CatDCD - Concatenate DCD files

Introduction

Catdcd functions much like the Unix "cat" command: it concatenates DCD files into a single DCD file. You can also use catdcd to write only selected atoms to the final DCD file. Starting with version 4.0, CatDCD is now built as part of the VMD Plugin tree, and shares the same reader/writer with VMD. CatDCD 4.0 can read/write any of the structure/trajectory formats that are supported by VMD by virtue of the plugin interface.

Contact

If you have questions please send email to vmd@ks.uiuc.edu

Download

License

UIUC Open Source License

Documentation

* catdcd *
* Written by Justin Gullingsrud, based on DCD I/O code from VMD

* FEATURES *
- catdcd functions much like the Unix "cat" command: it concatenates DCD files
into a single DCD file.  It also allows the user to specify which atoms and
which frames should be written into the output file; thus DCD's can be split
as well as combined.

* USAGE *
CatDCD 4.0
   catdcd -o outputfile [-otype <filetype>] [-i indexfile]
      [-stype <filetype>] [-s structurefile]
      [-first firstframe] [-last lastframe] [-stride stride]
      [-<filetype>] inputfile1 [-<filetype>] inputfile2 ...

Allowed input file types:
cpmd pdb dcd Alchemy AMBERPREP BallStick BiosymCAR Boogie
Cacao CADPAC CHARMm Chem3d-1 Chem3d-2 CSSR FDAT GSTAT Feature
Fractional GAMESSoutput Z-matrix Gaussianoutput HIN Isis MacMolecule
Macromodel MicroWorld MM2Input MM2Output MM3 MMADS MDLMOL MOLIN
MopacCartesian MopacInternal MopacOutput PCModel Quanta ShelX
Spartan SpartanSE SpartanMM Sybyl Sybyl2 Conjure Maccs2d Maccs3d
UniChemXYZ XYZ XED gro g96 trr xtc crd crdbox namdbin binpos
webpdb cube rst7 tinker dlpolyhist lammpstrj xyz cor molden
pqr mol2 car gamess xsf

Allowed output file types:
pdb dcd trr crd crdbox namdbin binpos rst7 xyz pqr

OR

catdcd -o <outputfile> [-i <indexfile>] [-first first] [-last last]
               [-stride stride] <inputfile1> <inputfile2> ...

OR

catdcd -num <inputfile1> <intputfile2> ...

-o <outputfile>: Specify the output file for CatDCD.  Required, unless -num
is present (see below).

-num: When present, no output file will be written.  Instead, CatDCD prints
the number of frames in each file, then exits.
 
-i <indexfile>
indexfile should contain the (zero-based) indices of the atoms in the
dcd files whose coordinates are to appear in the output file.  The indices
should be ASCII text, separated by whitespace.

-first first: Specify the first frame to be written to the output file.  
Default is 1 (write starting from the first frame read).

-last last: Specify the last frame to write.  Default is the last frame in 
the last file.

-stride stride: Specify how many frames to skip when writing.  Default is 1
(don't skip any frames).


* CAVEATS *
The input files may be any combination of charmm or xplor format, and big-
or little-endianness.  However, they must all have the same number of atoms.

The code uses only standard C library commands and should thus be portable to 
pretty much anywhere, including non-Unix platforms (I haven't tested this ;-)

* EXAMPLES *

catdcd -num eq01.dcd eq02.dcd

	Prints the number of frames in the two DCD files, then the total,
	then exits.

catdcd -o eq_all.dcd eq01.dcd eq02.dcd eq03.dcd

	Combines eq01.dcd, eq02.dcd, and eq03.dcd into eq_all.dcd.

catdcd -o eq_pro.dcd -i protein.ind eq01.dcd 

	Takes only the coordinates corresponding to the indices in 
	'protein.ind' from eq01.dcd and writes them to eq_pro.dcd

catdcd -o eq_first.dcd -first 1000 -last 2000 -stride 10 eq01.dcd eq02.dcd
	
	After skipping 999 frames, writes the 1000 frame and every 10th
	subsequent frame to eq_first.dcd, until a total of 2000 frames 
	have been read.  	

* Installation * 
Unpack the distribution package.  A directory named catdcd will be created.
Enter that directory and type "make".  To use a different compiler or compile
flags, edit the first three definitions in the Makefile.

New in version 4.0:
        * CatDCD is now integrated into the VMD plugin tree and is
          compiled as part of the standard plugin builds.

New in version 3.0:
        * Now uses the VMD plugins for file reading.  This makes it very easy
          to adapt the program to handle other file formats.
        * Use of VMD file readers means fixed atoms are handled automatically.
  
New in version 2.0:
	* New command line interface: The -o option is now required for 
	  setting the output file.
	* New -num option to print the number of frames in each file, as well
	  as the total.
	* Fixed a bug in the DCD reading code that caused misreading of the
	  DELTA parameter for byte-swapped Charmm DCD files; caused floating-
	  point exceptions on Alpha platforms.

New in Version 1.3:
	* Fixed free of uninitialized pointer when no -i option is set.
	* Fixed bug in reading of opposite-endian Charmm-format dcd files.

New in Version 1.2:
	* Fixed serious bug that appeared in 1.1; only frames from the first 
	  input file were being written to the output file.

New in Version 1.1:
	* Added -first, -last, and -stride flags.
	* Added version number information to the output.