Lin_F9 betascore

alphaspace2/LinF9data/Vina_atom_radii.dat

@@ -0,0 +1,40 @@
+#atom_type,Radii
+H,0.00
+HD,0.00   
+C,1.90 
+A,1.90 
+N,1.80 
+NA,1.80 
+O,1.70
+OA,1.70
+S,2.00
+SA,2.00
+P,2.10
+F,1.50
+Cl,1.80
+CL,1.80
+Br,2.00
+BR,2.00
+I,2.20
+Mn,1.20
+MN,1.20
+Mg,1.20
+MG,1.20
+Zn,1.20
+ZN,1.20
+Ca,1.20
+CA,1.20
+Fe,1.20
+FE,1.20
+Ni,1.20
+NI,1.20
+Na,1.20
+Co,1.20
+CO,1.20
+Cu,1.20
+CU,1.20
+Cd,1.20
+CD,1.20
+K,1.20
+SE,1.75
+Se,1.75

alphaspace2/LinF9data/colors_chimera.txt

@@ -0,0 +1,27 @@
+seagreen
+my_gold
+my_pink
+my_teal
+my_orange
+my_blue
+my_dkpurple
+my_ltblue
+my_peri
+my_peach
+tan
+plum
+my_ltgreen
+olivedrab
+firebrick
+pink
+dodgerblue
+mediumpurple
+my_lime
+goldenrod
+aquamarine
+my_rasp
+darkslateblue
+darkmagenta
+rosybrown
+my_coral
+my_foam

alphaspace2/LinF9data/colors_table.txt

@@ -0,0 +1,27 @@
+green
+yellow
+pink
+teal
+orange
+blue
+purple
+ltblue
+peri
+peach
+tan
+mauve
+ltgreen
+olive
+brick
+ltpink
+dodgerbl
+ltpurple
+lime
+gold
+aqua
+raspberry
+dkblue
+dkpruple
+rosybrown
+coral
+seafoam

