"Cavity" Users Guide for Version 4.6 / 5.0

$Id: index.html,v 1.1 1999/11/12 15:24:45 tnemoto Exp $

Introduction: What is Cavity ?
Install guide: Initial setting
User's manual: How to use
Download: Download program sources and executables with sample data

What is Cavity ?

Program 'cavity' calculates the reaction space(we call it "cavity") in the crystal. The shape and volume of a "cavity" can be obtained.

Original Cavity program is written by Mr. K. Yanagi in 1980 and Dr. T. Nemoto rewritten it in 1993 and meintains the program now.

Cite this program for publications:

J. Am. Chem. Soc. (1981) 103 5805-

Definition of Cavity

(Download figure written in PostScript)

"Cavity" is a space around the reactive group in a crystal. The Cavity is calculated in the following way.

Remove the reactive group from a molecule in a crystal.
Any space that is within van Der Waals radius + 1.2 Å from remaining atoms are omitted. If bond is defined, the bond length is taken as the radius.

Of course, any part of a molecule can be removed and the space that appears after removal can be visualized and it's volume can be calcuted.

The drawing of the Cavity is made a section by section, and all section is drawn together. Volume calculation is performed at the same time of drawing.

Install of Cavity

Latest version of Nov, 1999 is cavity 4.6a in fortran and cavity 5.0a in C. At first, download one of them from http://eels.kuicr.kyoto-u.ac.jp/~tnemoto/sv/download.html

Cavity 4.6 installation procedure is ...

uncompress cav4.6.tar.Z
tar xvf cav4.6.tar
cd cav
make

After that, an executable "cav4" appears. It is convenience copying this executable file to a directory in PATH (e.g. /usr/local/bin).

Cavity 5.0 installation procedure is ...

gzip -d cav5.0a.tar.gz
tar xvf cav5.0a.tar
cd cavity
make

After that, an executable "cav5" appears. It is convenience copying this executable file to a directory in PATH (e.g. /usr/local/bin). Since some program requirs "cav4", you should copy "cav5" as "cav4", or make symbolic link for convinience.

User's Manual

Cavity Calculation Procedure

Make a data file named "cav.dat" in the format described below.
Make a Control file named "cav.cnt" in the format described below.
Execute "cav4" (or cav5)
An ouput file named "cav.ps" containing PS drawing and cavity volume is obtained.

Control File "cav.cnt"

A line that begins with "#" is a comment and will be neglected.
The first line is a title (this line would be neglected but one line should be here for a dummy).
The following lines are for parameters in fixed format of (I7) or (F7.3).

Example of Control file

# Title
Cavity
# iview,  Manu,Volume,  Bond,  Test, ICAVE,N_Atom,N_Bond, N_Cav
      3      0      0      0      0      0     93     97      6
# Scale,Radius,CavPen,BondPn,CavBnP,CavAtP
    1.0  0.000      1      2      0      0
# Atom Number
      1      4      7     10     15     22     25     34     37     40
... omitted for clarity ...
    254    255    258    260    264    266    269    272    275    279
    281    282    283
# Bond Atom Number (Pair)
      1      4      1      7      1     10      1     15      1     99
... omitted for clarity ...
    264    269    264    272    272    275    272    279    272    281
    281    282    281    283
# Cavity Atom Number
    216    224    234    239    242    245
# Cavity Radi
  2.900  2.750  2.720  2.400  1.200
# Cavity Range
# X Min, X Max, Y Min, Y Max, Z Min, Z Max, Grid
 -1.718  5.825 -5.446  2.639 -4.944  3.608  0.200

Keywords in Control file

TITLE: Exact one line of title. Must.
IVIEW: Projection direction [1-3]. Usually use 3.
Manu: 0 for automatic determination of calculation range, 1 for manual mode.
Volume: 1 for volume calculation, 0 for only drawing.
Bond: 1 for drawing of bond, 0 for no bond.
Test: Usually 0
ICAVE: Usually 0
N_Atom: Number of atoms to be drawn
N_Bond: Number of bonds to be drawn
N_Cav: Number of atoms in the Cavity. That is, Number of atoms to be removed for the cavity.
Scale: Scale for drawing. Usually 1.
Radius: Radius of a atom in Å. Used to draw atoms.
CavPen: Pen number of Cavity drawing. Usually 1.
BondPn: Pen number of bond drawing. Usually 2.
CavBnP: Pen number of bond drawing within a Cavity. Usually 0.
CavAtP: Pen number of atom drawing.
Atom Number: Atom numbers to be drawn. The number of atoms to be drawn is written in N_ATOM.
Bond Atom Number (Pair): Pairs of atom numbers to be used for bond drawing. The number of pairs is written in N_Bond.
Cavity Atom Number: Atom numbers to be removed for cavity calculation. Number of atoms is written in N_Cav
Cavity Radi: Atomic radius for cavity calculation. Usually, specify Van Der Waals radius + 1.2 (Å).
Cavity Range: In manual mode, Specify calculation range. In automatic mode, dummy value.
Grid: grid size for volume calculation.

Data File "cav.dat"

Data file is for atomic coordinates and fixed format of (A6,I4,3F10.6). The coordinate of the origin and transformation matrix are written in the first 7 lines.

