1. Main
2. Files
3. Control Panel
4. Selecting
5. Move & Rotate
6. Display
7. Rendering
8. Tools
9. Mutations
10. Torsions
11. Preferences
12. Electrostatics
13. Surface
14. Scripting
15. Hardware stereo
16. Tips & Tricks
    
17. Download Manual
    

Język skryptów

Program Parser w języku skryptowym SPDBV został wygenerowany flex i yacc, której kombinacja pozwala budować bardzo zaawansowane analizatory składniowe. Język skryptowy jest dosyć łatwy dla osób, które znają jezyk programowania C lub perl . Język skryptowy obsługuje rozgałęzienia, pętle, tablice i dostęp do plików. Podprogramy są również obsługiwane, ale trzeba mieć świadomość, że wszystkie zmiany mają charakter globalny. Pomimo tego ograniczenia, pozwala to na wykonanie skryptów bardziej zwartych i czytelnych, a także może być użyty do przygotowania swego rodzaju "tablicy skoków" z ulubionymi funkcjami, które mogą być wykonane po klikając na ich nazwę z interfejsu SPDBV lub dodanego menu.

Skrypty mogą być zatrzymane w określonych momentach, aby dać możliwość użytkowanikom na interakcje z interfejsem graficznym przed wznowieniem operacji. Pozwala to między innymi na dostęp do poleceń, które nie są bezpośrednio dostępne w skrypcie, "wzięcie" danych wprowadzonych przez użytkownika, lub na wykonywanie innego polecenia nie zawartego w skryptach, poprzez wpisywanie ich bezpośrednio w opcji " Execute script command" z menu "Edit". Skrypty mogą być wczytywane jako plik tekstowy (z otwartą adnotacją w menu plik) lub w opcji "Script Run" z menu "File". W systemie unix, skrypty mogą być przekazywane jako ostatni parametr w wierszu polecenia ( opcjonalne po plikach PDB), miejsce na post i wymiany skryptów są na liście dyskusyjnej spdbv, którą prowadzi prof. Gale Rodos.

http://www.usm.maine.edu/~rhodes/SPVTut/text/DiscuSPV.html

Każdy z nas lubi zachowywać się grzecznie tak też skrypty muszą zaczynać się od "please do" i kończąc na "thank you".
Wszystkie instrukcje są zakończone średnikami.
Wszystkie informacje po # są ignorowane aż do końca linii.

Typy danych:

W podręczniku, typy danych występujące między < >. To oznacza, że wartość wymienionego typu jest oczekiwana (lub zwrócona). Tę wartość można uzyskać od zmiennej, lub też dostarczyć bezpośrednio.

Obsługiwane są typy:

Istnieją dwa rodzaje zmiennych: zmienne skryptu (które mogą być używane do przechowywania wartości w skryptach) oraz zmiennych programu (wewnętrzne zmienne spdbv).

Przypisanie wartości do zmiennej skryptu odbywa się poprzez:

$varname = value;

typy danych dla zmiennych są przypisywane domyślne podczas zadania.

$X = 1.0; przypisze wartość 1.0 typu <float> do $X.
$X = 1; przypisze wartość 1 typu <int> do $X.

Operacje na zmiennych (zwykle) są możliwe ale tylko do zmiennych tego samego typu, ale można wymusić wartość aby była innego typu poprzez zastosowanie podmienienia (typecasting) na przykład:

$X = (float)1; przypise wartość 1.0 typu do $X.

Prawidłowe podmienianie (typecast) to: (int) (float) (string)

Tablice:

Obecnie tablice: <int> <float> i <vector> są obsługiwane. Składnia jest następująca:

$X[<int>] = value;

Rodzaj tablicy jest automatycznie określana przy wartościach które wprowadziłeś do ich za pierwszym razem. Pamięć jest przydzielana dynamicznie i będzie uwolniona po komendzie 'thank you': jeżeli chcesz coś odzyskać (z pamięci) lepiej bądź grzeczny ;-)

Operacje:

Możliwe jest dodawanie, odejmowanie, mnożenie lub dzielenie typów danych. Przy niektórych operacjach jest to oczywiście nie możliwe (iloczyn dwóch ciągów lub przy zaznaczeniu dwóch atomów).

Dodanie dwóch łańcuchów, spowoduje konkatenacje.

