Author: bugman
Date: Mon Nov 17 12:04:25 2014
New Revision: 26597
URL: http://svn.gna.org/viewcvs/relax?rev=26597&view=rev
Log:
Updated the PDB file in the test_suite/shared_data/model_free/sphere/
directory.
The relax library is now being used to create the PDB file. Additional TER
and CONECT records are
now being created so the result is a more correct PDB file.
Modified:
trunk/test_suite/shared_data/model_free/sphere/create_sphere.py
(contents, props changed)
trunk/test_suite/shared_data/model_free/sphere/sphere.pdb
Modified: trunk/test_suite/shared_data/model_free/sphere/create_sphere.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/model_free/sphere/create_sphere.py?rev=26597&r1=26596&r2=26597&view=diff
==============================================================================
--- trunk/test_suite/shared_data/model_free/sphere/create_sphere.py
(original)
+++ trunk/test_suite/shared_data/model_free/sphere/create_sphere.py Mon
Nov 17 12:04:25 2014
@@ -1,35 +1,11 @@
-#!/usr/bin/python
+# relax script for creating the spherical PDB file.
+# Copyright 2004-2014, Edward d'Auvergne
-# Copyright 2004-2011, Edward d'Auvergne
-
+# Python module imports.
from math import acos, cos, pi, sin, sqrt
-
-def pdb_line(file=None, atom_num=0, atom=None, res_num=0, res_name=None,
vector=None):
- """Function for adding a line to the PDB file."""
-
- # ATOM.
- file.write('%-4s' % 'ATOM')
-
- # Atom number and type.
- file.write('%7i' % atom_num)
- file.write(' %-4s' % atom)
-
- # Residue number and name.
- file.write('%-4s' % res_name)
- file.write('%5i ' % res_num)
-
- # Vector.
- file.write('%8.3f' % vector[0])
- file.write('%8.3f' % vector[1])
- file.write('%8.3f' % vector[2])
-
- # I don't know what.
- file.write('%6.2f' % 1.0)
- file.write('%6.2f' % 0.0)
-
- # End of line.
- file.write('\n')
+# relax module imports.
+from lib.structure.pdb_write import atom, conect, ter
# Number of increments.
@@ -102,10 +78,10 @@
continue
# Nitrogen line.
- pdb_line(file=file, atom_num=atom_num, atom='N', res_num=res_num,
res_name='GLY', vector=[0.0, 0.0, 0.0])
+ atom(file=file, serial=atom_num, name='N', res_seq=res_num,
res_name='GLY', x=0.0, y=0.0, z=0.0)
# Hydrogen line.
- pdb_line(file=file, atom_num=atom_num+1, atom='H', res_num=res_num,
res_name='GLY', vector=vectors[i])
+ atom(file=file, serial=atom_num+1, name='H', res_seq=res_num,
res_name='GLY', x=vectors[i][0], y=vectors[i][1], z=vectors[i][2])
# Increment the atom number and residue number.
atom_num = atom_num + 2
@@ -115,8 +91,20 @@
used.append(vectors[i])
# Add a Trp indole NH for luck ;)
-pdb_line(file=file, atom_num=atom_num, atom='NE1', res_num=res_num-1,
res_name='GLY', vector=[0.0, 0.0, 0.0])
-pdb_line(file=file, atom_num=atom_num+1, atom='HE1', res_num=res_num-1,
res_name='GLY', vector=[1/sqrt(3), 1/sqrt(3), 1/sqrt(3)])
+atom(file=file, serial=atom_num, name='NE1', res_seq=res_num-1,
res_name='GLY', x=0.0, y=0.0, z=0.0)
+atom(file=file, serial=atom_num+1, name='HE1', res_seq=res_num-1,
res_name='GLY', x=1/sqrt(3), y=1/sqrt(3), z=1/sqrt(3))
+
+# Add a TER record.
+ter(file=file, serial=atom_num+2, res_name='GLY')
+
+# Connect everything.
+atom_num = 1
+for i in range(len(vectors)):
+ conect(file=file, serial=atom_num, bonded1=atom_num+1)
+ conect(file=file, serial=atom_num+1, bonded1=atom_num)
+ atom_num = atom_num + 2
+conect(file=file, serial=atom_num, bonded1=atom_num+1)
+conect(file=file, serial=atom_num+1, bonded1=atom_num)
