MAID does automatic fitting of protein X-ray crystallography electron density maps. It can correctly build about 60% of alpha carbons on medium-resolution maps and about 80% on high-resolution maps.

Package-Manager: portage-2.0.53

7 files changed, 1080 insertions, 0 deletions

diff --git a/sci-chemistry/maid/ChangeLog b/sci-chemistry/maid/ChangeLog
new file mode 100644
index 000000000000..8ffeed693bec
--- /dev/null
+++ b/sci-chemistry/maid/ChangeLog
@@ -0,0 +1,13 @@
+# ChangeLog for sci-chemistry/maid
+# Copyright 1999-2005 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/maid/ChangeLog,v 1.1 2005/12/15 20:33:37 spyderous Exp $
+
+*maid-20011112 (15 Dec 2005)
+
+  15 Dec 2005; Donnie Berkholz <spyderous@gentoo.org>;
+  +files/fix-compilation.patch, +files/fix-warnings.patch, +metadata.xml,
+  +maid-20011112.ebuild:
+  MAID does automatic fitting of protein X-ray crystallography electron
+  density maps. It can correctly build about 60% of alpha carbons on
+  medium-resolution maps and about 80% on high-resolution maps.
+
diff --git a/sci-chemistry/maid/Manifest b/sci-chemistry/maid/Manifest
new file mode 100644
index 000000000000..2369c2aa1ad8
--- /dev/null
+++ b/sci-chemistry/maid/Manifest
@@ -0,0 +1,6 @@
+MD5 bdf0475dbae5eb052a07b5867eaf848b ChangeLog 602
+MD5 ff5b0305adfcf24af5bdcabee62ebeb8 files/digest-maid-20011112 69
+MD5 d0c424b73bb547a1277338c40972d7ad files/fix-compilation.patch 22977
+MD5 bcc6fdf88e85ccb7f3a06ef3dd9011b7 files/fix-warnings.patch 17141
+MD5 1689aa68a1cafc5d932d148a1722a14a maid-20011112.ebuild 1366
+MD5 af1bfbb0777267a03e889b08173f2757 metadata.xml 248
diff --git a/sci-chemistry/maid/files/digest-maid-20011112 b/sci-chemistry/maid/files/digest-maid-20011112
new file mode 100644
index 000000000000..3df05a9dc28a
--- /dev/null
+++ b/sci-chemistry/maid/files/digest-maid-20011112
@@ -0,0 +1 @@
+MD5 23066037ad06f256d26e61a69d91c84a maid_unix_12nov01.tar.gz 480609
diff --git a/sci-chemistry/maid/files/fix-compilation.patch b/sci-chemistry/maid/files/fix-compilation.patch
new file mode 100644
index 000000000000..da280e4436f5
--- /dev/null
+++ b/sci-chemistry/maid/files/fix-compilation.patch
@@ -0,0 +1,570 @@
+diff -ur glmaid_dist.orig/drawwindow.c++ glmaid_dist/drawwindow.c++
+--- glmaid_dist.orig/drawwindow.c++	2001-11-12 05:35:50.000000000 -0800
++++ glmaid_dist/drawwindow.c++	2005-12-15 08:09:55.000000000 -0800
+@@ -659,7 +659,7 @@
+         { "OK",     fuse_ok_pushed,    NULL         },
+         { "PICK AGAIN",    pickagain_pushed ,NULL         },
+         { "QUIT", fuse_cancel_pushed,  NULL          },
+-        { "Help",   help,          "Help Button" },
++        { "Help",   help,          (void *) "Help Button" },
+     };
+     /* Create a TemplateDialog that will contain the control area
+      * and the action area buttons for the dialog
+@@ -737,7 +737,7 @@
+         { "OK",     assign_ok_pushed,     NULL          },
+         { "Clear",  clear_pushed,  NULL          },
+         { "Cancel", assignclose_dialog,  NULL          },
+-        { "Help",   help,          "Help Button" },
++        { "Help",   help,          (void *) "Help Button" },
+     };
+     /* Create a TemplateDialog that will contain the control area
+      * and the action area buttons for the dialog
+@@ -805,7 +805,7 @@
+         { "OK",     remove_ok_pushed,     NULL          },
+         { "Clear",  clear_pushed,  NULL          },
+         { "Cancel", removecancel_dialog,  NULL          },
+-        { "Help",   help,          "Help Button" },
++        { "Help",   help,          (void *) "Help Button" },
+     };
+     /* Create a TemplateDialog that will contain the control area
+      * and the action area buttons for the dialog
+diff -ur glmaid_dist.orig/fit.c++ glmaid_dist/fit.c++
+--- glmaid_dist.orig/fit.c++	2001-11-12 05:35:50.000000000 -0800
++++ glmaid_dist/fit.c++	2005-12-15 08:15:43.000000000 -0800
+@@ -305,7 +305,7 @@
+         { "OK",     inputfit_ok_pushed,     NULL          },
+         { "Clear",  clear_pushed,  NULL          },
+         { "Cancel", close_dialog,  NULL          },
+-        { "Help",   help,          "Help Button" },
++        { "Help",   help,          (void *) "Help Button" },
+     };
+     /* Create a TemplateDialog that will contain the control area
+      * and the action area buttons for the dialog
+@@ -430,7 +430,7 @@
+       fit[ii].val2= -1;
+    }
+    savefit(); //save the val2 segment unassignments
+-#endif;          
++#endif
+ #if 0
+      strcpy(ranknum,"rank1fit");
+      readset("set1",fitset);
+@@ -710,16 +710,16 @@
+    buildmenu=XmVaCreateSimplePulldownMenu (menubar, "build_menu", 3, build_cb,
+         XmVaPUSHBUTTON,traceonoff,'T', NULL, NULL,  // button_0
+         XmVaPUSHBUTTON,extend,'T', NULL, NULL,  // button_1
+-        XmVaPUSHBUTTON,fusepicks,'FP', NULL, NULL,  // button_2
++        XmVaPUSHBUTTON,fusepicks,"FP", NULL, NULL,  // button_2
+         XmVaPUSHBUTTON,recallfit,'F', NULL, NULL,  // button_3
+         XmVaPUSHBUTTON,recallbackupfit,'F', NULL, NULL,  // button_4
+-        XmVaCHECKBUTTON,drawfit,'DF', NULL, NULL,  // button_5
+-        XmVaCHECKBUTTON,pickfit,'DF', NULL, NULL,  // button_6
+-        XmVaPUSHBUTTON,inputfit,'DF', NULL, NULL,  // button_7
+-        XmVaPUSHBUTTON,drawrankfit,'DR', NULL, NULL,  // button_8
+-        XmVaPUSHBUTTON,drawrankset,'DR', NULL, NULL,  // button_9
+-        XmVaPUSHBUTTON,fittopdb,'DR', NULL, NULL,  // button_10
+-        XmVaPUSHBUTTON,deletefit,'DR', NULL, NULL,  // button_11
++        XmVaCHECKBUTTON,drawfit,"DF", NULL, NULL,  // button_5
++        XmVaCHECKBUTTON,pickfit,"DF", NULL, NULL,  // button_6
++        XmVaPUSHBUTTON,inputfit,"DF", NULL, NULL,  // button_7
