centroid = self._src_grp.centroid
+                # Define the centroid in a nucleophile with two atoms as the position of its more electronegative atom.
+                # Remember that the position in the interaction object matters. We have defined that the first group is always
+                # the nucleophile for both dipole-dipole and ion-dipole interactions.
+                if self.type in NUCLEOPHILE_INTERS and len(self.src_grp.atoms) == 2:
+                    dipole_atm = self.src_grp.atoms[0] if (self.src_grp.atoms[0].electronegativity
+                                                           > self.src_grp.atoms[1].electronegativity) else self.src_grp.atoms[1]
+                    src_centroid = dipole_atm.coord
+                # For unfavorable multipolar interactions, it may happen that the first atom group is an electrophile as well.
+                elif self.type == "Unfavorable electrophile-electrophile" and len(self.src_grp.atoms) == 2:
+                    dipole_atm = self.src_grp.atoms[0] if (self.src_grp.atoms[0].electronegativity
+                                                           < self.src_grp.atoms[1].electronegativity) else self.src_grp.atoms[1]
+                    src_centroid = dipole_atm.coord
+
+                self._src_centroid = src_centroid
         return self._src_centroid
 
     @src_centroid.setter
@@ -82,7 +108,22 @@ def trgt_centroid(self):
             if self._trgt_interacting_atms:
                 self._trgt_centroid = centroid(atom_coordinates(self._trgt_interacting_atms))
             else:
-                self._trgt_centroid = self._trgt_grp.centroid
+                trgt_centroid = self._trgt_grp.centroid
+
+                # Define the centroid in an electrophile with two atoms as the position of its less electronegative atom.
+                # Remember that the position in the interaction object matters. We have defined that the second group is always
+                # the electrophile for both dipole-dipole and ion-dipole interactions.
+                if self.type in ELECTROPHILE_INTERS and len(self.trgt_grp.atoms) == 2:
+                    dipole_atm = self.trgt_grp.atoms[0] if (self.trgt_grp.atoms[0].electronegativity
+                                                            < self.trgt_grp.atoms[1].electronegativity) else self.trgt_grp.atoms[1]
+                    trgt_centroid = dipole_atm.coord
+                # For unfavorable multipolar interactions, it may happen that the second atom group is a nucleophile as well.
+                elif self.type == "Unfavorable nucleophile-nucleophile" and len(self.trgt_grp.atoms) == 2:
+                    dipole_atm = self.trgt_grp.atoms[0] if (self.trgt_grp.atoms[0].electronegativity
+                                                            > self.trgt_grp.atoms[1].electronegativity) else self.trgt_grp.atoms[1]
+                    trgt_centroid = dipole_atm.coord
+
+                self._trgt_centroid = trgt_centroid
         return self._trgt_centroid
 
     @trgt_centroid.setter
@@ -133,6 +174,34 @@ def is_intramol_interaction(self):
     def is_intermol_interaction(self):
         return not self.is_intramol_interaction()
 
+    def show_src_centroid(self):
+        show_centroid = True
+
+        # Define the centroid in a nucleophile with two atoms as the position of its more electronegative atom.
+        # Remember that the position in the interaction object matters. We have defined that the first group is always
+        # the nucleophile for both dipole-dipole and ion-dipole interactions.
+        if self.type in NUCLEOPHILE_INTERS and len(self.src_grp.atoms) == 2:
+            show_centroid = False
+        # For unfavorable multipolar interactions, it may happen that the first atom group is an electrophile as well.
+        elif self.type == "Unfavorable electrophile-electrophile" and len(self.src_grp.atoms) == 2:
+            show_centroid = False
+
+        return show_centroid
+
+    def show_trgt_centroid(self):
+        show_centroid = True
+
+        # Define the centroid in an electrophile with two atoms as the position of its less electronegative atom.
+        # Remember that the position in the interaction object matters. We have defined that the second group is always
+        # the electrophile for both dipole-dipole and ion-dipole interactions.
+        if self.type in ELECTROPHILE_INTERS and len(self.trgt_grp.atoms) == 2:
+            show_centroid = False
+        # For unfavorable multipolar interactions, it may happen that the second atom group is a nucleophile as well.
+        elif self.type == "Unfavorable nucleophile-nucleophile" and len(self.trgt_grp.atoms) == 2:
+            show_centroid = False
+
+        return show_centroid
+
     def apply_refs(self):
         self.src_grp.add_interactions([self])
         self.trgt_grp.add_interactions([self])
@@ -145,11 +214,45 @@ def _expand_dict(self):
         for key in self._params:
             self.__dict__[key] = self._params[key]
 
+    def as_json(self):
+        inter_obj = {}
+        inter_obj["type"] = self.type
+
+        inter_obj["color"] = rgb2hex(*PYMOL_INTERACTION_COLOR_AS_RGB.get_unnormalized_color(self.type))
+        inter_obj["is_directional"] = self.is_directional()
+        inter_obj["is_intramol_interaction"] = self.is_intramol_interaction()
+        inter_obj["is_intermol_interaction"] = self.is_intermol_interaction()
+
+        src_grp_obj = self.src_grp.as_json()
+        src_grp_obj["add_pseudo_group"] = len(self.src_grp.atoms) > 1
+        src_grp_obj["centroid"] = self.src_centroid.tolist()
+        src_grp_obj["show_centroid"] = self.show_src_centroid()
+
+        if src_grp_obj["add_pseudo_group"]:
+            src_grp_obj["pseudo_group_name"] = "+".join([a.name for a in sorted(self.src_grp.atoms)])
+
+        inter_obj["src_grp"] = src_grp_obj
+
+        #
+        # Target atom group
+        #
+        trgt_grp_obj = self.trgt_grp.as_json()
+        trgt_grp_obj["add_pseudo_group"] = len(self.trgt_grp.atoms) > 1
+        trgt_grp_obj["centroid"] = self.trgt_centroid.tolist()
+        trgt_grp_obj["show_centroid"] = self.show_trgt_centroid()
+
+        if trgt_grp_obj["add_pseudo_group"]:
+            trgt_grp_obj["pseudo_group_name"] = "+".join([a.name for a in sorted(self.trgt_grp.atoms)])
+
+        inter_obj["trgt_grp"] = trgt_grp_obj
+
+        return inter_obj
+
     def __eq__(self, other):
         """Overrides the default implementation"""
         if isinstance(self, other.__class__):
-            is_equal_compounds = ((self.src_grp == other.src_grp and self.trgt_grp == other.trgt_grp) or
-                                  (self.src_grp == other.trgt_grp and self.trgt_grp == other.src_grp))
+            is_equal_compounds = ((self.src_grp == other.src_grp and self.trgt_grp == other.trgt_grp)
+                                  or (self.src_grp == other.trgt_grp and self.trgt_grp == other.src_grp))
 
             is_equal_interactions = self.type == other.type
             has_equal_params = self.params == other.params

luna/run.py

@@ -84,6 +84,9 @@ def main():
     parser.add_argument('--out_sim', dest="out_sim", action="store_true",
                         help="defines whether it should generate a similarity matrix")
 
+    parser.add_argument("--nproc", dest="nproc", type=int,
+                        help="the number of processors to use")
+
     args = parser.parse_args()
 
     proj_pkl_file = "%s/project_v%s.pkl.gz" % (args.working_path, version)
@@ -108,6 +111,9 @@ def main():
         opt["calc_ifp"] = False
         opt["out_pse"] = args.out_pse
 
+        if args.nproc:
+            opt["nproc"] = args.nproc
+
         if args.binding_modes_file:
             opt["binding_mode_filter"] = BindingModeFilter.from_config_file(args.binding_modes_file)
 

luna/util/__init__.py

@@ -3,6 +3,14 @@
 logger = logging.getLogger()
 
 
+def rgb2hex(r, g, b):
+    return "#{:02x}{:02x}{:02x}".format(r, g, b)
+
+
+def hex2rgb(hexcode):
+    return tuple(map(ord, hexcode[1:].decode('hex')))
+
+
 # TODO: Transform hex to rgb and vice versa
 class ColorPallete:
     def __init__(self, color_map=None, default_color=(255, 255, 255)):
@@ -21,6 +29,15 @@ def get_normalized_color(self, key):
             return color
         return tuple(c / 255 for c in color)
 
