The New Plan

ebuild branch has old ebuilds.  profiles dir still has CFLAGS.

Everything else is removed or modified for changing of upstream to
Alpine.

1 files changed, 0 insertions, 230 deletions

diff --git a/licenses/procheck b/licenses/procheck
deleted file mode 100644
index 793379cc3..000000000
--- a/licenses/procheck
+++ /dev/null
@@ -1,230 +0,0 @@
-
-
-	  PROCHECK - Stereochemical Quality of Protein Structures
-          -------------------------------------------------------
-			and AQUA for PROCHECK-NMR
-                        -------------------------
-
-			CONFIDENTIALITY AGREEMENT
-			-------------------------
-
-
-
-In regard to the PROCHECK suite of programs, specified in Appendix 1
-herewith and the AQUA suite of programs specified in Appendix 2 herewith
-(the Software) supplied to us, the copyright and other intellectual
-property rights to which belong to the authors, we
-
-    __________________________________________________________________
-
-undertake to the authors that we shall be bound by the following terms and
-conditions:-
-
-1. We will receive the Software and any related documentation in confidence
-and will not use the same except for the purpose of the department's own 
-research. The Software will be used only by such of our officers or
-employees to whom it must reasonably be communicated to enable us to
-undertake our research and who agree to be bound by the same confidence.
-The department shall procure and enforce such agreement from its staff for
-the benefit of the authors.
-
-2. The publication of research using the Software must reference
-
-   "Laskowski R A, MacArthur M W, Moss D S & Thornton J M (1993). PROCHECK:
-   a program to check the stereochemical quality of protein
-   structures. J. Appl.  Cryst., 26, 283-291."
-
-and
-
-   "Rullmann J A C (1996). AQUA, Computer Program, Department of NMR
-   Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht
-   University, The Netherlands."
-
-
-3. Research shall take place solely at the department's premises at
-
-    __________________________________________________________________
-
-4. All forms of the Software will be kept in a reasonably secure place to
-prevent unauthorised access.
-
-5. Each copy of the Software or, if not practicable then, any package
-associated therewith shall be suitably marked (and such marking maintained) 
-with the following copyright notice: " Copyright 1992 M W MacArthur, R A
-Laskowski, D S Moss, J A C Rullmann & J M Thornton All Rights Reserved".
-
-6. The Software may be modified but any changes made shall be made
-available to the authors.
-
-7. The Software shall be used exclusively for academic teaching and
-research. The Software will not be used for any commercial research or
-research associated with an industrial company.
-
-8. The confidentiality obligation in paragraph one shall not apply:
-
-   (i)  to information and data known to the department at the time of
-	receipt hereunder (as evidenced by its written records);
-
-  (ii)	to information and data which was at the time of receipt in the 
-	public domain or thereafter becomes so through no wrongful act of
-	the department;
-
- (iii)	to information and data which the department receives from a third
-	party not in breach of any obligation of confidentiality owed to
-	the authors.
-
-
-
-Please sign this Undertaking and return a copy of it to indicate that you 
-have read, understood and accepted the above terms.
-
-
-
-		      For and on behalf of _____________________________
-
-		      _________________________________________________
-		     
-		      ..................................................
-
-		      Dated ............................................
-
-
-
-
-APPENDIX 1 - DETAILS OF THE PROCHECK SUITE OF PROGRAMS PROVIDED (v.3.4.3)
----------------------------------------------------------------
-
-Files to be included
---------------------
-
-         1. anglen.f            }
-         2. anglen.inc          }
-         3. bplot.f             }
-         4. bplot.inc           }
-         5. brkcln.par          }
-         6. clean.f             }