$X = "Hello" + " World!"; jest równoznaczne z $X = "Hello World!";

W przypadku wektorów, mnożenie jest skalarne, gdy jeden z członków jest typu :

$X = <1.0,1.0,1.0> * 3.0; wprowadzi <3.0,3.0,3.0> w $X lub wykonuje iloczyn skalarny, jeśli operacja składa się z dwóch wektorów. (or performs a dot product if the operation involves two vectors.)

Iloczyn skalarny można uzyskać z operatorem 'X':

$X = <0.0,1.0,0.0> X <0.0,0.0,1.0>;

Ruchomy punkt i całość zmiennych może być: pre/post incremented with ++<var> and <var>++ respectively, or pre/post decremented with --<var> and <var>-- respectively. Jest to używane głównie do pętli.

Pozostała część (modułu) z cyfrowego podziału, może być udostępniona przy operatorach jak w

print 8 % 3;

co dało by nam 2

Komendy: (alfabetycznie)

WSTĘPNIE do wersji 3.7b1, niektóre polecenia mogą nie być wykonywalne na wszystkich platformach. Więcej poleceń, zostanie dodanych w razie potrzeb.

Można znaleźć kilka przykładów skryptów w katalogu skryptów SPDBV. Skrypty są nazywane bardzo oryginalnie: script01.txt, script02.txt itp. Dla każdego z poniższych poleceń, jest zanzaczone, w którym skrypcie można go znaleźć. Skrypty mają na celu stopniowo wprowadzać coraz więcej funkcji i są alternatywnym sposobem, aby nauczyć się tego języka. Należy zacząć od skryptu script01.txt

access acos angle align align_pos asin ask atan build center chain color compute clear close cos delete dist do else export fit get goto groupcount hide if inline is_selected layername max min minimize move mutate name normalize num omega open pause phi PI "please do" print psi readln redraw rename renumber res rotate return rms save selcount select set show silent sin ss stop sub substring superpose system tan torsion "thank you" while zoom

W trybie offline: aby otworzć wszystkie skrypty-przyklady można skorzysrtać z funkcji importu sieciowego do otwierania plików PDB. Jeśli pracujesz w trybie offline, można kopiować pliki np. na dysku lokalnym (w katalogu usrstuff spdbv) i zmienić odpowiednio skrypty: Zamiast

open pdb from net "1CRN";

powinno to wyglądać:

open pdb from usrstuff "1CRN.pdb";

access

uzyska względny dostęp względem reszt X, w porównaniu do warości 100% ref. Obliczanej w rozszerzonej konformacji w GGXGG (pentapeptydu). Zwracana wartość jest typu .

access(<selection>)

Alternatywnie, można uzyskać dostęp do specyficznych reszt z wybranej warstwy, co jest szybszą i poręczniejszą metodą w pętli z:

access(<layer>,<int>)

Podobne polecenia: name res ss
Udokumentowane na przykładzie w skrypcie: 11

acos

oblicza arcus cosines w wyrażeniach, gdzie wartości wyraża się w radianach

acos(<float>)

Podobne polecenia: : sin asin cos tan atan PI
Udokumentowane na przykładzie w skrypcie: brak

angle

oblicza kąty AOB w odniesieniu do trzech atomów (wektorów).

<floatvar> = angle(A,O,B);

gdzie A, O i B są jako wartości a wynik jest zwracany w stopniach.

Podobne polecenia: dist get torsion
Udokumentowane na przykładzie w skrypcie: brak

align

będzie podstawowym porównaniem sekwencji pomiędzy warstwami.

align <layer> onto <layer>;

gdzie zawiera pytania, które zostaną przedstawione dla użytkownika.

Podobne polecenia: align_pos
Udokumentowanie na przykładzie w skrypcie: brak

align_pos

będzie uzyskana pozycja przy porównywaniu reszt (wyrównanie w oknie). Wartość zwracana to typ int>.

align_pos(<selection>)

na przemian, można uzyskać dostęp bezpośrednio do konkretnej reszty z danej warstwy, metda ta jest jest szybsza i poręczniejsza w pętli z:

align_pos(<layer>,<int>)

Podobne polecenia: "generate structural alignment" superpose rms fit
Udokumentowanie na przykładzie w skrypcie: brak

asin

oblicza arcus sinus wyrażenia. Wartości są w radianach.

asin(<float>)

Podobne polecenia: : sin cos acos tan atan PI
Udokumentowanie w skrypcie: brak

ask

stworzy okno dialogowe (tak, nie) pojawiające się aby dać dla użytkowników urzyteczne informacje na temat efektów jego pracy.

