<p>Im trying to run ProtDeform on ubuntu 20.04
<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125161/" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125161/</a>
I need scoring function :/ to my project</p>
<p>But error occurs:</p>
<pre><code>(base) marcin@marcin-B550-AORUS-ELITE-AX-V2:~/ProtDeformV1.0$ ./install 
rm: cannot remove 'ProtDeform': No such file or directory
Compiling...
gcc -c  -g Matras.c Amino.c Vector.c GotohDPdis.c DiffStr.c BetaTopo.c RegressL.c Jacobi3.c SecStrEle.c ScoreENV.c ScoreDIS.c ScoreSSE.c BuildUpL.c DiheDis.c RMS.c OutAln.c StrLibL.c OutLibL.c LlistIO.c CalZsc.c LlistAlign.c MergeSort.c PairAli.c IO.c
Matras.c:77:1: warning: return type defaults to ‘int’ [-Wimplicit-int]
   77 | main(argc,argv)
      | ^~~~
Matras.c: In function ‘main’:
Matras.c:126:3: warning: implicit declaration of function ‘Set_AAnum’ [-Wimplicit-function-declaration]
  126 |   Set_AAnum();
      |   ^~~~~~~~~
Matras.c:390:27: warning: zero-length gnu_printf format string [-Wformat-zero-length]
  390 |         sprintf(envscfile,&quot;&quot;);
      |                           ^~
Matras.c:431:23: warning: zero-length gnu_printf format string [-Wformat-zero-length]
  431 |   sprintf(PAR.COMMAND,&quot;&quot;);
      |                       ^~
Matras.c:436:29: warning: implicit declaration of function ‘Get_Date_String’; did you mean ‘Get_Time_String’? [-Wimplicit-function-declaration]
  436 |   printf(&quot;#&lt;DATE&gt; \&quot;%s\&quot;\n&quot;,Get_Date_String());
      |                             ^~~~~~~~~~~~~~~
      |                             Get_Time_String
Matras.c:436:22: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=]
  436 |   printf(&quot;#&lt;DATE&gt; \&quot;%s\&quot;\n&quot;,Get_Date_String());
      |                     ~^      ~~~~~~~~~~~~~~~~~
      |                      |      |
      |                      char * int
      |                     %d
Matras.c:442:10: warning: too many arguments for format [-Wformat-extra-args]
  442 |   printf(&quot;# QueFile \&quot;%s\&quot; LibFile \&quot;%s\&quot;\n&quot;,MODE,QueFile,LibFile);
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Matras.c:498:4: warning: implicit declaration of function ‘Pairwise_3D_Alignment’ [-Wimplicit-function-declaration]
  498 |    Pairwise_3D_Alignment(&amp;proA,&amp;proB,&amp;DmapA,&amp;DmapB,&amp;AHead,&amp;SHead,inalifile,inssefile);
      |    ^~~~~~~~~~~~~~~~~~~~~
Matras.c:502:4: warning: implicit declaration of function ‘mainPD’; did you mean ‘main’? [-Wimplicit-function-declaration]
  502 |    mainPD(&amp;proA, &amp;proB, AHead.next, inalifile ); /* JR ProtDeform */
      |    ^~~~~~
      |    main
Matras.c:529:5: warning: implicit declaration of function ‘Output_Path_Horizontal_ClustalW’; did you mean ‘Output_Path_Horizontal_HTMLcolor’? [-Wimplicit-function-declaration]
  529 |     Output_Path_Horizontal_ClustalW(&amp;proA,&amp;proB,an,outclwfile);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |     Output_Path_Horizontal_HTMLcolor
Matras.c:726:6: warning: implicit declaration of function ‘Cal_Raw_MeanSD_Llist’; did you mean ‘Cal_Raw_Zscore_Llist’? [-Wimplicit-function-declaration]
  726 |      Cal_Raw_MeanSD_Llist(&amp;ALibHead,&amp;Mean,&amp;SD);
      |      ^~~~~~~~~~~~~~~~~~~~
      |      Cal_Raw_Zscore_Llist
Matras.c:512:26: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  512 |     sprintf(OutHead,&quot;%s%d&quot;,OheadStr,an-&gt;num);
      |                          ^
Matras.c:512:5: note: ‘sprintf’ output between 2 and 139 bytes into a destination of size 128
  512 |     sprintf(OutHead,&quot;%s%d&quot;,OheadStr,an-&gt;num);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Matras.c:587:43: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 113 and 240 [-Wformat-overflow=]
  587 |      { sprintf(command,&quot;perl %s/rotSTR.pl %s.mat %s -nc A -S B &gt; %s.pdb&quot;,
      |                                           ^~
  588 |              BASE_DIR,OutHead,proAfile,OutHead);
      |                       ~~~~~~~              
Matras.c:587:8: note: ‘sprintf’ output between 40 and 484 bytes into a destination of size 256
  587 |      { sprintf(command,&quot;perl %s/rotSTR.pl %s.mat %s -nc A -S B &gt; %s.pdb&quot;,
      |        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  588 |              BASE_DIR,OutHead,proAfile,OutHead);
      |              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Matras.c:590:62: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 33 and 223 [-Wformat-overflow=]
  590 |        sprintf(command,&quot;perl %s/rotSTR.pl - %s -nc B -S B &gt;&gt; %s.pdb&quot;,BASE_DIR,proBfile,OutHead);
      |                                                              ^~                        ~~~~~~~
Matras.c:590:8: note: ‘sprintf’ output between 38 and 355 bytes into a destination of size 256
  590 |        sprintf(command,&quot;perl %s/rotSTR.pl - %s -nc B -S B &gt;&gt; %s.pdb&quot;,BASE_DIR,proBfile,OutHead);
      |        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Matras.c:594:43: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 113 and 240 [-Wformat-overflow=]
  594 |      { sprintf(command,&quot;perl %s/rotSTR.pl %s.mat %s -nc A -S P -ch %c -H W &gt; %s.pdb&quot;,
      |                                           ^~
