opt_jobs added

denovo.py

@@ -80,6 +80,9 @@ def initialize(self):
                                  [1.0,-1.0,1.0], [-1.0,1.0,1.0], [-1.0,-1.0,-1.0], [-1.0,-1.0,1.0],
                                  [-1.0,1.0,-1.0], [1.0,-1.0,-1.0]])
 
+                #self.direcn = np.array([[1.0,0.0,0.0], [-1.0,0.0,0.0], [0.0,1.0,0.0], [0.0,-1.0,0.0],
+                #                 [0.0,0.0,1.0], [0.0,0.0,-1.0]])
+
                 if self.test:
                     self.res_d = np.load('models/res_d.npy').item()
                     chk = len(self.res_d)
@@ -218,7 +221,8 @@ def data_extraction(lines):
                                             s=line.strip().split()[-1]
                                             #print (line.strip())
                                             x, y, z = list(map(float, [x, y, z]))
-                                            if is_backbone(s, at):
+                                            if at == 'CA':# is_backbone(s, at):
+                                                            #print (at)
                                                             if rt+_0 not in d:
                                                                         l[len(d)] = rt+_0
                                                                         d[rt+_0]=[[x, y, z]]
@@ -583,7 +587,11 @@ def map_pdb(self):
                     new_cord = dis[i]*v + cords[i]
                     cords.append(new_cord)
 
-                r = animate.render(np.amax(cords)/2)
+                r = animate.render(abs(np.amax(cords)-np.amin(cords))/2)
+
+                print (np.array(cords))
+
+                np.save('map_grid.npy', {'gen':cords, 'org':self.ref_coord})
 
                 r.plot_final(cords, self.ref_coord)
 

opt_jobs.py

@@ -0,0 +1,51 @@
+import os
+import numpy as np
+
+
+class Work:
+	def __init__(self, seq, grid, name):
+		self.seq = seq
+		self.grid = grid
+		self.name = name
+
+	def gen_CA_pdb(self):
+		st = ''
+
+		for i in range (len(self.seq)):
+			l = ['ATOM', str(i+1), 'CA', self.seq[i], 'A', str(i+1), self.grid[i][0], self.grid[i][1], self.grid[i][2], '1.00', '0.00', 'C']
+			print ("{:>4}{:>7}{:>5}{:>4}{:>2}{:>4}{:>12}{:>8}{:>8}{:>6}{:>6}{:>12}".format(*l))
+			st += "{:>4}{:>7}{:>5}{:>4}{:>2}{:>4}{:>12}{:>8}{:>8}{:>6}{:>6}{:>12}".format(*l)+'\n'
+
+		st += 'TER\nEND'
+
+		g = open(self.name+'_CA.pdb','w')
+		g.write(st)
+		g.close()
+
+
+
+if __name__ == '__main__':
+	name = '1k43'
+	seq = ['ARG', 'GLY', 'LYS', 'TRP', 'THR', 'TYR', 'ASN', 'GLY', 'ILE', 'THR', 'TYR', 'GLU', 'GLY', 'ARG']
+	grid = np.array([[0.0, 0.0, 0.0],
+		[3.78, 0.0, 0.0],
+		[7.56, 0.0, 0.0],
+		[11.35, 0.0, 0.0],
+		[15.14, 0.0, 0.0],
+		[18.92, 0.0, 0.0],
+		[22.71, 0.0, 0.0],
+		[26.49, 0.0, 0.0],
+		[30.28, 0.0, 0.0],
+		[34.06, 0.0, 0.0],
+		[37.84, 0.0, 0.0],
+		[41.63, 0.0, 0.0],
+		[45.42, 0.0, 0.0],
+		[49.20, 0.0, 0.0]])
+
+	w = Work(seq, grid, name)
+
+	w.gen_CA_pdb()
+
+# for making pdb from CA
+# java apps.BBQ -bbq.fix_r12=T -ip=1k43_CA.pdb
+# add side chains via SCWRL