$int_varname = ask <string>;

gdzie zawiera pytania, które zostaną przedstawione dla użytkownika.

Podobne polecenia: if
Udokumentowanie w skrypcie: 08 and 10

atan

obliczenia arcus tangens wyrażenia. Wartości są w radianach.

atan(<float>)

Podobne polecenia: sin asin cos acos tan PI
Demonstrated in example script: none

build

dodaje różne obiekty, takie jak aminokwasy na powierzchnie molekularne.

build in <layer> molecular surface of quality <int>;

Podobne polecenia: delete
Demonstrated in example script: none

center

wyśrodkowuje widok na zaznaczone lub na widoczne grupy.

center on <selection>;
center on visible;

Udokumentowanie w skrypcie: 05 09 13

chain

otrzymamy nazwę łańcucha w pierwszej grupie znajdującej się w zaznaczeniu. Wartość zwracana jest w typie .

chain(<selection>)

alternatywmnie, można uzyskać bezpośredni dostęp do konkretnych reszt z danej warstwy, metoda ta jest szybsza i poręczniejsza w budowaniu pętli z:

chain(<layer>,<int>)

Podobne polecenia: name res ss access
Udokumentowanie w skrypcie: : 11

color

color some parts of the view. This is functionnally equivalent to the color column of the control panel.

color [in <layer>] <part> of <selection> by <vector>;
color <part> of <selection_variable> by <vector>;
color <part> of <selection_variable> in <color>;

when in <layer> is omitted, the current active layer is amumed.
<part> can be any combination of res,side,label,surface,ribbon,vdw.
<vector> is a rgb color (with intensity of each component are between 0.0 and 1.0.
<color> is any of the predefined kyewords: red green blue yellow white black grey cyan orange purple

example: color in "1crn" ribbon of res "F","N" by <1.0,0.0,0.0>;

Related commands: hide show
Demonstrated in example script: 05 13

compute

performs various computations on a protein.

compute in <layer> electrostatic potiential using "[coulomb|pb]" with "[partial|full]" charges;
compute in <layer> hbond;
<floatvar> = compute in <layer> energy;

Related commands: discard minimize
Demonstrated in example script: 07 and 09

clear

** USEFUL but DANGEROUS ** clear a file on disk.

clear file <string>;

where <string> is a variable that contains a filename.

Related commands: open close readln

close

close a layer or a file.

close <layer>;
close file <file>;

where <file> is a variable that contains a file previously open.

Related commands: open clear readln
Demonstrated in example script: 02 03 and 04

cos

compute the cosine of an expression. This returns the value in radians.

cos(<float>)
cos(<int>)

Related commands: sin asin acos tan atan PI
Demonstrated in example script: none

delete

delete selected residues, or hydrogens from a layer.

delete <selection>;
delete in <layer> hydrogen;
delete in <layer> molecular surface;
delete in <layer> electrostatic potential;

Related commands: build
Demonstrated in example script: none

dist

compute the distance between two atoms (vectors).

<floatvar> = dist(<vector>,<vector>);

Related commands: angle get torsion
Demonstrated in example script: 07

export

this command allows to save images or pov-ray scenes.

export image as <string>;
export stereo image as <string>;
export pov as <string> [and render];

where <string> contains the filename with full path. Alternately, you can save the file in one of the predifined directories [usrstuff|download|temp] with the following command

export pov in [usrstuff|download|temp] as <string> [and render];

See save for more explanations about path and filemames. note that the [and render option] will open the file for rendering on mac and pc, but will automatically launch pov on unix boxes provided you save the scene in the usrstuff directory.

Related commands: save
Demonstrated in example script: 09

fit

this command is equivalent to the fit (from selection) command of spdbv.

fit <layer> onto <layer> using <string>;

where <string> contains the method to be used ("CA", "backbone", "all").

Related commands: rms superpose
Demonstrated in example script: none

generate structural alignment

generate structural alignment;

Related commands: rms superpose fit
Demonstrated in example script: none

get

can access internal spdbv variables or atomic coordinates, retrieve aa sequences, or capture the current selection status of a specific layer (when modified directly from the graphical user interface). The list of internal variables that can be accessed is provided at the end of this guide.

