; LLVM IR from alexzheng42/sDMD :: src (Initialization)

; Unoptimized IR (clang -disable-llvm-passes):
target datalayout = "e-m:e-p270:32:32-p271:32:32-p272:64:64-i64:64-i128:128-f80:128-n8:16:32:64-S128"
target triple = "x86_64-unknown-linux-gnu"

%struct.REMDStr = type { i32, i32, i32, [50 x i8], [50 x i8], %struct.REMDTempStr }
%struct.REMDTempStr = type { i32, double }
%struct.AAStr = type { [5 x i8], i32, i32, i32, i32, double }
%struct.PepStr = type { i32, i32, i32, i32, double }

@.str.2 = external hidden unnamed_addr constant [71 x i8], align 1
@datadir = external global [1024 x i8], align 16
@.str.3 = external hidden unnamed_addr constant [3 x i8], align 1
@boxDimension = external global [4 x double], align 16
@REMDInfo = external global %struct.REMDStr, align 8
@.str.84 = external hidden unnamed_addr constant [2 x i8], align 1
@.str.94 = external hidden unnamed_addr constant [2 x i8], align 1
@atomnum = external global i32, align 4
@numofprotein = external global i32, align 4
@totalAminoAcids = external global i32, align 4
@protein = external global ptr, align 8
@aminoacid = external global ptr, align 8
@connectionMap = external global ptr, align 8
@Methodtype = external global [20 x i8], align 16
@.str.115 = external hidden unnamed_addr constant [10 x i8], align 1
@.str.128 = external hidden unnamed_addr constant [140 x i8], align 1
@.str.129 = external hidden unnamed_addr constant [18 x i8], align 1
@.str.130 = external hidden unnamed_addr constant [20 x i8], align 1
@.str.131 = external hidden unnamed_addr constant [2 x i8], align 1
@.str.132 = external hidden unnamed_addr constant [16 x i8], align 1
@.str.133 = external hidden unnamed_addr constant [4 x i8], align 1
@.str.134 = external hidden unnamed_addr constant [5 x i8], align 1
@.str.135 = external hidden unnamed_addr constant [11 x i8], align 1
@.str.136 = external hidden unnamed_addr constant [4 x i8], align 1
@.str.137 = external hidden unnamed_addr constant [24 x i8], align 1
@.str.138 = external hidden unnamed_addr constant [4 x i8], align 1
@.str.139 = external hidden unnamed_addr constant [58 x i8], align 1
@.str.140 = external hidden unnamed_addr constant [47 x i8], align 1
@.str.141 = external hidden unnamed_addr constant [9 x i8], align 1
@.str.142 = external hidden unnamed_addr constant [27 x i8], align 1
@.str.143 = external hidden unnamed_addr constant [36 x i8], align 1
@.str.144 = external hidden unnamed_addr constant [9 x i8], align 1
@.str.145 = external hidden unnamed_addr constant [4 x i8], align 1

; Function Attrs: nocallback nofree nosync nounwind willreturn memory(argmem: readwrite)
declare void @llvm.lifetime.start.p0(i64 immarg, ptr nocapture) #0

; Function Attrs: nounwind allocsize(0,1)
declare noalias ptr @calloc(i64 noundef, i64 noundef) #1

; Function Attrs: nounwind willreturn memory(read)
declare i32 @strcmp(ptr noundef, ptr noundef) #2

declare i32 @printf(ptr noundef, ...) #3

; Function Attrs: nounwind
declare i32 @sprintf(ptr noundef, ptr noundef, ...) #4

; Function Attrs: noreturn nounwind
declare void @exit(i32 noundef) #5

; Function Attrs: nounwind willreturn memory(read)
declare i32 @strncmp(ptr noundef, ptr noundef, i64 noundef) #2

declare noalias ptr @fopen(ptr noundef, ptr noundef) #3

declare i32 @fclose(ptr noundef) #3

; Function Attrs: nocallback nofree nosync nounwind willreturn memory(argmem: readwrite)
declare void @llvm.lifetime.end.p0(i64 immarg, ptr nocapture) #0

declare i32 @__isoc99_fscanf(ptr noundef, ptr noundef, ...) #3

declare ptr @fgets(ptr noundef, i32 noundef, ptr noundef) #3

; Function Attrs: nounwind uwtable
define dso_local void @ReadPDBFile(ptr noundef %0) #6 {
  %2 = alloca ptr, align 8
  %3 = alloca i32, align 4
  %4 = alloca i32, align 4
  %5 = alloca i32, align 4
  %6 = alloca [8 x i8], align 1
  %7 = alloca [8 x i8], align 1
  %8 = alloca [8 x i8], align 1
  %9 = alloca [256 x i8], align 16
  %10 = alloca [1024 x i8], align 16
  %11 = alloca [1024 x i8], align 16
  %12 = alloca [8 x i8], align 1
  %13 = alloca [20 x [8 x i8]], align 16
  %14 = alloca [3 x double], align 16
  %15 = alloca ptr, align 8
  %16 = alloca ptr, align 8
  %17 = alloca i32, align 4
  %18 = alloca i32, align 4
  %19 = alloca i32, align 4
  %20 = alloca i32, align 4
  store ptr %0, ptr %2, align 8, !tbaa !5
  call void @llvm.lifetime.start.p0(i64 4, ptr %3) #9
  store i32 0, ptr %3, align 4, !tbaa !9
  call void @llvm.lifetime.start.p0(i64 4, ptr %4) #9
  store i32 0, ptr %4, align 4, !tbaa !9
  call void @llvm.lifetime.start.p0(i64 4, ptr %5) #9
  call void @llvm.lifetime.start.p0(i64 8, ptr %6) #9
  call void @llvm.memset.p0.i64(ptr align 1 %6, i8 0, i64 8, i1 false)
  call void @llvm.lifetime.start.p0(i64 8, ptr %7) #9
  call void @llvm.lifetime.start.p0(i64 8, ptr %8) #9
  call void @llvm.lifetime.start.p0(i64 256, ptr %9) #9
  call void @llvm.memset.p0.i64(ptr align 16 %9, i8 0, i64 256, i1 false)
  call void @llvm.lifetime.start.p0(i64 1024, ptr %10) #9
  call void @llvm.lifetime.start.p0(i64 1024, ptr %11) #9
  call void @llvm.lifetime.start.p0(i64 8, ptr %12) #9
  call void @llvm.lifetime.start.p0(i64 160, ptr %13) #9
  call void @llvm.memset.p0.i64(ptr align 16 %13, i8 0, i64 160, i1 false)
  call void @llvm.lifetime.start.p0(i64 24, ptr %14) #9
  call void @llvm.lifetime.start.p0(i64 8, ptr %15) #9
  call void @llvm.lifetime.start.p0(i64 8, ptr %16) #9
  store ptr null, ptr %16, align 8, !tbaa !5
  %21 = load double, ptr getelementptr inbounds ([4 x double], ptr @boxDimension, i64 0, i64 1), align 8, !tbaa !11
  %22 = fcmp oeq double %21, 0.000000e+00
  br i1 %22, label %29, label %23

23:                                               ; preds = %1
  %24 = load double, ptr getelementptr inbounds ([4 x double], ptr @boxDimension, i64 0, i64 2), align 16, !tbaa !11
  %25 = fcmp oeq double %24, 0.000000e+00
  br i1 %25, label %29, label %26

26:                                               ; preds = %23
  %27 = load double, ptr getelementptr inbounds ([4 x double], ptr @boxDimension, i64 0, i64 3), align 8, !tbaa !11
  %28 = fcmp oeq double %27, 0.000000e+00
  br i1 %28, label %29, label %32

29:                                               ; preds = %26, %23, %1
  %30 = call i32 (ptr, ...) @printf(ptr noundef @.str.128)
  %31 = call i32 (ptr, ...) @printf(ptr noundef @.str.129, ptr noundef @.str.2, i32 noundef 785)
  call void @exit(i32 noundef 1) #10
  unreachable

32:                                               ; preds = %26
  %33 = getelementptr inbounds [1024 x i8], ptr %11, i64 0, i64 0
  %34 = call i32 (ptr, ptr, ...) @sprintf(ptr noundef %33, ptr noundef @.str.130, ptr noundef @datadir, ptr noundef getelementptr inbounds (%struct.REMDStr, ptr @REMDInfo, i32 0, i32 4)) #9
  %35 = getelementptr inbounds [1024 x i8], ptr %11, i64 0, i64 0
  %36 = call noalias ptr @fopen(ptr noundef %35, ptr noundef @.str.131)
  store ptr %36, ptr %15, align 8, !tbaa !5
  %37 = load ptr, ptr %15, align 8, !tbaa !5
  %38 = call i32 (ptr, ptr, ...) @fprintf(ptr noundef %37, ptr noundef @.str.132, ptr noundef @datadir) #9
  store i32 0, ptr @atomnum, align 4, !tbaa !9
  store i32 0, ptr @numofprotein, align 4, !tbaa !9
  store i32 0, ptr @totalAminoAcids, align 4, !tbaa !9
  store ptr null, ptr @protein, align 8, !tbaa !5
  store ptr null, ptr @aminoacid, align 8, !tbaa !5
  br label %39

39:                                               ; preds = %256, %134, %32
  %40 = load ptr, ptr %2, align 8, !tbaa !5
  %41 = getelementptr inbounds [1024 x i8], ptr %10, i64 0, i64 0
  %42 = call i32 (ptr, ptr, ...) @__isoc99_fscanf(ptr noundef %40, ptr noundef @.str.3, ptr noundef %41)
  %43 = icmp ne i32 %42, -1
  br i1 %43, label %44, label %48

44:                                               ; preds = %39
  %45 = getelementptr inbounds [1024 x i8], ptr %10, i64 0, i64 0
  %46 = call i32 @strncmp(ptr noundef %45, ptr noundef @.str.133, i64 noundef 3) #11
  %47 = icmp ne i32 %46, 0
  br label %48

48:                                               ; preds = %44, %39
  %49 = phi i1 [ false, %39 ], [ %47, %44 ]
  br i1 %49, label %50, label %260

50:                                               ; preds = %48
  %51 = getelementptr inbounds [1024 x i8], ptr %10, i64 0, i64 0
  %52 = call i32 @strcmp(ptr noundef %51, ptr noundef @.str.134) #11
  %53 = icmp eq i32 %52, 0
  br i1 %53, label %54, label %256

