Bug 145143

Summary: new port: science/p5-PerlMol and dependencies
Product: Ports & Packages Reporter: Steve Wills <steve>
Component: Individual Port(s)Assignee: freebsd-ports-bugs (Nobody) <ports-bugs>
Status: Closed FIXED    
Severity: Affects Only Me    
Priority: Normal    
Version: Latest   
Hardware: Any   
OS: Any   
Attachments:
Description Flags
file.shar none

Description Steve Wills 2010-03-29 00:40:08 UTC 
new port of perl project PerlMol. There are a bunch of ports here, hope it's OK to submit them all at once, but they're all interdependent and part of a single project.

Fix: see attached

Patch attached with submission follows:
Comment 1 dfilter service freebsd_committer freebsd_triage 2010-04-02 16:24:27 UTC 
miwi        2010-04-02 15:24:14 UTC

  FreeBSD ports repository

  Modified files:
    science              Makefile 
  Added files:
    science/p5-Chemistry-Bond-Find Makefile distinfo pkg-descr 
                                   pkg-plist 
  Log:
  Perl module which provides functions for detecting the bonds in a molecule from
  its 3D coordinates by using simple cutoffs, and for guessing the formal bond
  orders.
  
  WWW:    http://search.cpan.org/dist/Chemistry-Bond-Find/
  
  PR:             ports/145143
  Submitted by:   Steve Wills <steve at mouf.net>
  
  Revision  Changes    Path
  1.166     +1 -0      ports/science/Makefile
  1.1       +25 -0     ports/science/p5-Chemistry-Bond-Find/Makefile (new)
  1.1       +3 -0      ports/science/p5-Chemistry-Bond-Find/distinfo (new)
  1.1       +5 -0      ports/science/p5-Chemistry-Bond-Find/pkg-descr (new)
  1.1       +7 -0      ports/science/p5-Chemistry-Bond-Find/pkg-plist (new)
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Comment 2 dfilter service freebsd_committer freebsd_triage 2010-04-02 16:25:25 UTC 
miwi        2010-04-02 15:25:12 UTC

  FreeBSD ports repository

  Modified files:
    science              Makefile 
  Added files:
    science/p5-Chemistry-Canonicalize Makefile distinfo pkg-descr 
                                      pkg-plist 
  Log:
  Perl module which provides functions for "canonicalizing" a molecular
  structure; that is, to number the atoms in a unique way regardless of the
  input order.
  
  WWW:    http://search.cpan.org/dist/Chemistry-Canonicalize/
  
  PR:             ports/145143
  Submitted by:   Steve Wills <steve at mouf.net>
  
  Revision  Changes    Path
  1.167     +1 -0      ports/science/Makefile
  1.1       +25 -0     ports/science/p5-Chemistry-Canonicalize/Makefile (new)
  1.1       +3 -0      ports/science/p5-Chemistry-Canonicalize/distinfo (new)
  1.1       +5 -0      ports/science/p5-Chemistry-Canonicalize/pkg-descr (new)
  1.1       +4 -0      ports/science/p5-Chemistry-Canonicalize/pkg-plist (new)
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Comment 3 dfilter service freebsd_committer freebsd_triage 2010-04-02 16:26:08 UTC 
miwi        2010-04-02 15:25:56 UTC

  FreeBSD ports repository

  Modified files:
    science              Makefile 
  Added files:
    science/p5-Chemistry-Pattern Makefile distinfo pkg-descr 
                                 pkg-plist 
  Log:
  Perl module which implements basic pattern matching for molecules.
  
  WWW:    http://search.cpan.org/dist/Chemistry-Pattern/
  
  PR:             ports/145143
  Submitted by:   Steve Wills <steve at mouf.net>
  
  Revision  Changes    Path
  1.168     +1 -0      ports/science/Makefile
  1.1       +25 -0     ports/science/p5-Chemistry-Pattern/Makefile (new)
  1.1       +3 -0      ports/science/p5-Chemistry-Pattern/distinfo (new)
  1.1       +3 -0      ports/science/p5-Chemistry-Pattern/pkg-descr (new)
  1.1       +7 -0      ports/science/p5-Chemistry-Pattern/pkg-plist (new)
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Comment 4 dfilter service freebsd_committer freebsd_triage 2010-04-02 16:26:51 UTC 
miwi        2010-04-02 15:26:37 UTC

  FreeBSD ports repository

  Modified files:
    science              Makefile 
  Added files:
    science/p5-Chemistry-Isotope Makefile distinfo pkg-descr 
                                 pkg-plist 
  Log:
  Perl module which contains the exact mass data from the table of the isotopes.
  