  595 |            BASE_DIR,OutHead,proAfile,proA.chain,OutHead);
      |                     ~~~~~~~                
Matras.c:594:8: note: ‘sprintf’ output between 51 and 495 bytes into a destination of size 256
  594 |      { sprintf(command,&quot;perl %s/rotSTR.pl %s.mat %s -nc A -S P -ch %c -H W &gt; %s.pdb&quot;,
      |        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  595 |            BASE_DIR,OutHead,proAfile,proA.chain,OutHead);
      |            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Matras.c:597:73: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 23 and 213 [-Wformat-overflow=]
  597 |       sprintf(command,&quot;perl %s/rotSTR.pl - %s -nc B -S P -ch %c -H W&gt;&gt; %s.pdb&quot;,
      |                                                                        ^~

  598 |         BASE_DIR,proBfile,proB.chain,OutHead);
      |                                      ~~~~~~~                            

Matras.c:597:8: note: ‘sprintf’ output between 48 and 365 bytes into a destination of size 256
  597 |        sprintf(command,&quot;perl %s/rotSTR.pl - %s -nc B -S P -ch %c -H W&gt;&gt; %s.pdb&quot;,
      |        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  598 |          BASE_DIR,proBfile,proB.chain,OutHead);
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Amino.c: In function ‘Amino_Name’:
Amino.c:104:11: warning: implicit declaration of function ‘strncmp’ [-Wimplicit-function-declaration]
  104 |       if (strncmp(t,&quot;ALA&quot;,3)==0)  r = 'A';
      |           ^~~~~~~
Amino.c:104:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  104 |       if (strncmp(t,&quot;ALA&quot;,3)==0)  r = 'A';
      |                           ^
&lt;built-in&gt;: note: built-in ‘strncmp’ declared here
Amino.c:105:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  105 |  else if (strncmp(t,&quot;GLU&quot;,3)==0)  r = 'E';
      |                           ^
&lt;built-in&gt;: note: built-in ‘strncmp’ declared here
Amino.c:106:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  106 |  else if (strncmp(t,&quot;GLN&quot;,3)==0)  r = 'Q';
      |                           ^
&lt;built-in&gt;: note: built-in ‘strncmp’ declared here
Amino.c:107:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  107 |  else if (strncmp(t,&quot;ASP&quot;,3)==0)  r = 'D';
      |                           ^
&lt;built-in&gt;: note: built-in ‘strncmp’ declared here
Amino.c:108:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  108 |  else if (strncmp(t,&quot;ASN&quot;,3)==0)  r = 'N';
      |                           ^
&lt;built-in&gt;: note: built-in ‘strncmp’ declared here
Amino.c:109:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  109 |  else if (strncmp(t,&quot;LEU&quot;,3)==0)  r = 'L';
      |                           ^
&lt;built-in&gt;: note: built-in ‘strncmp’ declared here
Amino.c:110:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  110 |  else if (strncmp(t,&quot;GLY&quot;,3)==0)  r = 'G';
      |                           ^
&lt;built-in&gt;: note: built-in ‘strncmp’ declared here
Amino.c:111:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  111 |  else if (strncmp(t,&quot;LYS&quot;,3)==0)  r = 'K';
      |                           ^
&lt;built-in&gt;: note: built-in ‘strncmp’ declared here
Amino.c:112:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  112 |  else if (strncmp(t,&quot;SER&quot;,3)==0)  r = 'S';
      |                           ^
&lt;built-in&gt;: note: built-in ‘strncmp’ declared here
Amino.c:113:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  113 |  else if (strncmp(t,&quot;VAL&quot;,3)==0)  r = 'V';
      |                           ^
&lt;built-in&gt;: note: built-in ‘strncmp’ declared here
Amino.c:114:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  114 |  else if (strncmp(t,&quot;ARG&quot;,3)==0)  r = 'R';
      |                           ^
&lt;built-in&gt;: note: built-in ‘strncmp’ declared here
Amino.c:115:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  115 |  else if (strncmp(t,&quot;THR&quot;,3)==0)  r = 'T';
      |                           ^
&lt;built-in&gt;: note: built-in ‘strncmp’ declared here
Amino.c:116:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  116 |  else if (strncmp(t,&quot;PRO&quot;,3)==0)  r = 'P';
      |                           ^
&lt;built-in&gt;: note: built-in ‘strncmp’ declared here
Amino.c:117:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  117 |  else if (strncmp(t,&quot;ILE&quot;,3)==0)  r = 'I';
      |                           ^
&lt;built-in&gt;: note: built-in ‘strncmp’ declared here
Amino.c:118:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  118 |  else if (strncmp(t,&quot;MET&quot;,3)==0)  r = 'M';
      |                           ^
&lt;built-in&gt;: note: built-in ‘strncmp’ declared here
Amino.c:119:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  119 |  else if (strncmp(t,&quot;PHE&quot;,3)==0)  r = 'F';
      |                           ^
&lt;built-in&gt;: note: built-in ‘strncmp’ declared here
Amino.c:120:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  120 |  else if (strncmp(t,&quot;TYR&quot;,3)==0)  r = 'Y';
      |                           ^
&lt;built-in&gt;: note: built-in ‘strncmp’ declared here
