; 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.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.134 = external hidden unnamed_addr constant [5 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
@.str.146 = external hidden unnamed_addr constant [3 x i8], align 1
@.str.147 = external hidden unnamed_addr constant [11 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

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
declare i32 @__isoc99_sscanf(ptr noundef, ptr noundef, ...) #4

; Function Attrs: nounwind uwtable
define dso_local void @ReadGROFile(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 i32, align 4
  %7 = alloca [8 x i8], align 1
  %8 = alloca [256 x i8], align 16
  %9 = alloca [1024 x i8], align 16
  %10 = alloca [1024 x i8], align 16
  %11 = alloca [8 x i8], align 1
  %12 = alloca [20 x [8 x i8]], align 16
  %13 = alloca [3 x double], align 16
  %14 = alloca ptr, align 8
  %15 = alloca ptr, align 8
  %16 = alloca i32, align 4
  %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
  store i32 0, ptr %5, align 4, !tbaa !9
  call void @llvm.lifetime.start.p0(i64 4, ptr %6) #9
  call void @llvm.lifetime.start.p0(i64 8, ptr %7) #9
  call void @llvm.lifetime.start.p0(i64 256, ptr %8) #9
  call void @llvm.memset.p0.i64(ptr align 16 %8, i8 0, i64 256, i1 false)
  call void @llvm.lifetime.start.p0(i64 1024, ptr %9) #9
  call void @llvm.lifetime.start.p0(i64 1024, ptr %10) #9
  call void @llvm.lifetime.start.p0(i64 8, ptr %11) #9
  call void @llvm.lifetime.start.p0(i64 160, ptr %12) #9
  call void @llvm.memset.p0.i64(ptr align 16 %12, i8 0, i64 160, i1 false)
  call void @llvm.lifetime.start.p0(i64 24, ptr %13) #9
  call void @llvm.lifetime.start.p0(i64 8, ptr %14) #9
  call void @llvm.lifetime.start.p0(i64 8, ptr %15) #9
  store ptr null, ptr %15, align 8, !tbaa !5
  %21 = getelementptr inbounds [1024 x i8], ptr %10, i64 0, i64 0
  %22 = call i32 (ptr, ptr, ...) @sprintf(ptr noundef %21, ptr noundef @.str.130, ptr noundef @datadir, ptr noundef getelementptr inbounds (%struct.REMDStr, ptr @REMDInfo, i32 0, i32 4)) #9
  %23 = getelementptr inbounds [1024 x i8], ptr %10, i64 0, i64 0
  %24 = call noalias ptr @fopen(ptr noundef %23, ptr noundef @.str.131)
  store ptr %24, ptr %14, align 8, !tbaa !5
  %25 = load ptr, ptr %14, align 8, !tbaa !5
  %26 = call i32 (ptr, ptr, ...) @fprintf(ptr noundef %25, 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
  %27 = getelementptr inbounds [1024 x i8], ptr %9, i64 0, i64 0
  %28 = load ptr, ptr %2, align 8, !tbaa !5
  %29 = call ptr @fgets(ptr noundef %27, i32 noundef 1024, ptr noundef %28)
  %30 = load ptr, ptr %2, align 8, !tbaa !5
  %31 = call i32 (ptr, ptr, ...) @__isoc99_fscanf(ptr noundef %30, ptr noundef @.str.146, ptr noundef %4)
  call void @llvm.lifetime.start.p0(i64 4, ptr %16) #9
  store i32 1, ptr %16, align 4, !tbaa !9
  br label %32

32:                                               ; preds = %258, %1
  %33 = load i32, ptr %16, align 4, !tbaa !9
  %34 = load i32, ptr %4, align 4, !tbaa !9
  %35 = icmp sle i32 %33, %34
  br i1 %35, label %37, label %36

36:                                               ; preds = %32
  call void @llvm.lifetime.end.p0(i64 4, ptr %16) #9
  br label %261

37:                                               ; preds = %32
  %38 = getelementptr inbounds [8 x i8], ptr %11, i64 0, i64 0
  call void @llvm.memset.p0.i64(ptr align 1 %38, i8 0, i64 8, i1 false)
  %39 = getelementptr inbounds [8 x i8], ptr %7, i64 0, i64 0
  call void @llvm.memset.p0.i64(ptr align 1 %39, i8 0, i64 8, i1 false)
  %40 = load ptr, ptr %2, align 8, !tbaa !5
  %41 = getelementptr inbounds [8 x i8], ptr %11, i64 0, i64 0
  %42 = getelementptr inbounds [8 x i8], ptr %7, i64 0, i64 0
  %43 = getelementptr inbounds [1024 x i8], ptr %9, i64 0, i64 0
  %44 = call i32 (ptr, ptr, ...) @__isoc99_fscanf(ptr noundef %40, ptr noundef @.str.147, ptr noundef %6, ptr noundef %41, ptr noundef %42, ptr noundef %43)
  %45 = getelementptr inbounds [8 x i8], ptr %11, i64 0, i64 0
  call void @RemoveSpace(ptr noundef %45)
  %46 = getelementptr inbounds [8 x i8], ptr %7, i64 0, i64 0
  call void @RemoveSpace(ptr noundef %46)
  %47 = load i32, ptr %5, align 4, !tbaa !9
  %48 = load i32, ptr %6, align 4, !tbaa !9
  %49 = icmp ne i32 %47, %48
  br i1 %49, label %55, label %50

50:                                               ; preds = %37
  %51 = getelementptr inbounds [8 x i8], ptr %11, i64 0, i64 0
  %52 = getelementptr inbounds [256 x i8], ptr %8, i64 0, i64 0
  %53 = call i32 @strcmp(ptr noundef %51, ptr noundef %52) #10
  %54 = icmp ne i32 %53, 0
  br i1 %54, label %55, label %102

55:                                               ; preds = %50, %37
  %56 = getelementptr inbounds [8 x i8], ptr %11, i64 0, i64 0
  %57 = call i32 @strcmp(ptr noundef %56, ptr noundef @.str.136) #10
  %58 = icmp eq i32 %57, 0
  br i1 %58, label %59, label %62

59:                                               ; preds = %55
  %60 = getelementptr inbounds [1024 x i8], ptr %10, i64 0, i64 0
  %61 = call i32 (ptr, ptr, ...) @sprintf(ptr noundef %60, ptr noundef @.str.137, ptr noundef @datadir, ptr noundef @Methodtype, ptr noundef @.str.138) #9
  br label %66

62:                                               ; preds = %55
  %63 = getelementptr inbounds [1024 x i8], ptr %10, i64 0, i64 0
  %64 = getelementptr inbounds [8 x i8], ptr %11, i64 0, i64 0
  %65 = call i32 (ptr, ptr, ...) @sprintf(ptr noundef %63, ptr noundef @.str.137, ptr noundef @datadir, ptr noundef @Methodtype, ptr noundef %64) #9
  br label %66

66:                                               ; preds = %62, %59
  %67 = getelementptr inbounds [1024 x i8], ptr %10, i64 0, i64 0
  %68 = call noalias ptr @fopen(ptr noundef %67, ptr noundef @.str.94)
  store ptr %68, ptr %15, align 8, !tbaa !5
  %69 = load ptr, ptr %15, align 8, !tbaa !5
  %70 = icmp eq ptr %69, null
  br i1 %70, label %71, label %75

71:                                               ; preds = %66
  %72 = getelementptr inbounds [8 x i8], ptr %11, i64 0, i64 0
  %73 = call i32 (ptr, ...) @printf(ptr noundef @.str.139, ptr noundef %72, ptr noundef @datadir, ptr noundef @Methodtype)
  %74 = call i32 (ptr, ...) @printf(ptr noundef @.str.140, ptr noundef @.str.2, i32 noundef 920)
  call void @exit(i32 noundef 1) #11
  unreachable

75:                                               ; preds = %66
  %76 = getelementptr inbounds [1024 x i8], ptr %9, i64 0, i64 0
  %77 = load ptr, ptr %15, align 8, !tbaa !5
  %78 = call ptr @fgets(ptr noundef %76, i32 noundef 1024, ptr noundef %77)
  store i32 0, ptr %3, align 4, !tbaa !9
  br label %79