$sel = get selection of <layer>;
$varname = get <internal variable>;
$vector_varname = get coord <string> of <selection>;
$string_varname = get seq of <selection>;

where <string> contains the 4 characters atom name (for. ex " CA ") and selection a selection.

Related commands: set
Demonstrated in example script: 07 08 09 and 10

goto

one of the most useful (and controversal although it is one of the rare commands to be wired directly on any chip...) command that allow to continue the execution from a different point of the script.

goto <label>;

Execution will continue immediately after <label>, which must end with a colon. example:

goto elsewhere;
print "Never done";
elsewhere: print "welcome";

Related commands: sub do while return
Demonstrated in example script: none

groupcount

will return the number of groups in a layer. This is functionnally equivalent to a select all followed by a selcount, athough it is quicker.

$int_varname = groupcount of <layer>;

Related commands: selcount
Demonstrated in example script: 02 03 and 04

hide

hide some parts from the view. This is functionnally equivalent to the control panel.

hide <part> of <selection>;
hide in <layer> <part> of <selection>;

where <part> can be any combination of res,side,label,surface,ribbon,vdw.

Related commands: show color
Demonstrated in example script: 06

inline>
text
<inline

This is used in conjunction with the open command to load PDB files directly embedded in the script, which is useful mostly for web servers that need to return a script+pdb file in a single file.

Example:

open pdb INLINE> 
ATOM      1  N   THR     1      17.047  14.099   3.625  1.00 13.79
ATOM      2  CA  THR     1      16.967  12.784   4.338  1.00 10.80
ATOM      3  C   THR     1      15.685  12.755   5.133  1.00  9.19
ATOM      4  O   THR     1      15.268  13.825   5.594  1.00  9.85
ATOM      5  CB  THR     1      18.170  12.703   5.337  1.00 13.02
ATOM      6  OG1 THR     1      19.334  12.829   4.463  1.00 15.06
ATOM      7  CG2 THR     1      18.150  11.546   6.304  1.00 14.23
<INLINE;        

Related commands: open
Demonstrated in example script: none

is_selected

is_selected(<layer>,<int>)
is_selected(<int>)

When <layer> is omitted, the current active layer is used. Returned value is of type <int> and is 1 if the group is selected and 0 otherwise.

Related commands: select
Demonstrated in example script: 11

layername

will return the <string> value of the layer name

<string_var> = layername of <int>;

where int is the relative position of the layer from the first loaded which is number 0, of course.

Related commands:
Demonstrated in example script: none

max

will return the max value of two numbers or variables.

max of (<float>,<float>);
max of (<int>,<int>);

Related commands: min
Demonstrated in example script: none

min

will return the min value of two numbers or variables.

min of (<float>,<float>);
min of (<int>,<int>);

Related commands: max
Demonstrated in example script: none

minimize

performs an energy minimization using n cycles of steepest descent

minimize <selection> with <int> cycles;

Related commands: compute
Demonstrated in example script: 07

move

move a selection.

move <selection> by <vector>;

where <vector> contains the translation in angstroms.

Related commands: zoom rotate
Demonstrated in example script: 09

mutate

will mutate an amino acid to another. It is currently not possible to browse the rotamer library in a script.

mutate <selection> to <string>;

where <selection> must contain one valid amino acid (first selected is taken) and <string> contains the one letter code of the new residue.

Related commands:
Demonstrated in example script: none

name

will get the three letter name of the first selected group found in a selection. Returned value is of type <string> for ex: is 'ALA' or 'ATP'.

name(<selection>)

alternately, you can access directly a specific residue from a specific layer, which is faster and handy in loops with:

name(<layer>,<int>)

Related commands: num res chain ss access
Demonstrated in example script: 11

normalize

will normalize a vector. Returned value is of type <vector>.

normalize(<vector>)

Related commands: vector operations.
Demonstrated in example script: none

num

will get the number of the first selected group found in a selection. Returned value is of type <int>.

num(<selection>)

Alternately, you can access directly a specific residue from a specific layer, which is faster and handy in loops with:

num(<layer>,<int>)

related commands: name res chain ss access
Demonstrated in example script: 11

omega

will get the omega peptidic bond torsion angle for the first selected amino acid found in a selection. Returned value is of type <float> and is returned in degrees.

omega(<selection>)

Alternately, you can access directly a specific residue from a specific layer, which is faster and handy in loops with:

omega(<layer>,<int>)

Related commands: phi psi ss
Demonstrated in example script: none

open

load a pdb file in the workspace (next available layer).

open [pdb] from "disk|net" <string>;

To be able to use the "net" option, you have to set the correct server address in "Network Preferences". Note that it is possible to omit "pdb" as it is the default value. <string> contains the full filename (see below). The filename must be the absolute path of your file. Unix users will enderstand what I mean, but Mac users might be a little confused.