++        XmVaPUSHBUTTON,drawrankfit,"DR", NULL, NULL,  // button_8
++        XmVaPUSHBUTTON,drawrankset,"DR", NULL, NULL,  // button_9
++        XmVaPUSHBUTTON,fittopdb,"DR", NULL, NULL,  // button_10
++        XmVaPUSHBUTTON,deletefit,"DR", NULL, NULL,  // button_11
+         NULL);
+ #if 1
+     XmStringFree (traceonoff);   
+@@ -774,12 +774,12 @@
+         XmVaPUSHBUTTON,tordyncen,'M', NULL, NULL,  // button_3
+         XmVaCASCADEBUTTON,addcresidue,'W',   // button_4
+         XmVaCASCADEBUTTON,addnresidue,'W',   // button_5
+-        XmVaPUSHBUTTON,remcresidue,'RC', NULL, NULL,  // button_6
+-        XmVaPUSHBUTTON,remnresidue,'RN', NULL, NULL,  // button_7
+-        XmVaPUSHBUTTON,extendpickcterm,'RN', NULL, NULL,  // button_8
+-        XmVaCHECKBUTTON,drawgeo,'DF', NULL, NULL,  // button_9
+-        XmVaPUSHBUTTON,savepickfit,'DF', NULL, NULL,  // button_10
+-        XmVaPUSHBUTTON,drawrotomer,'DR', NULL, NULL,  // button_11
++        XmVaPUSHBUTTON,remcresidue,"RC", NULL, NULL,  // button_6
++        XmVaPUSHBUTTON,remnresidue,"RN", NULL, NULL,  // button_7
++        XmVaPUSHBUTTON,extendpickcterm,"RN", NULL, NULL,  // button_8
++        XmVaCHECKBUTTON,drawgeo,"DF", NULL, NULL,  // button_9
++        XmVaPUSHBUTTON,savepickfit,"DF", NULL, NULL,  // button_10
++        XmVaPUSHBUTTON,drawrotomer,"DR", NULL, NULL,  // button_11
+         NULL);
+ 
+   addcpullright = XmVaCreateSimplePulldownMenu (fitmenu,
+diff -ur glmaid_dist.orig/global.h glmaid_dist/global.h
+--- glmaid_dist.orig/global.h	2001-11-12 05:35:51.000000000 -0800
++++ glmaid_dist/global.h	2005-12-15 08:09:55.000000000 -0800
+@@ -6,7 +6,7 @@
+ #include  <assert.h>
+ #include <stdlib.h>
+ #include <stdio.h>
+-//#include <iostream.h>
++//#include <iostream>
+ //#include <iomanip.h>
+ #include <time.h>
+ #include <math.h>
+diff -ur glmaid_dist.orig/mainscreen.c++ glmaid_dist/mainscreen.c++
+--- glmaid_dist.orig/mainscreen.c++	2001-11-12 05:35:49.000000000 -0800
++++ glmaid_dist/mainscreen.c++	2005-12-15 08:09:55.000000000 -0800
+@@ -1,7 +1,7 @@
+ // mainscreen.c++  - Screen version  (most general) of maid
+ // the motif organizatrion was originally adapted from program levitt/motifman/ch04/dynapix.c
+ 
+-#include <CC/iostream.h>
++#include <iostream>
+ #include "Xgl.h"
+ #include "drawwindow.h"  // also calls global.h
+ #include "trace.h"
+@@ -53,7 +53,7 @@
+ int splitscreen =1; // if = 1 then use standard splitscreen stereo, 
+ //int splitscreen =0; // = 0 use wholescreen - also set geo.linewidth = 4 below
+ 
+-void main(int argc, char *argv[]) {
++int main(int argc, char *argv[]) {
+    
+     Arg resources[20];	
+     int n;
+@@ -209,5 +209,7 @@
+ #endif
+ #endif
+     XtAppMainLoop(sc.appctx);
++
++	return 0;
+ }
+ 
+diff -ur glmaid_dist.orig/makefile_graphics glmaid_dist/makefile_graphics
+--- glmaid_dist.orig/makefile_graphics	2001-11-12 05:35:52.000000000 -0800
++++ glmaid_dist/makefile_graphics	2005-12-15 08:16:00.000000000 -0800
+@@ -36,109 +36,111 @@
+ COMBINE = combine.h
+ SELENOMET = selenomet.h
+ 
+-CC = CC -c -O
++Cgeneric = gcc
++Clink = $(Cgeneric)
++Copt = $(Cgeneric) -c -O
+ 
+ 
+ auto:  $(OBJ) 
+-	CC $(OBJ) -lGLw -lGL -lGLU -lXm -lXt -lX11 -lm  -o maid
++	$(Clink) $(OBJ) -lGLw -lGL -lGLU -lXm -lXt -lX11 -lm  -o maid
+ 
+ mainscreen.o: mainscreen.c++  $(DRAWWIND) $(MATH)  $(CONTROL)  $(PEPTIDE) $(TORDYN) $(TRACE) $(ASSIGNSEQ) $(EXTENDFIT) $(EDITBONES)
+-	$(CC) mainscreen.c++
++	$(Copt) mainscreen.c++
+ 
+ symmate.o:  symmate.c++   $(GLOBAL) $(PEPTIDE) $(TRACE) $(MATH) $(PDBTOLEV) $(SYMMATE) $(COMBINE)
+-	$(CC) symmate.c++
++	$(Copt) symmate.c++
+ 
+ selenomet.o:  selenomet.c++   $(GLOBAL) $(MATH) $(SELENOMET)
+-	$(CC) selenomet.c++
++	$(Copt) selenomet.c++
+ 
+ combine.o:  combine.c++   $(GLOBAL) $(PEPTIDE) $(TRACE) $(MATH) $(COMBINE) $(SYMMATE) $(FITTOPDB)
+-	$(CC) combine.c++
++	$(Copt) combine.c++
+ 
+ control.o:  control.c++   $(GLOBAL) $(PEPTIDE) $(CONTROL) $(TORDYN) $(ASSIGNSEQ) $(PDBTOLEV) $(TRACE)  $(RANKSIDE) $(BONE)	
+-	$(CC) control.c++
++	$(Copt) control.c++
+ 
+ extend2.o:  extend2.c++  $(MATH) $(TRACE)  $(GLOBAL) $(EXTENDFIT) $(PEPTIDE)  $(BONE) $(EXTEND2) $(TORDYN) 	
+-	$(CC) extend2.c++
++	$(Copt) extend2.c++
+ 
+ checkfit.o:  checkfit.c++  $(MATH) $(TRACE)  $(GLOBAL) $(PEPTIDE) $(TORDYN) $(CHECKFIT) $(EDITBONES) $(BONE)
+-	$(CC) checkfit.c++
++	$(Copt) checkfit.c++
+ 
+ refine.o:  refine.c++  $(MATH) $(TRACE)  $(GLOBAL) $(REFINE) $(PEPTIDE) $(TORDYN)
+-	$(CC) refine.c++
++	$(Copt) refine.c++
+ 
+ rankside.o:  rankside.c++  $(PDBTOLEV) $(MATH) $(TRACE) $(RANKSIDE) $(GLOBAL) $(TORDYN) $(MODEL) $(PEPTIDE) $(EDITBONES) 
+-	$(CC) rankside.c++
++	$(Copt) rankside.c++
+ 
+ extendfit.o: extendfit.c++  $(DRAWWIND) $(SYMMATE) $(REFINE) $(MATH) $(BONE) $(PEPTIDE) $(TRACE) $(TORDYN) $(EXTENDFIT) $(FITTOPDB) $(EDITBONES) $(RANKSIDE) $(ASSIGNSEQ) 
+-	$(CC) extendfit.c++
++	$(Copt) extendfit.c++
+ 
+ editbones.o: editbones.c++  $(EDITBONES) $(DRAWWIND) $(MATH) $(BONE) $(PEPTIDE) $(TRACE) $(TORDYN) $(EXTENDFIT)
+-	$(CC) editbones.c++
++	$(Copt) editbones.c++
+ 
+ fittopdb.o: fittopdb.c++   $(DRAWWIND) $(PEPTIDE) $(FITTOPDB) $(PDBTOLEV)
+-	$(CC) fittopdb.c++
++	$(Copt) fittopdb.c++
+ 
+ tordyn.o: tordyn.c++  $(TORDYN)  $(DRAWWIND) $(PEPTIDE) $(MENU) $(TRACE) $(ASSIGNSEQ)  $(RUNTORDYN) $(EDITBONES) $(EXTENDFIT) $(REFINE)
+-	$(CC) tordyn.c++
++	$(Copt) tordyn.c++
+ 
+ runtordynnew.o: runtordynnew.c++   $(TRACE) $(TORDYN) $(RUNTORDYN) $(PEPTIDE) $(EDITBONES) $(REFINE) 
+-	$(CC) runtordynnew.c++
++	$(Copt) runtordynnew.c++
+ 
+ assignseq.o: assignseq.c++   $(PDBTOLEV) $(TRACE) $(ASSIGNSEQ) $(GLOBAL) $(TORDYN) $(MODEL) $(PEPTIDE) $(RANKSIDE)  $(EDITBONES) $(SYMMATE)