79:                                               ; preds = %90, %75
  %80 = load ptr, ptr %15, align 8, !tbaa !5
  %81 = getelementptr inbounds [1024 x i8], ptr %9, i64 0, i64 0
  %82 = call i32 (ptr, ptr, ...) @__isoc99_fscanf(ptr noundef %80, ptr noundef @.str.3, ptr noundef %81)
  %83 = icmp ne i32 %82, 0
  br i1 %83, label %84, label %88

84:                                               ; preds = %79
  %85 = getelementptr inbounds [1024 x i8], ptr %9, i64 0, i64 0
  %86 = call i32 @strcmp(ptr noundef @.str.134, ptr noundef %85) #10
  %87 = icmp eq i32 %86, 0
  br label %88

88:                                               ; preds = %84, %79
  %89 = phi i1 [ false, %79 ], [ %87, %84 ]
  br i1 %89, label %90, label %99

90:                                               ; preds = %88
  %91 = load ptr, ptr %15, align 8, !tbaa !5
  %92 = load i32, ptr %3, align 4, !tbaa !9
  %93 = add nsw i32 %92, 1
  store i32 %93, ptr %3, align 4, !tbaa !9
  %94 = sext i32 %92 to i64
  %95 = getelementptr inbounds [20 x [8 x i8]], ptr %12, i64 0, i64 %94
  %96 = getelementptr inbounds [8 x i8], ptr %95, i64 0, i64 0
  %97 = getelementptr inbounds [1024 x i8], ptr %9, i64 0, i64 0
  %98 = call i32 (ptr, ptr, ...) @__isoc99_fscanf(ptr noundef %91, ptr noundef @.str.141, ptr noundef %96, ptr noundef %97)
  br label %79, !llvm.loop !11

99:                                               ; preds = %88
  %100 = load ptr, ptr %15, align 8, !tbaa !5
  %101 = call i32 @fclose(ptr noundef %100)
  br label %102

102:                                              ; preds = %99, %50
  %103 = getelementptr inbounds [8 x i8], ptr %7, i64 0, i64 0
  %104 = getelementptr inbounds [20 x [8 x i8]], ptr %12, i64 0, i64 0
  %105 = load i32, ptr %3, align 4, !tbaa !9
  %106 = call i32 @CheckValidAtom(ptr noundef %103, ptr noundef %104, i32 noundef %105)
  %107 = icmp ne i32 %106, 0
  br i1 %107, label %108, label %137

108:                                              ; preds = %102
  %109 = load i32, ptr @atomnum, align 4, !tbaa !9
  %110 = add nsw i32 %109, 1
  store i32 %110, ptr @atomnum, align 4, !tbaa !9
  %111 = getelementptr inbounds [1024 x i8], ptr %9, i64 0, i64 0
  %112 = load ptr, ptr %2, align 8, !tbaa !5
  %113 = call ptr @fgets(ptr noundef %111, i32 noundef 1024, ptr noundef %112)
  %114 = getelementptr inbounds [1024 x i8], ptr %9, i64 0, i64 0
  %115 = getelementptr inbounds [3 x double], ptr %13, i64 0, i64 0
  %116 = getelementptr inbounds [3 x double], ptr %13, i64 0, i64 1
  %117 = getelementptr inbounds [3 x double], ptr %13, i64 0, i64 2
  %118 = call i32 (ptr, ptr, ...) @__isoc99_sscanf(ptr noundef %114, ptr noundef @.str.115, ptr noundef %115, ptr noundef %116, ptr noundef %117) #9
  %119 = getelementptr inbounds [3 x double], ptr %13, i64 0, i64 0
  %120 = load double, ptr %119, align 16, !tbaa !13
  %121 = fmul double %120, 1.000000e+01
  store double %121, ptr %119, align 16, !tbaa !13
  %122 = getelementptr inbounds [3 x double], ptr %13, i64 0, i64 1
  %123 = load double, ptr %122, align 8, !tbaa !13
  %124 = fmul double %123, 1.000000e+01
  store double %124, ptr %122, align 8, !tbaa !13
  %125 = getelementptr inbounds [3 x double], ptr %13, i64 0, i64 2
  %126 = load double, ptr %125, align 16, !tbaa !13
  %127 = fmul double %126, 1.000000e+01
  store double %127, ptr %125, align 16, !tbaa !13
  %128 = load ptr, ptr %14, align 8, !tbaa !5
  %129 = getelementptr inbounds [8 x i8], ptr %7, i64 0, i64 0
  %130 = getelementptr inbounds [3 x double], ptr %13, i64 0, i64 0
  %131 = load double, ptr %130, align 16, !tbaa !13
  %132 = getelementptr inbounds [3 x double], ptr %13, i64 0, i64 1
  %133 = load double, ptr %132, align 8, !tbaa !13
  %134 = getelementptr inbounds [3 x double], ptr %13, i64 0, i64 2
  %135 = load double, ptr %134, align 16, !tbaa !13
  %136 = call i32 (ptr, ptr, ...) @fprintf(ptr noundef %128, ptr noundef @.str.142, ptr noundef %129, double noundef %131, double noundef %133, double noundef %135) #9
  br label %141

137:                                              ; preds = %102
  %138 = getelementptr inbounds [1024 x i8], ptr %9, i64 0, i64 0
  %139 = load ptr, ptr %2, align 8, !tbaa !5
  %140 = call ptr @fgets(ptr noundef %138, i32 noundef 1024, ptr noundef %139)
  br label %141

141:                                              ; preds = %137, %108
  %142 = load i32, ptr %5, align 4, !tbaa !9
  %143 = load i32, ptr %6, align 4, !tbaa !9
  %144 = icmp ne i32 %142, %143
  br i1 %144, label %150, label %145

145:                                              ; preds = %141
  %146 = getelementptr inbounds [8 x i8], ptr %11, i64 0, i64 0
  %147 = getelementptr inbounds [256 x i8], ptr %8, i64 0, i64 0
  %148 = call i32 @strcmp(ptr noundef %146, ptr noundef %147) #10
  %149 = icmp ne i32 %148, 0
  br i1 %149, label %150, label %257

150:                                              ; preds = %145, %141
  %151 = load ptr, ptr @aminoacid, align 8, !tbaa !5
  %152 = load i32, ptr @totalAminoAcids, align 4, !tbaa !9
  %153 = add nsw i32 %152, 1
  store i32 %153, ptr @totalAminoAcids, align 4, !tbaa !9
  %154 = add nsw i32 %153, 1
  %155 = sext i32 %154 to i64
  %156 = mul i64 32, %155
  %157 = call ptr @realloc(ptr noundef %151, i64 noundef %156) #12
  store ptr %157, ptr @aminoacid, align 8, !tbaa !5
  %158 = load ptr, ptr @aminoacid, align 8, !tbaa !5
  %159 = load i32, ptr @totalAminoAcids, align 4, !tbaa !9
  %160 = sext i32 %159 to i64
  %161 = getelementptr inbounds %struct.AAStr, ptr %158, i64 %160
  %162 = getelementptr inbounds %struct.AAStr, ptr %161, i32 0, i32 0
  %163 = getelementptr inbounds [5 x i8], ptr %162, i64 0, i64 0
  %164 = getelementptr inbounds [8 x i8], ptr %11, i64 0, i64 0
  %165 = call i32 (ptr, ptr, ...) @sprintf(ptr noundef %163, ptr noundef @.str.3, ptr noundef %164) #9
  %166 = load i32, ptr %6, align 4, !tbaa !9
  %167 = load i32, ptr %5, align 4, !tbaa !9
  %168 = icmp slt i32 %166, %167
  br i1 %168, label %172, label %169

169:                                              ; preds = %150
  %170 = load i32, ptr @numofprotein, align 4, !tbaa !9
  %171 = icmp eq i32 %170, 0
  br i1 %171, label %172, label %175

172:                                              ; preds = %169, %150
  %173 = load i32, ptr @numofprotein, align 4, !tbaa !9
  %174 = add nsw i32 %173, 1
  br label %177

175:                                              ; preds = %169
  %176 = load i32, ptr @numofprotein, align 4, !tbaa !9
  br label %177