Amino.c:121:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  121 |  else if (strncmp(t,&quot;CYS&quot;,3)==0)  r = 'C';
      |                           ^
&lt;built-in&gt;: note: built-in ‘strncmp’ declared here
Amino.c:122:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  122 |  else if (strncmp(t,&quot;TRP&quot;,3)==0)  r = 'W';
      |                           ^
&lt;built-in&gt;: note: built-in ‘strncmp’ declared here
Amino.c:123:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  123 |  else if (strncmp(t,&quot;HIS&quot;,3)==0)  r = 'H';
      |                           ^
&lt;built-in&gt;: note: built-in ‘strncmp’ declared here
Amino.c:124:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  124 |  else if (strncmp(t,&quot;UNK&quot;,3)==0)  r = 'u';
      |                           ^
&lt;built-in&gt;: note: built-in ‘strncmp’ declared here
Amino.c:125:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  125 |  else if (strncmp(t,&quot;ACE&quot;,3)==0)  r = 'a';
      |                           ^
&lt;built-in&gt;: note: built-in ‘strncmp’ declared here
Amino.c:126:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  126 |  else if (strncmp(t,&quot;FOR&quot;,3)==0)  r = 'f';
      |                           ^
&lt;built-in&gt;: note: built-in ‘strncmp’ declared here
GotohDPdis.c: In function ‘GotohDP_Dscore_Iterative’:
GotohDPdis.c:202:3: warning: implicit declaration of function ‘ScoreDistanceSPair’; did you mean ‘ScoreDistanceS’? [-Wimplicit-function-declaration]
  202 |   ScoreDistanceSPair(proA,proB,an,DmapA,DmapB);
      |   ^~~~~~~~~~~~~~~~~~
      |   ScoreDistanceS
GotohDPdis.c: In function ‘GotohDP_Dscore’:
GotohDPdis.c:223:33: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=]
  223 |   { printf(&quot;#ERROR:PRE.MaxNali %s is less than Nali %d\n&quot;,PRE.MaxNali,an-&gt;Nali);
      |                                ~^                         ~~~~~~~~~~~
      |                                 |                            |
      |                                 char *                       int
      |                                %d
DiffStr.c: In function ‘Number_Sec’:
DiffStr.c:202:5: warning: type of ‘sym’ defaults to ‘int’ [-Wimplicit-int]
  202 | int Number_Sec(sym,Nstr)
      |     ^~~~~~~~~~
SecStrEle.c: In function ‘Output_SSE_PDB’:
SecStrEle.c:355:13: warning: too many arguments for format [-Wformat-extra-args]
  355 |  fprintf(fp,&quot;REMARK tFactor : 0 for Cend of SSE, 200 for  helix, 100 for sheet\n&quot;,pr-&gt;pname);
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ScoreENV.c: In function ‘Number_Sec’:
ScoreENV.c:313:5: warning: type of ‘sym’ defaults to ‘int’ [-Wimplicit-int]
  313 | int Number_Sec(sym,Nstr)
      |     ^~~~~~~~~~
ScoreENV.c: In function ‘Read_Env_Score’:
ScoreENV.c:264:22: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  264 |  sprintf(Fname,&quot;%s/%s&quot;,SCORE_DIR,fname);
      |                      ^
ScoreENV.c:264:2: note: ‘sprintf’ output 2 or more bytes (assuming 129) into a destination of size 128
  264 |  sprintf(Fname,&quot;%s/%s&quot;,SCORE_DIR,fname);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BuildUpL.c: In function ‘Build_Up_LL’:
BuildUpL.c:256:2: warning: implicit declaration of function ‘Merge_Sort_Double_Linked_List’ [-Wimplicit-function-declaration]
  256 |  Merge_Sort_Double_Linked_List(head,'R');
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BuildUpL.c: In function ‘Read_SSE_Alignment’:
BuildUpL.c:677:4: warning: implicit declaration of function ‘Get_Part_Of_Line’ [-Wimplicit-function-declaration]
  677 |    Get_Part_Of_Line(num1,word1,1,strlen(word1));
      |    ^~~~~~~~~~~~~~~~
OutAln.c: In function ‘Write_Rasmol_Color_Alignment’:
OutAln.c:564:34: warning: implicit declaration of function ‘Get_Date_String’ [-Wimplicit-function-declaration]
  564 |  fprintf(fp,&quot;# DATE      '%s'\n&quot;,Get_Date_String());
      |                                  ^~~~~~~~~~~~~~~
OutAln.c:564:28: warning: format ‘%s’ expects argument of type ‘char *’, but argument 3 has type ‘int’ [-Wformat=]
  564 |  fprintf(fp,&quot;# DATE      '%s'\n&quot;,Get_Date_String());
      |                           ~^     ~~~~~~~~~~~~~~~~~
      |                            |     |
      |                            |     int
      |                            char *
      |                           %d
OutAln.c: In function ‘Write_Rasmol_Color_Alignment_Each_Protein’:
OutAln.c:715:27: warning: format ‘%s’ expects argument of type ‘char *’, but argument 3 has type ‘int’ [-Wformat=]
  715 |  fprintf(fp,&quot;# DATE      %s\n&quot;,Get_Date_String());
      |                          ~^    ~~~~~~~~~~~~~~~~~
      |                           |    |
      |                           |    int
      |                           char *
      |                          %d
OutAln.c:731:10: warning: implicit declaration of function ‘Ncompare’ [-Wimplicit-function-declaration]
  731 |  Ncomp = Ncompare(a);
      |          ^~~~~~~~
OutAln.c: In function ‘Write_Molscript_Alignment_Each_Protein’:
OutAln.c:880:27: warning: format ‘%s’ expects argument of type ‘char *’, but argument 3 has type ‘int’ [-Wformat=]
  880 |  fprintf(fp,&quot;! DATE      %s\n&quot;,Get_Date_String());
      |                          ~^    ~~~~~~~~~~~~~~~~~
      |                           |    |