  WWW:    http://search.cpan.org/dist/Chemistry-Isotope/
  
  PR:             ports/145143
  Submitted by:   Steve Wills <steve at mouf.net>
  
  Revision  Changes    Path
  1.169     +1 -0      ports/science/Makefile
  1.1       +22 -0     ports/science/p5-Chemistry-Isotope/Makefile (new)
  1.1       +3 -0      ports/science/p5-Chemistry-Isotope/distinfo (new)
  1.1       +3 -0      ports/science/p5-Chemistry-Isotope/pkg-descr (new)
  1.1       +5 -0      ports/science/p5-Chemistry-Isotope/pkg-plist (new)
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Comment 5 dfilter service freebsd_committer freebsd_triage 2010-04-02 16:27:35 UTC 
miwi        2010-04-02 15:27:22 UTC

  FreeBSD ports repository

  Modified files:
    science              Makefile 
  Added files:
    science/p5-Chemistry-Ring Makefile distinfo pkg-descr 
                              pkg-plist 
  Log:
  Perl module which provides some basic methods for representing a ring.
  
  WWW:    http://search.cpan.org/dist/Chemistry-Ring/
  
  PR:             ports/145143
  Submitted by:   Steve Wills <steve at mouf.net>
  
  Revision  Changes    Path
  1.170     +1 -0      ports/science/Makefile
  1.1       +27 -0     ports/science/p5-Chemistry-Ring/Makefile (new)
  1.1       +3 -0      ports/science/p5-Chemistry-Ring/distinfo (new)
  1.1       +3 -0      ports/science/p5-Chemistry-Ring/pkg-descr (new)
  1.1       +5 -0      ports/science/p5-Chemistry-Ring/pkg-plist (new)
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Comment 6 dfilter service freebsd_committer freebsd_triage 2010-04-02 16:28:17 UTC 
miwi        2010-04-02 15:28:04 UTC

  FreeBSD ports repository

  Modified files:
    science              Makefile 
  Added files:
    science/p5-Chemistry-File-VRML Makefile distinfo pkg-descr 
                                   pkg-plist 
  Log:
  Generate VRML models for molecules
  
  WWW:    http://search.cpan.org/dist/Chemistry-File-VRML/
  
  PR:             ports/145143
  Submitted by:   Steve Wills <steve at mouf.net>
  
  Revision  Changes    Path
  1.171     +1 -0      ports/science/Makefile
  1.1       +25 -0     ports/science/p5-Chemistry-File-VRML/Makefile (new)
  1.1       +3 -0      ports/science/p5-Chemistry-File-VRML/distinfo (new)
  1.1       +3 -0      ports/science/p5-Chemistry-File-VRML/pkg-descr (new)
  1.1       +4 -0      ports/science/p5-Chemistry-File-VRML/pkg-plist (new)
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Comment 7 dfilter service freebsd_committer freebsd_triage 2010-04-02 16:28:55 UTC 
miwi        2010-04-02 15:28:42 UTC

  FreeBSD ports repository

  Modified files:
    science              Makefile 
  Added files:
    science/p5-Chemistry-File-XYZ Makefile distinfo pkg-descr 
                                  pkg-plist 
  Log:
  XYZ molecule format reader/writer
  
  WWW:    http://search.cpan.org/dist/Chemistry-File-XYZ/
  
  PR:             ports/145143
  Submitted by:   Steve Wills <steve at mouf.net>
  
  Revision  Changes    Path
  1.172     +1 -0      ports/science/Makefile
  1.1       +25 -0     ports/science/p5-Chemistry-File-XYZ/Makefile (new)
  1.1       +3 -0      ports/science/p5-Chemistry-File-XYZ/distinfo (new)
  1.1       +3 -0      ports/science/p5-Chemistry-File-XYZ/pkg-descr (new)
  1.1       +7 -0      ports/science/p5-Chemistry-File-XYZ/pkg-plist (new)
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Comment 8 dfilter service freebsd_committer freebsd_triage 2010-04-02 16:29:43 UTC 
miwi        2010-04-02 15:29:35 UTC