177:                                              ; preds = %175, %172
  %178 = phi i32 [ %174, %172 ], [ %176, %175 ]
  %179 = load ptr, ptr @aminoacid, align 8, !tbaa !5
  %180 = load i32, ptr @totalAminoAcids, align 4, !tbaa !9
  %181 = sext i32 %180 to i64
  %182 = getelementptr inbounds %struct.AAStr, ptr %179, i64 %181
  %183 = getelementptr inbounds %struct.AAStr, ptr %182, i32 0, i32 4
  store i32 %178, ptr %183, align 4, !tbaa !15
  %184 = load i32, ptr @atomnum, align 4, !tbaa !9
  %185 = sub nsw i32 %184, 1
  %186 = load ptr, ptr @aminoacid, align 8, !tbaa !5
  %187 = load i32, ptr @totalAminoAcids, align 4, !tbaa !9
  %188 = sub nsw i32 %187, 1
  %189 = sext i32 %188 to i64
  %190 = getelementptr inbounds %struct.AAStr, ptr %186, i64 %189
  %191 = getelementptr inbounds %struct.AAStr, ptr %190, i32 0, i32 3
  store i32 %185, ptr %191, align 8, !tbaa !17
  %192 = load i32, ptr @atomnum, align 4, !tbaa !9
  %193 = load ptr, ptr @aminoacid, align 8, !tbaa !5
  %194 = load i32, ptr @totalAminoAcids, align 4, !tbaa !9
  %195 = sext i32 %194 to i64
  %196 = getelementptr inbounds %struct.AAStr, ptr %193, i64 %195
  %197 = getelementptr inbounds %struct.AAStr, ptr %196, i32 0, i32 2
  store i32 %192, ptr %197, align 4, !tbaa !18
  %198 = load ptr, ptr @aminoacid, align 8, !tbaa !5
  %199 = load i32, ptr @totalAminoAcids, align 4, !tbaa !9
  %200 = sext i32 %199 to i64
  %201 = getelementptr inbounds %struct.AAStr, ptr %198, i64 %200
  %202 = getelementptr inbounds %struct.AAStr, ptr %201, i32 0, i32 0
  %203 = getelementptr inbounds [5 x i8], ptr %202, i64 0, i64 0
  %204 = call i32 @AAModel(ptr noundef %203)
  %205 = load ptr, ptr @aminoacid, align 8, !tbaa !5
  %206 = load i32, ptr @totalAminoAcids, align 4, !tbaa !9
  %207 = sext i32 %206 to i64
  %208 = getelementptr inbounds %struct.AAStr, ptr %205, i64 %207
  %209 = getelementptr inbounds %struct.AAStr, ptr %208, i32 0, i32 1
  store i32 %204, ptr %209, align 8, !tbaa !19
  %210 = load i32, ptr %6, align 4, !tbaa !9
  %211 = load i32, ptr %5, align 4, !tbaa !9
  %212 = icmp slt i32 %210, %211
  br i1 %212, label %216, label %213

213:                                              ; preds = %177
  %214 = load i32, ptr @numofprotein, align 4, !tbaa !9
  %215 = icmp eq i32 %214, 0
  br i1 %215, label %216, label %252

216:                                              ; preds = %213, %177
  %217 = load ptr, ptr @protein, align 8, !tbaa !5
  %218 = load i32, ptr @numofprotein, align 4, !tbaa !9
  %219 = add nsw i32 %218, 1
  store i32 %219, ptr @numofprotein, align 4, !tbaa !9
  %220 = add nsw i32 %219, 1
  %221 = sext i32 %220 to i64
  %222 = mul i64 24, %221
  %223 = call ptr @realloc(ptr noundef %217, i64 noundef %222) #12
  store ptr %223, ptr @protein, align 8, !tbaa !5
  %224 = load i32, ptr @totalAminoAcids, align 4, !tbaa !9
  %225 = sub nsw i32 %224, 1
  %226 = load ptr, ptr @protein, align 8, !tbaa !5
  %227 = load i32, ptr @numofprotein, align 4, !tbaa !9
  %228 = sub nsw i32 %227, 1
  %229 = sext i32 %228 to i64
  %230 = getelementptr inbounds %struct.PepStr, ptr %226, i64 %229
  %231 = getelementptr inbounds %struct.PepStr, ptr %230, i32 0, i32 3
  store i32 %225, ptr %231, align 4, !tbaa !20
  %232 = load i32, ptr @totalAminoAcids, align 4, !tbaa !9
  %233 = load ptr, ptr @protein, align 8, !tbaa !5
  %234 = load i32, ptr @numofprotein, align 4, !tbaa !9
  %235 = sext i32 %234 to i64
  %236 = getelementptr inbounds %struct.PepStr, ptr %233, i64 %235
  %237 = getelementptr inbounds %struct.PepStr, ptr %236, i32 0, i32 2
  store i32 %232, ptr %237, align 8, !tbaa !22
  %238 = load i32, ptr @atomnum, align 4, !tbaa !9
  %239 = sub nsw i32 %238, 1
  %240 = load ptr, ptr @protein, align 8, !tbaa !5
  %241 = load i32, ptr @numofprotein, align 4, !tbaa !9
  %242 = sub nsw i32 %241, 1
  %243 = sext i32 %242 to i64
  %244 = getelementptr inbounds %struct.PepStr, ptr %240, i64 %243
  %245 = getelementptr inbounds %struct.PepStr, ptr %244, i32 0, i32 1
  store i32 %239, ptr %245, align 4, !tbaa !23
  %246 = load i32, ptr @atomnum, align 4, !tbaa !9
  %247 = load ptr, ptr @protein, align 8, !tbaa !5
  %248 = load i32, ptr @numofprotein, align 4, !tbaa !9
  %249 = sext i32 %248 to i64
  %250 = getelementptr inbounds %struct.PepStr, ptr %247, i64 %249
  %251 = getelementptr inbounds %struct.PepStr, ptr %250, i32 0, i32 0
  store i32 %246, ptr %251, align 8, !tbaa !24
  br label %252

252:                                              ; preds = %216, %213
  %253 = load i32, ptr %6, align 4, !tbaa !9
  store i32 %253, ptr %5, align 4, !tbaa !9
  %254 = getelementptr inbounds [256 x i8], ptr %8, i64 0, i64 0
  %255 = getelementptr inbounds [8 x i8], ptr %11, i64 0, i64 0
  %256 = call i32 (ptr, ptr, ...) @sprintf(ptr noundef %254, ptr noundef @.str.3, ptr noundef %255) #9
  br label %257

257:                                              ; preds = %252, %145
  br label %258

258:                                              ; preds = %257
  %259 = load i32, ptr %16, align 4, !tbaa !9
  %260 = add nsw i32 %259, 1
  store i32 %260, ptr %16, align 4, !tbaa !9
  br label %32, !llvm.loop !25