-         7. gfac2pdb.f          }
-         8. gfac2pdb.inc        }
-         9. mplot.f             }
-        10. mplot.inc           } Source program files
-        11. nb.c                }
-        12. pplot.f             }
-        13. pplot.inc           }
-        14. ps.f                }
-        15. rmsdev.f            }
-        16. rmsdev.inc          }
-        17. secstr.f            }
-        18. sstruc.par          }
-        19. tplot.f             }
-        20. tplot.inc           }
-        21. viol2pdb.f          }
-        22. viol2pdb.inc        }
-        23. vplot.f             }
-        24. vplot.inc           }
-        25. gfac2pdb.scr        }
-        26. procheck.com      }
-        27. procheck.scr      }
-        28. procheck_comp.com }
-        29. procheck_comp.scr }
-        30. procheck_nmr.scr  }
-        31. proplot.com       }
-        32. proplot.scr       } Script files
-        33. proplot_comp.scr  }
-        34. proplot_nmr.scr   }
-        35. proplot_comp.com  }
-        36. prosub.com        }
-        37. setup.com         }
-        38. setup.scr         }
-        39. viol2pdb.scr      }
-        40. convax.for         }
-        41. procomp.com        } Installation files
-        42. procomp.scr        }
-        43. maninst.ps       }
-        44. manual.tar.Z     } Documentation files
-        45. nmr_manual.tar.Z }
-        46. procheck.dat       }
-        47. procheck.prm       } Data
-        48. procheck_comp.prm  } files
-        49. procheck_nmr.prm   }
-
-
-APPENDIX 2 - DETAILS OF THE AQUA SUITE OF PROGRAMS PROVIDED (v.0.40)
------------------------------------------------------------
-
-Files to be included
---------------------
-
-Source files:-
-------------
-
-AquaCalc.c            AquaCalc.h
-                      AquaData.h
-AquaDist.c            AquaDist.h    
-AquaFiles.c           AquaFiles.h     
-AquaFuncts.c          AquaFuncts.h      
-AquaFuncts_biosym.c   AquaFuncts_biosym.h             
-AquaFuncts_cv.c       AquaFuncts_cv.h         
-AquaFuncts_io.c       AquaFuncts_io.h         
-AquaFuncts_pdb.c      AquaFuncts_pdb.h          
-AquaFuncts_pdbmr.c    AquaFuncts_pdbmr.h            
-AquaHow.c             AquaHow.h
-                      AquaMacros.h   
-AquaPseudo.c          AquaPseudo.h      
-AquaStrucset.c        AquaStrucset.h
-                      AquaTypes.h        
-AquaWhat.c            AquaWhat.h    
-Qext.c                Qext.h
-Range.c               Range.h
-                      cv_subs.h 
-
-Script files:-
-------------
-ReadNrv.pm*           convDIANAtorsrestr    qdbext*
-aqdrst*               convDISGEOdistrestr   qguessc*
-aqpc*                 convDISGEOtorsrestr   qguessr*
-aqpcsel               convMRTABLE           qhelp*
-aquanal.pl*           convXPLORdistrestr    qmodr*
-clean0*               convXPLORtorsrestr    qsplitr*
-convBIOSYMdistrestr   makecmm*              qsumm*
-convBIOSYMtorsrestr   qconvert*             qsumm_aux1*
-convDIANAdistrestr    qconvr*               qsumm_aux2*
-
-Documentation:-
--------------
-README                 models.txt             qconvr.txt
-aqpc.txt               mr.txt                 qdbext.txt
-aqua_setup.txt         names.txt              qext.txt
-biosym.txt             overview.txt           qhelp.txt
-chains.txt             perl.txt               qsumm.txt
-conversion.txt         procheck.txt           restraint_format.txt
-dbas.txt               qanal.txt              setup.txt
-intro.txt              qclean.txt             torsion.txt
-log.txt                qconvert.txt           xplor.txt
-
-Extras:-
-------
-joinpdb*               splitpdb*
-
-
-
-Please complete the above form, sign it, and then send or fax to:-
-
-
-Roman Laskowski
-European Bioinformatics Institute,
-Wellcome Trust Genome Campus,
-Hinxton,
-Cambridge, CB10 1SD,
-United Kingdom
- 
-Fax:- +44 (0)1223 494 468
-
-If you have any problems either installing the software or running it,
-please e-mail your problems to:-
-
-    roman@ebi.ac.uk
-
-Questions about AQUA should be directed to Ton Rullmann at
-
-      rull@nmr.chem.ruu.nl
-