// File: /workspace/github_c_makefile_star2_O2/josch[P]stride/stride.c
// Function: PrintStrideHelp
void PrintStrideHelp(COMMAND *Cmd)
{

  fprintf(stderr,"\nAction: secondary structure assignment\n");
  fprintf(stderr,"Usage: stride [Options] InputFile [ > file ]\n");
  fprintf(stderr,"Options:  \n");
  fprintf(stderr,"  -fFile      Output file\n");
  fprintf(stderr,"  -mFile      MolScript file\n");
  fprintf(stderr,"  -o          Report secondary structure summary Only\n");
  fprintf(stderr,"  -h          Report Hydrogen bonds\n");
  fprintf(stderr,"  -rId1Id2..  Read only chains Id1, Id2 ...\n");
  fprintf(stderr,"  -cId1Id2..  Process only Chains Id1, Id2 ...\n");
  fprintf(stderr,"  -q[File]    Generate SeQuence file in FASTA format and die\n");
  fprintf(stderr,"\nOptions are position  and case insensitive\n");

  /*************** Private options - not for general use ****************/
  if( Cmd->Info ) {
    fprintf(stderr,"  -phFile        PhiPsiMap file for alpha helix\n");
    fprintf(stderr,"  -peFile        PhiPsiMap file for beta-sheet\n");
    fprintf(stderr,"  -pgFile        PhiPsiMap file for 3-1 helix\n");
    fprintf(stderr,"  -tha           treshold (Ener*Conf*Conf) for H\n");
    fprintf(stderr,"  -thc           treshold (Conf) for H\n");
    fprintf(stderr,"  -thd           treshold (Conf) for H\n");
    fprintf(stderr,"  -tea           treshold (Ener*Conf*Conf) for E\n");
    fprintf(stderr,"  -teb           treshold (Conf) for E\n");
    fprintf(stderr,"  -dFile         Dssp file\n");
    fprintf(stderr,"  -b             Include Brookhaven assignment\n");
    fprintf(stderr,"  -i             Print detailed information\n");
    fprintf(stderr,"  -llNumber      Sequence Length less then Number (with -s)\n");
    fprintf(stderr,"  -lgNumber      Sequence Length greater then Number (with -s)\n");
    fprintf(stderr,"  -ulNumber      ResolUtion less (better) then Number (with -s)\n");
    fprintf(stderr,"  -ugNumber      ResolUtion greater (worse) then Number (with -s)\n");
    fprintf(stderr,"  -s[xcnmapd]    Stringent: discard wrong or suspisious PDB files \n");
    fprintf(stderr,"       -x Process X-Ray structures\n");
    fprintf(stderr,"       -n Process NMR structures\n");
    fprintf(stderr,"       -m Process Model structures\n");
    fprintf(stderr,"       -c Exlude structures with only Calpha atoms\n");
    fprintf(stderr,"       -d Exculde structures with automatic secondary structure assignment\n");
    fprintf(stderr,"       -a Exclude structures without secondary structure assignment\n");
    fprintf(stderr,"       -p Exlude structures that are not published or in press\n");
    fprintf(stderr,"  -z             Measure differences with PDB and DSSP\n");
    
  }

  exit(0);

