analyze.pl - Revision history

Edit: /* Examples */

2009-08-01T01:04:00Z

Examples

Edit: /* Examples */

2009-07-28T01:40:39Z

Examples

Edit: /* Options */

2009-07-28T01:39:47Z

Options

Edit: /* Description */

2009-07-28T01:38:58Z

Description

Edit: /* Description */

2009-07-28T01:38:29Z

Description

Edit: /* Description */

2009-07-28T01:37:30Z

Description

Edit: /* Description */

2009-07-28T01:36:30Z

Description

Edit at 20:07, 27 July 2009

2009-07-27T20:07:30Z

New page

__NOTOC__
== Usage ==

<mmtsbToolUsage cmd="analyze.pl"></mmtsbToolUsage>

== Description ==

== Options ==

; -help : usage information

== Examples ==

←Older revision		Revision as of 01:04, 1 August 2009
Line 50:		Line 50:
	== Examples ==		== Examples ==

−	<mmtsbToolExample cmd="analyze.pl" set="~~/apps/mmtsb/bench/analyze.pl-test/~~test1"></mmtsbToolExample>	+	<mmtsbToolExample cmd="analyze.pl" set="test1"></mmtsbToolExample>

←Older revision		Revision as of 01:40, 28 July 2009
Line 49:		Line 49:

	== Examples ==		== Examples ==
		+
		+	<mmtsbToolExample cmd="analyze.pl" set="/apps/mmtsb/bench/analyze.pl-test/test1"></mmtsbToolExample>

@@ Line 10: / Line 10: @@
 values to be returned.
-An example for a function that calculates the end-to-end distance for the
+An example for a function that calculates the end-to-end distance between
 N- and C-terminal C-alpha atoms of the first chain from a given structure
 is given in the following:

@@ Line 24: / Line 24: @@
        $ca1=$atom->[$ia] if ($atom->[$ia]->{atomname} eq "CA");
+     }
-−
      my $ca2;
      for (my $ia=$res->[$#{$res}]->{start}; $ia<=$res->[$#{$res}]->{end}; $ia++) {
        $ca2=$atom->[$ia] if ($atom->[$ia]->{atomname} eq "CA");
+     }
-−
      my $dx=$ca1->{xcoor}-$ca2->{xcoor};
      my $dy=$ca1->{ycoor}-$ca2->{ycoor};
      my $dz=$ca1->{zcoor}-$ca2->{zcoor};
-−
      push(@data, sqrt($dx*$dx+$dy*$dy+$dz*$dz));
-−
      return @data;
+   }
-;
+An example of how to use such a function is given below.
 == Options ==

@@ Line 23: / Line 23: @@
      for (my $ia=$res->[0]->{start}; $ia<=$res->[0]->{end}; $ia++) {
        $ca1=$atom->[$ia] if ($atom->[$ia]->{atomname} eq "CA");
+     }
-  my $ca2;
+    my $ca2;
-  for (my $ia=$res->[$#{$res}]->{start}; $ia<=$res->[$#{$res}]->{end}; $ia++) {
+    for (my $ia=$res->[$#{$res}]->{start}; $ia<=$res->[$#{$res}]->{end}; $ia++) {
-    if ($atom->[$ia]->{atomname} eq "CA") {
+      $ca2=$atom->[$ia] if ($atom->[$ia]->{atomname} eq "CA");
+     }
-  my $dx=$ca1->{xcoor}-$ca2->{xcoor};
+    my $dx=$ca1->{xcoor}-$ca2->{xcoor};
-  my $dy=$ca1->{ycoor}-$ca2->{ycoor};
+    my $dy=$ca1->{ycoor}-$ca2->{ycoor};
-  my $dz=$ca1->{zcoor}-$ca2->{zcoor};
+    my $dz=$ca1->{zcoor}-$ca2->{zcoor};
-  push(@data, sqrt($dx*$dx+$dy*$dy+$dz*$dz));
+    push(@data, sqrt($dx*$dx+$dy*$dy+$dz*$dz));
-  return @data;
+    return @data;
-−
+  }
 ;
 == Options ==

@@ Line 46: / Line 46: @@
 ; -help : usage information
+; -function file : perl script file with function named analyze
 == Examples ==

←Older revision		Revision as of 01:36, 28 July 2009
Line 6:		Line 6:
	== Description ==		== Description ==

		+	This tool runs the perl function given in the script file for the structure given as argument. The perl function has to be named <TT>analyze</TT>. It is
		+	passed a <TT>Molecule</TT> object as argument and expects one or more
		+	values to be returned.
		+
		+	An example for a function that calculates the end-to-end distance for the
		+	N- and C-terminal C-alpha atoms of the first chain from a given structure
		+	is given in the following:
		+
		+	sub analyze {
		+	my $mol=shift;
		+	my @data=();
		+	my $res=$mol->{chain}->[0]->{res};
		+	my $atom=$mol->{chain}->[0]->{atom};
		+
		+	my $ca1;
		+	for (my $ia=$res->[0]->{start}; $ia<=$res->[0]->{end}; $ia++) {
		+	$ca1=$atom->[$ia] if ($atom->[$ia]->{atomname} eq "CA");
		+	$ca1=$atom->[$ia];
		+	}
		+	}
		+
		+	my $ca2;
		+	for (my $ia=$res->[$#{$res}]->{start}; $ia<=$res->[$#{$res}]->{end}; $ia++) {
		+	if ($atom->[$ia]->{atomname} eq "CA") {
		+	$ca2=$atom->[$ia];
		+	}
		+	}
		+
		+	my $dx=$ca1->{xcoor}-$ca2->{xcoor};
		+	my $dy=$ca1->{ycoor}-$ca2->{ycoor};
		+	my $dz=$ca1->{zcoor}-$ca2->{zcoor};
		+
		+	push(@data, sqrt($dx$dx+$dy$dy+$dz*$dz));
		+
		+	return @data;
		+	}
		+
		+	1;

	== Options ==		== Options ==