  FreeBSD ports repository

  Modified files:
    science              Makefile 
  Added files:
    science/p5-Chemistry-Mok Makefile distinfo pkg-descr pkg-plist 
  Log:
  Perl molecular awk interpreter
  
  WWW:    http://search.cpan.org/dist/Chemistry-Mok/
  
  PR:             ports/145143
  Submitted by:   Steve Wills <steve at mouf.net>
  
  Revision  Changes    Path
  1.173     +1 -0      ports/science/Makefile
  1.1       +32 -0     ports/science/p5-Chemistry-Mok/Makefile (new)
  1.1       +3 -0      ports/science/p5-Chemistry-Mok/distinfo (new)
  1.1       +3 -0      ports/science/p5-Chemistry-Mok/pkg-descr (new)
  1.1       +4 -0      ports/science/p5-Chemistry-Mok/pkg-plist (new)
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Comment 9 dfilter service freebsd_committer freebsd_triage 2010-04-02 16:31:42 UTC 
miwi        2010-04-02 15:31:34 UTC

  FreeBSD ports repository

  Modified files:
    science              Makefile 
  Added files:
    science/p5-Chemistry-FormulaPattern Makefile distinfo 
                                        pkg-descr pkg-plist 
  Log:
  Match molecule by formula
  
  WWW:    http://search.cpan.org/dist/Chemistry-ForumulaPattern/
  
  PR:             ports/145143
  Submitted by:   Steve Wills <steve at mouf.net>
  
  Revision  Changes    Path
  1.175     +1 -0      ports/science/Makefile
  1.1       +27 -0     ports/science/p5-Chemistry-FormulaPattern/Makefile (new)
  1.1       +3 -0      ports/science/p5-Chemistry-FormulaPattern/distinfo (new)
  1.1       +3 -0      ports/science/p5-Chemistry-FormulaPattern/pkg-descr (new)
  1.1       +5 -0      ports/science/p5-Chemistry-FormulaPattern/pkg-plist (new)
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Comment 10 dfilter service freebsd_committer freebsd_triage 2010-04-02 16:32:16 UTC 
miwi        2010-04-02 15:32:03 UTC

  FreeBSD ports repository

  Modified files:
    science              Makefile 
  Added files:
    science/p5-Chemistry-Reaction Makefile distinfo pkg-descr 
                                  pkg-plist 
  Log:
  Explicit chemical reactions
  
  WWW:    http://search.cpan.org/dist/Chemistry-Raction/
  
  PR:             ports/145143
  Submitted by:   Steve Wills <steve at mouf.net>
  
  Revision  Changes    Path
  1.176     +1 -0      ports/science/Makefile
  1.1       +31 -0     ports/science/p5-Chemistry-Reaction/Makefile (new)
  1.1       +3 -0      ports/science/p5-Chemistry-Reaction/distinfo (new)
  1.1       +3 -0      ports/science/p5-Chemistry-Reaction/pkg-descr (new)
  1.1       +4 -0      ports/science/p5-Chemistry-Reaction/pkg-plist (new)
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Comment 11 dfilter service freebsd_committer freebsd_triage 2010-04-02 16:32:33 UTC 
miwi        2010-04-02 15:32:24 UTC

  FreeBSD ports repository

  Modified files:
    science              Makefile 
  Added files:
    science/p5-Chemistry-File-Mopac Makefile distinfo pkg-descr 
                                    pkg-plist 
  Log:
  MOPAC 6 input file reader/writer
  
  WWW:    http://search.cpan.org/dist/Chemistry-File-Mopac/
  
  PR:             ports/145143
  Submitted by:   Steve Wills <steve at mouf.net>
  
  Revision  Changes    Path
  1.177     +1 -0      ports/science/Makefile
  1.1       +27 -0     ports/science/p5-Chemistry-File-Mopac/Makefile (new)
  1.1       +3 -0      ports/science/p5-Chemistry-File-Mopac/distinfo (new)
  1.1       +3 -0      ports/science/p5-Chemistry-File-Mopac/pkg-descr (new)
  1.1       +5 -0      ports/science/p5-Chemistry-File-Mopac/pkg-plist (new)
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Comment 12 dfilter service freebsd_committer freebsd_triage 2010-04-02 16:33:00 UTC 
miwi        2010-04-02 15:32:52 UTC

  FreeBSD ports repository

  Modified files:
    science              Makefile 
  Added files:
    science/p5-Chemistry-File-MDLMol Makefile distinfo pkg-descr 
                                     pkg-plist 
  Log:
  Perl module which will parse a SMARTS (SMiles ARbitrary Target Specification)
  string, generating a Chemistry::Pattern object. It is a file I/O driver for
  the PerlMol toolkit.
  
