Changeset fdb134b9 in sasview for sanscalculator

Timestamp:

Jan 20, 2013 12:50:50 PM (12 years ago)

Author:

Jae Cho <jhjcho@…>

Branches:

master, ESS_GUI, ESS_GUI_Docs, ESS_GUI_batch_fitting, ESS_GUI_bumps_abstraction, ESS_GUI_iss1116, ESS_GUI_iss879, ESS_GUI_iss959, ESS_GUI_opencl, ESS_GUI_ordering, ESS_GUI_sync_sascalc, costrafo411, magnetic_scatt, release-4.1.1, release-4.1.2, release-4.2.2, release_4.0.1, ticket-1009, ticket-1094-headless, ticket-1242-2d-resolution, ticket-1243, ticket-1249, ticket885, unittest-saveload

Children:

a30864b1

Parents:

afcb052

Message:

added bonding lines for pdb data if provided

File:

• sanscalculator/src/sans/calculator/sans_gen.py (modified) (7 diffs)

sanscalculator/src/sans/calculator/sans_gen.py

@@ -500 +500 @@
         vol_pix = numpy.zeros(0)
         pix_symbol = numpy.zeros(0)
+        x_line = numpy.zeros(0)
+        y_line = numpy.zeros(0)
+        z_line = numpy.zeros(0)
         try:
             input_f = open(path, 'rb')
@@ -507 +510 @@
             for line in lines:
                 try:
-                    #toks = line.split()
                     # check if line starts with "ATOM"
                     if line[0:6].strip().count('ATM') > 0 or \
@@ -553 +555 @@
                         sld_mz = numpy.append(sld_mz, 0)
                         pix_symbol = numpy.append(pix_symbol, atom_name)
+                    elif line[0:6].strip().count('CONECT') > 0 :
+                        toks = line.split()
+                        for val in toks[2:]:
+                            index = int(val) - 1
+                            num = int(toks[1]) - 1
+                            x_line = numpy.append(x_line, 
+                                                  [pos_x[num], pos_x[index]])
+                            y_line = numpy.append(y_line, 
+                                                  [pos_y[num], pos_y[index]])
+                            z_line = numpy.append(z_line, 
+                                                  [pos_z[num], pos_z[index]])        
                 except:
                     pass
@@ -561 +574 @@
 
             output = MagSLD(pos_x, pos_y, pos_z, sld_n, sld_mx, sld_my, sld_mz)
+            output.set_conect_lines(x_line, y_line, z_line)
             output.filename = os.path.basename(path)
             output.set_pix_type('atom')
@@ -834 +848 @@
         self.znodes = 10.0
         self.has_stepsize = False
+        self.has_conect = False
         self.pos_unit = self._pos_unit
         self.sld_unit = self._sld_unit
@@ -841 +856 @@
         self.pos_z = pos_z
         self.sld_n = sld_n
+        self.line_x = None
+        self.line_y = None
+        self.line_z = None
         self.sld_mx = sld_mx
         self.sld_my = sld_my
@@ -1017 +1035 @@
         return self.xstepsize, self.ystepsize, self.zstepsize
 
-    
+    def set_conect_lines(self, line_x, line_y, line_z):
+        """
+        Set bonding line data if taken from pdb
+        """
+        if line_x.__class__.__name__ != 'ndarray' or len(line_x) < 1:
+            return
+        if line_y.__class__.__name__ != 'ndarray' or len(line_y) < 1:
+            return
+        if line_z.__class__.__name__ != 'ndarray' or len(line_z) < 1:
+            return
+        self.has_conect = True
+        self.line_x = line_x 
+        self.line_y = line_y 
+        self.line_z = line_z
+        
+
 def test_load():
     from danse.common.plottools.arrow3d import Arrow3D