Babel version 1.6 Copyright (C) 1992-1996
				  by
		      Pat Walters and Matt Stahl

		   babel@mercury.aichem.arizona.edu


This software is provided on an "as is" basis, and without warranty of any 
kind, including but not limited to any implied warranty of merchantability 
or fitness for a particular purpose.

In no event shall the authors or the University of Arizona be liable for 
any direct, indirect, incidental, special, or consequential damages arising 
from use or distribution of this software. The University of Arizona also 
shall not be liable for any claim against any user of this program by any 
third party.

WHAT'S NEW 
-----------------
SMILES support - thanks Simon Kilvington
Gaussian 94 support
Command line arguments have changed a bit. See the section below on
multi-structure files.


PLEASE REGISTER
---------------
We don't want any money for Babel (unless of course you insist), but we
would like to know who has a copy so that we can notify people about updates 
and bug fixes.

You can register by sending e-mail to babel@mercury.aichem.arizona.edu and 
letting us know the following:
	-who you are
	-where you are
	-what platform you're running Babel on
	-which file conversions you commonly use

We are very open to suggestions.  If there's anything you like or don't 
like about the program please let us know.  Also if there are file formats
you would like to see supported let us know.
--------------------------------------------------------------------------

Thanks for downloading this copy of babel.  With this program we hope to
implement a general framework for converting between file formats used 
for molecular modeling.  


This manual is divided into 3 sections.

I. Installation
 A. Unix Installation
 B. DOS Installation
II. Using Babel
III. Other Stuff

I. INSTALLATION
--------------------------UNIX INSTALLATION-----------------------------
NOTE : If you downloded either sun-babel-1.0X.tar.Z or sgi-babel-1.0X.tar.Z 
please skip directly to step 3.

Installation is very simple. 

1. Special Instructions - Unless you have a Sun Workstaion with an old
Sabre C compiler (or other non-ansi C compiler) or a Dec machine running
Ultrix goto step 2.

SUN WORKSTATIONS WITH THE OLD (NON-ANSI) SABRE C COMPILER
If you have a Sun workstation with the old Sabre C compiler or another
non-ANSI C-compiler you must use gcc to compile babel. If you are using
gcc to compile babel, change line 10 in the makefile from

CC	      = cc

to

CC	      = gcc

DEC STATIONS RUNNING ULTRIX - If you have gcc follow the instructions above
to use gcc as the compiler.  Otherwise change line 1 in the Makefile from

CFLAGS        = -O 

to

CFLAGS        = -O -DULTRIX

2. Make the program by typing make.
3. Set the environment variable BABEL_DIR to point to the directory 
where the files types.lis and elements.lis are stored.
i.e. If the files are in /usr/local/babel type the following

setenv BABEL_DIR /usr/local/babel

If you plan to use babel frequently then you will probably want to
place the line above in your .cshrc file.


---------------------------DOS INSTALLATION------------------------------
1. Create a subdirectory for babel on your hard disk.
We will assume that you called the directory C:\BABEL.
2. Copy the files babel.exe, element.lis, and types.lis
into this directory.
3. Put the following line in your autoexec.bat file
SET BABEL_DIR=C:\BABEL
4. You're all set, have fun.

II. USING BABEL

The babel program may be invoked using command line options or menus. 

The menu interface can be accessed by typing:
babel -m

The command line input has the following format:
babel [-v] -i  [keywords] -o  [keywords2]

All arguments surrounded by [] are optional.
The -v flag is optional and is used to produce verbose output.
The -i flag is used to set the input type.  The following input type codes
are currently supported.

	alc -- Alchemy file
	prep -- AMBER PREP file
	bs -- Ball and Stick file
	bgf -- MSI BGF file
	car -- Biosym .CAR file
	boog -- Boogie file
	caccrt -- Cacao Cartesian file
	cadpac -- Cambridge CADPAC file
	charmm -- CHARMm file
	c3d1 -- Chem3D Cartesian 1 file
	c3d2 -- Chem3D Cartesian 2 file
	cssr -- CSD CSSR file
	fdat -- CSD FDAT file
	gstat -- CSD GSTAT file
	dock -- Dock Database file
	dpdb -- Dock PDB file
	feat -- Feature file
	fract -- Free Form Fractional file
	gamout -- GAMESS Output file
	gzmat -- Gaussian Z-Matrix file
	gauout -- Gaussian 92 Output file
	g94 -- Gaussian 94 Output file
	gr96A -- GROMOS96 (A) file
	gr96N -- GROMOS96 (nm) file
	hin -- Hyperchem HIN file
	sdf -- MDL Isis SDF file
	m3d -- M3D file
	macmol -- Mac Molecule file
	macmod -- Macromodel file
	micro -- Micro World file
	mm2in -- MM2 Input file
	mm2out -- MM2 Output file
	mm3 -- MM3 file
	mmads -- MMADS file
	mdl -- MDL MOLfile file
	molen -- MOLIN file
	mopcrt -- Mopac Cartesian file
	mopint -- Mopac Internal file
	mopout -- Mopac Output file
	pcmod -- PC Model file
	pdb -- PDB file
	psin -- PS-GVB Input file
	psout -- PS-GVB Output file
	msf -- Quanta MSF file
	schakal -- Schakal file
	shelx -- ShelX file
	smiles -- SMILES file
	spar -- Spartan file
	semi -- Spartan Semi-Empirical file
	spmm -- Spartan Mol. Mechanics file
	mol -- Sybyl Mol file
	mol2 -- Sybyl Mol2 file
	wiz -- Conjure file
	unixyz -- UniChem XYZ file
	xyz -- XYZ file
	xed -- XED file