      |                           |    int
      |                           char *
      |                          %d
OutAln.c:905:35: warning: implicit declaration of function ‘Remove_Space’ [-Wimplicit-function-declaration]
  905 |        if (OutProteinType == 'A') Remove_Space(rsta,pA-&gt;Rnum[a-&gt;nalA[i]]);
      |                                   ^~~~~~~~~~~~
OutAln.c: In function ‘Find_nal’:
OutAln.c:962:5: warning: type of ‘q’ defaults to ‘int’ [-Wimplicit-int]
  962 | int Find_nal(q,Nali,nalA)
      |     ^~~~~~~~
OutAln.c: In function ‘Output_Alignment_Information’:
OutAln.c:1058:2: warning: implicit declaration of function ‘Get_Part_Of_Line’ [-Wimplicit-function-declaration]
 1058 |  Get_Part_Of_Line(ln,pA-&gt;compnd,0,40);
      |  ^~~~~~~~~~~~~~~~
StrLibL.c: In function ‘Read_Library_List’:
StrLibL.c:75:5: warning: implicit declaration of function ‘Get_First_Field’ [-Wimplicit-function-declaration]
   75 |     Get_First_Field(name,tax,buffer);
      |     ^~~~~~~~~~~~~~~
StrLibL.c: In function ‘Check_Library_List’:
StrLibL.c:113:3: warning: implicit declaration of function ‘Get_Part_Of_Line’ [-Wimplicit-function-declaration]
  113 |   Get_Part_Of_Line(dir,bn-&gt;Name,1,2);
      |   ^~~~~~~~~~~~~~~~
OutLibL.c: In function ‘Output_Library_ClustalW’:
OutLibL.c:234:4: warning: implicit declaration of function ‘Get_Part_Of_Line’ [-Wimplicit-function-declaration]
  234 |    Get_Part_Of_Line(ln,bn-&gt;sim-&gt;Name,0,16);
      |    ^~~~~~~~~~~~~~~~
LlistIO.c: In function ‘Read_BSSP_File_LinearList’:
LlistIO.c:161:2: warning: implicit declaration of function ‘Set_SSE’ [-Wimplicit-function-declaration]
  161 |  Set_SSE(pr);
      |  ^~~~~~~
LlistIO.c:162:2: warning: implicit declaration of function ‘Set_Dis_bwn_SSE’ [-Wimplicit-function-declaration]
  162 |  Set_Dis_bwn_SSE(pr,'C');
      |  ^~~~~~~~~~~~~~~
LlistIO.c: In function ‘Translate_BSSP_File_LinearList’:
LlistIO.c:218:51: warning: implicit declaration of function ‘tolower’ [-Wimplicit-function-declaration]
  218 |             if (X-&gt;line[75]=='C') pr-&gt;Seq[Rnum] = tolower(pr-&gt;Seq[Rnum]);  /* for CIS conf */
      |                                                   ^~~~~~~
PairAli.c: In function ‘Pairwise_3D_Alignment’:
PairAli.c:188:3: warning: implicit declaration of function ‘Set_Value_AlignNode’; did you mean ‘Tail_Value_AlignNode’? [-Wimplicit-function-declaration]
  188 |   Set_Value_AlignNode(Ahead,'S');    /* JR  It was  D */
      |   ^~~~~~~~~~~~~~~~~~~
      |   Tail_Value_AlignNode
PairAli.c:189:3: warning: implicit declaration of function ‘Merge_Sort_Double_Linked_List’ [-Wimplicit-function-declaration]
  189 |   Merge_Sort_Double_Linked_List(Ahead,'R');
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IO.c: In function ‘Read_BSSP_File’:
IO.c:705:3: warning: implicit declaration of function ‘Set_SSE’ [-Wimplicit-function-declaration]
  705 |   Set_SSE(pr);
      |   ^~~~~~~
IO.c:706:3: warning: implicit declaration of function ‘Set_Dis_bwn_SSE’ [-Wimplicit-function-declaration]
  706 |   Set_Dis_bwn_SSE(pr,'C');
      |   ^~~~~~~~~~~~~~~
IO.c: In function ‘Read_Sequence’:
IO.c:886:13: warning: implicit declaration of function ‘isalpha’ [-Wimplicit-function-declaration]
  886 |    else if (isalpha(sym)!=0)
      |             ^~~~~~~
IO.c: In function ‘Read_Matras_Environment_File’:
IO.c:87:23: warning: ‘%s’ directive writing up to 63 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
   87 |   sprintf(Matfile,&quot;%s/%s&quot;,homedir,matfile);
      |                       ^~          ~~~~~~~
IO.c:87:3: note: ‘sprintf’ output between 2 and 192 bytes into a destination of size 128
   87 |   sprintf(Matfile,&quot;%s/%s&quot;,homedir,matfile);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IO.c: In function ‘Read_PDB_File’:
IO.c:378:20: warning: ‘%s’ directive writing up to 3 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  378 |  sprintf(Fname,&quot;%s/%s/%s&quot;,PDB_DIR,dir,fname);
      |                    ^~             ~~~
IO.c:378:2: note: ‘sprintf’ output 3 or more bytes (assuming 133) into a destination of size 128
  378 |  sprintf(Fname,&quot;%s/%s/%s&quot;,PDB_DIR,dir,fname);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c  -g vector.cpp TransSeq.cpp Geometry.cpp WriteDeformPDB.cpp Evaluation.cpp  -w
Geometry.cpp:30:31: error: ‘&lt;unnamed enum&gt; GEOMETRY’, declared using unnamed type, is used but never defined [-fpermissive]
   30 | extern enum { RIGID, AFFINE } GEOMETRY;
      |                               ^~~~~~~~
WriteDeformPDB.cpp:16:31: error: ‘&lt;unnamed enum&gt; GEOMETRY’, declared using unnamed type, is used but never defined [-fpermissive]
   16 | extern enum { RIGID, AFFINE } GEOMETRY;
      |                               ^~~~~~~~
make: *** [Makefile:125: ../ProtDeform] Error 1
</code></pre>
<p>I've contacted the program developers about this, but am still waiting for answer from them.</p>
<p>Can you help?</p>
<p>EDIT1:
ox
I've checked</p>
<p>Ubuntu 16.04 on virtualbox</p>
<p>Ubuntu 20.04 with i7</p>
<p>Ubuntu 20.04 with Ryzen 9</p>
<p>same error...</p>
<p>EDIT 2:</p>
<pre><code>I have found hidden file .matras:
###############################
### MATRAS ENVIRONMENT FILE ###
###############################

BASE_DIR .
SCORE_DIR  data_sc/ROM-04JAN29
TMP_DIR    .
