From 656badb8b0f18299175c4f57602e9ea9bd76f79b Mon Sep 17 00:00:00 2001
From: nzimmer3 <nathan.zimmerberg@mpibpc.mpg.de>
Date: Fri, 11 Aug 2017 16:36:17 -0400
Subject: [PATCH 1/3] Typo fix for assigning secondary structure

The secondary structure (ss) assignment had a typo that caused problems when the ss was assigned to multi chain models with different chain lengths. When chain.set_ss is run it must either have a input of length one or input length greater than or equal to the length of the chain.
---
 MAIN.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/MAIN.py b/MAIN.py
index e413178..9f40b4c 100644
--- a/MAIN.py
+++ b/MAIN.py
@@ -136,9 +136,10 @@ def main(options):
             # Now set the secondary structure for each of the chains
             sstmp = ss
             for chain in chains:
+                assert len(chain) <= len(sstmp) or len(sstmp) == 1, 'ss structure is not the right length'
                 ln = min(len(sstmp), len(chain))
                 chain.set_ss(sstmp[:ln])
-                sstmp = ss[:ln]
+                sstmp = sstmp[ln:]
         else:
             if options["-dssp"]:
                 method, executable = "dssp", options["-dssp"].value

From 5366f292eb459d8258e32ffd9e1761cb5b8d4989 Mon Sep 17 00:00:00 2001
From: nzimmer3 <nathan.zimmerberg@mpibpc.mpg.de>
Date: Fri, 11 Aug 2017 17:19:57 -0400
Subject: [PATCH 2/3] Two new tests for chains of different lengths

Two new tests on the snare complex 3IPD to justifiy the change to MAIN.py.

The chain22ss test outputs a pdb file that is missing a few atoms. With the fix it has the correct number of atoms.
---
 test/V2.7/chains22ss/.DS_Store | Bin 0 -> 6148 bytes
 test/test.sh                   |  22 ++++++++++++++++++++++
 2 files changed, 22 insertions(+)
 create mode 100644 test/V2.7/chains22ss/.DS_Store

diff --git a/test/V2.7/chains22ss/.DS_Store b/test/V2.7/chains22ss/.DS_Store
new file mode 100644
index 0000000000000000000000000000000000000000..4300f313d80f1442538b8aff403740f024caf0c2
GIT binary patch
literal 6148
zcmeHKOHRWu5PdFLL=>bhS!T%wB*X<mNekT}*i+Pxs!A2DP!Zc4gF|ru4!}Lio3T|=
znxrcbLNn6%`7<weo*PdMz_p)8XFv-;Oc#vyS(KQJi*H#Y^c)bKKI0S%j4<fU=EJRM
z>o5gOfxo7Je7iBu(ZdZg6u#fVY(C%^4+eKjJYK2k@|)}UK8Bc-v(Ob5-K|y?tR?1H
z$XW3<7v6+bnCp=1dScuXV@&agJ}x-ll<jX!_r8<aE@w9GcQP+4m>)ZtqG`!$Rh`$`
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z!+ARUlMt5%%sqNKT)2F=FtZCc6sNQE`H6<Zr5>#`1x$fW1@?TiCHcQoegEGiS<4hK
z1^$%+F3Rq*HeV^^)~%P5T$|7z=wcF=dsGUGkdCz?srZPl#<4^y#57>;kv%l~BcL)^
JVG8`J0-xzgxS{|6

literal 0
HcmV?d00001

diff --git a/test/test.sh b/test/test.sh
index a3c07b6..abf8f3f 100755
--- a/test/test.sh
+++ b/test/test.sh
@@ -109,6 +109,28 @@ diff *_cg.pdb ../../${DIFF}/${block}/*_cg.pdb >> ../${block}.diff
 diff *_cg.top ../../${DIFF}/${block}/*_cg.top >> ../${block}.diff
 cd ..
 
+# Test the seperate writing of chains of different lengths, position restraints, neutral termini. Use Mscl.
+block=chains22difflen
+echo '***************'${block}'*****************'
+mkdir $block
+cd $block
+pdbgett 3IPD
+$SCRIPT -f 3IPD.pdb -o 3IPD_cg.top -x 3IPD_cg.pdb -sep -nt -p All -pf 500 -dssp $DSSP -ff martini22
+diff *_cg.pdb ../../${DIFF}/${block}/*_cg.pdb >> ../${block}.diff
+diff *_cg.top ../../${DIFF}/${block}/*_cg.top >> ../${block}.diff
+cd ..
+
+# Multi chain and giving secondary sturcture as string.
+block=chains22ss
+echo '***************'${block}'*****************'
+mkdir $block
+cd $block
+pdbgett 3IPD
+$SCRIPT -f 3IPD.pdb -o 3IPD_cg.top -x 3IPD_cg.pdb -sep -ss HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC -ff martini22
+diff *_cg.pdb ../../${DIFF}/${block}/*_cg.pdb >> ../${block}.diff
+diff *_cg.top ../../${DIFF}/${block}/*_cg.top >> ../${block}.diff
+cd ..
+
 # Test cysteine bridge (between cys 9 and cys 164), naming protein and use dihedrals for extended regions. Use mutated lysozyme.
 block=Sbonds21
 echo '***************'${block}'*****************'

From 23aaabe8dff7d7d6fc437ab9e6c40359d809594f Mon Sep 17 00:00:00 2001
From: nzimmer3 <nathan.zimmerberg@mpibpc.mpg.de>
Date: Fri, 11 Aug 2017 17:25:19 -0400
Subject: [PATCH 3/3] Deleted extra folder

---
 test/V2.7/chains22ss/.DS_Store | Bin 6148 -> 0 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 test/V2.7/chains22ss/.DS_Store

diff --git a/test/V2.7/chains22ss/.DS_Store b/test/V2.7/chains22ss/.DS_Store
deleted file mode 100644
index 4300f313d80f1442538b8aff403740f024caf0c2..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 6148
zcmeHKOHRWu5PdFLL=>bhS!T%wB*X<mNekT}*i+Pxs!A2DP!Zc4gF|ru4!}Lio3T|=
znxrcbLNn6%`7<weo*PdMz_p)8XFv-;Oc#vyS(KQJi*H#Y^c)bKKI0S%j4<fU=EJRM
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JVG8`J0-xzgxS{|6