54:                                               ; preds = %50
  %55 = load ptr, ptr %2, align 8, !tbaa !5
  %56 = getelementptr inbounds [1024 x i8], ptr %10, i64 0, i64 0
  %57 = getelementptr inbounds [8 x i8], ptr %8, i64 0, i64 0
  %58 = getelementptr inbounds [8 x i8], ptr %12, i64 0, i64 0
  %59 = getelementptr inbounds [8 x i8], ptr %7, i64 0, i64 0
  %60 = call i32 (ptr, ptr, ...) @__isoc99_fscanf(ptr noundef %55, ptr noundef @.str.135, ptr noundef %56, ptr noundef %57, ptr noundef %58, ptr noundef %59, ptr noundef %5)
  %61 = load i32, ptr %4, align 4, !tbaa !9
  %62 = load i32, ptr %5, align 4, !tbaa !9
  %63 = icmp ne i32 %61, %62
  br i1 %63, label %64, label %111

64:                                               ; preds = %54
  %65 = getelementptr inbounds [8 x i8], ptr %12, i64 0, i64 0
  %66 = call i32 @strcmp(ptr noundef %65, ptr noundef @.str.136) #11
  %67 = icmp eq i32 %66, 0
  br i1 %67, label %68, label %71

68:                                               ; preds = %64
  %69 = getelementptr inbounds [1024 x i8], ptr %11, i64 0, i64 0
  %70 = call i32 (ptr, ptr, ...) @sprintf(ptr noundef %69, ptr noundef @.str.137, ptr noundef @datadir, ptr noundef @Methodtype, ptr noundef @.str.138) #9
  br label %75

71:                                               ; preds = %64
  %72 = getelementptr inbounds [1024 x i8], ptr %11, i64 0, i64 0
  %73 = getelementptr inbounds [8 x i8], ptr %12, i64 0, i64 0
  %74 = call i32 (ptr, ptr, ...) @sprintf(ptr noundef %72, ptr noundef @.str.137, ptr noundef @datadir, ptr noundef @Methodtype, ptr noundef %73) #9
  br label %75

75:                                               ; preds = %71, %68
  %76 = getelementptr inbounds [1024 x i8], ptr %11, i64 0, i64 0
  %77 = call noalias ptr @fopen(ptr noundef %76, ptr noundef @.str.94)
  store ptr %77, ptr %16, align 8, !tbaa !5
  %78 = load ptr, ptr %16, align 8, !tbaa !5
  %79 = icmp eq ptr %78, null
  br i1 %79, label %80, label %84

80:                                               ; preds = %75
  %81 = getelementptr inbounds [8 x i8], ptr %12, i64 0, i64 0
  %82 = call i32 (ptr, ...) @printf(ptr noundef @.str.139, ptr noundef %81, ptr noundef @datadir, ptr noundef @Methodtype)
  %83 = call i32 (ptr, ...) @printf(ptr noundef @.str.140, ptr noundef @.str.2, i32 noundef 812)
  call void @exit(i32 noundef 1) #10
  unreachable

84:                                               ; preds = %75
  %85 = getelementptr inbounds [1024 x i8], ptr %10, i64 0, i64 0
  %86 = load ptr, ptr %16, align 8, !tbaa !5
  %87 = call ptr @fgets(ptr noundef %85, i32 noundef 1024, ptr noundef %86)
  store i32 0, ptr %3, align 4, !tbaa !9
  br label %88

88:                                               ; preds = %99, %84
  %89 = load ptr, ptr %16, align 8, !tbaa !5
  %90 = getelementptr inbounds [1024 x i8], ptr %10, i64 0, i64 0
  %91 = call i32 (ptr, ptr, ...) @__isoc99_fscanf(ptr noundef %89, ptr noundef @.str.3, ptr noundef %90)
  %92 = icmp ne i32 %91, 0
  br i1 %92, label %93, label %97

93:                                               ; preds = %88
  %94 = getelementptr inbounds [1024 x i8], ptr %10, i64 0, i64 0
  %95 = call i32 @strcmp(ptr noundef @.str.134, ptr noundef %94) #11
  %96 = icmp eq i32 %95, 0
  br label %97

97:                                               ; preds = %93, %88
  %98 = phi i1 [ false, %88 ], [ %96, %93 ]
  br i1 %98, label %99, label %108

99:                                               ; preds = %97
  %100 = load ptr, ptr %16, align 8, !tbaa !5
  %101 = load i32, ptr %3, align 4, !tbaa !9
  %102 = add nsw i32 %101, 1
  store i32 %102, ptr %3, align 4, !tbaa !9
  %103 = sext i32 %101 to i64
  %104 = getelementptr inbounds [20 x [8 x i8]], ptr %13, i64 0, i64 %103
  %105 = getelementptr inbounds [8 x i8], ptr %104, i64 0, i64 0
  %106 = getelementptr inbounds [1024 x i8], ptr %10, i64 0, i64 0
  %107 = call i32 (ptr, ptr, ...) @__isoc99_fscanf(ptr noundef %100, ptr noundef @.str.141, ptr noundef %105, ptr noundef %106)
  br label %88, !llvm.loop !13

108:                                              ; preds = %97
  %109 = load ptr, ptr %16, align 8, !tbaa !5
  %110 = call i32 @fclose(ptr noundef %109)
  br label %111

111:                                              ; preds = %108, %54
  %112 = getelementptr inbounds [8 x i8], ptr %8, i64 0, i64 0
  %113 = getelementptr inbounds [20 x [8 x i8]], ptr %13, i64 0, i64 0
  %114 = load i32, ptr %3, align 4, !tbaa !9
  %115 = call i32 @CheckValidAtom(ptr noundef %112, ptr noundef %113, i32 noundef %114)
  %116 = icmp ne i32 %115, 0
  br i1 %116, label %117, label %134

117:                                              ; preds = %111
  %118 = load i32, ptr @atomnum, align 4, !tbaa !9
  %119 = add nsw i32 %118, 1
  store i32 %119, ptr @atomnum, align 4, !tbaa !9
  %120 = load ptr, ptr %2, align 8, !tbaa !5
  %121 = getelementptr inbounds [3 x double], ptr %14, i64 0, i64 0
  %122 = getelementptr inbounds [3 x double], ptr %14, i64 0, i64 1
  %123 = getelementptr inbounds [3 x double], ptr %14, i64 0, i64 2
  %124 = call i32 (ptr, ptr, ...) @__isoc99_fscanf(ptr noundef %120, ptr noundef @.str.115, ptr noundef %121, ptr noundef %122, ptr noundef %123)
  %125 = load ptr, ptr %15, align 8, !tbaa !5
  %126 = getelementptr inbounds [8 x i8], ptr %8, i64 0, i64 0
  %127 = getelementptr inbounds [3 x double], ptr %14, i64 0, i64 0
  %128 = load double, ptr %127, align 16, !tbaa !11
  %129 = getelementptr inbounds [3 x double], ptr %14, i64 0, i64 1
  %130 = load double, ptr %129, align 8, !tbaa !11
  %131 = getelementptr inbounds [3 x double], ptr %14, i64 0, i64 2
  %132 = load double, ptr %131, align 16, !tbaa !11
  %133 = call i32 (ptr, ptr, ...) @fprintf(ptr noundef %125, ptr noundef @.str.142, ptr noundef %126, double noundef %128, double noundef %130, double noundef %132) #9
  br label %138

134:                                              ; preds = %111
  %135 = getelementptr inbounds [1024 x i8], ptr %10, i64 0, i64 0
  %136 = load ptr, ptr %2, align 8, !tbaa !5
  %137 = call ptr @fgets(ptr noundef %135, i32 noundef 1024, ptr noundef %136)
  br label %39, !llvm.loop !15

138:                                              ; preds = %117
  %139 = load i32, ptr %4, align 4, !tbaa !9
  %140 = load i32, ptr %5, align 4, !tbaa !9
  %141 = icmp ne i32 %139, %140
  br i1 %141, label %147, label %142

142:                                              ; preds = %138
  %143 = getelementptr inbounds [8 x i8], ptr %12, i64 0, i64 0
  %144 = getelementptr inbounds [256 x i8], ptr %9, i64 0, i64 0
  %145 = call i32 @strcmp(ptr noundef %143, ptr noundef %144) #11
  %146 = icmp ne i32 %145, 0
  br i1 %146, label %147, label %255

147:                                              ; preds = %142, %138
  %148 = load ptr, ptr @aminoacid, align 8, !tbaa !5
  %149 = load i32, ptr @totalAminoAcids, align 4, !tbaa !9
  %150 = add nsw i32 %149, 1
  store i32 %150, ptr @totalAminoAcids, align 4, !tbaa !9
  %151 = add nsw i32 %150, 1
  %152 = sext i32 %151 to i64
  %153 = mul i64 32, %152
  %154 = call ptr @realloc(ptr noundef %148, i64 noundef %153) #12
  store ptr %154, ptr @aminoacid, align 8, !tbaa !5
  %155 = load ptr, ptr @aminoacid, align 8, !tbaa !5
  %156 = load i32, ptr @totalAminoAcids, align 4, !tbaa !9
  %157 = sext i32 %156 to i64
  %158 = getelementptr inbounds %struct.AAStr, ptr %155, i64 %157
  %159 = getelementptr inbounds %struct.AAStr, ptr %158, i32 0, i32 0
  %160 = getelementptr inbounds [5 x i8], ptr %159, i64 0, i64 0
  %161 = getelementptr inbounds [8 x i8], ptr %12, i64 0, i64 0
  %162 = call i32 (ptr, ptr, ...) @sprintf(ptr noundef %160, ptr noundef @.str.3, ptr noundef %161) #9
  %163 = getelementptr inbounds [8 x i8], ptr %7, i64 0, i64 0
  %164 = getelementptr inbounds [8 x i8], ptr %6, i64 0, i64 0
  %165 = call i32 @strcmp(ptr noundef %163, ptr noundef %164) #11
  %166 = icmp ne i32 %165, 0
  br i1 %166, label %174, label %167

167:                                              ; preds = %147
  %168 = load i32, ptr @numofprotein, align 4, !tbaa !9
  %169 = icmp eq i32 %168, 0
  br i1 %169, label %174, label %170

170:                                              ; preds = %167
  %171 = load i32, ptr %5, align 4, !tbaa !9
  %172 = load i32, ptr %4, align 4, !tbaa !9
  %173 = icmp slt i32 %171, %172
  br i1 %173, label %174, label %177

174:                                              ; preds = %170, %167, %147
  %175 = load i32, ptr @numofprotein, align 4, !tbaa !9
  %176 = add nsw i32 %175, 1
  br label %179

177:                                              ; preds = %170
  %178 = load i32, ptr @numofprotein, align 4, !tbaa !9
  br label %179