BSSP_DIR  /DB/BSSP
PDB_DIR   /DB/PDB
</code></pre>
<p>I'm checking to see if it simply requires PDB</p>

CC BY-SA 4.0
2023-09-13T01:54:33.760Z
What is ProtDeform? Why are you trying to use it? Can you give any additional context around your problem that would help in finding a solution?
gringer
CC BY-SA 4.0
2023-09-13T09:57:27.180Z
@gringer I add some information. Yes, still waiting for answer :/
MTG
CC BY-SA 4.0
2023-09-15T17:24:01.710Z
The tool is more than 10 years old, without documentation for compilation and without any documentation towards software versions. The paper has a single citation, indication it never has been adopted by the community. Hence, find something else that actually works. Not what you want to hear, I know.
ATpoint
CC BY-SA 4.0
2023-09-15T21:27:15.917Z
is this webserver giving any result with your input https://bioinfo.uib.es/~recerca/ProtDeform/
pippo1980
CC BY-SA 4.0
2023-09-15T21:29:40.973Z
are you trying to run or install the software ??
pippo1980
CC BY-SA 4.0
2023-09-16T07:36:50.373Z
@pippo1980 install to run :)
MTG
<proteins><protein-structure><bash><perl>
Old program make error ProtDeform
# Old program make error ProtDeform

(Asked by: username_0 on 2023-09-12)

Im trying to run ProtDeform on ubuntu 20.04
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125161/
I need scoring function :/ to my project
But error occurs:
(base) marcin@marcin-B550-AORUS-ELITE-AX-V2:~/ProtDeformV1.0$ ./install 
rm: cannot remove 'ProtDeform': No such file or directory
Compiling...
gcc -c  -g Matras.c Amino.c Vector.c GotohDPdis.c DiffStr.c BetaTopo.c RegressL.c Jacobi3.c SecStrEle.c ScoreENV.c ScoreDIS.c ScoreSSE.c BuildUpL.c DiheDis.c RMS.c OutAln.c StrLibL.c OutLibL.c LlistIO.c CalZsc.c LlistAlign.c MergeSort.c PairAli.c IO.c
Matras.c:77:1: warning: return type defaults to ‘int’ [-Wimplicit-int]
   77 | main(argc,argv)
      | ^~~~
Matras.c: In function ‘main’:
Matras.c:126:3: warning: implicit declaration of function ‘Set_AAnum’ [-Wimplicit-function-declaration]
  126 |   Set_AAnum();
      |   ^~~~~~~~~
Matras.c:390:27: warning: zero-length gnu_printf format string [-Wformat-zero-length]
  390 |         sprintf(envscfile,"");
      |                           ^~
Matras.c:431:23: warning: zero-length gnu_printf format string [-Wformat-zero-length]
  431 |   sprintf(PAR.COMMAND,"");
      |                       ^~
Matras.c:436:29: warning: implicit declaration of function ‘Get_Date_String’; did you mean ‘Get_Time_String’? [-Wimplicit-function-declaration]
  436 |   printf("# \"%s\"\n",Get_Date_String());
      |                             ^~~~~~~~~~~~~~~
      |                             Get_Time_String
Matras.c:436:22: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=]
  436 |   printf("# \"%s\"\n",Get_Date_String());
      |                     ~^      ~~~~~~~~~~~~~~~~~
      |                      |      |
      |                      char * int
      |                     %d
Matras.c:442:10: warning: too many arguments for format [-Wformat-extra-args]
  442 |   printf("# QueFile \"%s\" LibFile \"%s\"\n",MODE,QueFile,LibFile);
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Matras.c:498:4: warning: implicit declaration of function ‘Pairwise_3D_Alignment’ [-Wimplicit-function-declaration]
  498 |    Pairwise_3D_Alignment(&proA,&proB,&DmapA,&DmapB,&AHead,&SHead,inalifile,inssefile);
      |    ^~~~~~~~~~~~~~~~~~~~~
Matras.c:502:4: warning: implicit declaration of function ‘mainPD’; did you mean ‘main’? [-Wimplicit-function-declaration]
  502 |    mainPD(&proA, &proB, AHead.next, inalifile ); /* JR ProtDeform */
      |    ^~~~~~
      |    main
Matras.c:529:5: warning: implicit declaration of function ‘Output_Path_Horizontal_ClustalW’; did you mean ‘Output_Path_Horizontal_HTMLcolor’? [-Wimplicit-function-declaration]
  529 |     Output_Path_Horizontal_ClustalW(&proA,&proB,an,outclwfile);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |     Output_Path_Horizontal_HTMLcolor
Matras.c:726:6: warning: implicit declaration of function ‘Cal_Raw_MeanSD_Llist’; did you mean ‘Cal_Raw_Zscore_Llist’? [-Wimplicit-function-declaration]
  726 |      Cal_Raw_MeanSD_Llist(&ALibHead,&Mean,&SD);
      |      ^~~~~~~~~~~~~~~~~~~~
      |      Cal_Raw_Zscore_Llist
Matras.c:512:26: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  512 |     sprintf(OutHead,"%s%d",OheadStr,an->num);
      |                          ^
Matras.c:512:5: note: ‘sprintf’ output between 2 and 139 bytes into a destination of size 128
  512 |     sprintf(OutHead,"%s%d",OheadStr,an->num);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Matras.c:587:43: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 113 and 240 [-Wformat-overflow=]
  587 |      { sprintf(command,"perl %s/rotSTR.pl %s.mat %s -nc A -S B > %s.pdb",
      |                                           ^~
  588 |              BASE_DIR,OutHead,proAfile,OutHead);
      |                       ~~~~~~~              
Matras.c:587:8: note: ‘sprintf’ output between 40 and 484 bytes into a destination of size 256
  587 |      { sprintf(command,"perl %s/rotSTR.pl %s.mat %s -nc A -S B > %s.pdb",
      |        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  588 |              BASE_DIR,OutHead,proAfile,OutHead);
      |              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Matras.c:590:62: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 33 and 223 [-Wformat-overflow=]
  590 |        sprintf(command,"perl %s/rotSTR.pl - %s -nc B -S B >> %s.pdb",BASE_DIR,proBfile,OutHead);