+-	$(CC) assignseq.c++
++	$(Copt) assignseq.c++
+ 
+ peptide.o: peptide.c++  $(DRAWWIND) $(MATH) $(PEPTIDE)
+-	$(CC) peptide.c++
++	$(Copt) peptide.c++
+ 
+ initialize.o: initialize.c++ $(DRAWWIND) $(PEPTIDE) $(TORDYN) $(BONE) $(TRACE)
+-	$(CC) initialize.c++
++	$(Copt) initialize.c++
+ 
+ bone.o: bone.c++  $(DRAWWIND) $(MATH) $(BONE) 
+-	$(CC) bone.c++
++	$(Copt) bone.c++
+ 
+ trace.o: trace.c++   $(DRAWWIND) $(MATH) $(BONE) $(PEPTIDE) $(TRACE) $(TORDYN) $(EXTENDFIT)  $(CHECKFIT) $(FITTOPDB)
+-	$(CC) trace.c++
++	$(Copt) trace.c++
+ 
+ pdbtolev.o: pdbtolev.c++  $(INITIALIZE) $(PDBTOLEV) $(GLOBAL) $(MENU) $(DRAWWIND) $(PEPTIDE) $(FITTOPDB)
+-	$(CC) pdbtolev.c++
++	$(Copt) pdbtolev.c++
+ 
+ math.o: math.c++  $(MATH) $(PEPTIDE) $(TRACE)
+-	$(CC) math.c++
++	$(Copt) math.c++
+ 
+ global.o: global.c++  $(GLOBAL)
+-	$(CC) global.c++
++	$(Copt) global.c++
+ 
+ drawwindow.o: drawwindow.c++  $(MENU) $(DRAWWIND)  $(CUBE) $(PEPTIDE)  $(ASSIGNSEQ) $(FIT) $(EXTENDFIT)  $(EDITBONES)
+-	$(CC) drawwindow.c++
++	$(Copt) drawwindow.c++
+ 
+ 
+ mapmenu.o: mapmenu.c++ $(MAPMENU) $(DRAWWIND) $(MENU) $(CORE) $(COMBINE) $(PEPTIDE) $(EXTENDFIT) $(CONTROL)  $(EDITBONES) $(INITIALIZE)
+-	$(CC) mapmenu.c++
++	$(Copt) mapmenu.c++
+ 
+ 
+ menu.o: menu.c++ $(MENU) $(DRAWWIND) $(PDBTOLEV) $(MATH) $(MARCH) $(PEPTIDE) $(TRACE) $(INITIALIZE)
+-	$(CC) menu.c++
++	$(Copt) menu.c++
+ 
+ pdbmenu.o: pdbmenu.c++ $(PDBMENU) $(DRAWWIND) $(MENU) $(FITTOPDB) $(COMBINE) $(PEPTIDE)
+-	$(CC) pdbmenu.c++
++	$(Copt) pdbmenu.c++
+ 
+ sphere.o: sphere.c++ $(DRAWWIND) $(MATH) $(SPHERE)
+-	$(CC) sphere.c++
++	$(Copt) sphere.c++
+ 
+ cube.o: cube.c++  $(CUBE) $(DRAWWIND) 
+-	$(CC) cube.c++
++	$(Copt) cube.c++
+ 
+ model.o: model.c++ $(MODEL) $(DRAWWIND) $(PDBTOLEV) $(MATH)
+-	$(CC) model.c++
++	$(Copt) model.c++
+ 
+ fit.o: fit.c++ testfit.inc $(DRAWWIND) $(RANKSIDE) $(TRACE) $(FIT) $(MENU) $(BONE) $(TORDYN)  $(PEPTIDE) $(ASSIGNSEQ) $(FITTOPDB) $(EXTENDFIT) $(RANKSIDE)
+-	$(CC) fit.c++
++	$(Copt) fit.c++
+ 
+ contour.o: contour.c++ $(CONTOUR) $(DRAWWIND) $(TRACE) 
+-	$(CC) contour.c++
++	$(Copt) contour.c++
+ 
+ initializescreen.o: initializescreen.c++  $(INITIALIZESCREEN) $(DRAWWIND) $(PEPTIDE) $(TORDYN) $(BONE)
+-	$(CC) initializescreen.c++
+-
+-
++	$(Copt) initializescreen.c++
+ 
++clean:
++	rm -f *.o maid
+diff -ur glmaid_dist.orig/mapmenu.c++ glmaid_dist/mapmenu.c++
+--- glmaid_dist.orig/mapmenu.c++	2001-11-12 05:35:50.000000000 -0800
++++ glmaid_dist/mapmenu.c++	2005-12-15 08:09:55.000000000 -0800
+@@ -188,7 +188,7 @@
+         { "OK",     inputfitnum_ok_pushed,     NULL          },
+         { "Clear",  clear_pushed,  NULL          },
+         { "Cancel", close_dialog,  NULL          },
+-        { "Help",   help,          "Help Button" },
++        { "Help",   help,          (void *) "Help Button" },
+     };
+     /* Create a TemplateDialog that will contain the control area
+      * and the action area buttons for the dialog
+@@ -241,7 +241,7 @@
+         { "OK",     inputbone_ok_pushed,     NULL          },
+         { "Clear",  clear_pushed,  NULL          },
+         { "Cancel", close_dialog,  NULL          },
+-        { "Help",   help,          "Help Button" },
++        { "Help",   help,          (void *) "Help Button" },
+     };
+     /* Create a TemplateDialog that will contain the control area
+      * and the action area buttons for the dialog
+@@ -806,7 +806,7 @@
+              XmVaCASCADEBUTTON,contlevel,NULL,
+              XmVaCASCADEBUTTON,boneminset,NULL,
+              NULL);
+-   for(i=1;i<NMAPS;i++) // Turn off sensitivitivity  - look pale
++   for(int i=1;i<NMAPS;i++) // Turn off sensitivitivity  - look pale
+        XtSetSensitive(sc.mappullright[i],0);
+ 
+    colorpullright[1]=XmVaCreateSimplePulldownMenu (sc.mappullright[1],
+@@ -1156,11 +1156,11 @@
+             XtVaSetValues (widget, XmNset,False, NULL);
+   if (widget = XtNameToWidget (mapmenu,"button_9")) //DEFAULT:  Turn off check box for highlight bone point on/off button
+             XtVaSetValues (widget, XmNset,False, NULL);
+-    for(i=0;i<=6;i++){
++    for(int i=0;i<=6;i++){
+        XmStringFree (radius[i]);
+        XmStringFree (minden[i]);
+     }
+-    for(i=0;i<=9;i++){
++    for(int i=0;i<=9;i++){
+        XmStringFree (colorv[i]);
+        XmStringFree (level[i]);
+     }
+@@ -1175,7 +1175,7 @@
+     XmStringFree(editboneonoff);
+     XmStringFree(inputbonept);
+     XmStringFree(inputfitnum);
+-    for(i=1;i<NMAPS;i++)
++    for(int i=1;i<NMAPS;i++)
+        XmStringFree (xmpdb[i]);
+  }   
+     
+diff -ur glmaid_dist.orig/menu.c++ glmaid_dist/menu.c++
+--- glmaid_dist.orig/menu.c++	2001-11-12 05:35:50.000000000 -0800
++++ glmaid_dist/menu.c++	2005-12-15 08:09:55.000000000 -0800
+@@ -1,5 +1,5 @@
+ // This is primarily the menus associated with FILE pulldown menu
+-#include <CC/iostream.h>
++#include <iostream>
+ #include <stdlib.h>
+ #include <stdio.h>
+ #include <math.h>
+@@ -85,7 +85,7 @@
+         { "OK",     new_ok_pushed,     NULL          },
+         { "Clear",  clear_pushed,  NULL          },
+         { "Cancel", close_dialog,  NULL          },
+-        { "Help",   help,          "Help Button" },
++        { "Help",   help,          (void *) "Help Button" },
+     };
+     /* Create a TemplateDialog that will contain the control area
+      * and the action area buttons for the dialog
+@@ -159,7 +159,7 @@
+         { "OK",     old_ok_pushed,     NULL          },
+         { "Clear",  clear_pushed,  NULL          },
+         { "Cancel", close_dialog,  NULL          },
+-        { "Help",   help,          "Help Button" },
++        { "Help",   help,          (void *) "Help Button" },
+     };