Alternately, to be cross platform, you can also use one of the predetermined directories:

open [pdb] from usrstuff <string>;
open [pdb] from temp <string>;
open [pdb] from download <string>;

Constructing a full path on a Mac:

name_of_disl:name_of_folder:name_of_subfolder:name_of_subsubfolder:filename

For example, assume you store your pdb files in a folder named 'pdb' located in the 'System' disk. You can access the file '1crn.pdb' like this:

System:pdb:1crn.pdb

As you can see, Mac uses ':' as separator. This is of course different for unix which uses '/' and from windows which uses '\'. In order to make your scripts as portable as possible, I would recommend separating the file name from the path, which will let you (or other users) change just the path (one line) to make a generic script run on thieir machine.

Consider this example:

open "System:pdb:1crn.pdb";
open "System:pdb:1atp.pdb";

it is better rewriten like this:

$path = "System:pdb:"; # change this line to point to your pdb files directory.
open $path + "1crn.pdb";
open $path + "1atp.pdb";

The "open" command also allows to create files or open arbitrary text files for further processing, or allows to open a file as read-only.

$file_varname = open file <string>;
$file_varname = open file <string> for reading;

or allows to open a file as write (CAUTION WHEN USING THIS!).

$file_varname = open file <string> for writing;

or allows to append to a file (CAUTION WHEN USING THIS!).

$file_varname = open file <string> for appending;

In fact, using the full path of your file (directories+filename) is potentially dangerous if for some reason the filename get screwed up. Besides, it is not cross-platform and you likely wish to have your scripts running everywhere, I suggest that you and work with files store the files in your 'usrstuff' directory using the following equivalent commands:

$file_varname = open file <string> in usrstuff;
$file_varname = open file <string> in usrstuff for reading;
$file_varname = open file <string> in usrstuff for writing;
$file_varname = open file <string> in usrstuff for appending;

where <string> must *ONLY* contain the file name (no directory, no path) The open command can also be used to open a text file, which is only useful coupled with the graphical user interface.

open text <string>;
open text <string> in usrstuff;
open seq <string>;

this can be used to load a raw sequence to model. Sequence must be in format FASTA, SWISSPROT or SEQRES.

Related commands: close clear readln inline print save
Demonstrated in example script: all

pause

will stop the script execution for some seconds.

pause <float>;

Related commands: stop 'thank you' 'please do'
Demonstrated in example script: 05 06 07 09

phi

will get the phi torsion angle for the first selected amino acid found in a selection. Returned value is of type <float> and is returned in degrees.

phi(<selection>)

alternately, you can access directly a specific residue from a specific layer, which is faster and handy in loops with:

phi(<layer>,<int>)

Related commands: psi omega ss
Demonstrated in example script: 01 02 03 04

PI

return the value of PI.

related commands: sin asin cos acos tan atan
Demonstrated in example script:: none

please do

initiate a script, and reset all scripts variables. Note that this statement must be on the FIRST line of the script.

Related commands: stop pause 'thank you'
Demonstrated in example script: all

print

prints a value (string, variable, number etc..) onto stdout or in a spdbv communication dialog.

print on dialog; print on stdout;
print on <file> <expression>;
print <expression>;

where expression is any combination of aritmetic values or concatenation of strings. Note that a newline is printed after each print operation. You might then need to prepare a string (from concatenation) before printing.

Demonstrated in example script: 01 02 03 04 06 07 08 11

psi

will get the psi torsion angle for the first selected amino acid found in a selection. Returned value is of type <float> and is returned in degrees.

psi(<selection>)

alternately, you can access directly a specific residue from a specific layer, which is faster and handy in loops with:

psi(<layer>,<int>)

Related commands: phi omega
Demonstrated in example script: 03 04

readln

read the next line from a text file or from a dialog box.

$string_varname = readln from file <file>;
$string_varname = readln from user <string>;

where <file> is a file previously open with the open file command. and <string> is a prompt that will appear in the dialog.