179:                                              ; preds = %177, %174
  %180 = phi i32 [ %176, %174 ], [ %178, %177 ]
  %181 = load ptr, ptr @aminoacid, align 8, !tbaa !5
  %182 = load i32, ptr @totalAminoAcids, align 4, !tbaa !9
  %183 = sext i32 %182 to i64
  %184 = getelementptr inbounds %struct.AAStr, ptr %181, i64 %183
  %185 = getelementptr inbounds %struct.AAStr, ptr %184, i32 0, i32 4
  store i32 %180, ptr %185, align 4, !tbaa !16
  %186 = load i32, ptr @atomnum, align 4, !tbaa !9
  %187 = sub nsw i32 %186, 1
  %188 = load ptr, ptr @aminoacid, align 8, !tbaa !5
  %189 = load i32, ptr @totalAminoAcids, align 4, !tbaa !9
  %190 = sub nsw i32 %189, 1
  %191 = sext i32 %190 to i64
  %192 = getelementptr inbounds %struct.AAStr, ptr %188, i64 %191
  %193 = getelementptr inbounds %struct.AAStr, ptr %192, i32 0, i32 3
  store i32 %187, ptr %193, align 8, !tbaa !18
  %194 = load i32, ptr @atomnum, align 4, !tbaa !9
  %195 = load ptr, ptr @aminoacid, align 8, !tbaa !5
  %196 = load i32, ptr @totalAminoAcids, align 4, !tbaa !9
  %197 = sext i32 %196 to i64
  %198 = getelementptr inbounds %struct.AAStr, ptr %195, i64 %197
  %199 = getelementptr inbounds %struct.AAStr, ptr %198, i32 0, i32 2
  store i32 %194, ptr %199, align 4, !tbaa !19
  %200 = getelementptr inbounds [8 x i8], ptr %7, i64 0, i64 0
  %201 = getelementptr inbounds [8 x i8], ptr %6, i64 0, i64 0
  %202 = call i32 @strcmp(ptr noundef %200, ptr noundef %201) #11
  %203 = icmp ne i32 %202, 0
  br i1 %203, label %211, label %204

204:                                              ; preds = %179
  %205 = load i32, ptr @numofprotein, align 4, !tbaa !9
  %206 = icmp eq i32 %205, 0
  br i1 %206, label %211, label %207

207:                                              ; preds = %204
  %208 = load i32, ptr %5, align 4, !tbaa !9
  %209 = load i32, ptr %4, align 4, !tbaa !9
  %210 = icmp slt i32 %208, %209
  br i1 %210, label %211, label %250

211:                                              ; preds = %207, %204, %179
  %212 = getelementptr inbounds [8 x i8], ptr %6, i64 0, i64 0
  %213 = getelementptr inbounds [8 x i8], ptr %7, i64 0, i64 0
  %214 = call i32 (ptr, ptr, ...) @sprintf(ptr noundef %212, ptr noundef @.str.3, ptr noundef %213) #9
  %215 = load ptr, ptr @protein, align 8, !tbaa !5
  %216 = load i32, ptr @numofprotein, align 4, !tbaa !9
  %217 = add nsw i32 %216, 1
  store i32 %217, ptr @numofprotein, align 4, !tbaa !9
  %218 = add nsw i32 %217, 1
  %219 = sext i32 %218 to i64
  %220 = mul i64 24, %219
  %221 = call ptr @realloc(ptr noundef %215, i64 noundef %220) #12
  store ptr %221, ptr @protein, align 8, !tbaa !5
  %222 = load i32, ptr @totalAminoAcids, align 4, !tbaa !9
  %223 = sub nsw i32 %222, 1
  %224 = load ptr, ptr @protein, align 8, !tbaa !5
  %225 = load i32, ptr @numofprotein, align 4, !tbaa !9
  %226 = sub nsw i32 %225, 1
  %227 = sext i32 %226 to i64
  %228 = getelementptr inbounds %struct.PepStr, ptr %224, i64 %227
  %229 = getelementptr inbounds %struct.PepStr, ptr %228, i32 0, i32 3
  store i32 %223, ptr %229, align 4, !tbaa !20
  %230 = load i32, ptr @totalAminoAcids, align 4, !tbaa !9
  %231 = load ptr, ptr @protein, align 8, !tbaa !5
  %232 = load i32, ptr @numofprotein, align 4, !tbaa !9
  %233 = sext i32 %232 to i64
  %234 = getelementptr inbounds %struct.PepStr, ptr %231, i64 %233
  %235 = getelementptr inbounds %struct.PepStr, ptr %234, i32 0, i32 2
  store i32 %230, ptr %235, align 8, !tbaa !22
  %236 = load i32, ptr @atomnum, align 4, !tbaa !9
  %237 = sub nsw i32 %236, 1
  %238 = load ptr, ptr @protein, align 8, !tbaa !5
  %239 = load i32, ptr @numofprotein, align 4, !tbaa !9
  %240 = sub nsw i32 %239, 1
  %241 = sext i32 %240 to i64
  %242 = getelementptr inbounds %struct.PepStr, ptr %238, i64 %241
  %243 = getelementptr inbounds %struct.PepStr, ptr %242, i32 0, i32 1
  store i32 %237, ptr %243, align 4, !tbaa !23
  %244 = load i32, ptr @atomnum, align 4, !tbaa !9
  %245 = load ptr, ptr @protein, align 8, !tbaa !5
  %246 = load i32, ptr @numofprotein, align 4, !tbaa !9
  %247 = sext i32 %246 to i64
  %248 = getelementptr inbounds %struct.PepStr, ptr %245, i64 %247
  %249 = getelementptr inbounds %struct.PepStr, ptr %248, i32 0, i32 0
  store i32 %244, ptr %249, align 8, !tbaa !24
  br label %250

250:                                              ; preds = %211, %207
  %251 = load i32, ptr %5, align 4, !tbaa !9
  store i32 %251, ptr %4, align 4, !tbaa !9
  %252 = getelementptr inbounds [256 x i8], ptr %9, i64 0, i64 0
  %253 = getelementptr inbounds [8 x i8], ptr %12, i64 0, i64 0
  %254 = call i32 (ptr, ptr, ...) @sprintf(ptr noundef %252, ptr noundef @.str.3, ptr noundef %253) #9
  br label %255

255:                                              ; preds = %250, %142
  br label %256

256:                                              ; preds = %255, %50
  %257 = getelementptr inbounds [1024 x i8], ptr %10, i64 0, i64 0
  %258 = load ptr, ptr %2, align 8, !tbaa !5
  %259 = call ptr @fgets(ptr noundef %257, i32 noundef 1024, ptr noundef %258)
  br label %39, !llvm.loop !15

260:                                              ; preds = %48
  %261 = load i32, ptr @atomnum, align 4, !tbaa !9
  %262 = load ptr, ptr @aminoacid, align 8, !tbaa !5
  %263 = load i32, ptr @totalAminoAcids, align 4, !tbaa !9
  %264 = sext i32 %263 to i64
  %265 = getelementptr inbounds %struct.AAStr, ptr %262, i64 %264
  %266 = getelementptr inbounds %struct.AAStr, ptr %265, i32 0, i32 3
  store i32 %261, ptr %266, align 8, !tbaa !18
  %267 = load i32, ptr @totalAminoAcids, align 4, !tbaa !9
  %268 = load ptr, ptr @protein, align 8, !tbaa !5
  %269 = load i32, ptr @numofprotein, align 4, !tbaa !9
  %270 = sext i32 %269 to i64
  %271 = getelementptr inbounds %struct.PepStr, ptr %268, i64 %270
  %272 = getelementptr inbounds %struct.PepStr, ptr %271, i32 0, i32 3
  store i32 %267, ptr %272, align 4, !tbaa !20
  %273 = load i32, ptr @atomnum, align 4, !tbaa !9
  %274 = load ptr, ptr @protein, align 8, !tbaa !5
  %275 = load i32, ptr @numofprotein, align 4, !tbaa !9
  %276 = sext i32 %275 to i64
  %277 = getelementptr inbounds %struct.PepStr, ptr %274, i64 %276
  %278 = getelementptr inbounds %struct.PepStr, ptr %277, i32 0, i32 1
  store i32 %273, ptr %278, align 4, !tbaa !23
  %279 = load i32, ptr @atomnum, align 4, !tbaa !9
  %280 = add nsw i32 %279, 1
  %281 = sext i32 %280 to i64
  %282 = call noalias ptr @calloc(i64 noundef %281, i64 noundef 8) #13
  store ptr %282, ptr @connectionMap, align 8, !tbaa !5
  %283 = load i32, ptr @atomnum, align 4, !tbaa !9
  %284 = add nsw i32 %283, 1
  %285 = load i32, ptr @atomnum, align 4, !tbaa !9
  %286 = add nsw i32 %285, 1
  %287 = mul nsw i32 %284, %286
  %288 = sext i32 %287 to i64
  %289 = call noalias ptr @calloc(i64 noundef %288, i64 noundef 4) #13
  %290 = load ptr, ptr @connectionMap, align 8, !tbaa !5
  %291 = getelementptr inbounds ptr, ptr %290, i64 0
  store ptr %289, ptr %291, align 8, !tbaa !5
  call void @llvm.lifetime.start.p0(i64 4, ptr %17) #9
  store i32 1, ptr %17, align 4, !tbaa !9
  br label %292

292:                                              ; preds = %312, %260
  %293 = load i32, ptr %17, align 4, !tbaa !9
  %294 = load i32, ptr @atomnum, align 4, !tbaa !9
  %295 = add nsw i32 %294, 1
  %296 = icmp slt i32 %293, %295
  br i1 %296, label %298, label %297

297:                                              ; preds = %292
  call void @llvm.lifetime.end.p0(i64 4, ptr %17) #9
  br label %315

298:                                              ; preds = %292
  %299 = load ptr, ptr @connectionMap, align 8, !tbaa !5
  %300 = getelementptr inbounds ptr, ptr %299, i64 0
  %301 = load ptr, ptr %300, align 8, !tbaa !5
  %302 = load i32, ptr %17, align 4, !tbaa !9
  %303 = load i32, ptr @atomnum, align 4, !tbaa !9
  %304 = add nsw i32 %303, 1
  %305 = mul nsw i32 %302, %304
  %306 = sext i32 %305 to i64
  %307 = getelementptr inbounds i32, ptr %301, i64 %306
  %308 = load ptr, ptr @connectionMap, align 8, !tbaa !5
  %309 = load i32, ptr %17, align 4, !tbaa !9
  %310 = sext i32 %309 to i64
  %311 = getelementptr inbounds ptr, ptr %308, i64 %310
  store ptr %307, ptr %311, align 8, !tbaa !5
  br label %312