+     /* Create a TemplateDialog that will contain the control area
+      * and the action area buttons for the dialog
+@@ -211,7 +211,7 @@
+ 
+ 
+ /* The "ok" button was pushed or the user pressed Return */
+-static void old_ok_pushed(Widget w,XtPointer  client_data,XtPointer  call_data)
++extern void old_ok_pushed(Widget w,XtPointer  client_data,XtPointer  call_data)
+ {
+     char* text[5];
+     char text0[100];
+@@ -219,14 +219,14 @@
+         text[i] =   XmTextFieldGetString (ss.w[i]);
+       
+     strcpy(text0,text[0]);
+-    for( i = 0;i< ss.num;i++)
++    for(int i = 0;i< ss.num;i++)
+       XtFree (text[i]);
+     strcat(text0,".maid");
+     strcpy(maidfile.name,text0);
+ //    readmaidfile(maidfile,map,core);
+     readmaidfile(maidfile,map,bone);
+ printf(" npdbfile = %d\n",maidfile.npdb);
+-for(i=1;i<=maidfile.npdb;i++)
++for(int i=1;i<=maidfile.npdb;i++)
+    printf("pdbfilename%d = %s\n",i,maidfile.pdb[i].name);
+     Widget shell = (Widget) client_data;
+     XtDestroyWidget (shell);
+@@ -240,7 +240,7 @@
+ }
+ 
+ /* The "ok" button was pushed or the user pressed Return */
+-static void new_ok_pushed(Widget w,XtPointer  client_data,XtPointer  call_data)
++extern void new_ok_pushed(Widget w,XtPointer  client_data,XtPointer  call_data)
+ {
+     char* text[5];
+     char text0[100],ich[10];
+@@ -277,7 +277,7 @@
+     XtDestroyWidget (shell);
+ printf ("Name = %s pdbfile = %s mapfile = %s\n",
+       maidfile.name,maidfile.pdb[1].name,text[2]);
+-    for( i = 0;i< ss.num;i++)
++    for(int i = 0;i< ss.num;i++)
+       XtFree (text[i]);
+     maidfile.start=0;  // This starts routine (as set by RUN command)
+ }
+@@ -654,7 +654,7 @@
+     for(int i = 0;i< ss.num;i++)
+         text[i] =   XmTextFieldGetString (ss.w[i]);      
+     strcpy(text0,text[0]);
+-    for( i = 0;i< ss.num;i++)
++    for(int i = 0;i< ss.num;i++)
+       XtFree (text[i]);
+     
+     if( (fp=fopen(text[0],"r") ) ==NULL) { // check if file exists
+@@ -694,7 +694,7 @@
+         { "OK",     pdb_ok_pushed,     NULL          },
+         { "Clear",  clear_pushed,  NULL          },
+         { "Cancel", close_dialog,  NULL          },
+-        { "Help",   help,          "Help Button" },
++        { "Help",   help,          (void *) "Help Button" },
+     };
+     /* Create a TemplateDialog that will contain the control area
+      * and the action area buttons for the dialog
+@@ -749,7 +749,7 @@
+     for(int i = 0;i< ss.num;i++)
+         text[i] =   XmTextFieldGetString (ss.w[i]);      
+     strcpy(text0,text[0]);
+-    for( i = 0;i< ss.num;i++)
++    for(int i = 0;i< ss.num;i++)
+       XtFree (text[i]);
+ 
+     if( (fp=fopen(text0,"r") ) ==NULL) { // check if file exists
+@@ -788,7 +788,7 @@
+         { "OK",     map_ok_pushed,     NULL          },
+         { "Clear",  clear_pushed,  NULL          },
+         { "Cancel", close_dialog,  NULL          },
+-        { "Help",   help,          "Help Button" },
++        { "Help",   help,          (void *) "Help Button" },
+     };
+     /* Create a TemplateDialog that will contain the control area
+      * and the action area buttons for the dialog
+diff -ur glmaid_dist.orig/pdbmenu.c++ glmaid_dist/pdbmenu.c++
+--- glmaid_dist.orig/pdbmenu.c++	2001-11-12 05:35:50.000000000 -0800
++++ glmaid_dist/pdbmenu.c++	2005-12-15 08:09:55.000000000 -0800
+@@ -755,7 +755,7 @@
+              XmNradioBehavior, True,     /* RowColumn resources to enforce */
+              XmNradioAlwaysOne, True,    /* radio behavior in Menu */
+              NULL);   
+-    for(i=1;i<MAXPDB;i++){ // set default values for main color = yellow     
++    for(int i=1;i<MAXPDB;i++){ // set default values for main color = yellow     
+         if (widget = XtNameToWidget (colorpullright[i], "button_3")) 
+                 XtVaSetValues (widget, XmNset,True, NULL);
+     }
+@@ -895,11 +895,11 @@
+              XmNradioBehavior, True,     /* RowColumn resources to enforce */
+              XmNradioAlwaysOne, True,    /* radio behavior in Menu */
+              NULL);   
+-    for(i=1;i<MAXPDB;i++){ // set default values for side color = light blue     
++    for(int i=1;i<MAXPDB;i++){ // set default values for side color = light blue     
+         if (widget = XtNameToWidget (colorpullright[i], "button_2")) 
+                 XtVaSetValues (widget, XmNset,True, NULL);
+     }
+-    for(i=1;i<MAXPDB;i++){ // Turn off sensitivitivity  - look pale
++    for(int i=1;i<MAXPDB;i++){ // Turn off sensitivitivity  - look pale
+        XtSetSensitive(sc.pullright[i],0);
+     }
+    if (widget = XtNameToWidget (radpullright, "button_2"))
+@@ -917,11 +917,11 @@
+     XmStringFree (refineside);
+     XmStringFree (refineallside);
+     XmStringFree (rotatepdb);
+-    for(i=1;i<MAXPDB;i++)
++    for(int i=1;i<MAXPDB;i++)
+        XmStringFree (xmpdb[i]);
+-    for(i=0;i<=6;i++)
++    for(int i=0;i<=6;i++)
+        XmStringFree (radius[i]);
+-    for(i=0;i<=9;i++)
++    for(int i=0;i<=9;i++)
+        XmStringFree (colorv[i]);
+     XmStringFree( setradius); 
+     XmStringFree(maincolor);
+@@ -976,7 +976,7 @@
+        pdbn = 1;
+ printf("segn = %d  pdbn = %d\n",segn,pdbn);
+  
+-    for(i=1;i<=maidfile.pdb[pdbn].resdat[segn+1][0][0];i++) { 
++    for(int i=1;i<=maidfile.pdb[pdbn].resdat[segn+1][0][0];i++) { 
+        if(strcmp(text[0],maidfile.pdb[pdbn].resnumch[segn][i])== 0){
+           resn =i;
+           goto quiti;
+@@ -995,7 +995,7 @@
+          errormessage(toplevel,"You are near allowed limit of pdb labels.. 'Delete Label' and continue");
+     maidfile.pdb[pdbn].pickres[pnum].seg = segn;
+     maidfile.pdb[pdbn].pickres[pnum].num = resn;
+-    for(i=0;i<=2;i++)
++    for(int i=0;i<=2;i++)
