Convert gninatypes to xyz

Author: dkoes

types2xyz.py

@@ -0,0 +1,67 @@
+#!/usr/bin/env python3
+
+'''convert gninatypes file to xyz file'''
+import struct, sys, argparse
+from functools import partial
+import molgrid
+
+names = molgrid.GninaIndexTyper().get_type_names()
+
+def elem(t):
+    '''convert type index into element string'''
+    name = names[t]
+    if 'Hydrogen' in name:
+        return 'H'
+    elif 'Carbon' in name:
+        return 'C'
+    elif 'Nitrogen' in name:
+        return 'N'
+    elif 'Oxygen' in name:
+        return 'O'
+    elif 'Sulfur' in name:
+        return 'S'
+    elif 'Phosphorus' == name:
+        return 'P'
+    elif 'Fluorine' == name:
+        return 'F'
+    elif 'Chlorine' == name:
+        return 'Cl'
+    elif 'Bromine' == name:
+        return 'Br'
+    elif 'Iodine' == name:
+        return 'I'
+    elif 'Magnesium' == name:
+        return 'Mg'
+    elif 'Manganese' == name:
+        return 'Mn'
+    elif 'Zinc' == name:
+        return 'Zn'
+    elif 'Calcium' == name:
+        return 'Ca'
+    elif 'Iron' == name:
+        return 'Fe'
+    elif 'Boron' == name:
+        return 'B'
+    else:
+        return 'X'
+        
+
+parser = argparse.ArgumentParser()
+parser.add_argument('input',type=str,help='gninatypes file')
+parser.add_argument('output', default='-',nargs='?',type=argparse.FileType('w'),help='output xyz')
+
+args = parser.parse_args()
+
+
+struct_fmt = 'fffi'
+struct_len = struct.calcsize(struct_fmt)
+struct_unpack = struct.Struct(struct_fmt).unpack_from
+
+with open(args.input,'rb') as tfile:
+        results = [struct_unpack(chunk) for chunk in iter(partial(tfile.read, struct_len), b'')]
+
+args.output.write('%d\n'%len(results)) # number atoms
+args.output.write(args.input+'\n') #comment
+for x,y,z,t in results:
+    args.output.write('%s\t%f\t%f\t%f\n'%(elem(t),x,y,z))
+