312:                                              ; preds = %298
  %313 = load i32, ptr %17, align 4, !tbaa !9
  %314 = add nsw i32 %313, 1
  store i32 %314, ptr %17, align 4, !tbaa !9
  br label %292, !llvm.loop !25

315:                                              ; preds = %297
  call void @llvm.lifetime.start.p0(i64 4, ptr %18) #9
  store i32 1, ptr %18, align 4, !tbaa !9
  br label %316

316:                                              ; preds = %378, %315
  %317 = load i32, ptr %18, align 4, !tbaa !9
  %318 = load i32, ptr @numofprotein, align 4, !tbaa !9
  %319 = icmp sle i32 %317, %318
  br i1 %319, label %321, label %320

320:                                              ; preds = %316
  store i32 9, ptr %19, align 4
  call void @llvm.lifetime.end.p0(i64 4, ptr %18) #9
  br label %381

321:                                              ; preds = %316
  %322 = load i32, ptr %18, align 4, !tbaa !9
  %323 = load ptr, ptr @protein, align 8, !tbaa !5
  %324 = load i32, ptr %18, align 4, !tbaa !9
  %325 = sext i32 %324 to i64
  %326 = getelementptr inbounds %struct.PepStr, ptr %323, i64 %325
  %327 = getelementptr inbounds %struct.PepStr, ptr %326, i32 0, i32 0
  %328 = load i32, ptr %327, align 8, !tbaa !24
  %329 = load ptr, ptr @protein, align 8, !tbaa !5
  %330 = load i32, ptr %18, align 4, !tbaa !9
  %331 = sext i32 %330 to i64
  %332 = getelementptr inbounds %struct.PepStr, ptr %329, i64 %331
  %333 = getelementptr inbounds %struct.PepStr, ptr %332, i32 0, i32 2
  %334 = load i32, ptr %333, align 8, !tbaa !22
  %335 = load ptr, ptr @protein, align 8, !tbaa !5
  %336 = load i32, ptr %18, align 4, !tbaa !9
  %337 = sext i32 %336 to i64
  %338 = getelementptr inbounds %struct.PepStr, ptr %335, i64 %337
  %339 = getelementptr inbounds %struct.PepStr, ptr %338, i32 0, i32 1
  %340 = load i32, ptr %339, align 4, !tbaa !23
  %341 = load ptr, ptr @protein, align 8, !tbaa !5
  %342 = load i32, ptr %18, align 4, !tbaa !9
  %343 = sext i32 %342 to i64
  %344 = getelementptr inbounds %struct.PepStr, ptr %341, i64 %343
  %345 = getelementptr inbounds %struct.PepStr, ptr %344, i32 0, i32 3
  %346 = load i32, ptr %345, align 4, !tbaa !20
  %347 = call i32 (ptr, ...) @printf(ptr noundef @.str.143, i32 noundef %322, i32 noundef %328, i32 noundef %334, i32 noundef %340, i32 noundef %346)
  %348 = call i32 (ptr, ...) @printf(ptr noundef @.str.144)
  call void @llvm.lifetime.start.p0(i64 4, ptr %20) #9
  %349 = load ptr, ptr @protein, align 8, !tbaa !5
  %350 = load i32, ptr %18, align 4, !tbaa !9
  %351 = sext i32 %350 to i64
  %352 = getelementptr inbounds %struct.PepStr, ptr %349, i64 %351
  %353 = getelementptr inbounds %struct.PepStr, ptr %352, i32 0, i32 2
  %354 = load i32, ptr %353, align 8, !tbaa !22
  store i32 %354, ptr %20, align 4, !tbaa !9
  br label %355

355:                                              ; preds = %373, %321
  %356 = load i32, ptr %20, align 4, !tbaa !9
  %357 = load ptr, ptr @protein, align 8, !tbaa !5
  %358 = load i32, ptr %18, align 4, !tbaa !9
  %359 = sext i32 %358 to i64
  %360 = getelementptr inbounds %struct.PepStr, ptr %357, i64 %359
  %361 = getelementptr inbounds %struct.PepStr, ptr %360, i32 0, i32 3
  %362 = load i32, ptr %361, align 4, !tbaa !20
  %363 = icmp sle i32 %356, %362
  br i1 %363, label %365, label %364

364:                                              ; preds = %355
  store i32 12, ptr %19, align 4
  call void @llvm.lifetime.end.p0(i64 4, ptr %20) #9
  br label %376

365:                                              ; preds = %355
  %366 = load ptr, ptr @aminoacid, align 8, !tbaa !5
  %367 = load i32, ptr %20, align 4, !tbaa !9
  %368 = sext i32 %367 to i64
  %369 = getelementptr inbounds %struct.AAStr, ptr %366, i64 %368
  %370 = getelementptr inbounds %struct.AAStr, ptr %369, i32 0, i32 0
  %371 = getelementptr inbounds [5 x i8], ptr %370, i64 0, i64 0
  %372 = call i32 (ptr, ...) @printf(ptr noundef @.str.145, ptr noundef %371)
  br label %373

373:                                              ; preds = %365
  %374 = load i32, ptr %20, align 4, !tbaa !9
  %375 = add nsw i32 %374, 1
  store i32 %375, ptr %20, align 4, !tbaa !9
  br label %355, !llvm.loop !26

376:                                              ; preds = %364
  %377 = call i32 (ptr, ...) @printf(ptr noundef @.str.84)
  br label %378

378:                                              ; preds = %376
  %379 = load i32, ptr %18, align 4, !tbaa !9
  %380 = add nsw i32 %379, 1
  store i32 %380, ptr %18, align 4, !tbaa !9
  br label %316, !llvm.loop !27

381:                                              ; preds = %320
  %382 = load ptr, ptr %15, align 8, !tbaa !5
  %383 = call i32 @fclose(ptr noundef %382)
  call void @llvm.lifetime.end.p0(i64 8, ptr %16) #9
  call void @llvm.lifetime.end.p0(i64 8, ptr %15) #9
  call void @llvm.lifetime.end.p0(i64 24, ptr %14) #9
  call void @llvm.lifetime.end.p0(i64 160, ptr %13) #9
  call void @llvm.lifetime.end.p0(i64 8, ptr %12) #9
  call void @llvm.lifetime.end.p0(i64 1024, ptr %11) #9
  call void @llvm.lifetime.end.p0(i64 1024, ptr %10) #9
  call void @llvm.lifetime.end.p0(i64 256, ptr %9) #9
  call void @llvm.lifetime.end.p0(i64 8, ptr %8) #9
  call void @llvm.lifetime.end.p0(i64 8, ptr %7) #9
  call void @llvm.lifetime.end.p0(i64 8, ptr %6) #9
  call void @llvm.lifetime.end.p0(i64 4, ptr %5) #9
  call void @llvm.lifetime.end.p0(i64 4, ptr %4) #9
  call void @llvm.lifetime.end.p0(i64 4, ptr %3) #9
  ret void
}

; Function Attrs: nocallback nofree nounwind willreturn memory(argmem: write)
declare void @llvm.memset.p0.i64(ptr nocapture writeonly, i8, i64, i1 immarg) #7

; Function Attrs: nounwind
declare i32 @fprintf(ptr noundef, ptr noundef, ...) #4

; Function Attrs: nounwind uwtable
declare dso_local i32 @CheckValidAtom(ptr noundef, ptr noundef, i32 noundef) #6

; Function Attrs: nounwind allocsize(1)
declare ptr @realloc(ptr noundef, i64 noundef) #8

attributes #0 = { nocallback nofree nosync nounwind willreturn memory(argmem: readwrite) }
attributes #1 = { nounwind allocsize(0,1) "no-trapping-math"="true" "stack-protector-buffer-size"="8" "target-cpu"="x86-64" "target-features"="+cmov,+cx8,+fxsr,+mmx,+sse,+sse2,+x87" "tune-cpu"="generic" }
attributes #2 = { nounwind willreturn memory(read) "no-trapping-math"="true" "stack-protector-buffer-size"="8" "target-cpu"="x86-64" "target-features"="+cmov,+cx8,+fxsr,+mmx,+sse,+sse2,+x87" "tune-cpu"="generic" }
attributes #3 = { "no-trapping-math"="true" "stack-protector-buffer-size"="8" "target-cpu"="x86-64" "target-features"="+cmov,+cx8,+fxsr,+mmx,+sse,+sse2,+x87" "tune-cpu"="generic" }
attributes #4 = { nounwind "no-trapping-math"="true" "stack-protector-buffer-size"="8" "target-cpu"="x86-64" "target-features"="+cmov,+cx8,+fxsr,+mmx,+sse,+sse2,+x87" "tune-cpu"="generic" }
attributes #5 = { noreturn nounwind "no-trapping-math"="true" "stack-protector-buffer-size"="8" "target-cpu"="x86-64" "target-features"="+cmov,+cx8,+fxsr,+mmx,+sse,+sse2,+x87" "tune-cpu"="generic" }
attributes #6 = { nounwind uwtable "min-legal-vector-width"="0" "no-trapping-math"="true" "stack-protector-buffer-size"="8" "target-cpu"="x86-64" "target-features"="+cmov,+cx8,+fxsr,+mmx,+sse,+sse2,+x87" "tune-cpu"="generic" }
attributes #7 = { nocallback nofree nounwind willreturn memory(argmem: write) }
attributes #8 = { nounwind allocsize(1) "no-trapping-math"="true" "stack-protector-buffer-size"="8" "target-cpu"="x86-64" "target-features"="+cmov,+cx8,+fxsr,+mmx,+sse,+sse2,+x87" "tune-cpu"="generic" }
attributes #9 = { nounwind }
attributes #10 = { noreturn nounwind }
attributes #11 = { nounwind willreturn memory(read) }
attributes #12 = { nounwind allocsize(1) }
attributes #13 = { nounwind allocsize(0,1) }