+          sc.centerpos[i] = maidfile.pdb[pdbn].mainch[segn][resn][1][i];
+     if(sc.pdbwindow==1){ // Then window about centerpos
+           findpdbwind();
+@@ -1004,7 +1004,7 @@
+     }
+     else if (sc.pdbwindow !=1)
+            sc.windowselect = -1;
+-    for(i=1;i<= maidfile.nden;i++){ // contour about input fit
++    for(int i=1;i<= maidfile.nden;i++){ // contour about input fit
+             if(map[i].contonoff ==1)
+                 contourmap(map[i],sc.centerpos);
+             sc.drawcontour = 1; // Turn on drawing of contour
+@@ -1024,7 +1024,7 @@
+         { "OK",     center_ok_pushed,     NULL          },
+         { "Clear",  clear_pushed,  NULL          },
+         { "Cancel", close_dialog,  NULL          },
+-        { "Help",   help,          "Help Button" },
++        { "Help",   help,          (void *) "Help Button" },
+     };
+     /* Create a TemplateDialog that will contain the control area
+      * and the action area buttons for the dialog
+diff -ur glmaid_dist.orig/selenomet.c++ glmaid_dist/selenomet.c++
+--- glmaid_dist.orig/selenomet.c++	2001-11-12 05:35:50.000000000 -0800
++++ glmaid_dist/selenomet.c++	2005-12-15 08:18:11.000000000 -0800
+@@ -75,7 +75,7 @@
+         for (line_col = 0; line_col < LINE_WIDTH; line_col++) {
+ 
+                 digit = op_line[line_col];
+-                if (digit == NULL || digit == '\n') {
++                if (digit == 0 || digit == '\n') {
+                         break;
+                 }
+                 else if(digit == ',') {
+diff -ur glmaid_dist.orig/tordyn.c++ glmaid_dist/tordyn.c++
+--- glmaid_dist.orig/tordyn.c++	2001-11-12 05:35:49.000000000 -0800
++++ glmaid_dist/tordyn.c++	2005-12-15 08:13:32.000000000 -0800
+@@ -2748,7 +2748,7 @@
+ #if 1
+            if(geo.quit==1){
+                if(verbose>=2)// 30nov00 - do not print this line
+-                   printf(" For quitcond >2: NOTE NOTE!!  geo.quit = 1 after tordyn (near boundary??) - quitting\n");
++                   printf(" For quitcond >2: NOTE NOTE!!  geo.quit = 1 after tordyn (near boundary\?\?) - quitting\n");
+                goto quit1;
+            }
+            if(checkanglimit(tordata) ==1){
+@@ -2824,7 +2824,7 @@
+            runtordyn(den1,geo,tordata,tordata2);
+ #if 1
+            if(geo.quit==1){
+-               printf("NOTE  NOTE!!:  geo.quit = 1 after tordyn at 2 (near boundary??) - quitting\n");
++               printf("NOTE  NOTE!!:  geo.quit = 1 after tordyn at 2 (near boundary\?\?) - quitting\n");
+                goto quitwhile;
+            }
+            if(checkanglimit(tordata) ==1){
+diff -ur glmaid_dist.orig/Xgl.h glmaid_dist/Xgl.h
+--- glmaid_dist.orig/Xgl.h	2001-11-12 05:35:51.000000000 -0800
++++ glmaid_dist/Xgl.h	2005-12-15 08:09:55.000000000 -0800
+@@ -11,7 +11,7 @@
+ #include <Xm/RowColumn.h>
+ #include <Xm/MessageB.h>
+ #include <Xm/CascadeBG.h>
+-#include <X11/GLw/GLwMDrawA.h>
++#include <GL/GLwMDrawA.h>
+ #include <X11/keysym.h>
+ #include <X11/Xutil.h>
+ #include <GL/glx.h>
diff --git a/sci-chemistry/maid/files/fix-warnings.patch b/sci-chemistry/maid/files/fix-warnings.patch
new file mode 100644
index 000000000000..b4f48d244a69
--- /dev/null
+++ b/sci-chemistry/maid/files/fix-warnings.patch
@@ -0,0 +1,419 @@
+diff -ur glmaid_dist.orig/assignseq.c++ glmaid_dist/assignseq.c++
+--- glmaid_dist.orig/assignseq.c++	2005-12-15 08:09:55.000000000 -0800
++++ glmaid_dist/assignseq.c++	2005-12-15 08:36:47.000000000 -0800
+@@ -2630,9 +2630,9 @@
+    if(ibestden <= 1) // 0.8 or 1.0
+        *maxngap = geo.maxngap;
+    else if(ibestden ==2) // 1.2
+-       *maxngap = 1.5*geo.maxngap;
++       *maxngap = (int) (1.5*geo.maxngap);
+    else if (ibestden >2) // 1.4 or 1.6
+-       *maxngap = 2.0 *geo.maxngap;   
++       *maxngap = (int) (2.0 *geo.maxngap);   
+  }
+ #endif
+ 
+diff -ur glmaid_dist.orig/bone.c++ glmaid_dist/bone.c++
+--- glmaid_dist.orig/bone.c++	2005-12-15 08:09:55.000000000 -0800
++++ glmaid_dist/bone.c++	2005-12-15 08:31:26.000000000 -0800
+@@ -815,7 +815,7 @@
+    }
+ 
+ 
+-   bonemin = bone1.minden*maidfile.denscale;  // lower limit  used to make bone (round down) 
++   bonemin = (int) (bone1.minden*maidfile.denscale);  // lower limit  used to make bone (round down) 
+ fprintf(fpout,"bonemin = %d\n",bonemin);
+    defineiden(bone1,iden,den1,bonemin); // set point on boundary = REMOVE
+    bsort(den1,bone1,sortv,bonemin,sortnum,&maxsize);  // sort density into bins; sort[i] is vector of 1 ..... max
+diff -ur glmaid_dist.orig/checkfit.c++ glmaid_dist/checkfit.c++
+--- glmaid_dist.orig/checkfit.c++	2005-12-15 08:09:55.000000000 -0800
++++ glmaid_dist/checkfit.c++	2005-12-15 08:22:14.000000000 -0800
+@@ -2977,7 +2977,7 @@
+    *maxden = -1000.0;
+    xtof(den1,pos,fd); /* convert from double word to float sccreen*/
+    for(k=0;k<=2;k++)
+-       ir[k]=fd[k]+0.5; /*round  to integer*/
++       ir[k]=(int) (fd[k]+0.5); /*round  to integer*/
+    for(ii=ir[0]-2;ii<=ir[0]+2;ii++){
+      if( (ii>=1)&& (ii<=den1.amax[0]-den1.amin[0]-1) )
+         for(jj=ir[1]-2;jj<=ir[1]+2;jj++)
+diff -ur glmaid_dist.orig/extend2.c++ glmaid_dist/extend2.c++
+--- glmaid_dist.orig/extend2.c++	2005-12-15 08:09:55.000000000 -0800
++++ glmaid_dist/extend2.c++	2005-12-15 08:24:45.000000000 -0800
+@@ -363,7 +363,7 @@
+    nend[3]=geo.nend[1]+3;
+ #if 1  // Works well in most cases
+    mrot[0]= 2*nrot;
+-   mrot[1]= 1.5*nrot;
++   mrot[1]= (int) (1.5*nrot);
+    mrot[2]= nrot;
+    mrot[3]= nrot;
+ #endif
+diff -ur glmaid_dist.orig/extendfit.c++ glmaid_dist/extendfit.c++
+--- glmaid_dist.orig/extendfit.c++	2005-12-15 08:09:55.000000000 -0800
++++ glmaid_dist/extendfit.c++	2005-12-15 08:26:43.000000000 -0800