      |                                                              ^~                        ~~~~~~~
Matras.c:590:8: note: ‘sprintf’ output between 38 and 355 bytes into a destination of size 256
  590 |        sprintf(command,"perl %s/rotSTR.pl - %s -nc B -S B >> %s.pdb",BASE_DIR,proBfile,OutHead);
      |        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Matras.c:594:43: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 113 and 240 [-Wformat-overflow=]
  594 |      { sprintf(command,"perl %s/rotSTR.pl %s.mat %s -nc A -S P -ch %c -H W > %s.pdb",
      |                                           ^~
  595 |            BASE_DIR,OutHead,proAfile,proA.chain,OutHead);
      |                     ~~~~~~~                
Matras.c:594:8: note: ‘sprintf’ output between 51 and 495 bytes into a destination of size 256
  594 |      { sprintf(command,"perl %s/rotSTR.pl %s.mat %s -nc A -S P -ch %c -H W > %s.pdb",
      |        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  595 |            BASE_DIR,OutHead,proAfile,proA.chain,OutHead);
      |            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Matras.c:597:73: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 23 and 213 [-Wformat-overflow=]
  597 |       sprintf(command,"perl %s/rotSTR.pl - %s -nc B -S P -ch %c -H W>> %s.pdb",
      |                                                                        ^~

  598 |         BASE_DIR,proBfile,proB.chain,OutHead);
      |                                      ~~~~~~~                            

Matras.c:597:8: note: ‘sprintf’ output between 48 and 365 bytes into a destination of size 256
  597 |        sprintf(command,"perl %s/rotSTR.pl - %s -nc B -S P -ch %c -H W>> %s.pdb",
      |        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  598 |          BASE_DIR,proBfile,proB.chain,OutHead);
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Amino.c: In function ‘Amino_Name’:
Amino.c:104:11: warning: implicit declaration of function ‘strncmp’ [-Wimplicit-function-declaration]
  104 |       if (strncmp(t,"ALA",3)==0)  r = 'A';
      |           ^~~~~~~
Amino.c:104:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  104 |       if (strncmp(t,"ALA",3)==0)  r = 'A';
      |                           ^
: note: built-in ‘strncmp’ declared here
Amino.c:105:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  105 |  else if (strncmp(t,"GLU",3)==0)  r = 'E';
      |                           ^
: note: built-in ‘strncmp’ declared here
Amino.c:106:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  106 |  else if (strncmp(t,"GLN",3)==0)  r = 'Q';
      |                           ^
: note: built-in ‘strncmp’ declared here
Amino.c:107:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  107 |  else if (strncmp(t,"ASP",3)==0)  r = 'D';
      |                           ^
: note: built-in ‘strncmp’ declared here
Amino.c:108:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  108 |  else if (strncmp(t,"ASN",3)==0)  r = 'N';
      |                           ^
: note: built-in ‘strncmp’ declared here
Amino.c:109:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  109 |  else if (strncmp(t,"LEU",3)==0)  r = 'L';
      |                           ^
: note: built-in ‘strncmp’ declared here
Amino.c:110:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  110 |  else if (strncmp(t,"GLY",3)==0)  r = 'G';
      |                           ^
: note: built-in ‘strncmp’ declared here
Amino.c:111:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  111 |  else if (strncmp(t,"LYS",3)==0)  r = 'K';
      |                           ^
: note: built-in ‘strncmp’ declared here
Amino.c:112:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  112 |  else if (strncmp(t,"SER",3)==0)  r = 'S';
      |                           ^
: note: built-in ‘strncmp’ declared here
Amino.c:113:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  113 |  else if (strncmp(t,"VAL",3)==0)  r = 'V';
      |                           ^
: note: built-in ‘strncmp’ declared here
Amino.c:114:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  114 |  else if (strncmp(t,"ARG",3)==0)  r = 'R';
      |                           ^
: note: built-in ‘strncmp’ declared here
Amino.c:115:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  115 |  else if (strncmp(t,"THR",3)==0)  r = 'T';
      |                           ^
: note: built-in ‘strncmp’ declared here
Amino.c:116:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  116 |  else if (strncmp(t,"PRO",3)==0)  r = 'P';
      |                           ^
: note: built-in ‘strncmp’ declared here
Amino.c:117:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  117 |  else if (strncmp(t,"ILE",3)==0)  r = 'I';
      |                           ^
: note: built-in ‘strncmp’ declared here
Amino.c:118:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  118 |  else if (strncmp(t,"MET",3)==0)  r = 'M';
      |                           ^
: note: built-in ‘strncmp’ declared here
Amino.c:119:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  119 |  else if (strncmp(t,"PHE",3)==0)  r = 'F';
      |                           ^
: note: built-in ‘strncmp’ declared here
Amino.c:120:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  120 |  else if (strncmp(t,"TYR",3)==0)  r = 'Y';
      |                           ^
: note: built-in ‘strncmp’ declared here
Amino.c:121:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  121 |  else if (strncmp(t,"CYS",3)==0)  r = 'C';
      |                           ^
: note: built-in ‘strncmp’ declared here
