Double Quotes and Regular Expressions

Double quotes around a string are used to specify a regular expression search (compatible with Perl 5.005, using the Perl-compatible regular expressions library written by Philip Hazel). If you don't know how to use them, try consulting the man pages for ed, egrep, vi, or regex. If not, read the Perl docs, or get any one of a number of books including the O'Reilly and Associates Sed and Awk book. The following examples show just a few ways that regular expressions can be used within VMD.

Selection of all atoms with a name starting with C:

        name "C.*"

Segment names containing a number:

        segname ".*[0-9]+.*"

Multiple terms can be provided on the list of matching keywords. This example selects residues starting with an A, the glycine residues, and residues ending with a T. As with a string, a regular expression in a numeric context gets converted to an integer, which will always be zero:

        resname "A.*" GLY ".*T"

Selections containing special characters such as $+$ , $-$ , or $*$ , must be escaped with the \ character. In order to select atoms named Na+, one would use the selection:

        name "Na\+"

In brief, a regular selection allows matching to multiple possibilities, instead of just one character. Table 6.9 shows some of the methods that can be used.

Table 6.9: Regular expression methods.

Symbol	Example	Definition
.	. , A.C	match any character
[]	[ABCabc] , [A-Ca-c]	match any char in the list
[~]	[~Z] , [~XYZ] , [^x-z]	match all except the chars in the list
^	^C , ^A.*	next token must be the first part of string
$	[CO]G$	prev token must be the last part of string
*	C* , [ab]*	match 0 or more copies of prev char or
		regular expression token
+	C+ , [ab]+	match 1 or more copies of the prev token
\|	C\|O	match either the 1st token or the 2nd
\(\)	\(CA\)+	combines multiple tokens into one

There are many ways to do some selections. For example, choosing atoms with a name of either CA or CB can be done in the following ways:

        name CA CB
        name "CA|CB"
        name "C[AB]"
        name "C(A|B)"

Several caveats for those who already understand regular expressions. VMD automatically prepends ``^('' and appends ``)$'' to the selection string. This makes the selection O match only O and not OG or PRO. On the other hand, putting ^ and $ into the command won't really affect anything, selections that match on a substring must be preceded and followed by ``.*'', as in .*O.*, and some illegal selections could be accepted as correct, but strange, as in C)|(O , which gets converted to ^(C)|(O)$ and matches anything starting with a C or ending with an O.

A regular expression is similar to wildcard matching in X-PLOR. Table 6.10 is a list of conversions from X-PLOR style wildcards to the matching regular expression.

Table 6.10: Regular expression conversions.

X-PLOR Wildcard	Description	Regular Expression
*	matches any string	.*
%	matches a single character	.
+	matches any digit	[0-9]
#	matches any number	[0-9]+