Beautiful....Thanks very much, Bob....(I'm impressed -- that's not possible
with arrays in less flexible languages!) The only part that's going to be
hard to remember is to start counting from the beginning at 1 and not 0....
But, then again, I'm pretty used to getting my back end first...... :)
I've also added your JmolScript version to the wiki.
-Tom
On Tue, Sep 23, 2008 at 10:39 AM, Robert Hanson <[EMAIL PROTECTED]> wrote:
> sure - that would be fine. Please do add that. There are a lot of new
> capabilities lurking in Jmol 11.6 that I just have not had time to demo.
>
> x = (titleLines[3])[11][0].trim()
>
> [n] in general means "the nth element of" and can be applied to strings or
> lists. In this case we have a list of lines from a split() of a string. (The
> split function can take an argument, but without an argument "new line" is
> assumed.) These start at 1 for the first element and have the interesting
> capability of being able to count back from the last element using numbers
> less than or equal to 0. So "testing"[0] is "g" and "testing[-2] is "i".
>
> Two brackets in a row: [m][n] specify a range of elements of a list or a
> subset of characters of a string. The parentheses above are required to
> differentiate taking the last line of lines 3-11:
>
> (titleLines[3][11])[0]
>
> and taking the 11th through the last character of line 3:
>
> (titleLines[3])[11][0]
>
> which is what we want here.
>
> On Tue, Sep 23, 2008 at 11:43 AM, Thomas Stout <[EMAIL PROTECTED]>wrote:
>
>>
>> It looks to me like you're taking everything "extra" off the beginning and
>> ends of each line in the titleLines array, but it's the [11][0] syntax that
>> has me stumped....If they are positions in the line array, then is this a
>> selection from the beginning of the actual title text to the end of that
>> line?
>>
>
> you got it! I'm splitting off TITLE as well as the continuation line
> character in column 10 on the second an third lines.
>
>
>>
>> 12345678901
>> TITLE STRUCTURAL BASIS FOR THE PHOSPHOSERINE-PROLINE
>>
>> Thanks!
>> -Tom
>>
>>
>>
>>
>> On Mon, Sep 22, 2008 at 4:02 PM, Robert Hanson <[EMAIL PROTECTED]>wrote:
>>
>>> Nice. You can save yourself a little trouble with:
>>>
>>> var title =
>>> jmolEvaluate('getProperty("fileHeader").split().find("TITLE")')
>>>
>>> Also, realize that this goes back and retrieves the file again from its
>>> source. If you know you want to use the file header this way, it's more
>>> efficient to use
>>>
>>> set pdbGetHeader TRUE
>>>
>>> (uh, undocumented, I see...)
>>>
>>> This setting instructs Jmol to preserve the file header in memory when
>>> the file is loaded. It is used in Jmol Protein Explorer.
>>>
>>> Since you are really wanting to display this in Jmol, you might consider
>>> something like the following Jmol script, which requires no JavaScript:
>>>
>>> function getHeader()
>>> var titleLines =
>>> getProperty("fileHeader").split().find("TITLE").split()
>>> for (var i = 1; i <= titleLines.size;i = i + 1)
>>> titleLines[i] = (titleLines[i])[11][0].trim()
>>> end for
>>> return titleLines.join("|")
>>> end function
>>>
>>> set echo bottom left
>>> echo @{getheader()}
>>>
>>>
>>> Something like that....
>>>
>>>
>>> Bob
>>>
>>> On Mon, Sep 22, 2008 at 3:50 PM, Thomas Stout <[EMAIL PROTECTED]>wrote:
>>>
>>>>
>>>> Here, then -- with my thanks for all the help -- is a working method to
>>>> pull the "TITLE" lines from a PDB file and echo it to the bottom of the
>>>> Jmol
>>>> Applet window:
>>>>
>>>> var headerInfo = jmolGetPropertyAsString("fileHeader");
>>>> var cutUp = headerInfo.split("\n");
>>>>
>>>> var headerstring="";
>>>>
>>>> for (l=0;l<cutUp.length;l++) {
>>>> var regexp = new RegExp("TITLE.{5}(.*)\s*");
>>>> var temp = cutUp[l];
>>>>
>>>> if (temp.search(regexp) == 0) {
>>>> temp2 = RegExp.$1;
>>>> temp2.replace(/^\s+|\s+$/g, "").replace(/\s+/g, " ");
>>>> temp2 = temp2 + "|";
>>>> headerstring += temp2;
>>>> }
>>>> }
>>>>
>>>> headerstring.replace(/TITLE/, "");
>>>> jmolScript("set echo depth 0; set echo headerecho 2% 2%;
>>>> font echo 12 sanserif bolditalic; color echo green");
>>>> jmolScript('echo "' + headerstring + '"');
>>>>
>>>>
>>>> Cheers,
>>>> Tom
>>>>
>>>>
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>>>>
>>>
>>>
>>> --
>>> Robert M. Hanson
>>> Professor of Chemistry
>>> St. Olaf College
>>> Northfield, MN
>>> http://www.stolaf.edu/people/hansonr
>>>
>>>
>>> If nature does not answer first what we want,
>>> it is better to take what answer we get.
>>>
>>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>>
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>>
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>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
> -------------------------------------------------------------------------
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> challenge
> Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
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> _______________________________________________
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>
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