+@@ -4024,7 +4024,7 @@
+ ext.usenfits = 3;//  I do not think this makes any difference since it reset in other routines -Number of unassigned connected that must be linked to assigne seq. value
+    geo.deldist = sqrt( dot(den1.delx,den1.delx) ); // length of den1.delx vector = 1.445 for shad , res = 2.5
+    if(geo.deldist < 1.445)
+-      geo.gnmax = 7*(1.445/geo.deldist) +1;
++      geo.gnmax = (int) (7*(1.445/geo.deldist) +1);
+    else
+       geo.gnmax = 7;
+    geo.maxugap = 8;  //Maximum gap allowed to connect unassigned fits
+diff -ur glmaid_dist.orig/fit.c++ glmaid_dist/fit.c++
+--- glmaid_dist.orig/fit.c++	2005-12-15 08:15:43.000000000 -0800
++++ glmaid_dist/fit.c++	2005-12-15 08:36:24.000000000 -0800
+@@ -65,7 +65,7 @@
+ tordata.torconst=torconstorig;
+ tordata2.torconst=torconstorig;   
+ tordata.rfor=rfororig; //-BE CAREFUL - MUST BE SURE rfororig defined/geo.maxside = origmaxside;   
+-geo.maxside = origmaxside;   
++geo.maxside = (int) origmaxside;   
+     if (&client_data) {
+         XtRemoveWorkProc (work_id);
+     }
+diff -ur glmaid_dist.orig/initialize.c++ glmaid_dist/initialize.c++
+--- glmaid_dist.orig/initialize.c++	2005-12-15 08:09:55.000000000 -0800
++++ glmaid_dist/initialize.c++	2005-12-15 08:34:02.000000000 -0800
+@@ -300,7 +300,7 @@
+                            nless=nless+1;
+                            dds= -MAXCHAR+1;
+                       }
+-                      den1.den[i][j][k]=dds;
++                      den1.den[i][j][k]=(signed) dds;
+ 		     }
+ 		}
+ 	}
+Files glmaid_dist.orig/initialize.o and glmaid_dist/initialize.o differ
+diff -ur glmaid_dist.orig/mapmenu.c++ glmaid_dist/mapmenu.c++
+--- glmaid_dist.orig/mapmenu.c++	2005-12-15 08:09:55.000000000 -0800
++++ glmaid_dist/mapmenu.c++	2005-12-15 08:35:53.000000000 -0800
+@@ -430,7 +430,7 @@
+ {
+   int i;
+      for(i=0;i<3;i++)
+-     map.crange[i] = fcontradius[item_no]/map.delx[i];
++     map.crange[i] = (int) (fcontradius[item_no]/map.delx[i]);
+ //printf("map radius = %d\n",map.crange[0]);
+ }
+ 
+diff -ur glmaid_dist.orig/math.c++ glmaid_dist/math.c++
+--- glmaid_dist.orig/math.c++	2005-12-15 08:09:55.000000000 -0800
++++ glmaid_dist/math.c++	2005-12-15 08:31:55.000000000 -0800
+@@ -51,9 +51,9 @@
+   z=xx[2]/den1.cvz;
+   y=(xx[1]-z*den1.cvy)/den1.singam;
+   x=xx[0]-y*den1.cosgam-z*den1.cosbe;
+-  ijk[0]=x/den1.delx[0] - den1.amin[0];
+-  ijk[1]=y/den1.delx[1] - den1.amin[1];
+-  ijk[2]=z/den1.delx[2] - den1.amin[2];
++  ijk[0]=(int) (x/den1.delx[0] - den1.amin[0]);
++  ijk[1]=(int) (y/den1.delx[1] - den1.amin[1]);
++  ijk[2]=(int) (z/den1.delx[2] - den1.amin[2]);
+ }
+ 
+ void imcv(struct griddata& den1,int xi[3],float sx[3])  /*convert from  integer xi,xj (grid point)
+diff -ur glmaid_dist.orig/menu.c++ glmaid_dist/menu.c++
+--- glmaid_dist.orig/menu.c++	2005-12-15 08:09:55.000000000 -0800
++++ glmaid_dist/menu.c++	2005-12-15 08:35:15.000000000 -0800
+@@ -321,7 +321,7 @@
+ {
+    int i;  
+    sc.cubecol[0] += 0.01;
+-   i= sc.cubecol[0];
++   i= (int) sc.cubecol[0];
+    sc.cubecol[0]= sc.cubecol[0]-i;;
+    draw_screen(client_data);
+     return False; // Runs continually
+@@ -987,14 +987,14 @@
+     int i;
+ 
+     for(i=0;i<=2;i++) // Use default contour radius
+-          den1.crange[i]=sc.contourradius/den1.delx[i];
++          den1.crange[i]=(int) (sc.contourradius/den1.delx[i]);
+     den1.contonoff = -1;
+     den1.selectcontonoff = -1;
+     for(i=0;i<3;i++)
+        den1.color[i]=bluev[i];
+     den1.conlevel = sc.conlevel*maidfile.denscale;  // Set contourleve to default value
+     // Allocate arrays for contour routines
+-    den1.ntri = NTRI/(den1.delx[0]*den1.delx[1]*den1.delx[2]); // Scale ntri relative del = 1
++    den1.ntri = (int) (NTRI/(den1.delx[0]*den1.delx[1]*den1.delx[2])); // Scale ntri relative del = 1
+ printf("Allocating arrays for contour routines  ntriangles = %d\n",den1.ntri);
+     imat2(den1.tri,den1.ntri,9);
+ printf("   Done\n");
+diff -ur glmaid_dist.orig/pdbtolev.c++ glmaid_dist/pdbtolev.c++
+--- glmaid_dist.orig/pdbtolev.c++	2005-12-15 08:09:55.000000000 -0800
++++ glmaid_dist/pdbtolev.c++	2005-12-15 08:27:19.000000000 -0800
+@@ -645,7 +645,7 @@
+ {
+     int i,j,natot,bi;
+     float  bsqr;
+-    natot=subst[snum].pos[0][0]; /*total # of atoms*/
++    natot=(int) subst[snum].pos[0][0]; /*total # of atoms*/
+     bsqr=tsqr(bondlength);
+     for(i=1;i<=natot;i++)
+        cmat[i][0]=0; /*initally no connections to i*/
+diff -ur glmaid_dist.orig/rankside.c++ glmaid_dist/rankside.c++
+--- glmaid_dist.orig/rankside.c++	2005-12-15 08:09:55.000000000 -0800
++++ glmaid_dist/rankside.c++	2005-12-15 08:33:32.000000000 -0800
+@@ -201,13 +201,13 @@
+ #endif
+      tbad = fit.ibad[resn][a1] + fit.ibad[resn][a2] +fit.ibad[resn][a3];
+      if(tbad==0)
+-         return 0+iadd;    
++         return 0+(int) iadd;    
+      if(tbad ==1)
+-         return 1+iadd;
++         return 1+(int) iadd;
+      if(tbad==2)  
+-         return 2+iadd;
++         return 2+(int) iadd;
+      if(tbad==3)  
+-         return 4+iadd;
++         return 4+(int) iadd;
+      else if ((fit.ibad[resn][MET]==0)||(fit.ibad[resn][GLU]==0)||(fit.ibad[resn][GLN]==0) )
+          return 3;
+      else
+@@ -245,11 +245,11 @@
+         iadd = iadd+1;
+ #endif
+      if(fit.ibad[resn][a1]==0 ) 
+-         return 0+iadd;    
++         return 0+(int) iadd;    
+      else if( fit.ibad[resn][a2]==0 )
+-         return 1+iadd;
++         return 1+(int) iadd;
+      else if( fit.ibad[resn][a3]==0 )
+-         return 1+iadd;
++         return 1+(int) iadd;
+      else if ((fit.ibad[resn][MET]==0)||(fit.ibad[resn][GLU]==0)||(fit.ibad[resn][GLN]==0) )
+          return 3;