261:                                              ; preds = %36
  %262 = load ptr, ptr %2, align 8, !tbaa !5
  %263 = call i32 (ptr, ptr, ...) @__isoc99_fscanf(ptr noundef %262, ptr noundef @.str.115, ptr noundef getelementptr inbounds ([4 x double], ptr @boxDimension, i64 0, i64 1), ptr noundef getelementptr inbounds ([4 x double], ptr @boxDimension, i64 0, i64 2), ptr noundef getelementptr inbounds ([4 x double], ptr @boxDimension, i64 0, i64 3))
  %264 = load double, ptr getelementptr inbounds ([4 x double], ptr @boxDimension, i64 0, i64 1), align 8, !tbaa !13
  %265 = fmul double %264, 1.000000e+01
  store double %265, ptr getelementptr inbounds ([4 x double], ptr @boxDimension, i64 0, i64 1), align 8, !tbaa !13
  %266 = load double, ptr getelementptr inbounds ([4 x double], ptr @boxDimension, i64 0, i64 2), align 16, !tbaa !13
  %267 = fmul double %266, 1.000000e+01
  store double %267, ptr getelementptr inbounds ([4 x double], ptr @boxDimension, i64 0, i64 2), align 16, !tbaa !13
  %268 = load double, ptr getelementptr inbounds ([4 x double], ptr @boxDimension, i64 0, i64 3), align 8, !tbaa !13
  %269 = fmul double %268, 1.000000e+01
  store double %269, ptr getelementptr inbounds ([4 x double], ptr @boxDimension, i64 0, i64 3), align 8, !tbaa !13
  %270 = load i32, ptr @atomnum, align 4, !tbaa !9
  %271 = load ptr, ptr @aminoacid, align 8, !tbaa !5
  %272 = load i32, ptr @totalAminoAcids, align 4, !tbaa !9
  %273 = sext i32 %272 to i64
  %274 = getelementptr inbounds %struct.AAStr, ptr %271, i64 %273
  %275 = getelementptr inbounds %struct.AAStr, ptr %274, i32 0, i32 3
  store i32 %270, ptr %275, align 8, !tbaa !17
  %276 = load i32, ptr @totalAminoAcids, align 4, !tbaa !9
  %277 = load ptr, ptr @protein, align 8, !tbaa !5
  %278 = load i32, ptr @numofprotein, align 4, !tbaa !9
  %279 = sext i32 %278 to i64
  %280 = getelementptr inbounds %struct.PepStr, ptr %277, i64 %279
  %281 = getelementptr inbounds %struct.PepStr, ptr %280, i32 0, i32 3
  store i32 %276, ptr %281, align 4, !tbaa !20
  %282 = load i32, ptr @atomnum, align 4, !tbaa !9
  %283 = load ptr, ptr @protein, align 8, !tbaa !5
  %284 = load i32, ptr @numofprotein, align 4, !tbaa !9
  %285 = sext i32 %284 to i64
  %286 = getelementptr inbounds %struct.PepStr, ptr %283, i64 %285
  %287 = getelementptr inbounds %struct.PepStr, ptr %286, i32 0, i32 1
  store i32 %282, ptr %287, align 4, !tbaa !23
  %288 = load i32, ptr @atomnum, align 4, !tbaa !9
  %289 = add nsw i32 %288, 1
  %290 = sext i32 %289 to i64
  %291 = call noalias ptr @calloc(i64 noundef %290, i64 noundef 8) #13
  store ptr %291, ptr @connectionMap, align 8, !tbaa !5
  %292 = load i32, ptr @atomnum, align 4, !tbaa !9
  %293 = add nsw i32 %292, 1
  %294 = load i32, ptr @atomnum, align 4, !tbaa !9
  %295 = add nsw i32 %294, 1
  %296 = mul nsw i32 %293, %295
  %297 = sext i32 %296 to i64
  %298 = call noalias ptr @calloc(i64 noundef %297, i64 noundef 4) #13
  %299 = load ptr, ptr @connectionMap, align 8, !tbaa !5
  %300 = getelementptr inbounds ptr, ptr %299, i64 0
  store ptr %298, ptr %300, 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 %301

301:                                              ; preds = %321, %261
  %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 = icmp slt i32 %302, %304
  br i1 %305, label %307, label %306

306:                                              ; preds = %301
  call void @llvm.lifetime.end.p0(i64 4, ptr %17) #9
  br label %324

307:                                              ; preds = %301
  %308 = load ptr, ptr @connectionMap, align 8, !tbaa !5
  %309 = getelementptr inbounds ptr, ptr %308, i64 0
  %310 = load ptr, ptr %309, align 8, !tbaa !5
  %311 = load i32, ptr %17, align 4, !tbaa !9
  %312 = load i32, ptr @atomnum, align 4, !tbaa !9
  %313 = add nsw i32 %312, 1
  %314 = mul nsw i32 %311, %313
  %315 = sext i32 %314 to i64
  %316 = getelementptr inbounds i32, ptr %310, i64 %315
  %317 = load ptr, ptr @connectionMap, align 8, !tbaa !5
  %318 = load i32, ptr %17, align 4, !tbaa !9
  %319 = sext i32 %318 to i64
  %320 = getelementptr inbounds ptr, ptr %317, i64 %319
  store ptr %316, ptr %320, align 8, !tbaa !5
  br label %321

321:                                              ; preds = %307
  %322 = load i32, ptr %17, align 4, !tbaa !9
  %323 = add nsw i32 %322, 1
  store i32 %323, ptr %17, align 4, !tbaa !9
  br label %301, !llvm.loop !26

324:                                              ; preds = %306
  call void @llvm.lifetime.start.p0(i64 4, ptr %18) #9
  store i32 1, ptr %18, align 4, !tbaa !9
  br label %325

325:                                              ; preds = %387, %324
  %326 = load i32, ptr %18, align 4, !tbaa !9
  %327 = load i32, ptr @numofprotein, align 4, !tbaa !9
  %328 = icmp sle i32 %326, %327
  br i1 %328, label %330, label %329

329:                                              ; preds = %325
  store i32 10, ptr %19, align 4
  call void @llvm.lifetime.end.p0(i64 4, ptr %18) #9
  br label %390

330:                                              ; preds = %325
  %331 = load i32, ptr %18, align 4, !tbaa !9
  %332 = load ptr, ptr @protein, align 8, !tbaa !5
  %333 = load i32, ptr %18, align 4, !tbaa !9
  %334 = sext i32 %333 to i64
  %335 = getelementptr inbounds %struct.PepStr, ptr %332, i64 %334
  %336 = getelementptr inbounds %struct.PepStr, ptr %335, i32 0, i32 0
  %337 = load i32, ptr %336, align 8, !tbaa !24
  %338 = load ptr, ptr @protein, align 8, !tbaa !5
  %339 = load i32, ptr %18, align 4, !tbaa !9
  %340 = sext i32 %339 to i64
  %341 = getelementptr inbounds %struct.PepStr, ptr %338, i64 %340
  %342 = getelementptr inbounds %struct.PepStr, ptr %341, i32 0, i32 2
  %343 = load i32, ptr %342, align 8, !tbaa !22
  %344 = load ptr, ptr @protein, align 8, !tbaa !5
  %345 = load i32, ptr %18, align 4, !tbaa !9
  %346 = sext i32 %345 to i64
  %347 = getelementptr inbounds %struct.PepStr, ptr %344, i64 %346
  %348 = getelementptr inbounds %struct.PepStr, ptr %347, i32 0, i32 1
  %349 = load i32, ptr %348, align 4, !tbaa !23
  %350 = load ptr, ptr @protein, align 8, !tbaa !5
  %351 = load i32, ptr %18, align 4, !tbaa !9
  %352 = sext i32 %351 to i64
  %353 = getelementptr inbounds %struct.PepStr, ptr %350, i64 %352
  %354 = getelementptr inbounds %struct.PepStr, ptr %353, i32 0, i32 3
  %355 = load i32, ptr %354, align 4, !tbaa !20
  %356 = call i32 (ptr, ...) @printf(ptr noundef @.str.143, i32 noundef %331, i32 noundef %337, i32 noundef %343, i32 noundef %349, i32 noundef %355)
  %357 = call i32 (ptr, ...) @printf(ptr noundef @.str.144)
  call void @llvm.lifetime.start.p0(i64 4, ptr %20) #9
  %358 = load ptr, ptr @protein, align 8, !tbaa !5
  %359 = load i32, ptr %18, align 4, !tbaa !9
  %360 = sext i32 %359 to i64
  %361 = getelementptr inbounds %struct.PepStr, ptr %358, i64 %360
  %362 = getelementptr inbounds %struct.PepStr, ptr %361, i32 0, i32 2
  %363 = load i32, ptr %362, align 8, !tbaa !22
  store i32 %363, ptr %20, align 4, !tbaa !9
  br label %364

364:                                              ; preds = %382, %330
  %365 = load i32, ptr %20, align 4, !tbaa !9
  %366 = load ptr, ptr @protein, align 8, !tbaa !5
  %367 = load i32, ptr %18, align 4, !tbaa !9
  %368 = sext i32 %367 to i64
  %369 = getelementptr inbounds %struct.PepStr, ptr %366, i64 %368
  %370 = getelementptr inbounds %struct.PepStr, ptr %369, i32 0, i32 3
  %371 = load i32, ptr %370, align 4, !tbaa !20
  %372 = icmp sle i32 %365, %371
  br i1 %372, label %374, label %373

373:                                              ; preds = %364
  store i32 13, ptr %19, align 4
  call void @llvm.lifetime.end.p0(i64 4, ptr %20) #9
  br label %385

374:                                              ; preds = %364
  %375 = load ptr, ptr @aminoacid, align 8, !tbaa !5
  %376 = load i32, ptr %20, align 4, !tbaa !9
  %377 = sext i32 %376 to i64
  %378 = getelementptr inbounds %struct.AAStr, ptr %375, i64 %377
  %379 = getelementptr inbounds %struct.AAStr, ptr %378, i32 0, i32 0
  %380 = getelementptr inbounds [5 x i8], ptr %379, i64 0, i64 0
  %381 = call i32 (ptr, ...) @printf(ptr noundef @.str.145, ptr noundef %380)
  br label %382

382:                                              ; preds = %374
  %383 = load i32, ptr %20, align 4, !tbaa !9
  %384 = add nsw i32 %383, 1
  store i32 %384, ptr %20, align 4, !tbaa !9
  br label %364, !llvm.loop !27