  WWW:    http://search.cpan.org/dist/Chemistry-File-SMARTS/
  
  PR:             ports/145143
  Submitted by:   Steve Wills <steve at mouf.net>
  
  Revision  Changes    Path
  1.178     +1 -0      ports/science/Makefile
  1.1       +27 -0     ports/science/p5-Chemistry-File-MDLMol/Makefile (new)
  1.1       +3 -0      ports/science/p5-Chemistry-File-MDLMol/distinfo (new)
  1.1       +5 -0      ports/science/p5-Chemistry-File-MDLMol/pkg-descr (new)
  1.1       +6 -0      ports/science/p5-Chemistry-File-MDLMol/pkg-plist (new)
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Comment 13 dfilter service freebsd_committer freebsd_triage 2010-04-02 16:33:37 UTC 
miwi        2010-04-02 15:33:24 UTC

  FreeBSD ports repository

  Modified files:
    science              Makefile 
  Added files:
    science/p5-Chemistry-File-SLN Makefile distinfo pkg-descr 
                                  pkg-plist 
  Log:
  SLN linear notation parser/writer
  
  WWW:    http://search.cpan.org/dist/Chemistry-File-SLN/
  
  PR:             ports/145143
  Submitted by:   Steve Wills <steve at mouf.net>
  
  Revision  Changes    Path
  1.179     +1 -0      ports/science/Makefile
  1.1       +33 -0     ports/science/p5-Chemistry-File-SLN/Makefile (new)
  1.1       +3 -0      ports/science/p5-Chemistry-File-SLN/distinfo (new)
  1.1       +3 -0      ports/science/p5-Chemistry-File-SLN/pkg-descr (new)
  1.1       +6 -0      ports/science/p5-Chemistry-File-SLN/pkg-plist (new)
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Comment 14 dfilter service freebsd_committer freebsd_triage 2010-04-02 16:34:04 UTC 
miwi        2010-04-02 15:33:52 UTC

  FreeBSD ports repository

  Modified files:
    science              Makefile 
  Added files:
    science/p5-Chemistry-3DBuilder Makefile distinfo pkg-descr 
                                   pkg-plist 
  Log:
  Perl module which generates a three-dimensional molecular structure from a
  connection table, such as that obtained by a 2D representation of the
  molecule or from a SMILES string.
  
  WWW:    http://search.cpan.org/dist/Chemistry-3DBuilder/
  
  PR:             ports/145143
  Submitted by:   Steve Wills <steve at mouf.net
  
  Revision  Changes    Path
  1.180     +1 -0      ports/science/Makefile
  1.1       +35 -0     ports/science/p5-Chemistry-3DBuilder/Makefile (new)
  1.1       +3 -0      ports/science/p5-Chemistry-3DBuilder/distinfo (new)
  1.1       +5 -0      ports/science/p5-Chemistry-3DBuilder/pkg-descr (new)
  1.1       +3 -0      ports/science/p5-Chemistry-3DBuilder/pkg-plist (new)
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Comment 15 dfilter service freebsd_committer freebsd_triage 2010-04-02 16:34:51 UTC 
miwi        2010-04-02 15:34:39 UTC

  FreeBSD ports repository

  Modified files:
    science              Makefile 
  Added files:
    science/p5-Chemistry-File-SMARTS Makefile distinfo pkg-descr 
                                     pkg-plist 
  Log:
  Perl module which will parse a SMARTS (SMiles ARbitrary Target Specification)
  string, generating a Chemistry::Pattern object. It is a file I/O driver for
  the PerlMol toolkit.
  