+      else
+@@ -285,11 +285,11 @@
+         iadd = iadd+1;
+ #endif
+      if(fit.ibad[resn][a1]==0 ) 
+-         return 0+iadd;    
++         return 0+(int) iadd;    
+      else if( fit.ibad[resn][a2]==0 )
+-         return 1+iadd;
++         return 1+(int) iadd;
+      else if( fit.ibad[resn][a3]==0 )
+-         return 1+iadd;
++         return 1+(int) iadd;
+      else if ((fit.ibad[resn][MET]==0)||(fit.ibad[resn][GLU]==0)||(fit.ibad[resn][GLN]==0) )
+          return 3;
+      else
+@@ -316,11 +316,11 @@
+      if(valden> 1.1*ringden) //change2
+         iadd = iadd+1;
+      if(fit.ibad[resn][a1]==0 ) 
+-         return 0+iadd;    
++         return 0+(int) iadd;    
+      else if( fit.ibad[resn][a2]==0 )
+-         return 1+iadd;
++         return 1+(int) iadd;
+      else if( fit.ibad[resn][a3]==0 )
+-         return 1+iadd;
++         return 1+(int) iadd;
+      else if ((fit.ibad[resn][MET]==0)||(fit.ibad[resn][GLU]==0)||(fit.ibad[resn][GLN]==0) )
+          return 3;
+      else
+Files glmaid_dist.orig/rankside.o and glmaid_dist/rankside.o differ
+diff -ur glmaid_dist.orig/refine.c++ glmaid_dist/refine.c++
+--- glmaid_dist.orig/refine.c++	2005-12-15 08:09:55.000000000 -0800
++++ glmaid_dist/refine.c++	2005-12-15 08:26:15.000000000 -0800
+@@ -67,8 +67,8 @@
+ */
+ {
+    int ix,rnd;
+-   ix = floor(x);
+-   rnd = nn*(x-ix) + 0.5;
++   ix = (int) floor(x);
++   rnd = (int) (nn*(x-ix) + 0.5);
+    printf("nn = %d x = %5.3f  rnd = %d  Grid point %5.3f\n",nn,x,rnd,ix+(float)rnd/nn);
+    return rnd;
+ }
+@@ -82,8 +82,8 @@
+    int k;
+ 
+    for(k=0;k<=2;k++){
+-      ivec[k] = floor(fvec[k]);
+-      ival[k] = nn*(fvec[k]-ivec[k]) + 0.5;
++      ivec[k] = (int) floor(fvec[k]);
++      ival[k] = (int) (nn*(fvec[k]-ivec[k]) + 0.5);
+    }
+ }   
+ 
+@@ -115,9 +115,9 @@
+    }
+    for(k=0;k<=2;k++)
+        gzd.dvec[gzd.num][k] =ivec[k];
+-   gzd.den[gzd.num] = scalechar* exp(-rad*rad/bfact) +0.5; // mult by 100 and round
++   gzd.den[gzd.num] = (int) (scalechar* exp(-rad*rad/bfact) +0.5); // mult by 100 and round
+    for(k=0;k<=2;k++)
+-       gzd.forv[gzd.num][k] = 4.0*rad*gzd.den[gzd.num]*diffv[k]/bfact;   
++       gzd.forv[gzd.num][k] = (int) (4.0*rad*gzd.den[gzd.num]*diffv[k]/bfact);   
+ }
+ 
+ void assignforce(gzdhead)
+@@ -421,7 +421,7 @@
+    gzd[0].num = 0; 
+    oneatomgrid(den1,geo,ivec0,cenpos,gzd[0],bfact,countfunc);
+    printf("totnum = %d\n",gzd[0].num);
+-   maxgzd = gzd[0].num = 1.5*gzd[0].num; // increase by 15%
++   maxgzd = gzd[0].num = (int) (1.5*gzd[0].num); // increase by 15%
+    allocategzd(gzd[0].num);
+    del = 1.0/NDIV;
+    for(i=0;i<=NDIV;i++){
+diff -ur glmaid_dist.orig/sphere.c++ glmaid_dist/sphere.c++
+--- glmaid_dist.orig/sphere.c++	2005-12-15 08:09:55.000000000 -0800
++++ glmaid_dist/sphere.c++	2005-12-15 08:36:06.000000000 -0800
+@@ -95,7 +95,7 @@
+        fclose(fp);
+     } // spherefile opened
+     sc.isphere = maidfile.nsphere; // set active sphere to last read
+-    sc.drawspheres =1.0;
++    sc.drawspheres =1;
+     if (widget = XtNameToWidget (spheremenu,"button_0")) //DEFAULT:  Turn off check box for label on/off button
+             XtVaSetValues (widget, XmNset,TRUE, NULL);
+ }
+diff -ur glmaid_dist.orig/tordyn.c++ glmaid_dist/tordyn.c++
+--- glmaid_dist.orig/tordyn.c++	2005-12-15 08:13:32.000000000 -0800
++++ glmaid_dist/tordyn.c++	2005-12-15 08:28:27.000000000 -0800
+@@ -337,8 +337,8 @@
+     xtof(den1,apos,fd);
+ /* New version, interpolates all neighbors*/
+     for(k=0;k<=2;k++){
+-       ir[k]=fd[k]; /*round down*/
+-       irh[k]=fd[k]+0.5; /*round to next 1/2*/
++       ir[k]=(int) fd[k]; /*round down*/
++       irh[k]=(int) (fd[k]+0.5); /*round to next 1/2*/
+        if( (ir[k]<1)|| (irh[k]>den1.amax[k]-den1.amin[k]-1) ){
+ //         if(verbose>=1)
+          if(verbose>=2) // 30nov00 - do not print this line
+@@ -683,7 +683,7 @@
+    atomden = 0;
+    xtof(den1,pos,fd); /* convert from double word to float sccreen*/
+    for(kc=0;kc<=2;kc++)
+-       ir[kc]=fd[kc]; /*round down to integer*/
++       ir[kc]=(int) fd[kc]; /*round down to integer*/
+    for(k=0;k<=2;k++){ // check if pos in density range
+       if( (ir[k]<2)|| (ir[k]>den1.amax[k]-den1.amin[k]-2) ){
+          if(verbose>=2)
+@@ -2898,7 +2898,7 @@
+ //printf("oneside = %d geopos6(x) = geo.pos[geo.nend[0]+oneside][6][0] = %5.3f\n",geo.oneside,geo.pos[geo.nend[0]+geo.oneside][6][0]);
+    }
+    *returnden = bestden;  // return best cterm density
+-   *returnbad = bestbad;
++   *returnbad = (int) bestbad;
+  }// quitcont <5
+  quitrout:;
+  geo.fixend = origfixend; // set back to original value
+diff -ur glmaid_dist.orig/trace.c++ glmaid_dist/trace.c++
+--- glmaid_dist.orig/trace.c++	2005-12-15 08:09:55.000000000 -0800
++++ glmaid_dist/trace.c++	2005-12-15 08:31:07.000000000 -0800
+@@ -1079,7 +1079,7 @@
+ 
+    xtoi(den1,pos[resnum][atomnum],ig);
+    for(k=0;k<=2;k++)
+-     ig[k]=ig[k]+0.5; /*rounds to  nearest grid point*/
++     ig[k]=(int) (ig[k]+0.5); /*rounds to  nearest grid point*/
+    for(k=0;k<=2;k++){ // check if pos in density range
+       if( (ig[k]<2)|| (ig[k]>den1.amax[k]-den1.amin[k]-2) )
+          return 0;
+@@ -1099,7 +1099,7 @@
+ 
+    xtof(den1,pos,ijk); /*convert from world co-ord to floating grid i,j,k co-ord*/
+    for(k=0;k<=2;k++)
+-     ig[k]=ijk[k]+0.5; /*rounds to  nearest grid point*/
++     ig[k]=(int) (ijk[k]+0.5); /*rounds to  nearest grid point*/
+    for(k=0;k<=2;k++){ // check if pos in density range
+       if( (ig[k]<1)|| (ig[k]>den1.amax[k]-den1.amin[k]-1) ){
+          if(verbose>=2)
+@@ -1127,7 +1127,7 @@
+ 
+    xtof(den1,pos,ijk); /*convert from world co-ord to floating grid i,j,k co-ord*/
