// File: /workspace/github_c_makefile_star2_O3/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 %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
movq 0x1dd82(%rip), %r14     # 0x20ff0
movq (%r14), %rcx
leaq 0x15ed4(%rip), %rdi     # 0x1914c
movl $0x28, %esi
movl $0x1, %edx
callq 0x2240
movq (%r14), %rcx
leaq 0x15ee4(%rip), %rdi     # 0x19175
movl $0x2d, %esi
movl $0x1, %edx
callq 0x2240
movq (%r14), %rcx
leaq 0x15ef9(%rip), %rdi     # 0x191a3
movl $0xb, %esi
movl $0x1, %edx
callq 0x2240
movq (%r14), %rcx
leaq 0x15eec(%rip), %rdi     # 0x191af
movl $0x1a, %esi
movl $0x1, %edx
callq 0x2240
movq (%r14), %rcx
leaq 0x15eee(%rip), %rdi     # 0x191ca
movl $0x1d, %esi
movl $0x1, %edx
callq 0x2240
movq (%r14), %rcx
leaq 0x15ef3(%rip), %rdi     # 0x191e8
movl $0x36, %esi
movl $0x1, %edx
callq 0x2240
movq (%r14), %rcx
leaq 0x15f11(%rip), %rdi     # 0x1921f
movl $0x24, %esi
movl $0x1, %edx
callq 0x2240
movq (%r14), %rcx
leaq 0x15f1d(%rip), %rdi     # 0x19244
movl $0x2c, %esi
movl $0x1, %edx
callq 0x2240
movq (%r14), %rcx
leaq 0x15f31(%rip), %rdi     # 0x19271
movl $0x2f, %esi
movl $0x1, %edx
callq 0x2240
movq (%r14), %rcx
leaq 0x15f48(%rip), %rdi     # 0x192a1
movl $0x3d, %esi
movl $0x1, %edx
callq 0x2240
movq (%r14), %rcx
leaq 0x15f6d(%rip), %rdi     # 0x192df
movl $0x2c, %esi
movl $0x1, %edx
callq 0x2240
cmpl $0x0, 0x1d60(%rbx)
je 0x35e6
movq (%r14), %rcx
leaq 0x15f74(%rip), %rdi     # 0x1930c
movl $0x30, %esi
movl $0x1, %edx
callq 0x2240
movq (%r14), %rcx
leaq 0x15f8c(%rip), %rdi     # 0x1933d
movl $0x2f, %esi
movl $0x1, %edx
callq 0x2240
movq (%r14), %rcx
leaq 0x15fa3(%rip), %rdi     # 0x1936d
movl $0x2e, %esi
movl $0x1, %edx
callq 0x2240
movq (%r14), %rcx
leaq 0x15fb9(%rip), %rdi     # 0x1939c
movl $0x31, %esi
movl $0x1, %edx
callq 0x2240
movq (%r14), %rcx
leaq 0x15fd2(%rip), %rdi     # 0x193ce
movl $0x27, %esi
movl $0x1, %edx
callq 0x2240
movq (%r14), %rcx
leaq 0x15fe1(%rip), %rdi     # 0x193f6
movl $0x27, %esi
movl $0x1, %edx
callq 0x2240
movq (%r14), %rcx
leaq 0x15ff0(%rip), %rdi     # 0x1941e
movl $0x31, %esi
movl $0x1, %edx
callq 0x2240
movq (%r14), %rcx
leaq 0x16009(%rip), %rdi     # 0x19450
movl $0x27, %esi
movl $0x1, %edx
callq 0x2240
movq (%r14), %rcx
leaq 0x16018(%rip), %rdi     # 0x19478
movl $0x1b, %esi
movl $0x1, %edx
callq 0x2240
movq (%r14), %rcx
leaq 0x1601b(%rip), %rdi     # 0x19494
movl $0x2f, %esi
movl $0x1, %edx
callq 0x2240
movq (%r14), %rcx
leaq 0x16032(%rip), %rdi     # 0x194c4
movl $0x2c, %esi
movl $0x1, %edx
callq 0x2240
movq (%r14), %rcx
leaq 0x16046(%rip), %rdi     # 0x194f1
movl $0x3c, %esi
movl $0x1, %edx
callq 0x2240
movq (%r14), %rcx
leaq 0x1606a(%rip), %rdi     # 0x1952e
movl $0x3f, %esi
movl $0x1, %edx
callq 0x2240
movq (%r14), %rcx
leaq 0x16091(%rip), %rdi     # 0x1956e
movl $0x40, %esi
movl $0x1, %edx
callq 0x2240
movq (%r14), %rcx
leaq 0x160b9(%rip), %rdi     # 0x195af
movl $0x42, %esi
movl $0x1, %edx
callq 0x2240
movq (%r14), %rcx
leaq 0x160e3(%rip), %rdi     # 0x195f2
movl $0x43, %esi
movl $0x1, %edx
callq 0x2240
movq (%r14), %rcx
leaq 0x1610e(%rip), %rdi     # 0x19636
movl $0x23, %esi
movl $0x1, %edx
callq 0x2240
movq (%r14), %rcx
leaq 0x16119(%rip), %rdi     # 0x1965a
movl $0x21, %esi
movl $0x1, %edx
callq 0x2240
movq (%r14), %rcx
leaq 0x16122(%rip), %rdi     # 0x1967c
movl $0x23, %esi
movl $0x1, %edx
callq 0x2240
movq (%r14), %rcx
leaq 0x1612d(%rip), %rdi     # 0x196a0
movl $0x33, %esi
movl $0x1, %edx
callq 0x2240
movq (%r14), %rcx
leaq 0x16148(%rip), %rdi     # 0x196d4
movl $0x4b, %esi
movl $0x1, %edx
callq 0x2240
movq (%r14), %rcx
leaq 0x1617b(%rip), %rdi     # 0x19720
movl $0x44, %esi
movl $0x1, %edx
callq 0x2240
movq (%r14), %rcx
leaq 0x161a7(%rip), %rdi     # 0x19765
movl $0x3f, %esi
movl $0x1, %edx
callq 0x2240
movq (%r14), %rcx
leaq 0x161ce(%rip), %rdi     # 0x197a5
movl $0x37, %esi
movl $0x1, %edx
callq 0x2240
xorl %edi, %edi
callq 0x2230