385:                                              ; preds = %373
  %386 = call i32 (ptr, ...) @printf(ptr noundef @.str.84)
  br label %387

387:                                              ; preds = %385
  %388 = load i32, ptr %18, align 4, !tbaa !9
  %389 = add nsw i32 %388, 1
  store i32 %389, ptr %18, align 4, !tbaa !9
  br label %325, !llvm.loop !28

390:                                              ; preds = %329
  %391 = load ptr, ptr %14, align 8, !tbaa !5
  %392 = call i32 @fclose(ptr noundef %391)
  call void @llvm.lifetime.end.p0(i64 8, ptr %15) #9
  call void @llvm.lifetime.end.p0(i64 8, ptr %14) #9
  call void @llvm.lifetime.end.p0(i64 24, ptr %13) #9
  call void @llvm.lifetime.end.p0(i64 160, ptr %12) #9
  call void @llvm.lifetime.end.p0(i64 8, ptr %11) #9
  call void @llvm.lifetime.end.p0(i64 1024, ptr %10) #9
  call void @llvm.lifetime.end.p0(i64 1024, ptr %9) #9
  call void @llvm.lifetime.end.p0(i64 256, ptr %8) #9
  call void @llvm.lifetime.end.p0(i64 8, ptr %7) #9
  call void @llvm.lifetime.end.p0(i64 4, 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

; Function Attrs: nounwind uwtable
declare dso_local void @RemoveSpace(ptr noundef) #6

declare i32 @AAModel(ptr noundef) #3

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 = { nounwind willreturn memory(read) }
attributes #11 = { noreturn nounwind }
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 = distinct !{!11, !12}
!12 = !{!"llvm.loop.mustprogress"}
!13 = !{!14, !14, i64 0}
!14 = !{!"double", !7, i64 0}
!15 = !{!16, !10, i64 20}
!16 = !{!"AAStr", !7, i64 0, !10, i64 8, !10, i64 12, !10, i64 16, !10, i64 20, !14, i64 24}
!17 = !{!16, !10, i64 16}
!18 = !{!16, !10, i64 12}
!19 = !{!16, !10, i64 8}
!20 = !{!21, !10, i64 12}
!21 = !{!"PepStr", !10, i64 0, !10, i64 4, !10, i64 8, !10, i64 12, !14, i64 16}
!22 = !{!21, !10, i64 8}
!23 = !{!21, !10, i64 4}
!24 = !{!21, !10, i64 0}
!25 = distinct !{!25, !12}
!26 = distinct !{!26, !12}
!27 = distinct !{!27, !12}
!28 = distinct !{!28, !12}


; 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 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.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.134 = external hidden unnamed_addr constant [5 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
@.str.146 = external hidden unnamed_addr constant [3 x i8], align 1
@.str.147 = external hidden unnamed_addr constant [11 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: 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: nofree nounwind
declare noundef i32 @__isoc99_sscanf(ptr nocapture noundef readonly, ptr nocapture noundef readonly, ...) local_unnamed_addr #3

; Function Attrs: nounwind uwtable
define dso_local void @ReadGROFile(ptr noundef %0) local_unnamed_addr #6 {
  %2 = alloca i32, align 4
  %3 = alloca i32, align 4
  %4 = alloca [8 x i8], align 8
  %5 = alloca [256 x i8], align 16
  %6 = alloca [1024 x i8], align 16
  %7 = alloca [1024 x i8], align 16
  %8 = alloca [8 x i8], align 8
  %9 = alloca [20 x [8 x i8]], align 16
  %10 = alloca [3 x double], align 16
  call void @llvm.lifetime.start.p0(i64 4, ptr nonnull %2) #9
  store i32 0, ptr %2, align 4, !tbaa !5
  call void @llvm.lifetime.start.p0(i64 4, ptr nonnull %3) #9
  call void @llvm.lifetime.start.p0(i64 8, ptr nonnull %4) #9
  call void @llvm.lifetime.start.p0(i64 256, ptr nonnull %5) #9
  call void @llvm.memset.p0.i64(ptr noundef nonnull align 16 dereferenceable(256) %5, i8 0, i64 256, i1 false)
  call void @llvm.lifetime.start.p0(i64 1024, ptr nonnull %6) #9
  call void @llvm.lifetime.start.p0(i64 1024, ptr nonnull %7) #9
  call void @llvm.lifetime.start.p0(i64 8, ptr nonnull %8) #9
  call void @llvm.lifetime.start.p0(i64 160, ptr nonnull %9) #9
  call void @llvm.memset.p0.i64(ptr noundef nonnull align 16 dereferenceable(160) %9, i8 0, i64 160, i1 false)
  call void @llvm.lifetime.start.p0(i64 24, ptr nonnull %10) #9
  %11 = call i32 (ptr, ptr, ...) @sprintf(ptr noundef nonnull dereferenceable(1) %7, ptr noundef nonnull dereferenceable(1) @.str.130, ptr noundef nonnull @datadir, ptr noundef nonnull getelementptr inbounds (i8, ptr @REMDInfo, i64 62)) #9
  %12 = call noalias ptr @fopen(ptr noundef nonnull %7, ptr noundef nonnull @.str.131)
  %13 = tail call i32 (ptr, ptr, ...) @fprintf(ptr noundef %12, ptr noundef nonnull @.str.132, ptr noundef nonnull @datadir) #9
  store i32 0, ptr @atomnum, align 4, !tbaa !5
  store i32 0, ptr @numofprotein, align 4, !tbaa !5
  store i32 0, ptr @totalAminoAcids, align 4, !tbaa !5
  store ptr null, ptr @protein, align 8, !tbaa !9
  store ptr null, ptr @aminoacid, align 8, !tbaa !9
  %14 = call ptr @fgets(ptr noundef nonnull %6, i32 noundef 1024, ptr noundef %0)
  %15 = call i32 (ptr, ptr, ...) @__isoc99_fscanf(ptr noundef %0, ptr noundef nonnull @.str.146, ptr noundef nonnull %2) #9
  %16 = load i32, ptr %2, align 4, !tbaa !5
  %.not61 = icmp slt i32 %16, 1
  br i1 %.not61, label %._crit_edge, label %.lr.ph65

.lr.ph65:                                         ; preds = %1
  %17 = getelementptr inbounds i8, ptr %10, i64 8
  %18 = getelementptr inbounds i8, ptr %10, i64 16
  br label %48

._crit_edge:                                      ; preds = %156, %1
  %19 = call i32 (ptr, ptr, ...) @__isoc99_fscanf(ptr noundef %0, ptr noundef nonnull @.str.115, ptr noundef nonnull getelementptr inbounds (i8, ptr @boxDimension, i64 8), ptr noundef nonnull getelementptr inbounds (i8, ptr @boxDimension, i64 16), ptr noundef nonnull getelementptr inbounds (i8, ptr @boxDimension, i64 24)) #9
  %20 = load <2 x double>, ptr getelementptr inbounds (i8, ptr @boxDimension, i64 8), align 8, !tbaa !11
  %21 = fmul <2 x double> %20, <double 1.000000e+01, double 1.000000e+01>
  store <2 x double> %21, ptr getelementptr inbounds (i8, ptr @boxDimension, i64 8), align 8, !tbaa !11
  %22 = load double, ptr getelementptr inbounds (i8, ptr @boxDimension, i64 24), align 8, !tbaa !11
  %23 = fmul double %22, 1.000000e+01
  store double %23, ptr getelementptr inbounds (i8, ptr @boxDimension, i64 24), align 8, !tbaa !11
  %24 = load i32, ptr @atomnum, align 4, !tbaa !5
  %25 = load ptr, ptr @aminoacid, align 8, !tbaa !9
  %26 = load i32, ptr @totalAminoAcids, align 4, !tbaa !5
  %27 = sext i32 %26 to i64
  %28 = getelementptr inbounds %struct.AAStr, ptr %25, i64 %27, i32 3
  store i32 %24, ptr %28, align 8, !tbaa !13
  %29 = load i32, ptr @totalAminoAcids, align 4, !tbaa !5
  %30 = load ptr, ptr @protein, align 8, !tbaa !9
  %31 = load i32, ptr @numofprotein, align 4, !tbaa !5
  %32 = sext i32 %31 to i64
  %33 = getelementptr inbounds %struct.PepStr, ptr %30, i64 %32, i32 3
  store i32 %29, ptr %33, align 4, !tbaa !15
  %34 = load i32, ptr @atomnum, align 4, !tbaa !5
  %35 = load i32, ptr @numofprotein, align 4, !tbaa !5
  %36 = sext i32 %35 to i64
  %37 = getelementptr inbounds %struct.PepStr, ptr %30, i64 %36, i32 1
  store i32 %34, ptr %37, align 4, !tbaa !17
  %38 = add nsw i32 %34, 1
  %39 = sext i32 %38 to i64
  %40 = call noalias ptr @calloc(i64 noundef %39, i64 noundef 8) #10
  store ptr %40, ptr @connectionMap, align 8, !tbaa !9
  %41 = mul nsw i32 %38, %38
  %42 = zext nneg i32 %41 to i64
  %43 = call noalias ptr @calloc(i64 noundef %42, i64 noundef 4) #10
  store ptr %43, ptr %40, align 8, !tbaa !9
  %.not4866 = icmp slt i32 %34, 1
  br i1 %.not4866, label %.preheader, label %.lr.ph69.preheader

