Changeset 5fef0d7 for protein.py

Timestamp:

09/02/10 10:25:36 (14 years ago)

Author:

Jan Meinke <j.meinke@…>

Branches:

master

Children:

225475c

Parents:

3fbbfbb

Message:

Changed module name from smmp to smmp_p.

Fixed conversion to residue and atom names.

File:

• protein.py (modified) (3 diffs)

protein.py

@@ -6 +6 @@
 #
 import sys
+import numpy as np
 import smmp_p as smmp
 from math import *
@@ -52 +53 @@
         
     def name(self):
-        return ''.join([smmp.atm_c.nmat[i][self.__id] for i in range(0,4)]).strip()
+        return ''.join(smmp.atm_c.nmat[:,0].reshape([-1,4])[self.__id]).strip()
         
     def __str__(self):
@@ -174 +175 @@
     def residues(self):
         """Returns a list of the amino acids in this protein."""
-        seq = [str(c[0]) for c in smmp.res_c.seq]
+        seq = [''.join(l) for l in np.array([str(c[0]) for c in smmp.res_c.seq]).reshape([-1, 4])]
         first = smmp.mol_i.irsml1[self.__id]- 1
         last = smmp.mol_i.irsml2[self.__id] - 1
-        return ''.join(seq).split()[first:last]
+        return seq[first:last]
         
     def id(self):