# End of PDB.
file.write('END\n')
Propchange: trunk/test_suite/shared_data/model_free/sphere/create_sphere.py
------------------------------------------------------------------------------
--- svn:executable (original)
+++ svn:executable (removed)
@@ -1 +0,0 @@
-*
Modified: trunk/test_suite/shared_data/model_free/sphere/sphere.pdb
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/model_free/sphere/sphere.pdb?rev=26597&r1=26596&r2=26597&view=diff
==============================================================================
--- trunk/test_suite/shared_data/model_free/sphere/sphere.pdb (original)
+++ trunk/test_suite/shared_data/model_free/sphere/sphere.pdb Mon Nov 17
12:04:25 2014
@@ -1,21 +1,42 @@
-ATOM 1 N GLY 1 0.000 0.000 0.000 1.00 0.00
-ATOM 2 H GLY 1 0.745 0.000 -0.667 1.00 0.00
-ATOM 3 N GLY 2 0.000 0.000 0.000 1.00 0.00
-ATOM 4 H GLY 2 -0.373 0.645 -0.667 1.00 0.00
-ATOM 5 N GLY 3 0.000 0.000 0.000 1.00 0.00
-ATOM 6 H GLY 3 -0.373 -0.645 -0.667 1.00 0.00
-ATOM 7 N GLY 4 0.000 0.000 0.000 1.00 0.00
-ATOM 8 H GLY 4 1.000 0.000 0.000 1.00 0.00
-ATOM 9 N GLY 5 0.000 0.000 0.000 1.00 0.00
-ATOM 10 H GLY 5 -0.500 0.866 0.000 1.00 0.00
-ATOM 11 N GLY 6 0.000 0.000 0.000 1.00 0.00
-ATOM 12 H GLY 6 -0.500 -0.866 0.000 1.00 0.00
-ATOM 13 N GLY 7 0.000 0.000 0.000 1.00 0.00
-ATOM 14 H GLY 7 0.745 0.000 0.667 1.00 0.00
-ATOM 15 N GLY 8 0.000 0.000 0.000 1.00 0.00
-ATOM 16 H GLY 8 -0.373 0.645 0.667 1.00 0.00
-ATOM 17 N GLY 9 0.000 0.000 0.000 1.00 0.00
-ATOM 18 H GLY 9 -0.373 -0.645 0.667 1.00 0.00
-ATOM 19 NE1 GLY 9 0.000 0.000 0.000 1.00 0.00
-ATOM 20 HE1 GLY 9 0.577 0.577 0.577 1.00 0.00
+ATOM 1 N GLY 1 0.000 0.000 0.000 1.00 0.00
+ATOM 2 H GLY 1 0.745 0.000 -0.667 1.00 0.00
+ATOM 3 N GLY 2 0.000 0.000 0.000 1.00 0.00
+ATOM 4 H GLY 2 -0.373 0.645 -0.667 1.00 0.00
+ATOM 5 N GLY 3 0.000 0.000 0.000 1.00 0.00
+ATOM 6 H GLY 3 -0.373 -0.645 -0.667 1.00 0.00
+ATOM 7 N GLY 4 0.000 0.000 0.000 1.00 0.00
+ATOM 8 H GLY 4 1.000 0.000 0.000 1.00 0.00
+ATOM 9 N GLY 5 0.000 0.000 0.000 1.00 0.00
+ATOM 10 H GLY 5 -0.500 0.866 0.000 1.00 0.00
+ATOM 11 N GLY 6 0.000 0.000 0.000 1.00 0.00
+ATOM 12 H GLY 6 -0.500 -0.866 0.000 1.00 0.00
+ATOM 13 N GLY 7 0.000 0.000 0.000 1.00 0.00
+ATOM 14 H GLY 7 0.745 0.000 0.667 1.00 0.00
+ATOM 15 N GLY 8 0.000 0.000 0.000 1.00 0.00
+ATOM 16 H GLY 8 -0.373 0.645 0.667 1.00 0.00
+ATOM 17 N GLY 9 0.000 0.000 0.000 1.00 0.00
+ATOM 18 H GLY 9 -0.373 -0.645 0.667 1.00 0.00
+ATOM 19 NE1 GLY 9 0.000 0.000 0.000 1.00 0.00
+ATOM 20 HE1 GLY 9 0.577 0.577 0.577 1.00 0.00
+TER 21 GLY
+CONECT 1 2
+CONECT 2 1
+CONECT 3 4
+CONECT 4 3
+CONECT 5 6
+CONECT 6 5
+CONECT 7 8
+CONECT 8 7
+CONECT 9 10
+CONECT 10 9
+CONECT 11 12
+CONECT 12 11
+CONECT 13 14
+CONECT 14 13
+CONECT 15 16
+CONECT 16 15
+CONECT 17 18
+CONECT 18 17
+CONECT 19 20
+CONECT 20 19
END
r26597 - in /trunk/test_suite/shared_data/model_free/sphere: create_sphere.py sphere.pdb