The -o flag is used to set the output file type.  The following output 
type codes are currently supported.

	diag -- DIAGNOTICS file
	t -- Alchemy file
	bs -- Ball and Stick file
	bmin -- Batchmin Command file
	caccrt -- Cacao Cartesian file
	cacint -- Cacao Internal file
	cache -- CAChe MolStruct file
	c3d1 -- Chem3D Cartesian 1 file
	c3d2 -- Chem3D Cartesian 2 file
	d -- ChemDraw Conn. Table file
	con -- Conjure file
	contmp -- Conjure Template file
	cssr -- CSD CSSR file
	feat -- Feature file
	fhz -- Fenske-Hall ZMatrix file
	gamin -- Gamess Input file
	gcart -- Gaussian Cartesian file
	g -- Gaussian Z-matrix file
	gotmp -- Gaussian Z-matrix tmplt file
	hin -- Hyperchem HIN file
	icon -- Icon 8 file
	i -- IDATM file
	macmol -- Mac Molecule file
	k -- Macromodel file
	micro -- Micro World file
	mi -- MM2 Input file
	mo -- MM2 Ouput file
	mm3 -- MM3 file
	mmads -- MMADS file
	mdl -- MDL Molfile file
	ac -- Mopac Cartesian file
	ai -- Mopac Internal file
	pc -- PC Model file
	p -- PDB file
	report -- Report file
	spar -- Spartan file
	mol -- Sybyl Mol file
	mol2 -- Sybyl Mol2 file
	maccs -- MDL Maccs file file
	xed -- XED file
	unixyz -- UniChem XYZ file
	x -- XYZ file

To convert an MM2 output file named mm2.grf to a MOPAC internal coordinate 
input file named mopac.dat the user would enter:
babel -imm2out mm2.grf -omopint mopac.dat

To perform the above conversion with the keywords PM3 GEO-OK T=30000 in the
file mopac.dat the user would enter:
babel -imm2out mm2.grf -omopint mopac.dat "PM3 GEO-OK T=30000"
Note the use of the double quotes around the keywords.


Z-MATRIX RENUMBERING
--------------------
I have received mail from a number of people who have complained that the Z-matrix
created by Babel contains very long "bonds" (often 5 to 10 angstroms).  This is
not a bug in the Cartesian to internal algorithm.  It is actually brought about by
a poorly numbered structure.

The Cartesian to internal algorithm goes kind of like this :
        put atom 1 at the origin
        for i = 2 to num_atoms
         {
          find the closest atom with atom number < i
          call that atom NA(i)
         }

If atoms are not numbered properly you end up with very long bonds.
Having these "bonds" in your Z-matrix tends to create all sorts of
problems during geometry optimization.

I've added a new flag, "-renum" to Babel.  If this flag is used, Babel
will attempt to renumber the structure so that the Z-matrix is
contiguous.

Renumbering in Babel 1.1 is accomplished using the -renum flag. There are
two ways to this.  If you use -renum by itself, Babel will use atom 1 in
the input structure as atom 1 in the Z-matrix.  If you use -renum X where
X is an integer, Babel will use atom X as atom 1 in the Z-matrix.

Examples:

babel -ixyz myfile.xyz -renum -omopint myfile.dat "AM1 MMOK T=30000"

will create a MOPAC input file with atom 1 from myfile.xyz as atom 1
in myfile.dat.

babel -ixyz myfile.xyz -renum 9 -omopint myfile.dat "AM1 MMOK T=30000"

will create a MOPAC input file with atom 9 from myfile.xyz as atom 1
in myfile.dat.

There is currently one limitiation to the -renum flag.  The file must
be contiguous.  The method won't currently work for bimolecular complexes
or anything like that.  I'll try and fix this up in the near future.