Related commands: open close clear substring
Demonstrated in example script: 04 06

redraw

will force the main window to be refreshed. Useful only in the interactive mode.

Related commands: show
Demonstrated in example script: 05 07

rename

rename chain of <selection> as <string>;

will change the chain name of the selected residues.

rename <layer> as <string>;

will change the layer name.

Related commands: renumber
Demonstrated in example script: none

renumber

renumber <selection> from <int>;
renumber <selection> add <int>;

will change the residue number of selected residues.

Related commands: rename
Demonstrated in example script: none

res

will get the one letter name of the first selected group found in a selection. Returned value is of type <string> e.g.: 'A' or 'C' or 'D',...

res(<selection>)

alternately, you can access directly a specific residue from a specific layer, which is faster and handy in loops with:

res(<layer>,<int>)

Related commands: num name chain ss access
Demonstrated in example script: 11

rotate

rotate the view successively around axis x,y,z:

rotate <vector>;

where <vector> contains rotation angles in degrees. This command can also be used to rotate a selection around a specific axis.

rotate <selection> by <float> [deg|rad] around axis <vector> <vector>;

or to do a torsion (rotate atoms downstream a bond around this bond) using the following syntax:

rotate atoms of <selection> by <float> [deg|rad] around bond <string> <string>;

Related commands: zoom move
Demonstrated in example script: 05 06 09

return

It will resume execution where it was before entering the subroutine. See sub for more explanations

Related commands: goto do while sub
Demonstrated in example script: 08 10

rms

this command is equivalent to the RMS command of spdbv.

rms of <layer> and <layer> using <string>;
<floatvar> = rms of <layer> and <layer> using <string>;

where <string> contains the method to be used ("CA", "backbone", "all").

Related commands: fit superpose
Demonstrated in example script: 05

save

save a all or part of pdb files from some layers.

save <layer> as <string>;
save selection of <layer> as <string>;

where <string> contains the full filename (see discussion in open). An alternative set of commands that will save files in predifined directories located under the spddbv main directory is available. Directories can be usrstuff,temp or download:

save <layer> in [usrstuff|temp|download] as <string> ;
save selection of <layer> in [usrstuff|temp|download] as <string> ;

in this case <string> must contain *ONLY* the filename, as the directory is implicit. This is very useful to make scripts portable among the various OS supported (Windows, Macintosh, IRIX and Linux).

Related commands: open
Demonstrated in example script: 06

search

*This function is not yet available.* allows to search 3D patterns in pdb files.

search in <layer> <string>;
search in <layer> <string> >> <string>;

where the first <string> contains the filename of the 3Dsearch pattern description file, and the second (optional) string appends the output to a file (that might be worth clearing before with the clear command).

Demonstrated in example script: none

selcount

will return the number of selected groups in a layer.

$int_varname = selcount of <layer>;

Related commands: groupcount
Demonstrated in example script: 06

select

allow to select specific residues and perform logical operations on them. This can then be used to color or hide residues, among other things.

<var> = select [in <layer>] <selection>;
select <var>;

when [in <layer>] is ommitted, the current active layer is assumed. <var> must contain a selection and <selection> can be any combination of:

example:

$sel1 = select in "1ATP" res "Y" and chain "I";

It is currently not possible to provide very complex selections in one operation, but this is easily overcomed as selections can be added or substracted: Example:

$sel = $sel1 + $sel2 + sel3 - sel4;

A special case allows to get the current selection state of a layer into a variable. This is useful to capture a selection made directly from the user graphical interface.

$sel = get selection of <layer>;

Related commands: selcount
Demonstrated in example script: all

set

can set internal spdbv variables or atomic coordinates. The list of internal variables that can be accessed is provided at the end of this guide.

set <internal variable> = $varname;
set coord <string> of <selection> = $vector_varname;

where <string> contains the 4 characters atom name (for. ex " CA ") and selection a selection. It also allows to toggle the backbone representation for a layer to "ca_trace":

set ca_trace [ON|OFF] for <layer>;

Related commands: get
Demonstrated in example script: 07

show

show some parts from the view. This is functionnally equivalent to the control panel.

show <part> of <selection>;
show in <layer> <part> of <selection>;

where <part> can be any combination of res, side ,label, surface, ribbon, vdw.

