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author | Donnie Berkholz <dberkholz@gentoo.org> | 2005-12-15 20:33:37 +0000 |
---|---|---|
committer | Donnie Berkholz <dberkholz@gentoo.org> | 2005-12-15 20:33:37 +0000 |
commit | 7491ec27723e236090c9936e6c4c8d2d23605985 (patch) | |
tree | fadfcbace971aa399bc834b5a2e2c2f37a950c57 /sci-chemistry | |
parent | New upstream version (diff) | |
download | historical-7491ec27723e236090c9936e6c4c8d2d23605985.tar.gz historical-7491ec27723e236090c9936e6c4c8d2d23605985.tar.bz2 historical-7491ec27723e236090c9936e6c4c8d2d23605985.zip |
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
Diffstat (limited to 'sci-chemistry')
-rw-r--r-- | sci-chemistry/maid/ChangeLog | 13 | ||||
-rw-r--r-- | sci-chemistry/maid/Manifest | 6 | ||||
-rw-r--r-- | sci-chemistry/maid/files/digest-maid-20011112 | 1 | ||||
-rw-r--r-- | sci-chemistry/maid/files/fix-compilation.patch | 570 | ||||
-rw-r--r-- | sci-chemistry/maid/files/fix-warnings.patch | 419 | ||||
-rw-r--r-- | sci-chemistry/maid/maid-20011112.ebuild | 62 | ||||
-rw-r--r-- | sci-chemistry/maid/metadata.xml | 9 |
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> |