Bug 204341 - biology/molden: Update to 5.4
Summary: biology/molden: Update to 5.4
Status: Closed FIXED
Alias: None
Product: Ports & Packages
Classification: Unclassified
Component: Individual Port(s) (show other bugs)
Version: Latest
Hardware: Any Any
: --- Affects Only Me
Assignee: Kurt Jaeger
URL:
Keywords: needs-qa, patch
Depends on:
Blocks:
 
Reported: 2015-11-06 19:42 UTC by Kurt Jaeger
Modified: 2016-01-18 19:33 UTC (History)
0 users

See Also:


Attachments
patch (61.07 KB, patch)
2015-11-06 19:42 UTC, Kurt Jaeger
koobs: maintainer-approval+
Details | Diff

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Description Kurt Jaeger freebsd_committer 2015-11-06 19:42:21 UTC
Created attachment 162857 [details]
patch

Changes:
- Missing hydrogens atoms of HETATM molecules (pdb files) are stored locally.
- Pdb files can now be clipped. 
- Fixes missing residues. Introduces an alternative way of generating rotamers,
  without using z-matrices. This potentially a faster algorithm.
- Supports Movie making through avconv/ffmpeg.
- calculates the Electron Localization Function (ELF).
- Updated code of ambfor/ambmd to speed up optimisations/MD of proteins
  solvated in water (Jan, 2014).

test-builds @work, needs some users that can test the application itself.
Comment 1 Kurt Jaeger freebsd_committer 2015-11-07 17:06:28 UTC
Test-builds on 11-amd64, 10.2a+i, 9.3a are fine, waiting for some
test-run-reports.
Comment 2 Kubilay Kocak freebsd_committer freebsd_triage 2015-11-08 08:25:54 UTC
Comment on attachment 162857 [details]
patch

Un-maintained port, implicit approval
Comment 3 Kurt Jaeger freebsd_committer 2015-11-08 08:46:33 UTC
I asked the user from

https://lists.freebsd.org/pipermail/freebsd-ports/2015-November/101012.html

to test the updated port and wait for him to report back.
Comment 4 commit-hook freebsd_committer 2016-01-18 19:32:47 UTC
A commit references this bug:

Author: pi
Date: Mon Jan 18 19:32:37 UTC 2016
New revision: 406605
URL: https://svnweb.freebsd.org/changeset/ports/406605

Log:
  biology/molden: 5.0.7 -> 5.4

  Changes:
  - Missing hydrogens atoms of HETATM molecules (pdb files) are stored locally.
  - Pdb files can now be clipped.
  - Fixes missing residues. Introduces an alternative way of generating rotamers,
    without using z-matrices. This potentially a faster algorithm.
  - Supports Movie making through avconv/ffmpeg.
  - calculates the Electron Localization Function (ELF).
  - Updated code of ambfor/ambmd to speed up optimisations/MD of proteins
    solvated in water (Jan, 2014).

  PR:		204341

Changes:
  head/biology/molden/Makefile
  head/biology/molden/distinfo
  head/biology/molden/files/patch-ambfor-makefile
  head/biology/molden/files/patch-surf-Makefile
  head/biology/molden/files/patch-surf-makefile