next up gif contents index
Next: PhiMap file (.phi) files Up: File Formats Previous: File Formats


Interactions file

  The interactions file contains a list of interaction records. Interactions are described in §6.4.12. An interaction file is an ASCII text file, where each line describes one interaction, unless that line starts with an exclamation point and is therefore treated as a comment and ignored. For maximum flexibility, each line is basically free format after the first character. The first character identifies an interaction as either an intensity interaction I, or a distance interaction D.

A distance interaction record has three fields separated by colons ":". The first field is the type I or D already described. The next two fields are spock selection strings identifying the atoms that are involved in the interaction. When an interaction file is read, if there is more than one atom that matches the given selection, the first atom in the sequence is used.

An intensity interaction record is nearly identical except that the first character is I and there are two extra fields (colon-delimited again) for the interaction type number and the intensity of the interaction.

Here's a sample interactions file:

! interaction file written by spock v1.0, Copyright 1997, Jon A. Christopher
I : r=ALA,rn=    1,ch=_,a= CB  : r=HOH,rn=  174,ch=_,a= O   : 1 : 1.000000
I : r=SER,rn=   35,ch=_,a= OG  : r=HOH,rn=  196,ch=_,a= O   : 5 : 2.000000
D : r=LYS,rn=   41,ch=_,a= NZ  : r=PRO,rn=   55,ch=_,a= CD 
D : r=ASP,rn=   66,ch=_,a= OD1 : r=HOH,rn=  155,ch=_,a= O  
I : r=HOH,rn=  124,ch=_,a= O   : r=HOH,rn=  192,ch=_,a= O   : 3 : 0.000000
D : r=HOH,rn=  181,ch=_,a= O   : r=SER,rn=   64,ch=_,a= O  
I : r=HOH,rn=  192,ch=_,a= O   : r=HOH,rn=  193,ch=_,a= O   : 2 : 0.000000

Jon Christopher
Tue Sep 14 16:44:48 CDT 1999