Minor cleanup and fixes.

clauswilke · Feb 17, 2014 · 9f6d25f · 9f6d25f
1 parent 5896357
commit 9f6d25f
Show file tree

Hide file tree

Showing 13 changed files with 12 additions and 21,605 deletions.
diff --git a/PDBs/1aq7_clean.pdb b/PDBs/1aq7_clean.pdb
diff --git a/PDBs/1gfl_clean.pdb b/PDBs/1gfl_clean.pdb
diff --git a/PDBs/1nbw_clean.pdb b/PDBs/1nbw_clean.pdb
diff --git a/PDBs/1vca_clean.pdb b/PDBs/1vca_clean.pdb
diff --git a/PDBs/2o6r_clean.pdb b/PDBs/2o6r_clean.pdb
diff --git a/PDBs/2r83_clean.pdb b/PDBs/2r83_clean.pdb
diff --git a/PDBs/3cap_clean.pdb b/PDBs/3cap_clean.pdb
diff --git a/PDBs/3cuq_clean.pdb b/PDBs/3cuq_clean.pdb
diff --git a/PDBs/3vni_clean.pdb b/PDBs/3vni_clean.pdb
diff --git a/PDBs/7tim_clean.pdb b/PDBs/7tim_clean.pdb
diff --git a/PeptideBuilder.py b/PeptideBuilder.py
@@ -225,7 +225,7 @@ def makeIle(segID, N, CA, C, O, geo):
     CB_CG1_length=geo.CB_CG1_length
     CA_CB_CG1_angle=geo.CA_CB_CG1_angle
     N_CA_CB_CG1_diangle=geo.N_CA_CB_CG1_diangle 
-        
+
     CB_CG2_length=geo.CB_CG2_length
     CA_CB_CG2_angle=geo.CA_CB_CG2_angle
     N_CA_CB_CG2_diangle= geo.N_CA_CB_CG2_diangle

diff --git a/README.txt b/README.txt
@@ -1,6 +1,10 @@
 This is the PeptideBuilder library, written by Matthew Z. Tien,
 Dariya K. Sydykova, Austin G. Meyer, and Claus O. Wilke.
 
+Reference:
+M. Z. Tien, D. K. Sydykova, A. G. Meyer, C. O. Wilke (2013). PeptideBuilder:
+A simple Python library to generate model peptides. PeerJ 1:e80.
+
 The software is provided to you under the GNU General Public
 License, version 2.0 or later. The most up-to-date version of this software is
 available at https://github.com/mtien/PeptideBuilder.
@@ -18,5 +22,11 @@ a unix machine unix, the shell script 'runUnitTests.sh' will do that for you.
 If the shell script doesn't find any differences (prints out only empty lines)
 then everything is working correctly.
 
+**Note:** Apparently some versions of Biopython add a line containing 'END' to
+end of created PDB files, and this breaks the unit tests. If all your unit tests
+fail, check whether that's the reason why. Simply check manually whether the
+files in folder 'unitTests.expected' look like the files generated by the script
+'runUnitTests.sh'.
+
 The script 'evaluation.py' reproduces the results presented in Table 1 of the
 PeptideBuilder manuscript.
diff --git a/runUnitTests.sh b/runUnitTests.sh
@@ -1,4 +1,4 @@
-#!/usr/bin/sh
+#!/bin/sh
 
 # remove results from prior tests
 rm -f test?.*