Related commands: hide color
Demonstrated in example script: 06 09 13

silent

can be used in conjunction witht the stop command to prevent any feedback of which line the script was stopped.

silent stop;

Related commands: stop
Demonstrated in example script: 08 10

sin

compute the sinus of an expression.

sin(<float>) sin(<int>)

This returns the value in radians.

Related commands: asin cos acos tan atan PI
Demonstrated in example script: none

ss

will get the secondary structure assignment of the first selected amino acid found in a selection. Returned value is of type <string> and is 'h' 's' or 'c'.

ss(<selection>)

alternately, you can access directly a specific residue from a specific layer, which is faster and handy in loops with:

ss(<layer>,<int>)

Related commands: phi psi omega
Demonstrated in example script: 11

stop

will stop the script in a way that it can be continued from the graphical user interface with "shift" open script. Very convenient if you want to interactively inspect a molecule before resuming the script flow.

Related commands: 'please do' 'thank you' pause silent
Demonstrated in example script: 06 08

sub

this command is nothing else than a goto that remembers where it was before. It will resume execution where it was before entering the subroutine as soon as a return statement is reached.

sub <label>; <--- note that this must be the only command on a line

Execution will continue immediately after <label>, which must end with a colon.

Note that subroutines must be located at the end of the script (after the thank you statement). All variables beeing global, be very careful when you use them, especially loops variables). Example:

 please do 
 sub elsewhere; 
 thank you 

 elsewhere: 
 { 
      print "Is grass really greener here?";
      return; 
 }

Related commands: goto do while return
Demonstrated in example script: 08 10

substring

allow to access substrings within a string by position. Substrings are separated by spaces and numbering start from 0.

$string_varname = substring <int> of <string>;

Examples:

$X = substring 0 of "Hello World!"; will put "Hello" into $X.

$X = substring 1 of "Hello World!"; will put "World!" into $X.

Demonstrated in example script: 04

superpose

this command is equivalent to the magic fit of spdbv.

<int> = superpose <layer> onto <layer> using <string>;

where <string> contains the method to be used ("CA", "backbone", "all","ss"). This returns the number of solutions as an int.
When "ss" is used, and more than one solution is possible, a temp file "match.txt" is written and a window will be opened with one solution per line.

Related commands: rms fit
Demonstrated in example script: 05

system

** USEFUL but DANGEROUS **. Executes a shell system command.

system <string>;

This command is supported only for SGI and Linux versions. It is mainly useful to execute a script that will put results into a file that can then be open as read-only with the open file command and read line by line with readln.

Demonstrated in example script: none

tan

compute the tangent of an expression. Returns the value in radians.

tan(<float>)
tan(<int>)

Related commands: sin asin cos acos atan PI
Demonstrated in example script: none

torsion

compute the torsion angle ABCD between four atoms (vectors). In other words, the angle between planes ABC and BCD.

<floatvar> = torsion(A,B,C,D);

where A,B,C and D are <vector> values. Result is returned in degrees.

Related commands: dist get
Demonstrated in example script: none

thank you

polite way of ending a script, which will also free any memory assigned for arrays.

Related commands: 'please do'
Demonstrated in example script: all

zoom

this command changes the camera position to zoom in or out

zoom <float>;

where <float> is the percent change. 100.0 means no change, 110.0 will do a close-up (enlarge the image by 10%) 90.0 will zoom out (decrease the image size by 10%).

Related commands: rotate move
Demonstrated in example script: 05

Tests (conditionnal execution):

 if (expression test expression) 
 { 
 } 
 else 
 { 
 } 

Where test can be

Demonstrated in example script: 04 06 08

Loops:

Two kinds of loops are supported that allow to cope with any situation. The higher level for(;;) statement is not implemented:

In the following case, statements will be executed at least once, and more depending on the result of the test.

 do 
 { <-- note that statements must start on the next line. 
   statements; 
 } 
 while (expression test expression); <-- note the semicolon

In the following case, statements may not be executed at all, depending on the result of the test.

 while (expression test expression) 
 { 
    statements;
 } 

Demonstrated in example script: 01 02 03 04 05 06 07 09

Internal variables:

This is the list of recognized internal spdbv variables, that can be accessed by the get and set commands. Access to additional variables will be added in the future, as needed.

The following variables affect the behaviour of alerts presented during the load of a protein:

Demonstrated in example script: 08 10

Last modified 20 / Jul /2001
by Torsten Schwede and Nicolas Guex