alphaspace2/LinF9data/hp_types_dict.dat

@@ -0,0 +1,203 @@
+#RES_name,ATOM_name,ATOM_element,for_ACC,for_DON
+ALA,C,C,NNP,NNP
+ALA,CA,C,NNP,NNP
+ALA,CB,C,NP,NP
+ALA,N,N,NNP,P
+ALA,O,OA,P,NPP
+ARG,C,C,NNP,NNP
+ARG,CA,C,NNP,NNP
+ARG,CB,C,NP,NP
+ARG,CD,C,NNP,NNP
+ARG,CG,C,NP,NP
+ARG,CZ,C,NNP,NNP
+ARG,N,N,NNP,P
+ARG,NE,N,NNP,P
+ARG,NH1,N,NNP,P
+ARG,NH2,N,NNP,P
+ARG,O,OA,P,NPP
+ASN,C,C,NNP,NNP
+ASN,CA,C,NNP,NNP
+ASN,CB,C,NP,NP
+ASN,CG,C,NNP,NNP
+ASN,N,N,NNP,P
+ASN,ND2,N,NNP,P
+ASN,O,OA,P,NPP   
+ASN,OD1,OA,P,NNP
+ASP,C,C,NNP,NNP
+ASP,CA,C,NNP,NNP
+ASP,CB,C,NP,NP
+ASP,CG,C,NNP,NNP
+ASP,N,N,NNP,P
+ASP,O,OA,P,NPP   
+ASP,OD1,OA,P,NNP
+ASP,OD2,OA,P,NNP
+CYS,C,C,NNP,NNP
+CYS,CA,C,NNP,NNP
+CYS,CB,C,NNP,NNP
+CYS,N,N,NNP,P
+CYS,O,OA,P,NPP  
+CYS,SG,S,NNP,NNP
+GLN,C,C,NNP,NNP
+GLN,CA,C,NNP,NNP
+GLN,CB,C,NP,NP
+GLN,CD,C,NNP,NNP
+GLN,CG,C,NP,NP
+GLN,N,N,NNP,P
+GLN,NE2,N,NNP,P
+GLN,O,OA,P,NPP   
+GLN,OE1,OA,P,NNP
+GLU,C,C,NNP,NNP
+GLU,CA,C,NNP,NNP
+GLU,CB,C,NP,NP
+GLU,CD,C,NNP,NNP
+GLU,CG,C,NP,NP
+GLU,N,N,NNP,P
+GLU,O,OA,P,NPP   
+GLU,OE1,OA,P,NNP
+GLU,OE2,OA,P,NNP
+GLY,C,C,NNP,NNP
+GLY,CA,C,NNP,NNP
+GLY,N,N,NNP,P
+GLY,O,OA,P,NPP   
+HID,C,C,NNP,NNP
+HID,CA,C,NNP,NNP
+HID,CB,C,NP,NP
+HID,CD2,A,NNP,NNP
+HID,CE1,A,NNP,NNP
+HID,CG,A,NNP,NNP
+HID,N,N,NNP,P
+HID,ND1,N,P,P
+HID,NE2,N,P,P
+HID,O,OA,P,NPP  
+HIE,C,C,NNP,NNP
+HIE,CA,C,NNP,NNP
+HIE,CB,C,NP,NP
+HIE,CD2,A,NNP,NNP
+HIE,CE1,A,NNP,NNP
+HIE,CG,A,NNP,NNP
+HIE,N,N,NNP,P
+HIE,ND1,N,P,P
+HIE,NE2,N,P,P
+HIE,O,OA,P,NPP  
+HIP,C,C,NNP,NNP
+HIP,CA,C,NNP,NNP
+HIP,CB,C,NP,NP
+HIP,CD2,A,NNP,NNP
+HIP,CE1,A,NNP,NNP
+HIP,CG,A,NNP,NNP
+HIP,N,N,NNP,P
+HIP,ND1,N,P,P
+HIP,NE2,N,P,P
+HIP,O,OA,P,NPP  
+HIS,C,C,NNP,NNP
+HIS,CA,C,NNP,NNP
+HIS,CB,C,NP,NP
+HIS,CD2,A,NNP,NNP
+HIS,CE1,A,NNP,NNP
+HIS,CG,A,NNP,NNP
+HIS,N,N,NNP,P
+HIS,ND1,N,P,P
+HIS,NE2,N,P,P
+HIS,O,OA,P,NPP   
+ILE,C,C,NNP,NNP
+ILE,CA,C,NNP,NNP
+ILE,CB,C,NP,NP
+ILE,CD1,C,NP,NP
+ILE,CG1,C,NP,NP
+ILE,CG2,C,NP,NP
+ILE,N,N,NNP,P
+ILE,O,OA,P,NPP   
+LEU,C,C,NNP,NNP
+LEU,CA,C,NNP,NNP
+LEU,CB,C,NP,NP
+LEU,CD1,C,NP,NP
+LEU,CD2,C,NP,NP
+LEU,CG,C,NP,NP
+LEU,N,N,NNP,P
+LEU,O,OA,P,NPP     
+LYS,C,C,NNP,NNP
+LYS,CA,C,NNP,NNP
+LYS,CB,C,NP,NP
+LYS,CD,C,NP,NP
+LYS,CE,C,NNP,NNP
+LYS,CG,C,NP,NP
+LYS,N,N,NNP,P
+LYS,NZ,N,NNP,P  
+LYS,O,OA,P,NPP  
+MET,C,C,NNP,NNP
+MET,CA,C,NNP,NNP
+MET,CB,C,NP,NP
+MET,CE,C,NNP,NNP
+MET,CG,C,NNP,NNP
+MET,N,N,NNP,P
+MET,O,OA,P,NPP   
+MET,SD,S,NNP,NNP
+PHE,C,C,NNP,NNP
+PHE,CA,C,NNP,NNP
+PHE,CB,C,NP,NP
+PHE,CD1,A,NP,NP
+PHE,CD2,A,NP,NP
+PHE,CE1,A,NP,NP
+PHE,CE2,A,NP,NP
+PHE,CG,A,NP,NP
+PHE,CZ,A,NP,NP
+PHE,N,N,NNP,P
+PHE,O,OA,P,NPP    
+PRO,C,C,NNP,NNP
+PRO,CA,C,NNP,NNP
+PRO,CB,C,NP,NP
+PRO,CD,C,NNP,NNP
+PRO,CG,C,NP,NP
+PRO,N,N,P,NNP
+PRO,O,OA,P,NPP 
+SER,C,C,NNP,NNP
+SER,CA,C,NNP,NNP
+SER,CB,C,NNP,NNP
+SER,N,N,NNP,P
+SER,O,OA,P,NPP  
+SER,OG,OA,P,P
+THR,C,C,NNP,NNP
+THR,CA,C,NNP,NNP
+THR,CB,C,NNP,NNP
+THR,CG2,C,NP,NP
+THR,N,N,NNP,P
+THR,O,OA,P,NPP 
+THR,OG1,OA,P,P
+TRP,C,C,NNP,NNP
+TRP,CA,C,NNP,NNP
+TRP,CB,C,NP,NP
+TRP,CD1,A,NNP,NNP
+TRP,CD2,A,NP,NP
+TRP,CE2,A,NNP,NNP
+TRP,CE3,A,NP,NP
+TRP,CG,A,NP,NP
+TRP,CH2,A,NP,NP
+TRP,CZ2,A,NP,NP
+TRP,CZ3,A,NP,NP
+TRP,N,N,NNP,P
+TRP,NE1,N,NNP,P
+TRP,O,OA,P,NPP   
+TYR,C,C,NNP,NNP
+TYR,CA,C,NNP,NNP
+TYR,CB,C,NP,NP
+TYR,CD1,A,NP,NP
+TYR,CD2,A,NP,NP
+TYR,CE1,A,NP,NP
+TYR,CE2,A,NP,NP
+TYR,CG,A,NP,NP
+TYR,CZ,A,NNP,NNP
+TYR,N,N,NNP,P
+TYR,O,OA,P,NPP 
+TYR,OH,OA,P,P
+VAL,C,C,NNP,NNP
+VAL,CA,C,NNP,NNP
+VAL,CB,C,NP,NP
+VAL,CG1,C,NP,NP
+VAL,CG2,C,NP,NP
+VAL,N,N,NNP,P
+VAL,O,OA,P,NPP
+ZN,ZN,Zn,NNP,PP
+FE,FE,Fe,NNP,PP
+MG,MG,Mg,NNP,PP
+MN,MN,Mn,NNP,PP
+CA,CA,Ca,NNP,PP

alphaspace2/Snapshot.py

@@ -129,8 +129,13 @@ def genPockets(self):
             self._pocket_xyz[i] = np.mean(self._alpha_xyz[indices], axis=0)
             self._pocket_space[i] = np.sum(self._alpha_space[indices], axis=0)
 
-    def genBScore(self, receptor):
-        from .VinaScoring import _pre_process_pdbqt, _get_probe_score
+    def genBScore(self, receptor, score_function="Vina"):
+        if score_function == "Vina":
+            from .VinaScoring import _pre_process_pdbqt, _get_probe_score
+        elif score_function == "Lin_F9":
+            from .LinF9Scoring import _pre_process_pdbqt, _get_probe_score
+        else:
+            raise ValueError("The scoring function " + score_function + " has not been implemented yet")
 
         if hasattr(receptor, 'adv_atom_types'):
             logging.debug('Vina Atom type found, calculating beta scores')
@@ -165,15 +170,15 @@ def calculateContact(self, coords):
         self._pocket_contact = np.array(
             [np.any(self._alpha_contact[alpha_indices]) for alpha_indices in self._pocket_alpha_index_list])
 
-    def run(self, receptor, binder=None):
+    def run(self, receptor, binder=None, score_function="Vina"):
 
         self.genAlphas(receptor)
 
         self.genPockets()
 
         self.genBetas()
 
-        self.genBScore(receptor)
+        self.genBScore(receptor, score_function=score_function)
 
         if binder is not None:
             self.calculateContact(coords=binder.xyz[0] * 10)

alphaspace2/VinaScoring.py

@@ -414,11 +414,11 @@ def annotateVinaAtomTypes(receptor, pdbqt):
         adv_atom_type = line[77:79].strip()
         adv_atom_types.append(adv_atom_type)
 
-        if receptor.top.n_atoms < len(adv_atom_types):
-            print("Redundant Atom types in pdbqt file found, trimming last {} entries".format(
-                {receptor.top.n_atoms - len(adv_atom_types)}))
-            adv_atom_types = adv_atom_types[:receptor.top.n_atoms]
-            partial_charges = partial_charges[:receptor.top.n_atoms]
+    if receptor.top.n_atoms < len(adv_atom_types):
+        print("Redundant Atom types in pdbqt file found, trimming last {} entries".format(
+            {receptor.top.n_atoms - len(adv_atom_types)}))
+        adv_atom_types = adv_atom_types[:receptor.top.n_atoms]
+        partial_charges = partial_charges[:receptor.top.n_atoms]
 
     receptor.partial_charges = partial_charges
     receptor.adv_atom_types = adv_atom_types

alphaspace2/functions.py

@@ -446,7 +446,7 @@ def _findInRange(query_points, ref_points, cutoff):
 
 def _markInRange(query_points, ref_points, cutoff):
     indices = _findInRange(query_points, ref_points, cutoff)
-    query_bool = np.zeros(len(query_points), dtype=np.bool)
+    query_bool = np.zeros(len(query_points), dtype=bool)
     query_bool[indices] = 1
     return query_bool