!llvm.module.flags = !{!0, !1, !2, !3}
!llvm.ident = !{!4}

!0 = !{i32 1, !"wchar_size", i32 4}
!1 = !{i32 8, !"PIC Level", i32 2}
!2 = !{i32 7, !"PIE Level", i32 2}
!3 = !{i32 7, !"uwtable", i32 2}
!4 = !{!"clang version 19.1.0 (git@github.com:llvm/llvm-project.git a4bf6cd7cfb1a1421ba92bca9d017b49936c55e4)"}
!5 = !{!6, !6, i64 0}
!6 = !{!"any pointer", !7, i64 0}
!7 = !{!"omnipotent char", !8, i64 0}
!8 = !{!"Simple C/C++ TBAA"}
!9 = !{!10, !10, i64 0}
!10 = !{!"int", !7, i64 0}
!11 = !{!12, !12, i64 0}
!12 = !{!"double", !7, i64 0}
!13 = distinct !{!13, !14}
!14 = !{!"llvm.loop.mustprogress"}
!15 = distinct !{!15, !14}
!16 = !{!17, !10, i64 20}
!17 = !{!"AAStr", !7, i64 0, !10, i64 8, !10, i64 12, !10, i64 16, !10, i64 20, !12, i64 24}
!18 = !{!17, !10, i64 16}
!19 = !{!17, !10, i64 12}
!20 = !{!21, !10, i64 12}
!21 = !{!"PepStr", !10, i64 0, !10, i64 4, !10, i64 8, !10, i64 12, !12, i64 16}
!22 = !{!21, !10, i64 8}
!23 = !{!21, !10, i64 4}
!24 = !{!21, !10, i64 0}
!25 = distinct !{!25, !14}
!26 = distinct !{!26, !14}
!27 = distinct !{!27, !14}


; Optimized IR (opt -passes='default<O3>'):
target datalayout = "e-m:e-p270:32:32-p271:32:32-p272:64:64-i64:64-i128:128-f80:128-n8:16:32:64-S128"
target triple = "x86_64-unknown-linux-gnu"

%struct.REMDStr = type { i32, i32, i32, [50 x i8], [50 x i8], %struct.REMDTempStr }
%struct.REMDTempStr = type { i32, double }
%struct.AAStr = type { [5 x i8], i32, i32, i32, i32, double }
%struct.PepStr = type { i32, i32, i32, i32, double }

@.str.2 = external hidden unnamed_addr constant [71 x i8], align 1
@datadir = external global [1024 x i8], align 16
@.str.3 = external hidden unnamed_addr constant [3 x i8], align 1
@boxDimension = external local_unnamed_addr global [4 x double], align 16
@REMDInfo = external global %struct.REMDStr, align 8
@.str.84 = external hidden unnamed_addr constant [2 x i8], align 1
@.str.94 = external hidden unnamed_addr constant [2 x i8], align 1
@atomnum = external local_unnamed_addr global i32, align 4
@numofprotein = external local_unnamed_addr global i32, align 4
@totalAminoAcids = external local_unnamed_addr global i32, align 4
@protein = external local_unnamed_addr global ptr, align 8
@aminoacid = external local_unnamed_addr global ptr, align 8
@connectionMap = external local_unnamed_addr global ptr, align 8
@Methodtype = external global [20 x i8], align 16
@.str.115 = external hidden unnamed_addr constant [10 x i8], align 1
@.str.128 = external hidden unnamed_addr constant [140 x i8], align 1
@.str.129 = external hidden unnamed_addr constant [18 x i8], align 1
@.str.130 = external hidden unnamed_addr constant [20 x i8], align 1
@.str.131 = external hidden unnamed_addr constant [2 x i8], align 1
@.str.132 = external hidden unnamed_addr constant [16 x i8], align 1
@.str.133 = external hidden unnamed_addr constant [4 x i8], align 1
@.str.134 = external hidden unnamed_addr constant [5 x i8], align 1
@.str.135 = external hidden unnamed_addr constant [11 x i8], align 1
@.str.136 = external hidden unnamed_addr constant [4 x i8], align 1
@.str.137 = external hidden unnamed_addr constant [24 x i8], align 1
@.str.138 = external hidden unnamed_addr constant [4 x i8], align 1
@.str.139 = external hidden unnamed_addr constant [58 x i8], align 1
@.str.140 = external hidden unnamed_addr constant [47 x i8], align 1
@.str.141 = external hidden unnamed_addr constant [9 x i8], align 1
@.str.142 = external hidden unnamed_addr constant [27 x i8], align 1
@.str.143 = external hidden unnamed_addr constant [36 x i8], align 1
@.str.144 = external hidden unnamed_addr constant [9 x i8], align 1
@.str.145 = external hidden unnamed_addr constant [4 x i8], align 1

; Function Attrs: mustprogress nocallback nofree nosync nounwind willreturn memory(argmem: readwrite)
declare void @llvm.lifetime.start.p0(i64 immarg, ptr nocapture) #0

; Function Attrs: mustprogress nofree nounwind willreturn allockind("alloc,zeroed") allocsize(0,1) memory(inaccessiblemem: readwrite)
declare noalias noundef ptr @calloc(i64 noundef, i64 noundef) local_unnamed_addr #1

; Function Attrs: mustprogress nofree nounwind willreturn memory(argmem: read)
declare i32 @strcmp(ptr nocapture noundef, ptr nocapture noundef) local_unnamed_addr #2

; Function Attrs: nofree nounwind
declare noundef i32 @printf(ptr nocapture noundef readonly, ...) local_unnamed_addr #3

; Function Attrs: nofree nounwind
declare noundef i32 @sprintf(ptr noalias nocapture noundef writeonly, ptr nocapture noundef readonly, ...) local_unnamed_addr #3

; Function Attrs: noreturn nounwind
declare void @exit(i32 noundef) local_unnamed_addr #4

; Function Attrs: mustprogress nofree nounwind willreturn memory(argmem: read)
declare i32 @strncmp(ptr nocapture noundef, ptr nocapture noundef, i64 noundef) local_unnamed_addr #2

; Function Attrs: nofree nounwind
declare noalias noundef ptr @fopen(ptr nocapture noundef readonly, ptr nocapture noundef readonly) local_unnamed_addr #3

; Function Attrs: nofree nounwind
declare noundef i32 @fclose(ptr nocapture noundef) local_unnamed_addr #3

; Function Attrs: mustprogress nocallback nofree nosync nounwind willreturn memory(argmem: readwrite)
declare void @llvm.lifetime.end.p0(i64 immarg, ptr nocapture) #0

declare i32 @__isoc99_fscanf(ptr noundef, ptr noundef, ...) local_unnamed_addr #5

; Function Attrs: nofree nounwind
declare noundef ptr @fgets(ptr noundef, i32 noundef, ptr nocapture noundef) local_unnamed_addr #3

; Function Attrs: nounwind uwtable
define dso_local void @ReadPDBFile(ptr noundef %0) local_unnamed_addr #6 {
  %2 = alloca i32, align 4
  %3 = alloca [8 x i8], align 8
  %4 = alloca [8 x i8], align 1
  %5 = alloca [8 x i8], align 1
  %6 = alloca [256 x i8], align 16
  %7 = alloca [1024 x i8], align 16
  %8 = alloca [1024 x i8], align 16
  %9 = alloca [8 x i8], align 1
  %10 = alloca [20 x [8 x i8]], align 16
  %11 = alloca [3 x double], align 16
  call void @llvm.lifetime.start.p0(i64 4, ptr nonnull %2) #9
  call void @llvm.lifetime.start.p0(i64 8, ptr nonnull %3) #9
  store i64 0, ptr %3, align 8
  call void @llvm.lifetime.start.p0(i64 8, ptr nonnull %4) #9
  call void @llvm.lifetime.start.p0(i64 8, ptr nonnull %5) #9
  call void @llvm.lifetime.start.p0(i64 256, ptr nonnull %6) #9
  call void @llvm.memset.p0.i64(ptr noundef nonnull align 16 dereferenceable(256) %6, i8 0, i64 256, i1 false)
  call void @llvm.lifetime.start.p0(i64 1024, ptr nonnull %7) #9
  call void @llvm.lifetime.start.p0(i64 1024, ptr nonnull %8) #9
  call void @llvm.lifetime.start.p0(i64 8, ptr nonnull %9) #9
  call void @llvm.lifetime.start.p0(i64 160, ptr nonnull %10) #9
  call void @llvm.memset.p0.i64(ptr noundef nonnull align 16 dereferenceable(160) %10, i8 0, i64 160, i1 false)
  call void @llvm.lifetime.start.p0(i64 24, ptr nonnull %11) #9
  %12 = load double, ptr getelementptr inbounds (i8, ptr @boxDimension, i64 8), align 8, !tbaa !5
  %13 = fcmp oeq double %12, 0.000000e+00
  %14 = load double, ptr getelementptr inbounds (i8, ptr @boxDimension, i64 16), align 16
  %15 = fcmp oeq double %14, 0.000000e+00
  %or.cond = select i1 %13, i1 true, i1 %15
  %16 = load double, ptr getelementptr inbounds (i8, ptr @boxDimension, i64 24), align 8
  %17 = fcmp oeq double %16, 0.000000e+00
  %or.cond3 = select i1 %or.cond, i1 true, i1 %17
  br i1 %or.cond3, label %18, label %21

18:                                               ; preds = %1
  %19 = tail call i32 (ptr, ...) @printf(ptr noundef nonnull dereferenceable(1) @.str.128)
  %20 = tail call i32 (ptr, ...) @printf(ptr noundef nonnull dereferenceable(1) @.str.129, ptr noundef nonnull @.str.2, i32 noundef 785)
  tail call void @exit(i32 noundef 1) #10
  unreachable

21:                                               ; preds = %1
  %22 = call i32 (ptr, ptr, ...) @sprintf(ptr noundef nonnull dereferenceable(1) %8, ptr noundef nonnull dereferenceable(1) @.str.130, ptr noundef nonnull @datadir, ptr noundef nonnull getelementptr inbounds (i8, ptr @REMDInfo, i64 62)) #9
  %23 = call noalias ptr @fopen(ptr noundef nonnull %8, ptr noundef nonnull @.str.131)
  %24 = tail call i32 (ptr, ptr, ...) @fprintf(ptr noundef %23, ptr noundef nonnull @.str.132, ptr noundef nonnull @datadir) #9
  store i32 0, ptr @atomnum, align 4, !tbaa !9
  store i32 0, ptr @numofprotein, align 4, !tbaa !9
  store i32 0, ptr @totalAminoAcids, align 4, !tbaa !9
  store ptr null, ptr @protein, align 8, !tbaa !11
  store ptr null, ptr @aminoacid, align 8, !tbaa !11
  %25 = call i32 (ptr, ptr, ...) @__isoc99_fscanf(ptr noundef %0, ptr noundef nonnull @.str.3, ptr noundef nonnull %7) #9
  %.not7175 = icmp eq i32 %25, -1
  br i1 %.not7175, label %.critedge, label %.lr.ph73.lr.ph

.lr.ph73.lr.ph:                                   ; preds = %21
  %26 = getelementptr inbounds i8, ptr %11, i64 8
  %27 = getelementptr inbounds i8, ptr %11, i64 16
  br label %.lr.ph73