Amino.c:122:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  122 |  else if (strncmp(t,"TRP",3)==0)  r = 'W';
      |                           ^
: note: built-in ‘strncmp’ declared here
Amino.c:123:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  123 |  else if (strncmp(t,"HIS",3)==0)  r = 'H';
      |                           ^
: note: built-in ‘strncmp’ declared here
Amino.c:124:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  124 |  else if (strncmp(t,"UNK",3)==0)  r = 'u';
      |                           ^
: note: built-in ‘strncmp’ declared here
Amino.c:125:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  125 |  else if (strncmp(t,"ACE",3)==0)  r = 'a';
      |                           ^
: note: built-in ‘strncmp’ declared here
Amino.c:126:27: warning: ‘strncmp’ argument 3 type is ‘int’ where ‘long unsigned int’ is expected in a call to built-in function declared without prototype [-Wbuiltin-declaration-mismatch]
  126 |  else if (strncmp(t,"FOR",3)==0)  r = 'f';
      |                           ^
: note: built-in ‘strncmp’ declared here
GotohDPdis.c: In function ‘GotohDP_Dscore_Iterative’:
GotohDPdis.c:202:3: warning: implicit declaration of function ‘ScoreDistanceSPair’; did you mean ‘ScoreDistanceS’? [-Wimplicit-function-declaration]
  202 |   ScoreDistanceSPair(proA,proB,an,DmapA,DmapB);
      |   ^~~~~~~~~~~~~~~~~~
      |   ScoreDistanceS
GotohDPdis.c: In function ‘GotohDP_Dscore’:
GotohDPdis.c:223:33: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=]
  223 |   { printf("#ERROR:PRE.MaxNali %s is less than Nali %d\n",PRE.MaxNali,an->Nali);
      |                                ~^                         ~~~~~~~~~~~
      |                                 |                            |
      |                                 char *                       int
      |                                %d
DiffStr.c: In function ‘Number_Sec’:
DiffStr.c:202:5: warning: type of ‘sym’ defaults to ‘int’ [-Wimplicit-int]
  202 | int Number_Sec(sym,Nstr)
      |     ^~~~~~~~~~
SecStrEle.c: In function ‘Output_SSE_PDB’:
SecStrEle.c:355:13: warning: too many arguments for format [-Wformat-extra-args]
  355 |  fprintf(fp,"REMARK tFactor : 0 for Cend of SSE, 200 for  helix, 100 for sheet\n",pr->pname);
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ScoreENV.c: In function ‘Number_Sec’:
ScoreENV.c:313:5: warning: type of ‘sym’ defaults to ‘int’ [-Wimplicit-int]
  313 | int Number_Sec(sym,Nstr)
      |     ^~~~~~~~~~
ScoreENV.c: In function ‘Read_Env_Score’:
ScoreENV.c:264:22: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  264 |  sprintf(Fname,"%s/%s",SCORE_DIR,fname);
      |                      ^
ScoreENV.c:264:2: note: ‘sprintf’ output 2 or more bytes (assuming 129) into a destination of size 128
  264 |  sprintf(Fname,"%s/%s",SCORE_DIR,fname);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BuildUpL.c: In function ‘Build_Up_LL’:
BuildUpL.c:256:2: warning: implicit declaration of function ‘Merge_Sort_Double_Linked_List’ [-Wimplicit-function-declaration]
  256 |  Merge_Sort_Double_Linked_List(head,'R');
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BuildUpL.c: In function ‘Read_SSE_Alignment’:
BuildUpL.c:677:4: warning: implicit declaration of function ‘Get_Part_Of_Line’ [-Wimplicit-function-declaration]
  677 |    Get_Part_Of_Line(num1,word1,1,strlen(word1));
      |    ^~~~~~~~~~~~~~~~
OutAln.c: In function ‘Write_Rasmol_Color_Alignment’:
OutAln.c:564:34: warning: implicit declaration of function ‘Get_Date_String’ [-Wimplicit-function-declaration]
  564 |  fprintf(fp,"# DATE      '%s'\n",Get_Date_String());
      |                                  ^~~~~~~~~~~~~~~
OutAln.c:564:28: warning: format ‘%s’ expects argument of type ‘char *’, but argument 3 has type ‘int’ [-Wformat=]
  564 |  fprintf(fp,"# DATE      '%s'\n",Get_Date_String());
      |                           ~^     ~~~~~~~~~~~~~~~~~
      |                            |     |
      |                            |     int
      |                            char *
      |                           %d
OutAln.c: In function ‘Write_Rasmol_Color_Alignment_Each_Protein’:
OutAln.c:715:27: warning: format ‘%s’ expects argument of type ‘char *’, but argument 3 has type ‘int’ [-Wformat=]
  715 |  fprintf(fp,"# DATE      %s\n",Get_Date_String());
      |                          ~^    ~~~~~~~~~~~~~~~~~
      |                           |    |
      |                           |    int
      |                           char *
      |                          %d
OutAln.c:731:10: warning: implicit declaration of function ‘Ncompare’ [-Wimplicit-function-declaration]
  731 |  Ncomp = Ncompare(a);
      |          ^~~~~~~~
OutAln.c: In function ‘Write_Molscript_Alignment_Each_Protein’:
OutAln.c:880:27: warning: format ‘%s’ expects argument of type ‘char *’, but argument 3 has type ‘int’ [-Wformat=]
  880 |  fprintf(fp,"! DATE      %s\n",Get_Date_String());
      |                          ~^    ~~~~~~~~~~~~~~~~~
      |                           |    |
      |                           |    int
      |                           char *
      |                          %d
OutAln.c:905:35: warning: implicit declaration of function ‘Remove_Space’ [-Wimplicit-function-declaration]
  905 |        if (OutProteinType == 'A') Remove_Space(rsta,pA->Rnum[a->nalA[i]]);
      |                                   ^~~~~~~~~~~~
OutAln.c: In function ‘Find_nal’:
OutAln.c:962:5: warning: type of ‘q’ defaults to ‘int’ [-Wimplicit-int]
  962 | int Find_nal(q,Nali,nalA)
      |     ^~~~~~~~