If you run into any problems with this, please don't hesitate to contact me.

MULTI-STRUCTURE FILES
---------------------
Most file formats are now supported as multi-structure.  With this type of 
file, the user has two output options
	- produce one output file for each structure in the file
	- produce a multi-structure output file.

When converting a multi structure file it is sometimes necessary to supply a 
keyword after the input file name.  This keyword specifies the number
of files to extract from the input file. Hopefully the examples below 
will make this a little more clear.

To extract all the structures from a multi-structure Macromodel file 
called mols.out and write the structures as pdb files the user would 
type:

babel -imacmod mols.out all -op mols.pdb

To extract the structures into a series of single structure files
use the -split keyword.

babel -imacmod mols.out all -op mols.pdb -split

To extract only the first five structures from a multi-structure 
Macromodel file and write the structures as a MOPAC internal coordinate
file the user would type
babel -imacmod mols.out "1-5" -oai mols.int



HYDROGEN ADDITION/DELETION
--------------------------
Babel has the ability to add and delete hydrogens from any file format.  
Hydrogens can be added by supplying the -h flag, hydrogens may be deleted 
by supplying the -d flag.

To add hydrogens a CSD fractional coordinate file called input.cssr and 
output the file as a MOPAC internal coordinate input file named output.add 
the user would type:
babel -icf input.cssr -h -oai output.add 

To delete hydrogens from a Macromodel file named benzene.dat and 
output the file as an XYZ file name benzene.new the user would type
babel -imacmod benzene.dat -d -oxyz benzene.new

CONVERTING THE NCI DATABASE
---------------------------
Now that Professor Gasteiger's group has made the NCI database available
as 3D structures, I'm sure that alot of people will be interested in 
converting the database to other formats.  Many people people also want to
add the hydrogens which are missing in the NCI 3D database.

Babel is capable of reading the NCI database using the -imaccs 
flag.  Here are a couple of examples of how to convert NCI 3D.

If you want to convert the entire database to one huge Sybyl mol2 file, you
would type the following:

babel -imaccs nci3d.mol -omol2 nci3d.mol2

If you want to convert the entire database to one huge Sybyl mol2 file and
add hydrogens, you would do the following:

babel -h -imaccs nci3d.mol -omol2  nci3d.mol2

Let's say you're slightly less ambitious and you only want to look at the 
first 500 structures.  Then you would do this:

babel -h -imaccs nci3d.mol "1-500" -omol2 CON > nci3d.mol2

If you wanted to look at the next 500 structures you would do this:

babel -h -imaccs nci3d.mol "501-1000" -omol2 CON > nci3d.mol2

To read the first 100 structures and output them to individual MacroModel
files named nci0001.dat, nci0002.dat, nci0003.dat, etc., you would type:

babel -h -imaccs nci3d.mol "1-100" -omacmod nci.dat

MACMOLECULE FILES
-----------------
Since MacMolecule only uses single letter it is often necessary to use
different names (i.e. X for Cl).  The user can specify substituted atom
names on the command line.  

To read a MacMolecule file named foo.bar where X is substituted for Cl
and Y is substitued for Cobalt and write an MM2 output type file named
bar.baz the user would type:
babel -imacmol "X/Cl Y/Co" foo.bar -omo bar.baz  

CHEMDRAW FILES
--------------
The user can supply a keyword to indicate the viewing axis for the 
ChemDraw projection by supplying a keyword.  To convert an XYZ file
named test.xyz to a ChemDraw file named test.cdy with the view down the
y axis the user would type:
babel -ix test.xyz -od test.cdx x

The default view is down the z axis.  Babel will also write MDL Molfile
type files which can be read by ChemDraw, ChemIntosh, ChemWindow, and 
Chem3D.

GAMESS FILES
------------
---GAMESS Output Files---
The output files are the .log files created by redirecting screen output.  
Babel first looks for a set of geometry optimized coordinates.  If the 
output file does not contain geometry optimized coordiantes Babel will 
use the input coordiantes. If Babel uses the input coordiantes it will 
convert from Bohr to Angstroms.

To read a GAMESS output file named exam01.log and convert it to an XYZ 
file named exam01.xyz the user would type:
babel -igamout exam01.log -ox exam01.xyz

---GAMESS Input Files---
Babel is capable of creating three types of GAMESS input files
COORD=CART Cartesian Coordinates
COORD=ZMAT Gaussian Style Z-matrix
COORD=ZMTPC MOPAC Style Z-matrix

Babel does not calculate the point group for you.  You'll have to pull
out your copy of Cotton and insert that manually. You'll also have to 
specify your own $SYSTEM, $BASIS, $SCF, $GUESS, etc. cards.