.lr.ph73:                                         ; preds = %.lr.ph73.lr.ph, %.outer
  %.045.ph77 = phi i32 [ 0, %.lr.ph73.lr.ph ], [ %.3, %.outer ]
  %.046.ph76 = phi i32 [ 0, %.lr.ph73.lr.ph ], [ %.147, %.outer ]
  br label %28

28:                                               ; preds = %.lr.ph73, %66
  %.04572 = phi i32 [ %.045.ph77, %.lr.ph73 ], [ %.2, %66 ]
  %29 = call i32 @strncmp(ptr noundef nonnull dereferenceable(1) %7, ptr noundef nonnull dereferenceable(1) @.str.133, i64 noundef 3) #11
  %.not51 = icmp eq i32 %29, 0
  br i1 %.not51, label %.critedge, label %30

30:                                               ; preds = %28
  %31 = call i32 @strcmp(ptr noundef nonnull dereferenceable(1) %7, ptr noundef nonnull dereferenceable(1) @.str.134) #11
  %32 = icmp eq i32 %31, 0
  br i1 %32, label %33, label %.outer

33:                                               ; preds = %30
  %34 = call i32 (ptr, ptr, ...) @__isoc99_fscanf(ptr noundef %0, ptr noundef nonnull @.str.135, ptr noundef nonnull %7, ptr noundef nonnull %5, ptr noundef nonnull %9, ptr noundef nonnull %4, ptr noundef nonnull %2) #9
  %35 = load i32, ptr %2, align 4, !tbaa !9
  %.not55 = icmp eq i32 %.046.ph76, %35
  br i1 %.not55, label %55, label %36

36:                                               ; preds = %33
  %37 = call i32 @strcmp(ptr noundef nonnull dereferenceable(1) %9, ptr noundef nonnull dereferenceable(1) @.str.136) #11
  %38 = icmp eq i32 %37, 0
  %.str.138. = select i1 %38, ptr @.str.138, ptr %9
  %39 = call i32 (ptr, ptr, ...) @sprintf(ptr noundef nonnull dereferenceable(1) %8, ptr noundef nonnull dereferenceable(1) @.str.137, ptr noundef nonnull @datadir, ptr noundef nonnull @Methodtype, ptr noundef nonnull %.str.138.) #9
  %40 = call noalias ptr @fopen(ptr noundef nonnull %8, ptr noundef nonnull @.str.94)
  %41 = icmp eq ptr %40, null
  br i1 %41, label %42, label %45

42:                                               ; preds = %36
  %43 = call i32 (ptr, ...) @printf(ptr noundef nonnull dereferenceable(1) @.str.139, ptr noundef nonnull %9, ptr noundef nonnull @datadir, ptr noundef nonnull @Methodtype)
  %44 = call i32 (ptr, ...) @printf(ptr noundef nonnull dereferenceable(1) @.str.140, ptr noundef nonnull @.str.2, i32 noundef 812)
  call void @exit(i32 noundef 1) #10
  unreachable

45:                                               ; preds = %36
  %46 = call ptr @fgets(ptr noundef nonnull %7, i32 noundef 1024, ptr noundef nonnull %40)
  %47 = call i32 (ptr, ptr, ...) @__isoc99_fscanf(ptr noundef nonnull %40, ptr noundef nonnull @.str.3, ptr noundef nonnull %7) #9
  %.not5667 = icmp eq i32 %47, 0
  br i1 %.not5667, label %.critedge5, label %.lr.ph

.lr.ph:                                           ; preds = %45, %50
  %indvars.iv = phi i64 [ %indvars.iv.next, %50 ], [ 0, %45 ]
  %48 = call i32 @strcmp(ptr noundef nonnull dereferenceable(1) @.str.134, ptr noundef nonnull dereferenceable(1) %7) #11
  %49 = icmp eq i32 %48, 0
  br i1 %49, label %50, label %.critedge5.loopexit

50:                                               ; preds = %.lr.ph
  %indvars.iv.next = add nuw nsw i64 %indvars.iv, 1
  %51 = getelementptr inbounds [20 x [8 x i8]], ptr %10, i64 0, i64 %indvars.iv
  %52 = call i32 (ptr, ptr, ...) @__isoc99_fscanf(ptr noundef nonnull %40, ptr noundef nonnull @.str.141, ptr noundef nonnull %51, ptr noundef nonnull %7) #9
  %53 = call i32 (ptr, ptr, ...) @__isoc99_fscanf(ptr noundef nonnull %40, ptr noundef nonnull @.str.3, ptr noundef nonnull %7) #9
  %.not56 = icmp eq i32 %53, 0
  br i1 %.not56, label %.critedge5.loopexit, label %.lr.ph, !llvm.loop !13

.critedge5.loopexit:                              ; preds = %50, %.lr.ph
  %.1.lcssa.ph.in = phi i64 [ %indvars.iv, %.lr.ph ], [ %indvars.iv.next, %50 ]
  %.1.lcssa.ph = trunc i64 %.1.lcssa.ph.in to i32
  br label %.critedge5

.critedge5:                                       ; preds = %.critedge5.loopexit, %45
  %.1.lcssa = phi i32 [ 0, %45 ], [ %.1.lcssa.ph, %.critedge5.loopexit ]
  %54 = call i32 @fclose(ptr noundef nonnull %40)
  br label %55

55:                                               ; preds = %.critedge5, %33
  %.2 = phi i32 [ %.1.lcssa, %.critedge5 ], [ %.04572, %33 ]
  %56 = call i32 @CheckValidAtom(ptr noundef nonnull %5, ptr noundef nonnull %10, i32 noundef %.2)
  %.not57 = icmp eq i32 %56, 0
  br i1 %.not57, label %66, label %57

57:                                               ; preds = %55
  %58 = load i32, ptr @atomnum, align 4, !tbaa !9
  %59 = add nsw i32 %58, 1
  store i32 %59, ptr @atomnum, align 4, !tbaa !9
  %60 = call i32 (ptr, ptr, ...) @__isoc99_fscanf(ptr noundef %0, ptr noundef nonnull @.str.115, ptr noundef nonnull %11, ptr noundef nonnull %26, ptr noundef nonnull %27) #9
  %61 = load double, ptr %11, align 16, !tbaa !5
  %62 = load double, ptr %26, align 8, !tbaa !5
  %63 = load double, ptr %27, align 16, !tbaa !5
  %64 = call i32 (ptr, ptr, ...) @fprintf(ptr noundef %23, ptr noundef nonnull @.str.142, ptr noundef nonnull %5, double noundef %61, double noundef %62, double noundef %63) #9
  %65 = load i32, ptr %2, align 4, !tbaa !9
  %.not58 = icmp eq i32 %.046.ph76, %65
  br i1 %.not58, label %69, label %71

66:                                               ; preds = %55
  %67 = call ptr @fgets(ptr noundef nonnull %7, i32 noundef 1024, ptr noundef %0)
  %68 = call i32 (ptr, ptr, ...) @__isoc99_fscanf(ptr noundef %0, ptr noundef nonnull @.str.3, ptr noundef nonnull %7) #9
  %.not = icmp eq i32 %68, -1
  br i1 %.not, label %.critedge, label %28, !llvm.loop !15

69:                                               ; preds = %57
  %70 = call i32 @strcmp(ptr noundef nonnull dereferenceable(1) %9, ptr noundef nonnull dereferenceable(1) %6) #11
  %.not59 = icmp eq i32 %70, 0
  br i1 %.not59, label %.outer, label %71

71:                                               ; preds = %69, %57
  %72 = load ptr, ptr @aminoacid, align 8, !tbaa !11
  %73 = load i32, ptr @totalAminoAcids, align 4, !tbaa !9
  %74 = add nsw i32 %73, 1
  store i32 %74, ptr @totalAminoAcids, align 4, !tbaa !9
  %75 = add nsw i32 %73, 2
  %76 = sext i32 %75 to i64
  %77 = shl nsw i64 %76, 5
  %78 = call ptr @realloc(ptr noundef %72, i64 noundef %77) #12
  store ptr %78, ptr @aminoacid, align 8, !tbaa !11
  %79 = load i32, ptr @totalAminoAcids, align 4, !tbaa !9
  %80 = sext i32 %79 to i64
  %81 = getelementptr inbounds %struct.AAStr, ptr %78, i64 %80
  %82 = call i32 (ptr, ptr, ...) @sprintf(ptr noundef nonnull dereferenceable(1) %81, ptr noundef nonnull dereferenceable(1) @.str.3, ptr noundef nonnull %9) #9
  %83 = call i32 @strcmp(ptr noundef nonnull dereferenceable(1) %4, ptr noundef nonnull dereferenceable(1) %3) #11
  %84 = icmp ne i32 %83, 0
  %85 = load i32, ptr @numofprotein, align 4
  %86 = icmp eq i32 %85, 0
  %or.cond7 = select i1 %84, i1 true, i1 %86
  %87 = load i32, ptr %2, align 4
  %88 = icmp slt i32 %87, %.046.ph76
  %or.cond61 = select i1 %or.cond7, i1 true, i1 %88
  %89 = zext i1 %or.cond61 to i32
  %90 = add nsw i32 %85, %89
  %91 = load ptr, ptr @aminoacid, align 8, !tbaa !11
  %92 = load i32, ptr @totalAminoAcids, align 4, !tbaa !9
  %93 = sext i32 %92 to i64
  %94 = getelementptr inbounds %struct.AAStr, ptr %91, i64 %93, i32 4
  store i32 %90, ptr %94, align 4, !tbaa !16
  %95 = load i32, ptr @atomnum, align 4, !tbaa !9
  %96 = add nsw i32 %95, -1
  %97 = load i32, ptr @totalAminoAcids, align 4, !tbaa !9
  %98 = sext i32 %97 to i64
  %99 = getelementptr %struct.AAStr, ptr %91, i64 %98
  %100 = getelementptr i8, ptr %99, i64 -16
  store i32 %96, ptr %100, align 8, !tbaa !18
  %101 = load i32, ptr @atomnum, align 4, !tbaa !9
  %102 = load i32, ptr @totalAminoAcids, align 4, !tbaa !9
  %103 = sext i32 %102 to i64
  %104 = getelementptr inbounds %struct.AAStr, ptr %91, i64 %103, i32 2
  store i32 %101, ptr %104, align 4, !tbaa !19
  %105 = call i32 @strcmp(ptr noundef nonnull dereferenceable(1) %4, ptr noundef nonnull dereferenceable(1) %3) #11
  %106 = icmp ne i32 %105, 0
  %107 = load i32, ptr @numofprotein, align 4
  %108 = icmp eq i32 %107, 0
  %or.cond9 = select i1 %106, i1 true, i1 %108
  %109 = load i32, ptr %2, align 4
  %110 = icmp slt i32 %109, %.046.ph76
  %or.cond63 = select i1 %or.cond9, i1 true, i1 %110
  br i1 %or.cond63, label %111, label %130