  WWW:    http://search.cpan.org/dist/Chemistry-File-SMARTS/
  
  PR:             ports/145143
  Submitted by:   Steve Wills <steve at mouf.net>
  
  Revision  Changes    Path
  1.181     +1 -0      ports/science/Makefile
  1.1       +31 -0     ports/science/p5-Chemistry-File-SMARTS/Makefile (new)
  1.1       +3 -0      ports/science/p5-Chemistry-File-SMARTS/distinfo (new)
  1.1       +5 -0      ports/science/p5-Chemistry-File-SMARTS/pkg-descr (new)
  1.1       +4 -0      ports/science/p5-Chemistry-File-SMARTS/pkg-plist (new)
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Comment 16 dfilter service freebsd_committer freebsd_triage 2010-04-02 16:35:31 UTC 
miwi        2010-04-02 15:35:23 UTC

  FreeBSD ports repository

  Modified files:
    science              Makefile 
  Added files:
    science/p5-Chemistry-InternalCoords Makefile distinfo 
                                        pkg-descr pkg-plist 
  Log:
  Perl module implements an object class for representing internal
  coordinates and provides methods for converting them to Cartesian
  coordinates.
  
  WWW:    http://search.cpan.org/dist/Chemistry-InternalCoords/
  
  PR:             ports/145143
  Submitted by:   Steve Wills <steve at mouf.net>
  
  Revision  Changes    Path
  1.182     +1 -0      ports/science/Makefile
  1.1       +29 -0     ports/science/p5-Chemistry-InternalCoords/Makefile (new)
  1.1       +3 -0      ports/science/p5-Chemistry-InternalCoords/distinfo (new)
  1.1       +5 -0      ports/science/p5-Chemistry-InternalCoords/pkg-descr (new)
  1.1       +7 -0      ports/science/p5-Chemistry-InternalCoords/pkg-plist (new)
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Comment 17 dfilter service freebsd_committer freebsd_triage 2010-04-02 16:35:55 UTC 
miwi        2010-04-02 15:35:47 UTC

  FreeBSD ports repository

  Modified files:
    science              Makefile 
  Added files:
    science/p5-Chemistry-File-SMILES Makefile distinfo pkg-descr 
                                     pkg-plist 
  Log:
  Perl module which parses a SMILES (Simplified Molecular Input Line Entry
  Specification) string.
  
  WWW:    http://search.cpan.org/dist/Chemistry-File-SMILES/
  
  PR:             ports/145143
  Submitted by:   Steve Wills <steve at mouf.net>
  
  Revision  Changes    Path
  1.183     +1 -0      ports/science/Makefile
  1.1       +31 -0     ports/science/p5-Chemistry-File-SMILES/Makefile (new)
  1.1       +3 -0      ports/science/p5-Chemistry-File-SMILES/distinfo (new)
  1.1       +4 -0      ports/science/p5-Chemistry-File-SMILES/pkg-descr (new)
  1.1       +6 -0      ports/science/p5-Chemistry-File-SMILES/pkg-plist (new)
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Comment 18 Martin Wilke freebsd_committer freebsd_triage 2010-04-02 16:36:31 UTC 
State Changed
From-To: open->closed

Committed. Thanks!
Comment 19 dfilter service freebsd_committer freebsd_triage 2010-04-02 16:36:39 UTC 
miwi        2010-04-02 15:36:26 UTC

  FreeBSD ports repository

  Modified files:
    science              Makefile 
  Added files:
    science/p5-PerlMol   Makefile distinfo pkg-descr pkg-plist 
    science/p5-PerlMol/files patch-Makefile.PL 
  Log:
  Perl modules for molecular chemistry
  
  WWW:    http://search.cpan.org/dist/PerlMol/
  
  PR:             ports/145143
  Submitted by:   Steve Wills <steve at mouf.net>
  
  Revision  Changes    Path
  1.184     +1 -0      ports/science/Makefile
  1.1       +69 -0     ports/science/p5-PerlMol/Makefile (new)
  1.1       +3 -0      ports/science/p5-PerlMol/distinfo (new)
  1.1       +37 -0     ports/science/p5-PerlMol/files/patch-Makefile.PL (new)
  1.1       +3 -0      ports/science/p5-PerlMol/pkg-descr (new)
  1.1       +3 -0      ports/science/p5-PerlMol/pkg-plist (new)
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