+    def get_unnormalized_color(self, key):
+        color = self.get_color(key)
+
+        if isinstance(color, str):
+            return color
+        elif all([x > 1 for x in color]):
+            return color
+        return tuple(int(c * 255) for c in color)
+
     def get_color(self, key):
         if key in self.color_map:
             return self.color_map[key]

luna/util/default_values.py

@@ -213,3 +213,50 @@
     "Aromatic bond": "black",
     "Other bond": "black",
 }, "white")
+
+PYMOL_INTERACTION_COLOR_AS_RGB = ColorPallete({
+    "Proximal": (0.6, 0.6, 0.6),
+    "Hydrogen bond": (0.3, 0.3, 1.0),
+    "Water-bridged hydrogen bond": (0.75, 0.75, 1.0),
+    "Weak hydrogen bond": (0.4, 0.7, 0.7),
+    "Ionic": (0.0, 1.0, 0.0),
+    "Salt bridge": (0.2, 0.6, 0.2),
+    "Cation-pi": (1.0, 0.6, 0.6),
+    "Amide-aromatic stacking": (0.70, 0.30, 0.40),
+    "Hydrophobic": (1.0, 0.5, 0.0),
+    "Halogen bond": (0.5, 1, 1),
+    "Halogen-pi": (0.5, 1, 1),
+    "Chalcogen bond": (1.0, 0.8, 0.5),
+    "Chalcogen-pi": (1.0, 0.8, 0.5),
+    "Repulsive": (0.55, 0.25, 0.60),
+    "Covalent bond": (0.0, 0.0, 0.0),
+    "Atom overlap": (0.4, 0.4, 0.4),
+    "Van der Waals clash": (0.9, 0.9, 0.9),
+    "Van der Waals": (0.5, 0.5, 0.5),
+    "Orthogonal multipolar": (1.0, 1.0, 0.5),
+    "Parallel multipolar": (1.0, 1.0, 0.5),
+    "Antiparallel multipolar": (1.0, 1.0, 0.5),
+    "Tilted multipolar": (1.0, 1.0, 0.5),
+    "Multipolar": (1.0, 1.0, 0.5),
+    "Unfavorable nucleophile-nucleophile": (0.70, 0.50, 0.50),
+    "Unfavorable electrophile-electrophile": (0.70, 0.50, 0.50),
+    "Cation-nucleophile": (0.65, 0.9, 0.65),
+    "Anion-electrophile": (0.65, 0.9, 0.65),
+    "Unfavorable anion-nucleophile": (0.70, 0.50, 0.50),
+    "Unfavorable cation-electrophile": (0.70, 0.50, 0.50),
+    "Pi-stacking": (1.0, 0.2, 0.2),
+    "Face-to-face pi-stacking": (1.0, 0.2, 0.2),
+    "Face-to-edge pi-stacking": (1.0, 0.2, 0.2),
+    "Face-to-slope pi-stacking": (1.0, 0.2, 0.2),
+    "Edge-to-edge pi-stacking": (1.0, 0.2, 0.2),
+    "Edge-to-face pi-stacking": (1.0, 0.2, 0.2),
+    "Edge-to-slope pi-stacking": (1.0, 0.2, 0.2),
+    "Displaced face-to-face pi-stacking": (1.0, 0.2, 0.2),
+    "Displaced face-to-edge pi-stacking": (1.0, 0.2, 0.2),
+    "Displaced face-to-slope pi-stacking": (1.0, 0.2, 0.2),
+    "Single bond": (0.0, 0.0, 0.0),
+    "Double bond": (0.0, 0.0, 0.0),
+    "Triple bond": (0.0, 0.0, 0.0),
+    "Aromatic bond": (0.0, 0.0, 0.0),
+    "Other bond": (0.0, 0.0, 0.0),
+}, (1.0, 1.0, 1.0))