From 063ccd95873ec0d81d39d372ea9cefff25decffb Mon Sep 17 00:00:00 2001
From: Kurt Glaesmann <kurt.glaesemann@pnnl.gov>
Date: Thu, 2 Jul 2009 20:26:51 +0000
Subject: [PATCH] Add support for PDB files that left justify atomic type

---
 src/prepar/ChangeLog    |  3 ++-
 src/prepar/pre_pdbseq.F | 24 ++++++++++++++++++++++++
 src/prepar/pre_rdpdb.F  | 24 ++++++++++++++++++++++++
 3 files changed, 50 insertions(+), 1 deletion(-)

diff --git a/src/prepar/ChangeLog b/src/prepar/ChangeLog
index b331610cd9..8a187489cf 100644
--- a/src/prepar/ChangeLog
+++ b/src/prepar/ChangeLog
@@ -117,4 +117,5 @@ Jan 14 1999	 Add zeros for nsp,npmf,npmfi
 Jan 29 1999	 Add MODEL option
 		 Add input LINK command
 		 Add CHAIN option
-		 Change in topology format
\ No newline at end of file
+		 Change in topology format
+Jul  2 2009      Add support for PDB files that left justify atomic type
diff --git a/src/prepar/pre_pdbseq.F b/src/prepar/pre_pdbseq.F
index 49e60f3b8d..d4f22e1799 100644
--- a/src/prepar/pre_pdbseq.F
+++ b/src/prepar/pre_pdbseq.F
@@ -186,6 +186,18 @@ c      if(nchain.eq.1) cseq(1,iseq)(4:5)='_N'
       latm(2,iatm)=pre_atnum(card(77:78))
       if(latm(2,iatm).eq.0) latm(2,iatm)=pre_atnum(card(13:14))
       catm(1,iatm)(1:4)=card(13:16)
+c     shift it to get justifcation correct
+      if (catm(1,iatm)(2:2) .eq. ' ') then
+        catm(1,iatm)(2:2) = catm(1,iatm)(3:3)
+        catm(1,iatm)(3:3) = catm(1,iatm)(4:4)
+        catm(1,iatm)(4:4) = ' '
+      endif
+      if (catm(1,iatm)(2:2) .eq. ' ') then
+        catm(1,iatm)(2:2) = catm(1,iatm)(3:3)
+        catm(1,iatm)(3:3) = catm(1,iatm)(4:4)
+        catm(1,iatm)(4:4) = ' '
+      endif
+c
       read(card(31:54),'(3f8.3)') (xatm(j,iatm),j=1,3)
       endif
       goto 1
@@ -230,6 +242,18 @@ c      if(nchain.eq.1) cseq(1,iseq)(4:5)='_N'
       latm(2,iatm)=pre_atnum(card(77:78))
       if(latm(2,iatm).eq.0) latm(2,iatm)=pre_atnum(card(13:14))
       catm(1,iatm)(1:4)=card(13:16)
+c     shift it to get justifcation correct
+      if (catm(1,iatm)(2:2) .eq. ' ') then
+        catm(1,iatm)(2:2) = catm(1,iatm)(3:3)
+        catm(1,iatm)(3:3) = catm(1,iatm)(4:4)
+        catm(1,iatm)(4:4) = ' '
+      endif
+      if (catm(1,iatm)(2:2) .eq. ' ') then
+        catm(1,iatm)(2:2) = catm(1,iatm)(3:3)
+        catm(1,iatm)(3:3) = catm(1,iatm)(4:4)
+        catm(1,iatm)(4:4) = ' '
+      endif
+c
       read(card(31:54),'(3f8.3)') (xatm(j,iatm),j=1,3)
       endif
       goto 1
diff --git a/src/prepar/pre_rdpdb.F b/src/prepar/pre_rdpdb.F
index be41cd8ffb..9af2b3f9d6 100644
--- a/src/prepar/pre_rdpdb.F
+++ b/src/prepar/pre_rdpdb.F
@@ -149,6 +149,18 @@ c
       endif
  1002 format(a6,6x,a4,a1,a3,1x,a1,i4,4x,3f8.3)
  2002 format(a6,6x,a4,a1,a3,i6,4x,3f8.3)
+c     shift it to get justifcation correct
+      if (nama(2:2) .eq. ' ') then
+        nama(2:2) = nama(3:3)
+        nama(3:3) = nama(4:4)
+        nama(4:4) = ' '
+      endif
+      if (nama(2:2) .eq. ' ') then
+        nama(2:2) = nama(3:3)
+        nama(3:3) = nama(4:4)
+        nama(4:4) = ' '
+      endif
+c
       if(util_print('where',print_debug)) then
       if(lrgpdb.eq.0) then
       write(lfnout,1002) hdr,nama,alocal,namr,achain,num,x,y,z
@@ -156,6 +168,18 @@ c
       write(lfnout,2002) hdr,nama,alocal,namr,num,x,y,z
       endif
       endif
+c     shift it to get justifcation correct
+      if (nama(2:2) .eq. ' ') then
+        nama(2:2) = nama(3:3)
+        nama(3:3) = nama(4:4)
+        nama(4:4) = ' '
+      endif
+      if (nama(2:2) .eq. ' ') then
+        nama(2:2) = nama(3:3)
+        nama(3:3) = nama(4:4)
+        nama(4:4) = ' '
+      endif
+c
       if(alocal.ne.' '.and.alocal.ne.altloc.and.altloc.ne.'*') goto 100
       if(achain.ne.' '.and.achain.ne.chain.and.chain.ne.'*') goto 100
 c