.lr.ph69.preheader:                               ; preds = %._crit_edge
  %44 = zext nneg i32 %38 to i64
  %45 = add nsw i64 %44, -1
  %46 = add nsw i64 %44, -2
  %xtraiter = and i64 %45, 3
  %47 = icmp ult i64 %46, 3
  br i1 %47, label %.preheader.loopexit.unr-lcssa, label %.lr.ph69.preheader.new

.lr.ph69.preheader.new:                           ; preds = %.lr.ph69.preheader
  %unroll_iter = and i64 %45, -4
  br label %.lr.ph69

48:                                               ; preds = %.lr.ph65, %156
  %.04264 = phi i32 [ 1, %.lr.ph65 ], [ %157, %156 ]
  %.04363 = phi i32 [ 0, %.lr.ph65 ], [ %.2, %156 ]
  %.04462 = phi i32 [ 0, %.lr.ph65 ], [ %.145, %156 ]
  store i64 0, ptr %8, align 8
  store i64 0, ptr %4, align 8
  %49 = call i32 (ptr, ptr, ...) @__isoc99_fscanf(ptr noundef %0, ptr noundef nonnull @.str.147, ptr noundef nonnull %3, ptr noundef nonnull %8, ptr noundef nonnull %4, ptr noundef nonnull %6) #9
  call void @RemoveSpace(ptr noundef nonnull %8)
  call void @RemoveSpace(ptr noundef nonnull %4)
  %50 = load i32, ptr %3, align 4, !tbaa !5
  %.not51 = icmp eq i32 %.04462, %50
  br i1 %.not51, label %51, label %53

51:                                               ; preds = %48
  %52 = call i32 @strcmp(ptr noundef nonnull dereferenceable(1) %8, ptr noundef nonnull dereferenceable(1) %5) #11
  %.not52 = icmp eq i32 %52, 0
  br i1 %.not52, label %72, label %53

53:                                               ; preds = %51, %48
  %54 = call i32 @strcmp(ptr noundef nonnull dereferenceable(1) %8, ptr noundef nonnull dereferenceable(1) @.str.136) #11
  %55 = icmp eq i32 %54, 0
  %.str.138. = select i1 %55, ptr @.str.138, ptr %8
  %56 = call i32 (ptr, ptr, ...) @sprintf(ptr noundef nonnull dereferenceable(1) %7, ptr noundef nonnull dereferenceable(1) @.str.137, ptr noundef nonnull @datadir, ptr noundef nonnull @Methodtype, ptr noundef nonnull %.str.138.) #9
  %57 = call noalias ptr @fopen(ptr noundef nonnull %7, ptr noundef nonnull @.str.94)
  %58 = icmp eq ptr %57, null
  br i1 %58, label %59, label %62

59:                                               ; preds = %53
  %60 = call i32 (ptr, ...) @printf(ptr noundef nonnull dereferenceable(1) @.str.139, ptr noundef nonnull %8, ptr noundef nonnull @datadir, ptr noundef nonnull @Methodtype)
  %61 = call i32 (ptr, ...) @printf(ptr noundef nonnull dereferenceable(1) @.str.140, ptr noundef nonnull @.str.2, i32 noundef 920)
  call void @exit(i32 noundef 1) #12
  unreachable

62:                                               ; preds = %53
  %63 = call ptr @fgets(ptr noundef nonnull %6, i32 noundef 1024, ptr noundef nonnull %57)
  %64 = call i32 (ptr, ptr, ...) @__isoc99_fscanf(ptr noundef nonnull %57, ptr noundef nonnull @.str.3, ptr noundef nonnull %6) #9
  %.not5357 = icmp eq i32 %64, 0
  br i1 %.not5357, label %.critedge, label %.lr.ph

.lr.ph:                                           ; preds = %62, %67
  %indvars.iv = phi i64 [ %indvars.iv.next, %67 ], [ 0, %62 ]
  %65 = call i32 @strcmp(ptr noundef nonnull dereferenceable(1) @.str.134, ptr noundef nonnull dereferenceable(1) %6) #11
  %66 = icmp eq i32 %65, 0
  br i1 %66, label %67, label %.critedge.loopexit

67:                                               ; preds = %.lr.ph
  %indvars.iv.next = add nuw nsw i64 %indvars.iv, 1
  %68 = getelementptr inbounds [20 x [8 x i8]], ptr %9, i64 0, i64 %indvars.iv
  %69 = call i32 (ptr, ptr, ...) @__isoc99_fscanf(ptr noundef nonnull %57, ptr noundef nonnull @.str.141, ptr noundef nonnull %68, ptr noundef nonnull %6) #9
  %70 = call i32 (ptr, ptr, ...) @__isoc99_fscanf(ptr noundef nonnull %57, ptr noundef nonnull @.str.3, ptr noundef nonnull %6) #9
  %.not53 = icmp eq i32 %70, 0
  br i1 %.not53, label %.critedge.loopexit, label %.lr.ph, !llvm.loop !18

.critedge.loopexit:                               ; preds = %67, %.lr.ph
  %.1.lcssa.ph.in = phi i64 [ %indvars.iv, %.lr.ph ], [ %indvars.iv.next, %67 ]
  %.1.lcssa.ph = trunc i64 %.1.lcssa.ph.in to i32
  br label %.critedge

.critedge:                                        ; preds = %.critedge.loopexit, %62
  %.1.lcssa = phi i32 [ 0, %62 ], [ %.1.lcssa.ph, %.critedge.loopexit ]
  %71 = call i32 @fclose(ptr noundef nonnull %57)
  br label %72

72:                                               ; preds = %.critedge, %51
  %.2 = phi i32 [ %.1.lcssa, %.critedge ], [ %.04363, %51 ]
  %73 = call i32 @CheckValidAtom(ptr noundef nonnull %4, ptr noundef nonnull %9, i32 noundef %.2)
  %.not54 = icmp eq i32 %73, 0
  br i1 %.not54, label %86, label %74

74:                                               ; preds = %72
  %75 = load i32, ptr @atomnum, align 4, !tbaa !5
  %76 = add nsw i32 %75, 1
  store i32 %76, ptr @atomnum, align 4, !tbaa !5
  %77 = call ptr @fgets(ptr noundef nonnull %6, i32 noundef 1024, ptr noundef %0)
  %78 = call i32 (ptr, ptr, ...) @__isoc99_sscanf(ptr noundef nonnull %6, ptr noundef nonnull @.str.115, ptr noundef nonnull %10, ptr noundef nonnull %17, ptr noundef nonnull %18) #9
  %79 = load <2 x double>, ptr %10, align 16, !tbaa !11
  %80 = fmul <2 x double> %79, <double 1.000000e+01, double 1.000000e+01>
  store <2 x double> %80, ptr %10, align 16, !tbaa !11
  %81 = load double, ptr %18, align 16, !tbaa !11
  %82 = fmul double %81, 1.000000e+01
  store double %82, ptr %18, align 16, !tbaa !11
  %83 = extractelement <2 x double> %80, i64 0
  %84 = extractelement <2 x double> %80, i64 1
  %85 = call i32 (ptr, ptr, ...) @fprintf(ptr noundef %12, ptr noundef nonnull @.str.142, ptr noundef nonnull %4, double noundef %83, double noundef %84, double noundef %82) #9
  br label %88