The type of input file is controlled by specifying a keyword on the 
Babel command line.  The keywords are
	cart - Cartesian 
	zmt - Gaussian style Z-matrix
	zmtmpc - MOPAC style Z-matrix

To read an xyz file named coords.xyz and convert it to a GAMESS input
file in Cartesian coordiantes named coords.in the user would type:
babel -ixyz coords.xzy -ogamin coords.in cart

To do the same conversion by have the GAMESS input in Gaussian Z-matrix
style the user would type
babel -ixyz coords.xzy -ogamin coords.in zmt

If no keyword is specified the input file will be in Cartesian Coordiantes.

GAUSSIAN FILES
--------------
NOTE : The output file format for Gaussian94 in different from
that used by previous versions of Gaussain.  Use the -g94 flag
to read Gaussian94 output files.

Babel 1.6 features a number of improvements aimed at the Gaussian
user.

1.  A (hopefully) bulletproof Gaussian reader.
2.  A new reader for gaussian output files which reads all the
steps from a minimization. These steps can then be written to
a multistructure file which can be animated with X-mol or whatever.
To extract all the steps from a Gaussian output file into a single muti
structure XYZ file you would do this:

babel -igauout file.out all -oxyz file.xyz

To extract all the steps from a Gaussian output file into a series of
files called file0001.xyz, file0002.xyz, etc.  You would do this:

babel -igauout file.out all -oxyz file.xyz

To extract only the last step from a Gaussian output file you would do
this:

babel -igauout file.out last -oxyz file.xyz

3. We  added the facility to define the header information for your
Gaussian files.  To do this you need to have a file with the header info
in either the current directory (checked first) or the directory pointed
to by the BABEL_DIR environment variable (checked second).  If the header
file isn't present Babel just puts in its default header information.
This can be handy if you constantly use the same basis sets and run the
same sorts of jobs.  There is a sample gauss.hdr in the archive.

QUANTA FILES
------------
Quanta files are binary and different systems use different binary
representations (big endian vs. little endian).  So, if you are going to use
Babel on a Quanta file you should run Babel on the same type of machine which
created the Quanta file.

I made a few concessions with this file format.  First,  I just translated the 
Quanta atom types to element types and let Babel assign hybridizations.  Quanta
has alot of strange atom types (i.e. Carbon with 2 Flourines attached) which 
don't translate easily to the hybidizized types we use.  Second, I found that 
the bonding information found in the Quanta files was not alway reliable so I
had Babel assign connectivities.  

There is a file called quanta.lis which should be kept in the directory 
pointed to by BABEL_DIR.  This file contains the numeric quanta type and 
corresponding element type.  If anything is missing or incorrect you can just 
edit this file and fix it.

III. OTHER STUFF
---------------
CURRENT LIMITATIONS
Macromodel - bond orders are not always correctly assigned for conjugated
pi systems.  

PDB files - When reading PDB files Babel assigns bonds are examining 
interatomic distances and assigning a bond where the interatomic distance
is less than the sum of the atoms convalent radii.  There is code in read_pdb.c
to read connections specified in CONECT records, but this code is commented
out.  We did this because a number of files available from Brookhaven have
CONECT records specified for only a few of the bonds in the molecule.  We
realize that we could determine connectivity in the PDB file by looking
at atom ids and residue types, but we have put this in yet.  This feature 
will probably be added soon.  If you would like to use the explicit CONECT
records in a PDB file see Appendix A.  When writing PDB files all residue
types are assigned as UNK.

REPORTING BUGS
Noone is perfect, and we're sure that there are still a few glitches in this
program.  If you happen to find such a glitch please send a mail message to
babel@mercury.aichem.arizona.edu describing the nature of the problem.  If 
possible please include the input file so we can use it to determine the 
cause of the problem.

CREDIT WHERE CREDIT IS DUE
Babel began it's life a program called convert written by Ajay Shah.  
Babel in its current form was written by Pat Walters and Matt Stahl.

COMING ATTRACTIONS
We consider Babel to be a constantly evolving program.  Hopefully 
modules to handle new file formats will be contributed and the program 
will become useful to an even wider range of chemists.  We currently have 
a number of additions to Babel underway at the
U of A.  Among these are:
1.  A real users manual 
2.  A developers guide which will assist programmers in creating new 
modules (Actually I have finished a draft of the Babel Developers Guide.
If you'd like a copy send me some mail - pat@mercury.aichem.arizona.edu).

PLEASE WRITE
We would really appreciate any and all input from babel users.  Please
send comments, praise, flames, and job offers :-) to 
babel@mercury.aichem.arizona.edu

Have fun,

Pat Walters
Chief Cook and Bottle-Washer