111:                                              ; preds = %71
  %112 = call i32 (ptr, ptr, ...) @sprintf(ptr noundef nonnull dereferenceable(1) %3, ptr noundef nonnull dereferenceable(1) @.str.3, ptr noundef nonnull %4) #9
  %113 = load ptr, ptr @protein, align 8, !tbaa !11
  %114 = load i32, ptr @numofprotein, align 4, !tbaa !9
  %115 = add nsw i32 %114, 1
  store i32 %115, ptr @numofprotein, align 4, !tbaa !9
  %116 = add nsw i32 %114, 2
  %117 = sext i32 %116 to i64
  %118 = mul nsw i64 %117, 24
  %119 = call ptr @realloc(ptr noundef %113, i64 noundef %118) #12
  store ptr %119, ptr @protein, align 8, !tbaa !11
  %120 = load i32, ptr @totalAminoAcids, align 4, !tbaa !9
  %121 = add nsw i32 %120, -1
  %122 = load i32, ptr @numofprotein, align 4, !tbaa !9
  %123 = sext i32 %122 to i64
  %124 = getelementptr %struct.PepStr, ptr %119, i64 %123
  %125 = getelementptr i8, ptr %124, i64 -12
  store i32 %121, ptr %125, align 4, !tbaa !20
  %126 = getelementptr inbounds %struct.PepStr, ptr %119, i64 %123, i32 2
  store i32 %120, ptr %126, align 8, !tbaa !22
  %127 = load i32, ptr @atomnum, align 4, !tbaa !9
  %128 = add nsw i32 %127, -1
  %129 = getelementptr i8, ptr %124, i64 -20
  store i32 %128, ptr %129, align 4, !tbaa !23
  store i32 %127, ptr %124, align 8, !tbaa !24
  %.pre = load i32, ptr %2, align 4, !tbaa !9
  br label %130

130:                                              ; preds = %71, %111
  %131 = phi i32 [ %109, %71 ], [ %.pre, %111 ]
  %132 = call i32 (ptr, ptr, ...) @sprintf(ptr noundef nonnull dereferenceable(1) %6, ptr noundef nonnull dereferenceable(1) @.str.3, ptr noundef nonnull %9) #9
  br label %.outer

.outer:                                           ; preds = %30, %69, %130
  %.147 = phi i32 [ %131, %130 ], [ %.046.ph76, %69 ], [ %.046.ph76, %30 ]
  %.3 = phi i32 [ %.2, %130 ], [ %.2, %69 ], [ %.04572, %30 ]
  %133 = call ptr @fgets(ptr noundef nonnull %7, i32 noundef 1024, ptr noundef %0)
  %134 = call i32 (ptr, ptr, ...) @__isoc99_fscanf(ptr noundef %0, ptr noundef nonnull @.str.3, ptr noundef nonnull %7) #9
  %.not71 = icmp eq i32 %134, -1
  br i1 %.not71, label %.critedge, label %.lr.ph73, !llvm.loop !15

.critedge:                                        ; preds = %.outer, %28, %66, %21
  %135 = load i32, ptr @atomnum, align 4, !tbaa !9
  %136 = load ptr, ptr @aminoacid, align 8, !tbaa !11
  %137 = load i32, ptr @totalAminoAcids, align 4, !tbaa !9
  %138 = sext i32 %137 to i64
  %139 = getelementptr inbounds %struct.AAStr, ptr %136, i64 %138, i32 3
  store i32 %135, ptr %139, align 8, !tbaa !18
  %140 = load i32, ptr @totalAminoAcids, align 4, !tbaa !9
  %141 = load ptr, ptr @protein, align 8, !tbaa !11
  %142 = load i32, ptr @numofprotein, align 4, !tbaa !9
  %143 = sext i32 %142 to i64
  %144 = getelementptr inbounds %struct.PepStr, ptr %141, i64 %143, i32 3
  store i32 %140, ptr %144, align 4, !tbaa !20
  %145 = load i32, ptr @atomnum, align 4, !tbaa !9
  %146 = load i32, ptr @numofprotein, align 4, !tbaa !9
  %147 = sext i32 %146 to i64
  %148 = getelementptr inbounds %struct.PepStr, ptr %141, i64 %147, i32 1
  store i32 %145, ptr %148, align 4, !tbaa !23
  %149 = add nsw i32 %145, 1
  %150 = sext i32 %149 to i64
  %151 = call noalias ptr @calloc(i64 noundef %150, i64 noundef 8) #13
  store ptr %151, ptr @connectionMap, align 8, !tbaa !11
  %152 = mul nsw i32 %149, %149
  %153 = zext nneg i32 %152 to i64
  %154 = call noalias ptr @calloc(i64 noundef %153, i64 noundef 4) #13
  store ptr %154, ptr %151, align 8, !tbaa !11
  %.not5278 = icmp slt i32 %145, 1
  br i1 %.not5278, label %.preheader, label %.lr.ph80.preheader

.lr.ph80.preheader:                               ; preds = %.critedge
  %155 = zext nneg i32 %149 to i64
  %156 = add nsw i64 %155, -1
  %157 = add nsw i64 %155, -2
  %xtraiter = and i64 %156, 3
  %158 = icmp ult i64 %157, 3
  br i1 %158, label %.preheader.loopexit.unr-lcssa, label %.lr.ph80.preheader.new

.lr.ph80.preheader.new:                           ; preds = %.lr.ph80.preheader
  %unroll_iter = and i64 %156, -4
  br label %.lr.ph80

.preheader.loopexit.unr-lcssa:                    ; preds = %.lr.ph80, %.lr.ph80.preheader
  %indvars.iv93.unr = phi i64 [ 1, %.lr.ph80.preheader ], [ %indvars.iv.next94.3, %.lr.ph80 ]
  %lcmp.mod.not = icmp eq i64 %xtraiter, 0
  br i1 %lcmp.mod.not, label %.preheader, label %.lr.ph80.epil

.lr.ph80.epil:                                    ; preds = %.preheader.loopexit.unr-lcssa, %.lr.ph80.epil
  %indvars.iv93.epil = phi i64 [ %indvars.iv.next94.epil, %.lr.ph80.epil ], [ %indvars.iv93.unr, %.preheader.loopexit.unr-lcssa ]
  %epil.iter = phi i64 [ %epil.iter.next, %.lr.ph80.epil ], [ 0, %.preheader.loopexit.unr-lcssa ]
  %159 = load ptr, ptr @connectionMap, align 8, !tbaa !11
  %160 = load ptr, ptr %159, align 8, !tbaa !11
  %161 = mul nuw nsw i64 %indvars.iv93.epil, %155
  %162 = getelementptr inbounds i32, ptr %160, i64 %161
  %163 = getelementptr inbounds ptr, ptr %159, i64 %indvars.iv93.epil
  store ptr %162, ptr %163, align 8, !tbaa !11
  %indvars.iv.next94.epil = add nuw nsw i64 %indvars.iv93.epil, 1
  %epil.iter.next = add i64 %epil.iter, 1
  %epil.iter.cmp.not = icmp eq i64 %epil.iter.next, %xtraiter
  br i1 %epil.iter.cmp.not, label %.preheader, label %.lr.ph80.epil, !llvm.loop !25

.preheader:                                       ; preds = %.preheader.loopexit.unr-lcssa, %.lr.ph80.epil, %.critedge
  %164 = load i32, ptr @numofprotein, align 4, !tbaa !9
  %.not5384 = icmp slt i32 %164, 1
  br i1 %.not5384, label %._crit_edge87, label %.lr.ph86

.lr.ph80:                                         ; preds = %.lr.ph80, %.lr.ph80.preheader.new
  %indvars.iv93 = phi i64 [ 1, %.lr.ph80.preheader.new ], [ %indvars.iv.next94.3, %.lr.ph80 ]
  %niter = phi i64 [ 0, %.lr.ph80.preheader.new ], [ %niter.next.3, %.lr.ph80 ]
  %165 = load ptr, ptr @connectionMap, align 8, !tbaa !11
  %166 = load ptr, ptr %165, align 8, !tbaa !11
  %167 = mul nuw nsw i64 %indvars.iv93, %155
  %168 = getelementptr inbounds i32, ptr %166, i64 %167
  %169 = getelementptr inbounds ptr, ptr %165, i64 %indvars.iv93
  store ptr %168, ptr %169, align 8, !tbaa !11
  %indvars.iv.next94 = add nuw nsw i64 %indvars.iv93, 1
  %170 = load ptr, ptr @connectionMap, align 8, !tbaa !11
  %171 = load ptr, ptr %170, align 8, !tbaa !11
  %172 = mul nuw nsw i64 %indvars.iv.next94, %155
  %173 = getelementptr inbounds i32, ptr %171, i64 %172
  %174 = getelementptr inbounds ptr, ptr %170, i64 %indvars.iv.next94
  store ptr %173, ptr %174, align 8, !tbaa !11
  %indvars.iv.next94.1 = add nuw nsw i64 %indvars.iv93, 2
  %175 = load ptr, ptr @connectionMap, align 8, !tbaa !11
  %176 = load ptr, ptr %175, align 8, !tbaa !11
  %177 = mul nuw nsw i64 %indvars.iv.next94.1, %155
  %178 = getelementptr inbounds i32, ptr %176, i64 %177
  %179 = getelementptr inbounds ptr, ptr %175, i64 %indvars.iv.next94.1
  store ptr %178, ptr %179, align 8, !tbaa !11
  %indvars.iv.next94.2 = add nuw nsw i64 %indvars.iv93, 3
  %180 = load ptr, ptr @connectionMap, align 8, !tbaa !11
  %181 = load ptr, ptr %180, align 8, !tbaa !11
  %182 = mul nuw nsw i64 %indvars.iv.next94.2, %155
  %183 = getelementptr inbounds i32, ptr %181, i64 %182
  %184 = getelementptr inbounds ptr, ptr %180, i64 %indvars.iv.next94.2
  store ptr %183, ptr %184, align 8, !tbaa !11
  %indvars.iv.next94.3 = add nuw nsw i64 %indvars.iv93, 4
  %niter.next.3 = add i64 %niter, 4
  %niter.ncmp.3 = icmp eq i64 %niter.next.3, %unroll_iter
  br i1 %niter.ncmp.3, label %.preheader.loopexit.unr-lcssa, label %.lr.ph80, !llvm.loop !27

