I want to align to ligands in PyMOL like one would do it with protein structures, but I get an error message:
ExecutiveAlign: mobile selection must derive from one object only
I also copied the ligands into separate PDB files, renamed the HETATM entries to ATOM, but still I get this error. I am wondering why PyMOL has problems aligning those small molecules.
PS: Those ligands have similar structure, only different coordinates.
When you align with the align function pymol seeds the structural alignment by doing a sequence alignment first.
You can use the pair_fit function but will have to specify the corespondency between atoms. This function takes two selections, one for each element, that have the same number of atoms.
If the ligands have the exact same chemical structure you can pass the objects directly, if not you will have to make the appropriate selections.
Did you do this through the GUI? That's a bug, the align function never works from the GUI. Try doing it by command line.
align mol1, mol2
Related
[![enter image description here][4]][4][![enter image description here][5]][5]I have a PDF that has tabular data that runs over 50+ pages, i want to extract this table into an excel file using Automation Anywhere. (i am using community version of AA 11.3). I watched videos of the PDF integration command but haven't had any success trying this for tabular data.
Requesting assistance.
Thanks.
I am afraid that your case will be quite challenging... and the main reason for that are the values that contains multiple lines. You can still achieve what you need, and with good performance, but the code itself will not be pretty. You will also be facing challanges with Automation Anywhere, since it does not really provide the right tools to do such a thing and you may need to resort to scripting (VBScripts) or Metabots.
Solution 1
This one will try to use purely text extraction and Regular expressions. Mainly standard functionality, nothing too "dirty".
First you need to realise how do the exported data look like. You can see that you can export to Plain or Structured.
The Plain one is not useful at all as the data is all over the place, without any clear pattern.
The Structured one is much better as the data structure resembles the data from the original document. From looking at the data you can make these observations:
Each row contains 5 columns
All columns are always filled (at least in the visible sample set)
The last two columns can serve as a pattern "anchor" (identifier), because they contain a clear pattern (a number followed by minimum of two spaces followed by a dollar sign and another number)
Rows with data are separated by a blank row
The text columns may contain a multiline value, which will duplicate the rows (this one thing makes it especially tricky)
First wou need to ensure that the Structured data contain only the table, nothing else. You can probably use the Before-After string command for that.
Then you need to check if you can reliably identify the character width of every column. You can try this for yourself if you copy the text into Excel, use the Text to Columns with the Fixed Width option and try to play around with the sliders
The you need to try to find a way how to reliably identify each row and prepare it for the Split command in AA. For that you need to have a delimiter. But since each data row can actually consists of multiple text rows, you need to create a delimiter of your own. I used the Replace function with Regular Expression option and replace a specific pattern for a delimiter (pipe). See here.
Now that you have added a custom delimiter, you can use the Split command to add each row into a list and loop through it.
Because each data row may consists of several rows, you will need to use Split again, this time use the [ENTER] as delimiter. Now you need to loop through each of the text line of a single data line and use the Substring function to extract data based on column width and concatenate them to a single value that you store somewhere else.
All in all, a painful process.
Solution 2
This may not be applicable, but it's worth a try - open the PDF in Microsoft Word. It will give you a warning, ignore it. Word will attempt to open the document and, if you're lucky, it will recognise your table as a table. If it works, it will make the data extraction much easier an you will be able to use Macros/VBA or even simple Copy&Paste. I tried it on a random PDF of my own and it works quite well.
I know that when we implement a ParDo transform, we pick up individual elements from our data(basically separated by "\n"). But what if I have an element that occupies two lines in my file. Can I apply my own condition to pick elements according to it? Or is it always necessary to have an element in a single line?
Reading of text files is controlled by TextIO, not by ParDo - I suppose that's what you meant. Indeed right now TextIO splits files into 1 element per line, however there is work in progress on changing that. You can follow the work at https://issues.apache.org/jira/browse/BEAM-2802.
It would be useful for that work, if you told more about your file format, to make sure it is in scope.
As the title says, I would like to know what is the meaning of the pipe (or tube) "|" in a Delphi code. See that screenshot :
I know the meaning of "*" which is a wild card for one or more characters, but I can't find what means "|".