86:                                               ; preds = %72
  %87 = call ptr @fgets(ptr noundef nonnull %6, i32 noundef 1024, ptr noundef %0)
  br label %88

88:                                               ; preds = %86, %74
  %89 = load i32, ptr %3, align 4, !tbaa !5
  %.not55 = icmp eq i32 %.04462, %89
  br i1 %.not55, label %90, label %92

90:                                               ; preds = %88
  %91 = call i32 @strcmp(ptr noundef nonnull dereferenceable(1) %8, ptr noundef nonnull dereferenceable(1) %5) #11
  %.not56 = icmp eq i32 %91, 0
  br i1 %.not56, label %156, label %92

92:                                               ; preds = %90, %88
  %93 = load ptr, ptr @aminoacid, align 8, !tbaa !9
  %94 = load i32, ptr @totalAminoAcids, align 4, !tbaa !5
  %95 = add nsw i32 %94, 1
  store i32 %95, ptr @totalAminoAcids, align 4, !tbaa !5
  %96 = add nsw i32 %94, 2
  %97 = sext i32 %96 to i64
  %98 = shl nsw i64 %97, 5
  %99 = call ptr @realloc(ptr noundef %93, i64 noundef %98) #13
  store ptr %99, ptr @aminoacid, align 8, !tbaa !9
  %100 = load i32, ptr @totalAminoAcids, align 4, !tbaa !5
  %101 = sext i32 %100 to i64
  %102 = getelementptr inbounds %struct.AAStr, ptr %99, i64 %101
  %103 = call i32 (ptr, ptr, ...) @sprintf(ptr noundef nonnull dereferenceable(1) %102, ptr noundef nonnull dereferenceable(1) @.str.3, ptr noundef nonnull %8) #9
  %104 = load i32, ptr %3, align 4, !tbaa !5
  %105 = icmp slt i32 %104, %.04462
  %106 = load i32, ptr @numofprotein, align 4
  %107 = icmp eq i32 %106, 0
  %or.cond = select i1 %105, i1 true, i1 %107
  %108 = zext i1 %or.cond to i32
  %109 = add nsw i32 %106, %108
  %110 = load ptr, ptr @aminoacid, align 8, !tbaa !9
  %111 = load i32, ptr @totalAminoAcids, align 4, !tbaa !5
  %112 = sext i32 %111 to i64
  %113 = getelementptr inbounds %struct.AAStr, ptr %110, i64 %112, i32 4
  store i32 %109, ptr %113, align 4, !tbaa !20
  %114 = load i32, ptr @atomnum, align 4, !tbaa !5
  %115 = add nsw i32 %114, -1
  %116 = load i32, ptr @totalAminoAcids, align 4, !tbaa !5
  %117 = sext i32 %116 to i64
  %118 = getelementptr %struct.AAStr, ptr %110, i64 %117
  %119 = getelementptr i8, ptr %118, i64 -16
  store i32 %115, ptr %119, align 8, !tbaa !13
  %120 = load i32, ptr @atomnum, align 4, !tbaa !5
  %121 = load i32, ptr @totalAminoAcids, align 4, !tbaa !5
  %122 = sext i32 %121 to i64
  %123 = getelementptr inbounds %struct.AAStr, ptr %110, i64 %122, i32 2
  store i32 %120, ptr %123, align 4, !tbaa !21
  %124 = load i32, ptr @totalAminoAcids, align 4, !tbaa !5
  %125 = sext i32 %124 to i64
  %126 = getelementptr inbounds %struct.AAStr, ptr %110, i64 %125
  %127 = call i32 @AAModel(ptr noundef %126) #9
  %128 = load ptr, ptr @aminoacid, align 8, !tbaa !9
  %129 = load i32, ptr @totalAminoAcids, align 4, !tbaa !5
  %130 = sext i32 %129 to i64
  %131 = getelementptr inbounds %struct.AAStr, ptr %128, i64 %130, i32 1
  store i32 %127, ptr %131, align 8, !tbaa !22
  %132 = load i32, ptr %3, align 4, !tbaa !5
  %133 = icmp slt i32 %132, %.04462
  %134 = load i32, ptr @numofprotein, align 4
  %135 = icmp eq i32 %134, 0
  %or.cond3 = select i1 %133, i1 true, i1 %135
  br i1 %or.cond3, label %136, label %153

136:                                              ; preds = %92
  %137 = load ptr, ptr @protein, align 8, !tbaa !9
  %138 = add nsw i32 %134, 1
  store i32 %138, ptr @numofprotein, align 4, !tbaa !5
  %139 = add nsw i32 %134, 2
  %140 = sext i32 %139 to i64
  %141 = mul nsw i64 %140, 24
  %142 = call ptr @realloc(ptr noundef %137, i64 noundef %141) #13
  store ptr %142, ptr @protein, align 8, !tbaa !9
  %143 = load i32, ptr @totalAminoAcids, align 4, !tbaa !5
  %144 = add nsw i32 %143, -1
  %145 = load i32, ptr @numofprotein, align 4, !tbaa !5
  %146 = sext i32 %145 to i64
  %147 = getelementptr %struct.PepStr, ptr %142, i64 %146
  %148 = getelementptr i8, ptr %147, i64 -12
  store i32 %144, ptr %148, align 4, !tbaa !15
  %149 = getelementptr inbounds %struct.PepStr, ptr %142, i64 %146, i32 2
  store i32 %143, ptr %149, align 8, !tbaa !23
  %150 = load i32, ptr @atomnum, align 4, !tbaa !5
  %151 = add nsw i32 %150, -1
  %152 = getelementptr i8, ptr %147, i64 -20
  store i32 %151, ptr %152, align 4, !tbaa !17
  store i32 %150, ptr %147, align 8, !tbaa !24
  %.pre = load i32, ptr %3, align 4, !tbaa !5
  br label %153

153:                                              ; preds = %92, %136
  %154 = phi i32 [ %132, %92 ], [ %.pre, %136 ]
  %155 = call i32 (ptr, ptr, ...) @sprintf(ptr noundef nonnull dereferenceable(1) %5, ptr noundef nonnull dereferenceable(1) @.str.3, ptr noundef nonnull %8) #9
  br label %156

156:                                              ; preds = %90, %153
  %.145 = phi i32 [ %154, %153 ], [ %.04462, %90 ]
  %157 = add nuw nsw i32 %.04264, 1
  %158 = load i32, ptr %2, align 4, !tbaa !5
  %.not.not = icmp slt i32 %.04264, %158
  br i1 %.not.not, label %48, label %._crit_edge, !llvm.loop !25

.preheader.loopexit.unr-lcssa:                    ; preds = %.lr.ph69, %.lr.ph69.preheader
  %indvars.iv80.unr = phi i64 [ 1, %.lr.ph69.preheader ], [ %indvars.iv.next81.3, %.lr.ph69 ]
  %lcmp.mod.not = icmp eq i64 %xtraiter, 0
  br i1 %lcmp.mod.not, label %.preheader, label %.lr.ph69.epil

.lr.ph69.epil:                                    ; preds = %.preheader.loopexit.unr-lcssa, %.lr.ph69.epil
  %indvars.iv80.epil = phi i64 [ %indvars.iv.next81.epil, %.lr.ph69.epil ], [ %indvars.iv80.unr, %.preheader.loopexit.unr-lcssa ]
  %epil.iter = phi i64 [ %epil.iter.next, %.lr.ph69.epil ], [ 0, %.preheader.loopexit.unr-lcssa ]
  %159 = load ptr, ptr @connectionMap, align 8, !tbaa !9
  %160 = load ptr, ptr %159, align 8, !tbaa !9
  %161 = mul nuw nsw i64 %indvars.iv80.epil, %44
  %162 = getelementptr inbounds i32, ptr %160, i64 %161
  %163 = getelementptr inbounds ptr, ptr %159, i64 %indvars.iv80.epil
  store ptr %162, ptr %163, align 8, !tbaa !9
  %indvars.iv.next81.epil = add nuw nsw i64 %indvars.iv80.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.ph69.epil, !llvm.loop !26

.preheader:                                       ; preds = %.preheader.loopexit.unr-lcssa, %.lr.ph69.epil, %._crit_edge
  %164 = load i32, ptr @numofprotein, align 4, !tbaa !5
  %.not4975 = icmp slt i32 %164, 1
  br i1 %.not4975, label %._crit_edge78, label %.lr.ph77