OutAln.c: In function ‘Output_Alignment_Information’:
OutAln.c:1058:2: warning: implicit declaration of function ‘Get_Part_Of_Line’ [-Wimplicit-function-declaration]
 1058 |  Get_Part_Of_Line(ln,pA->compnd,0,40);
      |  ^~~~~~~~~~~~~~~~
StrLibL.c: In function ‘Read_Library_List’:
StrLibL.c:75:5: warning: implicit declaration of function ‘Get_First_Field’ [-Wimplicit-function-declaration]
   75 |     Get_First_Field(name,tax,buffer);
      |     ^~~~~~~~~~~~~~~
StrLibL.c: In function ‘Check_Library_List’:
StrLibL.c:113:3: warning: implicit declaration of function ‘Get_Part_Of_Line’ [-Wimplicit-function-declaration]
  113 |   Get_Part_Of_Line(dir,bn->Name,1,2);
      |   ^~~~~~~~~~~~~~~~
OutLibL.c: In function ‘Output_Library_ClustalW’:
OutLibL.c:234:4: warning: implicit declaration of function ‘Get_Part_Of_Line’ [-Wimplicit-function-declaration]
  234 |    Get_Part_Of_Line(ln,bn->sim->Name,0,16);
      |    ^~~~~~~~~~~~~~~~
LlistIO.c: In function ‘Read_BSSP_File_LinearList’:
LlistIO.c:161:2: warning: implicit declaration of function ‘Set_SSE’ [-Wimplicit-function-declaration]
  161 |  Set_SSE(pr);
      |  ^~~~~~~
LlistIO.c:162:2: warning: implicit declaration of function ‘Set_Dis_bwn_SSE’ [-Wimplicit-function-declaration]
  162 |  Set_Dis_bwn_SSE(pr,'C');
      |  ^~~~~~~~~~~~~~~
LlistIO.c: In function ‘Translate_BSSP_File_LinearList’:
LlistIO.c:218:51: warning: implicit declaration of function ‘tolower’ [-Wimplicit-function-declaration]
  218 |             if (X->line[75]=='C') pr->Seq[Rnum] = tolower(pr->Seq[Rnum]);  /* for CIS conf */
      |                                                   ^~~~~~~
PairAli.c: In function ‘Pairwise_3D_Alignment’:
PairAli.c:188:3: warning: implicit declaration of function ‘Set_Value_AlignNode’; did you mean ‘Tail_Value_AlignNode’? [-Wimplicit-function-declaration]
  188 |   Set_Value_AlignNode(Ahead,'S');    /* JR  It was  D */
      |   ^~~~~~~~~~~~~~~~~~~
      |   Tail_Value_AlignNode
PairAli.c:189:3: warning: implicit declaration of function ‘Merge_Sort_Double_Linked_List’ [-Wimplicit-function-declaration]
  189 |   Merge_Sort_Double_Linked_List(Ahead,'R');
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IO.c: In function ‘Read_BSSP_File’:
IO.c:705:3: warning: implicit declaration of function ‘Set_SSE’ [-Wimplicit-function-declaration]
  705 |   Set_SSE(pr);
      |   ^~~~~~~
IO.c:706:3: warning: implicit declaration of function ‘Set_Dis_bwn_SSE’ [-Wimplicit-function-declaration]
  706 |   Set_Dis_bwn_SSE(pr,'C');
      |   ^~~~~~~~~~~~~~~
IO.c: In function ‘Read_Sequence’:
IO.c:886:13: warning: implicit declaration of function ‘isalpha’ [-Wimplicit-function-declaration]
  886 |    else if (isalpha(sym)!=0)
      |             ^~~~~~~
IO.c: In function ‘Read_Matras_Environment_File’:
IO.c:87:23: warning: ‘%s’ directive writing up to 63 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
   87 |   sprintf(Matfile,"%s/%s",homedir,matfile);
      |                       ^~          ~~~~~~~
IO.c:87:3: note: ‘sprintf’ output between 2 and 192 bytes into a destination of size 128
   87 |   sprintf(Matfile,"%s/%s",homedir,matfile);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IO.c: In function ‘Read_PDB_File’:
IO.c:378:20: warning: ‘%s’ directive writing up to 3 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  378 |  sprintf(Fname,"%s/%s/%s",PDB_DIR,dir,fname);
      |                    ^~             ~~~
IO.c:378:2: note: ‘sprintf’ output 3 or more bytes (assuming 133) into a destination of size 128
  378 |  sprintf(Fname,"%s/%s/%s",PDB_DIR,dir,fname);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c  -g vector.cpp TransSeq.cpp Geometry.cpp WriteDeformPDB.cpp Evaluation.cpp  -w
Geometry.cpp:30:31: error: ‘ GEOMETRY’, declared using unnamed type, is used but never defined [-fpermissive]
   30 | extern enum { RIGID, AFFINE } GEOMETRY;
      |                               ^~~~~~~~
WriteDeformPDB.cpp:16:31: error: ‘ GEOMETRY’, declared using unnamed type, is used but never defined [-fpermissive]
   16 | extern enum { RIGID, AFFINE } GEOMETRY;
      |                               ^~~~~~~~
make: *** [Makefile:125: ../ProtDeform] Error 1

I've contacted the program developers about this, but am still waiting for answer from them.
Can you help?
EDIT1:
ox
I've checked
Ubuntu 16.04 on virtualbox
Ubuntu 20.04 with i7
Ubuntu 20.04 with Ryzen 9
same error...
EDIT 2:
I have found hidden file .matras:
###############################
### MATRAS ENVIRONMENT FILE ###
###############################

BASE_DIR .
SCORE_DIR  data_sc/ROM-04JAN29
TMP_DIR    .
BSSP_DIR  /DB/BSSP
PDB_DIR   /DB/PDB

I'm checking to see if it simply requires PDB

**Tags:** proteins, protein-structure, bash, perl
> **Comments:**
> **username_1**: What is ProtDeform? Why are you trying to use it? Can you give any additional context around your problem that would help in finding a solution?  
> **username_0**: @gringer I add some information. Yes, still waiting for answer :/  
> **username_2**: The tool is more than 10 years old, without documentation for compilation and without any documentation towards software versions. The paper has a single citation, indication it never has been adopted by the community. Hence, find something else that actually works. Not what you want to hear, I know.  
> **username_3**: is this webserver giving any result with your input https://bioinfo.uib.es/~recerca/ProtDeform/  
> **username_3**: are you trying to run or install the software ??  
> **username_0**: @pippo1980 install to run :)  

---

## 0 answers