}

// Assembly:
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
movq %rdi, %rbx
movq 0x1d2de(%rip), %r13     # 0x1fff0
movq (%r13), %rcx
leaq 0x1542f(%rip), %rdi     # 0x1814c
pushq $0x28
popq %rsi
pushq $0x1
popq %r14
movq %r14, %rdx
callq 0x2250
movq (%r13), %rcx
leaq 0x1543e(%rip), %rdi     # 0x18175
pushq $0x2d
popq %rsi
movq %r14, %rdx
callq 0x2250
movq (%r13), %rcx
leaq 0x15456(%rip), %rdi     # 0x181a3
pushq $0xb
popq %rsi
movq %r14, %rdx
callq 0x2250
movq (%r13), %rcx
leaq 0x1544c(%rip), %rdi     # 0x181af
pushq $0x1a
popq %rsi
movq %r14, %rdx
callq 0x2250
movq (%r13), %rcx
leaq 0x15451(%rip), %rdi     # 0x181ca
pushq $0x1d
popq %rsi
movq %r14, %rdx
callq 0x2250
movq (%r13), %rcx
leaq 0x15459(%rip), %rdi     # 0x181e8
pushq $0x36
popq %rsi
movq %r14, %rdx
callq 0x2250
movq (%r13), %rcx
leaq 0x1547a(%rip), %rdi     # 0x1821f
pushq $0x24
popq %rsi
movq %r14, %rdx
callq 0x2250
movq (%r13), %rcx
leaq 0x15489(%rip), %rdi     # 0x18244
pushq $0x2c
popq %r15
movq %r15, %rsi
movq %r14, %rdx
callq 0x2250
movq (%r13), %rcx
leaq 0x1549c(%rip), %rdi     # 0x18271
pushq $0x2f
popq %rsi
movq %r14, %rdx
callq 0x2250
movq (%r13), %rcx
leaq 0x154b6(%rip), %rdi     # 0x182a1
pushq $0x3d
popq %rsi
movq %r14, %rdx
callq 0x2250
movq (%r13), %rcx
leaq 0x154de(%rip), %rdi     # 0x182df
movq %r15, %rsi
movq %r14, %rdx
callq 0x2250
cmpl $0x0, 0x1d60(%rbx)
je 0x3040
movq (%r13), %rcx
leaq 0x154e8(%rip), %rdi     # 0x1830c
pushq $0x30
popq %rsi
pushq $0x1
popq %rbx
movq %rbx, %rdx
callq 0x2250
movq (%r13), %rcx
leaq 0x15500(%rip), %rdi     # 0x1833d
pushq $0x2f
popq %r14
movq %r14, %rsi
movq %rbx, %rdx
callq 0x2250
movq (%r13), %rcx
leaq 0x15516(%rip), %rdi     # 0x1836d
pushq $0x2e
popq %rsi
movq %rbx, %rdx
callq 0x2250
movq (%r13), %rcx
leaq 0x1552f(%rip), %rdi     # 0x1839c
pushq $0x31
popq %r15
movq %r15, %rsi
movq %rbx, %rdx
callq 0x2250
movq (%r13), %rcx
leaq 0x15547(%rip), %rdi     # 0x183ce
pushq $0x27
popq %r12
movq %r12, %rsi
movq %rbx, %rdx
callq 0x2250
movq (%r13), %rcx
leaq 0x15555(%rip), %rdi     # 0x183f6
movq %r12, %rsi
movq %rbx, %rdx
callq 0x2250
movq (%r13), %rcx
leaq 0x15567(%rip), %rdi     # 0x1841e
movq %r15, %rsi
movq %rbx, %rdx
callq 0x2250
movq (%r13), %rcx
leaq 0x15583(%rip), %rdi     # 0x18450
movq %r12, %rsi
movq %rbx, %rdx
callq 0x2250
movq (%r13), %rcx
leaq 0x15595(%rip), %rdi     # 0x18478
pushq $0x1b
popq %rsi
movq %rbx, %rdx
callq 0x2250
movq (%r13), %rcx
leaq 0x1559b(%rip), %rdi     # 0x18494
movq %r14, %rsi
movq %rbx, %rdx
callq 0x2250
movq (%r13), %rcx
leaq 0x155b5(%rip), %rdi     # 0x184c4
pushq $0x2c
popq %rsi
movq %rbx, %rdx
callq 0x2250
movq (%r13), %rcx
leaq 0x155cc(%rip), %rdi     # 0x184f1
pushq $0x3c
popq %rsi
movq %rbx, %rdx
callq 0x2250
movq (%r13), %rcx
leaq 0x155f3(%rip), %rdi     # 0x1852e
pushq $0x3f
popq %r14
movq %r14, %rsi
movq %rbx, %rdx
callq 0x2250
movq (%r13), %rcx
leaq 0x15619(%rip), %rdi     # 0x1856e
pushq $0x40
popq %rsi
movq %rbx, %rdx
callq 0x2250
movq (%r13), %rcx
leaq 0x15644(%rip), %rdi     # 0x185af
pushq $0x42
popq %rsi
movq %rbx, %rdx
callq 0x2250
movq (%r13), %rcx
leaq 0x15671(%rip), %rdi     # 0x185f2
pushq $0x43
popq %rsi
movq %rbx, %rdx
callq 0x2250
movq (%r13), %rcx
leaq 0x1569f(%rip), %rdi     # 0x18636
pushq $0x23
popq %r15
movq %r15, %rsi
movq %rbx, %rdx
callq 0x2250
movq (%r13), %rcx
leaq 0x156a9(%rip), %rdi     # 0x1865a
pushq $0x21
popq %rsi
movq %rbx, %rdx
callq 0x2250
movq (%r13), %rcx
leaq 0x156b5(%rip), %rdi     # 0x1867c
movq %r15, %rsi
movq %rbx, %rdx
callq 0x2250
movq (%r13), %rcx
leaq 0x156c3(%rip), %rdi     # 0x186a0
pushq $0x33
popq %rsi
movq %rbx, %rdx
callq 0x2250
movq (%r13), %rcx
leaq 0x156e1(%rip), %rdi     # 0x186d4
pushq $0x4b
popq %rsi
movq %rbx, %rdx
callq 0x2250
movq (%r13), %rcx
leaq 0x15717(%rip), %rdi     # 0x18720
pushq $0x44
popq %rsi
movq %rbx, %rdx
callq 0x2250
movq (%r13), %rcx
leaq 0x15746(%rip), %rdi     # 0x18765
movq %r14, %rsi
movq %rbx, %rdx
callq 0x2250
movq (%r13), %rcx
leaq 0x15770(%rip), %rdi     # 0x187a5
pushq $0x37
popq %rsi
movq %rbx, %rdx
callq 0x2250
xorl %edi, %edi
callq 0x2240