.lr.ph69:                                         ; preds = %.lr.ph69, %.lr.ph69.preheader.new
  %indvars.iv80 = phi i64 [ 1, %.lr.ph69.preheader.new ], [ %indvars.iv.next81.3, %.lr.ph69 ]
  %niter = phi i64 [ 0, %.lr.ph69.preheader.new ], [ %niter.next.3, %.lr.ph69 ]
  %165 = load ptr, ptr @connectionMap, align 8, !tbaa !9
  %166 = load ptr, ptr %165, align 8, !tbaa !9
  %167 = mul nuw nsw i64 %indvars.iv80, %44
  %168 = getelementptr inbounds i32, ptr %166, i64 %167
  %169 = getelementptr inbounds ptr, ptr %165, i64 %indvars.iv80
  store ptr %168, ptr %169, align 8, !tbaa !9
  %indvars.iv.next81 = add nuw nsw i64 %indvars.iv80, 1
  %170 = load ptr, ptr @connectionMap, align 8, !tbaa !9
  %171 = load ptr, ptr %170, align 8, !tbaa !9
  %172 = mul nuw nsw i64 %indvars.iv.next81, %44
  %173 = getelementptr inbounds i32, ptr %171, i64 %172
  %174 = getelementptr inbounds ptr, ptr %170, i64 %indvars.iv.next81
  store ptr %173, ptr %174, align 8, !tbaa !9
  %indvars.iv.next81.1 = add nuw nsw i64 %indvars.iv80, 2
  %175 = load ptr, ptr @connectionMap, align 8, !tbaa !9
  %176 = load ptr, ptr %175, align 8, !tbaa !9
  %177 = mul nuw nsw i64 %indvars.iv.next81.1, %44
  %178 = getelementptr inbounds i32, ptr %176, i64 %177
  %179 = getelementptr inbounds ptr, ptr %175, i64 %indvars.iv.next81.1
  store ptr %178, ptr %179, align 8, !tbaa !9
  %indvars.iv.next81.2 = add nuw nsw i64 %indvars.iv80, 3
  %180 = load ptr, ptr @connectionMap, align 8, !tbaa !9
  %181 = load ptr, ptr %180, align 8, !tbaa !9
  %182 = mul nuw nsw i64 %indvars.iv.next81.2, %44
  %183 = getelementptr inbounds i32, ptr %181, i64 %182
  %184 = getelementptr inbounds ptr, ptr %180, i64 %indvars.iv.next81.2
  store ptr %183, ptr %184, align 8, !tbaa !9
  %indvars.iv.next81.3 = add nuw nsw i64 %indvars.iv80, 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.ph69, !llvm.loop !28

._crit_edge78:                                    ; preds = %._crit_edge74, %.preheader
  %185 = call i32 @fclose(ptr noundef %12)
  call void @llvm.lifetime.end.p0(i64 24, ptr nonnull %10) #9
  call void @llvm.lifetime.end.p0(i64 160, ptr nonnull %9) #9
  call void @llvm.lifetime.end.p0(i64 8, ptr nonnull %8) #9
  call void @llvm.lifetime.end.p0(i64 1024, ptr nonnull %7) #9
  call void @llvm.lifetime.end.p0(i64 1024, ptr nonnull %6) #9
  call void @llvm.lifetime.end.p0(i64 256, ptr nonnull %5) #9
  call void @llvm.lifetime.end.p0(i64 8, ptr nonnull %4) #9
  call void @llvm.lifetime.end.p0(i64 4, ptr nonnull %3) #9
  call void @llvm.lifetime.end.p0(i64 4, ptr nonnull %2) #9
  ret void

.lr.ph77:                                         ; preds = %.preheader, %._crit_edge74
  %indvars.iv88 = phi i64 [ %indvars.iv.next89, %._crit_edge74 ], [ 1, %.preheader ]
  %186 = load ptr, ptr @protein, align 8, !tbaa !9
  %187 = getelementptr inbounds %struct.PepStr, ptr %186, i64 %indvars.iv88
  %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 !23
  %191 = getelementptr inbounds i8, ptr %187, i64 4
  %192 = load i32, ptr %191, align 4, !tbaa !17
  %193 = getelementptr inbounds i8, ptr %187, i64 12
  %194 = load i32, ptr %193, align 4, !tbaa !15
  %195 = trunc nuw nsw i64 %indvars.iv88 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 !9
  %199 = getelementptr inbounds %struct.PepStr, ptr %198, i64 %indvars.iv88, i32 2
  %200 = load i32, ptr %199, align 8, !tbaa !23
  %201 = getelementptr inbounds %struct.PepStr, ptr %198, i64 %indvars.iv88, i32 3
  %202 = load i32, ptr %201, align 4, !tbaa !15
  %.not5070 = icmp sgt i32 %200, %202
  br i1 %.not5070, label %._crit_edge74, label %.lr.ph73.preheader

.lr.ph73.preheader:                               ; preds = %.lr.ph77
  %203 = sext i32 %200 to i64
  br label %.lr.ph73

._crit_edge74:                                    ; preds = %.lr.ph73, %.lr.ph77
  %204 = call i32 (ptr, ...) @printf(ptr noundef nonnull dereferenceable(1) @.str.84)
  %indvars.iv.next89 = add nuw nsw i64 %indvars.iv88, 1
  %205 = load i32, ptr @numofprotein, align 4, !tbaa !5
  %206 = sext i32 %205 to i64
  %.not49.not = icmp slt i64 %indvars.iv88, %206
  br i1 %.not49.not, label %.lr.ph77, label %._crit_edge78, !llvm.loop !29

.lr.ph73:                                         ; preds = %.lr.ph73.preheader, %.lr.ph73
  %indvars.iv84 = phi i64 [ %203, %.lr.ph73.preheader ], [ %indvars.iv.next85, %.lr.ph73 ]
  %207 = load ptr, ptr @aminoacid, align 8, !tbaa !9
  %208 = getelementptr inbounds %struct.AAStr, ptr %207, i64 %indvars.iv84
  %209 = call i32 (ptr, ...) @printf(ptr noundef nonnull dereferenceable(1) @.str.145, ptr noundef %208)
  %indvars.iv.next85 = add nsw i64 %indvars.iv84, 1
  %210 = load ptr, ptr @protein, align 8, !tbaa !9
  %211 = getelementptr inbounds %struct.PepStr, ptr %210, i64 %indvars.iv88, i32 3
  %212 = load i32, ptr %211, align 4, !tbaa !15
  %213 = sext i32 %212 to i64
  %.not50.not = icmp slt i64 %indvars.iv84, %213
  br i1 %.not50.not, label %.lr.ph73, label %._crit_edge74, !llvm.loop !30
}

; 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

; Function Attrs: nounwind uwtable
declare dso_local void @RemoveSpace(ptr noundef) local_unnamed_addr #6

declare i32 @AAModel(ptr noundef) local_unnamed_addr #5

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 = { nounwind allocsize(0,1) }
attributes #11 = { nounwind willreturn memory(read) }
attributes #12 = { noreturn nounwind }
attributes #13 = { nounwind allocsize(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 = !{!"int", !7, i64 0}
!7 = !{!"omnipotent char", !8, i64 0}
!8 = !{!"Simple C/C++ TBAA"}
!9 = !{!10, !10, i64 0}
!10 = !{!"any pointer", !7, i64 0}
!11 = !{!12, !12, i64 0}
!12 = !{!"double", !7, i64 0}
!13 = !{!14, !6, i64 16}
!14 = !{!"AAStr", !7, i64 0, !6, i64 8, !6, i64 12, !6, i64 16, !6, i64 20, !12, i64 24}
!15 = !{!16, !6, i64 12}
!16 = !{!"PepStr", !6, i64 0, !6, i64 4, !6, i64 8, !6, i64 12, !12, i64 16}
!17 = !{!16, !6, i64 4}
!18 = distinct !{!18, !19}
!19 = !{!"llvm.loop.mustprogress"}
!20 = !{!14, !6, i64 20}
!21 = !{!14, !6, i64 12}
!22 = !{!14, !6, i64 8}
!23 = !{!16, !6, i64 8}
!24 = !{!16, !6, i64 0}
!25 = distinct !{!25, !19}
!26 = distinct !{!26, !27}
!27 = !{!"llvm.loop.unroll.disable"}
!28 = distinct !{!28, !19}
!29 = distinct !{!29, !19}
!30 = distinct !{!30, !19}


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