sci-chemistry / pdbcat

Manipulate and process PDB files using tools such as Perl, awk, etc

Official package sites : http://www.ks.uiuc.edu/Development/MDTools/pdbcat/ ·

The Brookhaven Protein Data Bank stores atomic coordinate information for protein structures in a column based format. This is designed to be read easily read by FORTRAN programs. Indeed, if you get the format description (from anonymous ftp to ftp.pdb.bnl.gov, the file /pub/format.desc.ps) they show the single input line needed to read each record type. However, I am a C/C++ programmer in the Unix environment. It is a easier for me to deal with field based input than column based ones. If the fields are white space delimited I can easily use awk and perl to manipulate the coordinate information. So I needed some way to convert the ATOM and HETATM records of PDB files from the standard column based format to a field based one and back again. It needed to denote missing fields if they exist. That converter is `pdbcat'.

v1.3 :: 0 :: gentoo

Modified
License
free-noncomm
Keywords
~amd64 ~amd64-linux ~x86 ~x86-linux

dev-util / cmake : Cross platform Make

sys-devel / make : Standard tool to compile source trees

Robin H. Johnson · gentoo
Drop $Id$ per council decision in bug #611234.
Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
Johannes Huber · gentoo
sci-chemistry/pdbcat: Shorten DESCRIPTION
Package-Manager: Portage-2.3.3, Repoman-2.3.1
Johannes Huber · gentoo
sci-chemistry/pdbcat: EAPI 6
Package-Manager: Portage-2.3.3, Repoman-2.3.1
Robin H. Johnson · gentoo
proj/gentoo: Initial commit
This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson <robbat2@gentoo.org> X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed