science/vmd: unbreak build

- Remove patches that are not required with the new sources for stride
 - Add stride license test

science/vmd/files/patch-lib_stride_Makefile

@@ -0,0 +1,26 @@
+--- lib/stride/Makefile.orig	2003-04-08 12:03:14 UTC
++++ lib/stride/Makefile
+@@ -1,12 +1,12 @@
+ #FLAGS = -lm -L/usr/pub/lib -lefence -o
+ #CC = cc -O2 -fullwarn -TENV:large_GOT
+ #CC = cc -g -Wall
+-CC = gcc -O2  # at least for SunOS
++#CC = gcc -O2  # at least for SunOS
+ #CC = cc -g
+ 
+ #CC = cc -O2 -fullwarn
+ 
+-#CC = cc -O2
++CC = cc ${CFLAGS} -O2
+ FLAGS = -lm  -o
+ 
+ SOURCE = stride.c splitstr.c rdpdb.c initchn.c geometry.c thr2one.c one2thr.c filename.c tolostr.c strutil.c place_h.c hbenergy.c memory.c helix.c sheet.c rdmap.c phipsi.c command.c molscr.c die.c hydrbond.c mergepat.c fillasn.c escape.c p_jrnl.c p_rem.c p_atom.c p_helix.c p_sheet.c p_turn.c p_ssbond.c p_expdta.c p_model.c p_compnd.c report.c nsc.c area.c ssbond.c chk_res.c chk_atom.c turn.c pdbasn.c dssp.c outseq.c chkchain.c elem.c measure.c asngener.c p_endmdl.c stred.c contact_order.c contact_map.c
+@@ -20,7 +20,7 @@ BINDIR = .
+ 
+ 
+ stride : $(OBJECT)
+-	$(CC) $(OBJECT) $(FLAGS)  $(BINDIR)/stride${ARCH}
++	$(CC) $(OBJECT) $(FLAGS)  $(BINDIR)/stride
+ 
+ $(OBJECT) : stride.h protot.h
+ 

science/vmd/files/patch-plugins__hesstrans__Makefile

@@ -1,11 +0,0 @@
---- ../plugins/hesstrans/Makefile.orig	2012-03-19 19:58:44.000000000 -0400
-+++ ../plugins/hesstrans/Makefile	2012-03-19 19:59:01.000000000 -0400
-@@ -12,7 +12,7 @@
- ARCHDIR=${COMPILEDIR}/lib_${ARCH}/tcl/hesstrans$(VERSION)
- SRCDIR=src
- INCDIR=-Isrc
--CXXFLAGS = -g $(CXXFLAGS)
-+CXXFLAGS += -g
- VPATH = src ${ARCHDIR}
- 
- ##

science/vmd/files/patch-stride.c

@@ -1,11 +0,0 @@
---- lib/stride/stride.c-xxx	Fri Dec 17 18:18:42 2004
-+++ lib/stride/stride.c	Fri Dec 17 18:19:21 2004
-@@ -93,7 +93,7 @@
-   for( i=0; i<NHBond; i++ ) free(HBond[i]);
-   free(Cmd);
- 
--  return(SUCCESS);
-+  return(0);
- }
- 
- void ProcessStrideOptions(char **List, int ListLength, COMMAND *Cmd)

science/vmd/files/patch-stride.h

@@ -1,11 +0,0 @@
---- lib/stride/stride.h-xxx	Fri Dec 17 18:18:07 2004
-+++ lib/stride/stride.h	Fri Dec 17 18:18:30 2004
-@@ -40,7 +40,7 @@
- #define MAX_BOND                  100
- #define MAX_ASSIGN                300
- #define MAX_INFO                  100
--#define MAX_AT_IN_RES             50
-+#define MAX_AT_IN_RES             75
- #define MAX_AT_IN_HETERORES       200
- #define MAXRESDNR                 6
- #define MAXRESACC                 6 

science/vmd/files/patch-stride_Makefile

@@ -1,10 +0,0 @@
---- lib/stride/Makefile-orig	Fri Mar 25 17:51:11 2005
-+++ lib/stride/Makefile	Fri Mar 25 17:49:22 2005
-@@ -1,6 +1,6 @@
- #CC = gcc -O2  # ->> for DJGPP compiler under DOS and for SunOS; also suitable for other machines
- 
--CC = cc -O2
-+CC = cc ${CFLAGS} -O2
- FLAGS = -lm  -o
- 
- SOURCE = stride.c splitstr.c rdpdb.c initchn.c geometry.c thr2one.c one2thr.c filename.c tolostr.c strutil.c place_h.c hbenergy.c memory.c helix.c sheet.c rdmap.c phipsi.c command.c molscr.c die.c hydrbond.c mergepat.c fillasn.c escape.c p_jrnl.c p_rem.c p_atom.c p_helix.c p_sheet.c p_turn.c p_ssbond.c p_expdta.c p_model.c p_compnd.c report.c nsc.c area.c ssbond.c chk_res.c chk_atom.c turn.c pdbasn.c dssp.c outseq.c chkchain.c elem.c measure.c asngener.c p_endmdl.c stred.c

science/vmd/files/stride.txt

@@ -0,0 +1,24 @@
+All rights reserved, whether the whole  or  part  of  the  program  is
+concerned.  Permission  to use, copy, and modify this software and its
+documentation is granted for academic use, provided that:
+
+  i.  this copyright notice appears in all copies of the software  and
+      related documentation;
+
+ ii.  the reference given below (Frishman and  Argos,  1995)  must  be
+      cited  in any publication of scientific results based in part or
+      completely on the use of the program;
+
+iii.  bugs will be reported to the authors.
+
+The use of the  software  in  commercial  activities  is  not  allowed
+without a prior written commercial license agreement.
+
+WARNING: STRIDE is provided "as-is" and without warranty of any kind,
+express,  implied  or  otherwise,  including  without  limitation  any
+warranty of merchantability or fitness for a particular purpose. In no
+event will the authors be liable for any special, incidental, indirect
+or consequential damages  of  any  kind,  or  any  damages  whatsoever
+resulting  from loss of data or profits, whether or not advised of the
+possibility of damage, and on any theory of liability, arising out  of
+or in connection with the use or performance of this software.