Thanks
This is a question that can be answered by reading the documentation. It can be found here:
Vcl.Dialogs.TOpenDialog.Filter
To create file masks in program code, assign a value to the Filter
property that consists of a description and a mask separated by a
vertical bar (pipe) character. Do not include spaces around the
vertical bar. For example,
OpenDialog1.Filter := 'Text files (*.txt)|*.TXT';
Multiple filters should be separated by vertical bars. For example,
OpenDialog1.Filter := 'Text files (*.txt)|*.TXT|Pascal files (*.pas)|*.PAS';
To include multiple masks in a single filter, separate the masks with
semicolons. This works both in the Object Inspector and in program
code. For example,
OpenDialog1.Filter := 'Pascal files|*.PAS;*.DPK;*.DPR';
You might like to absorb the hints found here (How can I search for Delphi documentation?) in order to help you in the future.
In Delphi, the | character is often used as separator in certain string properties to differentiate between:
The description and the mask of a file filter, as used in TOpenDialog.Filter.
The short part, the long part and the image index of a hint text, as used in all Hint properties.
The pipe separates the filter expression (on the right) from the caption the user will see (on the left). If you want to apply more than one filter, just append it, also separated by pipes.
For TOpenDialog this is just a syntax to specify in one line of Filter both:
friendly type name (here: Regles de chaurfage)
file extension related to the type (here .fuz)
This is not language operator. This is just some kind of convention TOpenDialog is using.
Multiple filters should be separated by vertical bars.
http://docs.embarcadero.com/products/rad_studio/delphiAndcpp2009/HelpUpdate2/EN/html/delphivclwin32/Dialogs_TOpenDialog_Filter.html
Using libclang, I have a cursor into a AST, which corresponds to the statement resulting from a macro expansion. I want to retrieve the original, unexpanded macro text.
I've looked for a libclang API to do this, and can't find one. Am I missing something?
Assuming such an API doesn't exist, I see a couple of ways to go about doing this, both based on using clang_getCursorExtent() to obtain the source range of the cursor - which is, presumably, the range of the original text.
The first idea is to use clang_getFileLocation() to obtain the filename and position od the range start and end, and to read the text directly from the file. If I've compiled from unsaved files then i need to deal with that, but my main concern with this approach is that it just doesn't seem right to be going outside to the filesystem when I'm sure clang holds all this information internally. There also would be implications if the AST has been loaded rather than generated, or if the source files have been modified since they were parsed.
The second approach is to call clang_tokenize() on the cursor extent. I tried doing this, and found that it fails to produce a token list for most of the cursors in the AST. Tracing into the code, it turns out that internally clang_tokenize() manipulates the supplied range and ends up concluding that it spans multiple files (presumably due to some effect of the macro expansion), and aborts. This seems incorrect to me, but I do feel that in any case I'm abusing clang_tokenize() trying to do this.
So, what's the best approach?
This is the only way I've found.
So you get the top level cursor with clang_getTranslationUnitCursor(). Then, you do clang_visitChildren(), with the visitor function passed into this returning CXChildVisit_Continue so that only the immediate children are returned. Among the children, you see the usual cursor types for top level declarations (like CXCursor_TypedefDecl, CXCursor_EnumDecl) but among them there's also CXCursor_MacroExpansion. Every single macro expansion appears to show up in a cursor with this type. You can then call clang_tokenize() on any of these cursors and it gives you the unexpanded macro text.
I have no idea why macro expansions get stuck near the top of the AST instead of within elements where they get used, it makes things pretty awkward. Example:
enum someEnum{
one = SOMEMACRO,
two,
three
}
It'd be nice if the macro expansion cursor for SOMEMACRO were within the enum declaration instead of being a sibling to it.
(I realize this is ridiculously late but I'm hoping this gets libclang more exposure, maybe someone more experienced with it can provide more insight).
I tried tikz/pgf a bit but have not had much luck creating a nice diagram to visualize bitfields or byte fields of packed data structures (i.e. in memory). Essentially I want a set of rectangles representing ranges of bits with labels inside, and offsets along the top. There should be multiple rows for each word of the data structure. This is similar to most of the diagrams in most processor manuals labeling opcode encoding etc.
Has anyone else tried to do this using latex or is there a package for this?
I have successfully used the bytefield package for something like this. If it doesn't do exactly what you want, please extend your question with an example...
You will find several examples with both tikz code source and a visual rendering of this code at http://www.texample.net/tikz/examples/