._crit_edge87:                                    ; preds = %._crit_edge, %.preheader
  %185 = call i32 @fclose(ptr noundef %23)
  call void @llvm.lifetime.end.p0(i64 24, ptr nonnull %11) #9
  call void @llvm.lifetime.end.p0(i64 160, ptr nonnull %10) #9
  call void @llvm.lifetime.end.p0(i64 8, ptr nonnull %9) #9
  call void @llvm.lifetime.end.p0(i64 1024, ptr nonnull %8) #9
  call void @llvm.lifetime.end.p0(i64 1024, ptr nonnull %7) #9
  call void @llvm.lifetime.end.p0(i64 256, ptr nonnull %6) #9
  call void @llvm.lifetime.end.p0(i64 8, ptr nonnull %5) #9
  call void @llvm.lifetime.end.p0(i64 8, ptr nonnull %4) #9
  call void @llvm.lifetime.end.p0(i64 8, ptr nonnull %3) #9
  call void @llvm.lifetime.end.p0(i64 4, ptr nonnull %2) #9
  ret void

.lr.ph86:                                         ; preds = %.preheader, %._crit_edge
  %indvars.iv101 = phi i64 [ %indvars.iv.next102, %._crit_edge ], [ 1, %.preheader ]
  %186 = load ptr, ptr @protein, align 8, !tbaa !11
  %187 = getelementptr inbounds %struct.PepStr, ptr %186, i64 %indvars.iv101
  %188 = load i32, ptr %187, align 8, !tbaa !24
  %189 = getelementptr inbounds i8, ptr %187, i64 8
  %190 = load i32, ptr %189, align 8, !tbaa !22
  %191 = getelementptr inbounds i8, ptr %187, i64 4
  %192 = load i32, ptr %191, align 4, !tbaa !23
  %193 = getelementptr inbounds i8, ptr %187, i64 12
  %194 = load i32, ptr %193, align 4, !tbaa !20
  %195 = trunc nuw nsw i64 %indvars.iv101 to i32
  %196 = call i32 (ptr, ...) @printf(ptr noundef nonnull dereferenceable(1) @.str.143, i32 noundef %195, i32 noundef %188, i32 noundef %190, i32 noundef %192, i32 noundef %194)
  %197 = call i32 (ptr, ...) @printf(ptr noundef nonnull dereferenceable(1) @.str.144)
  %198 = load ptr, ptr @protein, align 8, !tbaa !11
  %199 = getelementptr inbounds %struct.PepStr, ptr %198, i64 %indvars.iv101, i32 2
  %200 = load i32, ptr %199, align 8, !tbaa !22
  %201 = getelementptr inbounds %struct.PepStr, ptr %198, i64 %indvars.iv101, i32 3
  %202 = load i32, ptr %201, align 4, !tbaa !20
  %.not5481 = icmp sgt i32 %200, %202
  br i1 %.not5481, label %._crit_edge, label %.lr.ph83.preheader

.lr.ph83.preheader:                               ; preds = %.lr.ph86
  %203 = sext i32 %200 to i64
  br label %.lr.ph83

._crit_edge:                                      ; preds = %.lr.ph83, %.lr.ph86
  %204 = call i32 (ptr, ...) @printf(ptr noundef nonnull dereferenceable(1) @.str.84)
  %indvars.iv.next102 = add nuw nsw i64 %indvars.iv101, 1
  %205 = load i32, ptr @numofprotein, align 4, !tbaa !9
  %206 = sext i32 %205 to i64
  %.not53.not = icmp slt i64 %indvars.iv101, %206
  br i1 %.not53.not, label %.lr.ph86, label %._crit_edge87, !llvm.loop !28

.lr.ph83:                                         ; preds = %.lr.ph83.preheader, %.lr.ph83
  %indvars.iv97 = phi i64 [ %203, %.lr.ph83.preheader ], [ %indvars.iv.next98, %.lr.ph83 ]
  %207 = load ptr, ptr @aminoacid, align 8, !tbaa !11
  %208 = getelementptr inbounds %struct.AAStr, ptr %207, i64 %indvars.iv97
  %209 = call i32 (ptr, ...) @printf(ptr noundef nonnull dereferenceable(1) @.str.145, ptr noundef %208)
  %indvars.iv.next98 = add nsw i64 %indvars.iv97, 1
  %210 = load ptr, ptr @protein, align 8, !tbaa !11
  %211 = getelementptr inbounds %struct.PepStr, ptr %210, i64 %indvars.iv101, i32 3
  %212 = load i32, ptr %211, align 4, !tbaa !20
  %213 = sext i32 %212 to i64
  %.not54.not = icmp slt i64 %indvars.iv97, %213
  br i1 %.not54.not, label %.lr.ph83, label %._crit_edge, !llvm.loop !29
}

; Function Attrs: mustprogress nocallback nofree nounwind willreturn memory(argmem: write)
declare void @llvm.memset.p0.i64(ptr nocapture writeonly, i8, i64, i1 immarg) #7

; Function Attrs: nofree nounwind
declare noundef i32 @fprintf(ptr nocapture noundef, ptr nocapture noundef readonly, ...) local_unnamed_addr #3

; Function Attrs: nounwind uwtable
declare dso_local i32 @CheckValidAtom(ptr noundef, ptr noundef, i32 noundef) local_unnamed_addr #6

; Function Attrs: mustprogress nounwind willreturn allockind("realloc") allocsize(1) memory(argmem: readwrite, inaccessiblemem: readwrite)
declare noalias noundef ptr @realloc(ptr allocptr nocapture noundef, i64 noundef) local_unnamed_addr #8

attributes #0 = { mustprogress nocallback nofree nosync nounwind willreturn memory(argmem: readwrite) }
attributes #1 = { mustprogress nofree nounwind willreturn allockind("alloc,zeroed") allocsize(0,1) memory(inaccessiblemem: readwrite) "alloc-family"="malloc" "no-trapping-math"="true" "stack-protector-buffer-size"="8" "target-cpu"="x86-64" "target-features"="+cmov,+cx8,+fxsr,+mmx,+sse,+sse2,+x87" "tune-cpu"="generic" }
attributes #2 = { mustprogress nofree nounwind willreturn memory(argmem: read) "no-trapping-math"="true" "stack-protector-buffer-size"="8" "target-cpu"="x86-64" "target-features"="+cmov,+cx8,+fxsr,+mmx,+sse,+sse2,+x87" "tune-cpu"="generic" }
attributes #3 = { nofree nounwind "no-trapping-math"="true" "stack-protector-buffer-size"="8" "target-cpu"="x86-64" "target-features"="+cmov,+cx8,+fxsr,+mmx,+sse,+sse2,+x87" "tune-cpu"="generic" }
attributes #4 = { noreturn nounwind "no-trapping-math"="true" "stack-protector-buffer-size"="8" "target-cpu"="x86-64" "target-features"="+cmov,+cx8,+fxsr,+mmx,+sse,+sse2,+x87" "tune-cpu"="generic" }
attributes #5 = { "no-trapping-math"="true" "stack-protector-buffer-size"="8" "target-cpu"="x86-64" "target-features"="+cmov,+cx8,+fxsr,+mmx,+sse,+sse2,+x87" "tune-cpu"="generic" }
attributes #6 = { nounwind uwtable "min-legal-vector-width"="0" "no-trapping-math"="true" "stack-protector-buffer-size"="8" "target-cpu"="x86-64" "target-features"="+cmov,+cx8,+fxsr,+mmx,+sse,+sse2,+x87" "tune-cpu"="generic" }
attributes #7 = { mustprogress nocallback nofree nounwind willreturn memory(argmem: write) }
attributes #8 = { mustprogress nounwind willreturn allockind("realloc") allocsize(1) memory(argmem: readwrite, inaccessiblemem: readwrite) "alloc-family"="malloc" "no-trapping-math"="true" "stack-protector-buffer-size"="8" "target-cpu"="x86-64" "target-features"="+cmov,+cx8,+fxsr,+mmx,+sse,+sse2,+x87" "tune-cpu"="generic" }
attributes #9 = { nounwind }
attributes #10 = { noreturn nounwind }
attributes #11 = { nounwind willreturn memory(read) }
attributes #12 = { nounwind allocsize(1) }
attributes #13 = { nounwind allocsize(0,1) }

!llvm.module.flags = !{!0, !1, !2, !3}
!llvm.ident = !{!4}

!0 = !{i32 1, !"wchar_size", i32 4}
!1 = !{i32 8, !"PIC Level", i32 2}
!2 = !{i32 7, !"PIE Level", i32 2}
!3 = !{i32 7, !"uwtable", i32 2}
!4 = !{!"clang version 19.1.0 (git@github.com:llvm/llvm-project.git a4bf6cd7cfb1a1421ba92bca9d017b49936c55e4)"}
!5 = !{!6, !6, i64 0}
!6 = !{!"double", !7, i64 0}
!7 = !{!"omnipotent char", !8, i64 0}
!8 = !{!"Simple C/C++ TBAA"}
!9 = !{!10, !10, i64 0}
!10 = !{!"int", !7, i64 0}
!11 = !{!12, !12, i64 0}
!12 = !{!"any pointer", !7, i64 0}
!13 = distinct !{!13, !14}
!14 = !{!"llvm.loop.mustprogress"}
!15 = distinct !{!15, !14}
!16 = !{!17, !10, i64 20}
!17 = !{!"AAStr", !7, i64 0, !10, i64 8, !10, i64 12, !10, i64 16, !10, i64 20, !6, i64 24}
!18 = !{!17, !10, i64 16}
!19 = !{!17, !10, i64 12}
!20 = !{!21, !10, i64 12}
!21 = !{!"PepStr", !10, i64 0, !10, i64 4, !10, i64 8, !10, i64 12, !6, i64 16}
!22 = !{!21, !10, i64 8}
!23 = !{!21, !10, i64 4}
!24 = !{!21, !10, i64 0}
!25 = distinct !{!25, !26}
!26 = !{!"llvm.loop.unroll.disable"}
!27 = distinct !{!27, !14}
!28 = distinct !{!28, !14}
!29 = distinct !{!29, !14}


; Effective O3 passes: EarlyCSEPass,GVNPass,GlobalOptPass,IPSCCPPass,IndVarSimplifyPass,InferAlignmentPass,InferFunctionAttrsPass,InstCombinePass,InstSimplifyPass,JumpThreadingPass,LCSSAPass,LICMPass,LoopRotatePass,LoopSimplifyPass,LoopUnrollPass,ReassociatePass,SROAPass,SimplifyCFGPass,TailCallElimPass