Example of Control file

ORIGIN      5.601346  6.952534  3.076390
VMT0        1.000000  0.000000  0.000000
VMT1        0.000000  1.000000  0.000000
VMT2        0.000000  0.000000  1.000000
RVMT0       1.000000 -0.000000  0.000000
RVMT1      -0.000000  1.000000 -0.000000
RVMT2       0.000000 -0.000000  1.000000
CO1B     5  5.779318 10.785900  3.980696
SPHERE      9.000000
CO1B     5 11.639863  4.597915 -3.980696
CO1B     5 11.639863  4.597915  7.399224
N1B      2  4.433502 12.081833  3.715771
N1B      2 10.294047  3.301982 -3.715771
N1B      2 10.294047  3.301982  7.664149
N2B      2  4.276440  9.655498  4.063769
N2B      2 10.136985  5.728317 -4.063769
... omitted for clarity ...
H6A2     4  4.032875  0.992564  1.966336
H6A2     4  1.827670 -0.992564 -3.723624
H6A2     4  1.827670 -0.992564  7.656296
H6A2     4 13.548760 -0.992564 -3.723624
H6A2     4 13.548760 -0.992564  7.656296

Key word for Data file

ORIGIN: The origine coordinates of the drawing. Calculation range in cav.cnt should be taken from this.
VMT: Matrix to determin projection (section) direction
RVMT: Inverse matrix of the above matrix
SPHERE: (Optional) limit the calculation range to a sphere of radius of r Å from the origin.SPHERE This keyword require exact four spaces between keyword and the radius.
ATOM: (A6)AtomName (I4)AtomTypeNumber in cav.cnt (3F10.6)Cartesian coordinate in Å.

Example of Output File "cav.ps"

The output file is as following format.

header: Header for Post Script printing.
data: Cavity drawing and a volume in each section.
result: Volume of the cavity
footer: Footer for Post Script printing.

The linesbegins with "%#" is a comment that shows the progress of the calculations.

%!PS-Adobe-3.0 EPSF-3.0
%%Creater: PS-META-FILE(CAV4)
... omitted for clarity ...
    1.0000    1.0000 scale
    0.0000    0.0000 translate
%%EndProlog
%# StartData
%# ORIGIN=  5.601346  6.952534  3.076390
cc /mesh {3} def
cc save mesh 3 ne { 
cc -100 -100 m 0 0 rl 0 0 rl 0 0 rl 0 0 rl clip newpath } if
%# RVMT1 =  1.000000  0.000000  0.000000
%# RVMT2 =  0.000000  1.000000  0.000000
%# RVMT3 =  0.000000  0.000000  1.000000
cp        1 p
ct (Cavity                                  ) tt
%# mess Cavity Start                            
%# mess Z =  -3.444 (   1/  27) IView=3         
%# mess Volume/Plane =  0.000                   
%# mess Z =  -3.244 (   2/  27) IView=3         
%# mess Volume/Plane =  0.000                   
%# mess Z =  -3.044 (   3/  27) IView=3         
%# mess Volume/Plane =  0.000                   
%# mess Z =  -2.844 (   4/  27) IView=3         
%# mess Volume/Plane =  0.000                   
%# mess Z =  -2.644 (   5/  27) IView=3         
ca     0.903  -2.177   2.378   34   35 a %   -2.644    O1A   
ca     0.903  -2.177   2.378   70   73 a %   -2.644    O1A   
ca    -0.880  -1.166   2.808   27   32 a %   -2.644    C1A   
ca     3.037   1.708   2.070  223  231 a %   -2.644    C6A   
ca     3.272   0.849   1.722  206  208 a %   -2.644    H6A1  
%# mess Volume/Plane =  0.000                   
%# mess Z =  -2.444 (   6/  27) IView=3         
ca     4.935  -2.151   2.296  149  153 a %   -2.444    C11B  
ca    -0.312   2.448   2.828  310  315 a %   -2.444    C11C  

... omitted for clarity ...

ca     1.440  -1.611   1.008  178  192 a %    1.556    H6B1  
ca    -1.305  -1.120   1.794  339  346 a %    1.556    H7B1  
ca     3.585   1.373   2.315  261  262 a %    1.556    H7B3  
ca     4.770  -1.771   1.751  151  153 a %    1.556    H5B1  
ca    -0.692  -4.233   2.680   65   67 a %    1.556    O3A   
%# mess Volume/Plane =  0.000                   
%# mess Z =   1.756 (  27/  27) IView=3         
%# mess Volume/Plane =  0.000                   
%# mess Z =   1.956 (  28/  27) IView=3         
%# mess Volume/Plane =  0.000                   
cc restore
%# mess XRANGE =    -0.1360    3.7172           
%# mess YRANGE =    -3.0786    1.1391           
%# mess ZRANGE =    -3.0440    1.9560           
%# EndData
restore
showpage
%%EOF

Cavity Program source

This chapter explains each source file.

Initialize, finish-up: cavini.f/cavini.c
Definition of Common Data Block: cavity.inc / cavity.h, global.h (If you need to calculate large data, edit there files)
Read data: readdt.f / readdt.c
Main loop / Draw bonds / Generate atoms on each plane: cvmain.f/cvmain.c
Calculation of each plane / Draw cavity: cavity.f/cavity.c
Output graphics data to file: error.f, plot.f / plot.c (Default is PostScript. If you need to output another format, edit these files)

If you have questions, or you find bugs, and so on, please ask me.

Takashi NEMOTO

tnemoto@eels.kuicr.kyoto-u.ac.jp

"Cavity" Users Guide for Version 4.6 / 5.0

Contents

Cavity 4.6 installation procedure is ...

Cavity 5.0 installation procedure is ...

Cavity Calculation Procedure

Example of Input Files

Example of Control file

Keywords in Control file

Example of Control file

Key word for Data file