+    for(k=0;k<=2;k++)
+-     ig[k]=ijk[k]+0.5; /*rounds to  nearest grid point*/
++     ig[k]=(int) (ijk[k]+0.5); /*rounds to  nearest grid point*/
+    for(k=0;k<=2;k++){ // check if pos in density range
+       if( (ig[k]<1)|| (ig[k]>den1.amax[k]-den1.amin[k]-1) ){
+          if(verbose>=2)
+@@ -1204,7 +1204,7 @@
+ 
+    xtof(den1,pos,ijk); /*convert from world co-ord to floating grid i,j,k co-ord*/
+    for(k=0;k<=2;k++)
+-     ig[k]=ijk[k]+0.5; /*rounds to  nearest grid point*/
++     ig[k]=(int) (ijk[k]+0.5); /*rounds to  nearest grid point*/
+    for(k=0;k<=2;k++){ // check if pos in density range
+       if( ((ig[k]-geo.setrad)<0)|| ((ig[k]+geo.setrad)>den1.griddim[k]-1) ){
+          if(verbose>=2)
+@@ -2543,7 +2543,7 @@
+    atomden = 0;
+    xtof(den1,pos,fd); /* convert from double word to float sccreen*/
+    for(kc=0;kc<=2;kc++)
+-       ir[kc]=fd[kc]; /*round down to integer*/
++       ir[kc]=(int) fd[kc]; /*round down to integer*/
+    for(k=0;k<=2;k++){ // check if pos in density range
+       if( (ir[k]<1)|| (ir[k]>den1.amax[k]-den1.amin[k]-1) ){
+ //if(verbose>=2)
+@@ -2569,7 +2569,7 @@
+    atomden = 0;
+    xtof(den1,pos[inum][itype],fd); /* convert from double word to float sccreen*/
+    for(kc=0;kc<=2;kc++)
+-       ir[kc]=fd[kc]; /*round down to integer*/
++       ir[kc]=(int) fd[kc]; /*round down to integer*/
+    for(k=0;k<=2;k++){ // check if pos in density range
+       if( (ir[k]<1)|| (ir[k]>den1.amax[k]-den1.amin[k]-1) ){
+         if(verbose>=2)
+@@ -3438,7 +3438,7 @@
+     dist =distv(pos[1][1],pos[n0+1][1]); // distance from Ca[geo.cafix] to Ca[1]
+ dist = dist/2.0;
+     thdel = rotdel/dist; // step size of theta rotation
+-    mth =1+ thtot/thdel; // max # of theta steps  - round up
++    mth =1+ (int) (thtot/thdel); // max # of theta steps  - round up
+     thdel = thtot/mth; // reset th del so that equal steps from 0 to thttot
+     maxden = -10000.0;
+ for(iaxis=0;iaxis<8;iaxis++){// rotate about origingalca1 caend axis
+@@ -3455,7 +3455,7 @@
+        }
+        else{
+          delph = rotdel/(dist*sin(th));//the delta phi angle step
+-         mphi = phitot/delph +1; // round up
++         mphi = (int) (phitot/delph) +1; // round up
+          delph = phitot/mphi; // make phitot = mphi*delph 
+        }
+        for(iph = 0;iph<=mphi;iph++){ // the phi step 
+@@ -3545,7 +3545,7 @@
+     dist =distv(pos[1][1],pos[n0+1][1]); // distance from Ca[geo.cafix] to Ca[1]
+ dist = dist/2.0;
+     thdel = rotdel/dist; // step size of theta rotation
+-    mth =1+ thtot/thdel; // max # of theta steps  - round up
++    mth =1+ (int) (thtot/thdel); // max # of theta steps  - round up
+     thdel = thtot/mth; // reset th del so that equal steps from 0 to thttot
+     maxden = -10000.0;
+ for(iaxis=0;iaxis<8;iaxis++){// rotate about origingalca1 caend axis
+@@ -3562,7 +3562,7 @@
+        }
+        else{
+          delph = rotdel/(dist*sin(th));//the delta phi angle step
+-         mphi = phitot/delph +1; // round up
++         mphi = (int) (phitot/delph) +1; // round up
+          delph = phitot/mphi; // make phitot = mphi*delph 
+        }
+        for(iph = 0;iph<=mphi;iph++){ // the phi step 
+@@ -6905,8 +6905,8 @@
+   for(i=0;i<=2;i++)
+     avegrid = avegrid+den1.delx[i];
+   avegrid = avegrid/3.0;
+-  geo.nihel = 0.5 + geo.curdist[1]/(1.414*avegrid); // 0.5 so that rounds to nearest int
+-  geo.nisheet = geo.curdist[2]/(1.414*avegrid);
++  geo.nihel = (int) (0.5 + geo.curdist[1]/(1.414*avegrid)); // 0.5 so that rounds to nearest int
++  geo.nisheet = (int) (geo.curdist[2]/(1.414*avegrid));
+ printf("\nGRID SIZE:  %5.3f %5.3f %5.3f avegrid = %5.3f  nihel = %d\n", 
+       den1.delx[0],den1.delx[1],den1.delx[2],avegrid,geo.nihel);
+ 
+Files glmaid_dist.orig/trace.o and glmaid_dist/trace.o differ
diff --git a/sci-chemistry/maid/maid-20011112.ebuild b/sci-chemistry/maid/maid-20011112.ebuild
new file mode 100644
index 000000000000..2c76a5c00c4e
--- /dev/null
+++ b/sci-chemistry/maid/maid-20011112.ebuild
@@ -0,0 +1,62 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/maid/maid-20011112.ebuild,v 1.1 2005/12/15 20:33:37 spyderous Exp $
+
+inherit eutils toolchain-funcs
+
+MY_PN="${PN}_unix"
+MY_PV="${PV:6:2}nov${PV:0:2}"
+MY_P="${MY_PN}_${MY_PV}"
+DESCRIPTION="Automates the fitting of protein X-ray crystallographic electron density maps"
+HOMEPAGE="http://www.msi.umn.edu/~levitt/"
+SRC_URI="http://www.msi.umn.edu/~levitt/maid_unix_12nov01.tar.gz"
+LICENSE="molmol"
+SLOT="0"
+KEYWORDS="~x86"
+IUSE="X"
+DEPEND="X? ( virtual/motif
+		virtual/glu
+		virtual/opengl
+		|| ( x11-libs/libXt virtual/x11 )
+	)"
+S="${WORKDIR}/glmaid_dist"
+
+src_unpack() {
+	if best_version virtual/opengl | grep mesa; then
+		if ! built_with_use media-libs/mesa motif; then
+			msg="Build media-libs/mesa with USE=motif"
+			eerror "${msg}"
+			die "${msg}"
+		fi
+	fi
+
+	unpack ${A}
+	cd ${S}
+
+	epatch ${FILESDIR}/fix-compilation.patch
+	epatch ${FILESDIR}/fix-warnings.patch
+
+	if use X; then
+		ln -s makefile_graphics makefile
+	else
+		ln -s makefile_batch makefile
+	fi
+
+	sed -i \
+		-e "s:^Cgeneric = .*:Cgeneric = $(tc-getCXX):g" \
+		-e "s:\(Copt.*\)-O:\1${CFLAGS}:g" \
+		makefile
+}
+
+src_compile() {
+	emake || die "emake failed"
+}
+
+src_install() {
+	dodoc MANUAL*
+	if use X; then
+		dobin maid
+	else
+		dobin maidbatch
+	fi
+}
diff --git a/sci-chemistry/maid/metadata.xml b/sci-chemistry/maid/metadata.xml
new file mode 100644
index 000000000000..211b8bd0f0a4
--- /dev/null
+++ b/sci-chemistry/maid/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<maintainer>
+<email>spyderous@gentoo.org</email>
+<name>Donnie Berkholz</name>
+</maintainer>
+</pkgmetadata>