Smormo-Ed's Command Language

1 Introduction
2 Procedures
3 Examples
- 3.1 version
- 3.2 read and write smiles

1 Introduction

Smormo-Ed has a simple interpreter built into it. It accepts commands as s-expressions (like lisp or scheme). There is a "scratch area", which holds a molecule in the program's internal data structures. If the GUI is enabled, this is what can be seen in the window. Some commands accept or return molecules encoded as s-expression, and others operate on the molecule in the scratch area. mol->sexp and sexp->mol can be used to transfer a molecule into or out of the scratch area. Each atom in the scratch area has a flag indication if it is "selected" or not. Some procedures operation only on selected atoms.

Here is an example of a molecule encoded as an s-expression. (molecule (atom (element C) (x -137.64) (y -40.36) (tag A0)) (atom (element C) (x -95.64) (y -40.36) (tag A1)) (atom (element O) (x -53.64) (y -40.36) (tag A2)) (bond (tag A0) (tag A1)) (bond (tag A1) (tag A2)))

This molecule has 3 atoms and 2 bonds.

2 Procedures

2.1 Stopping

2.1.1 quit

(quit) End the program.

2.1.2 exit

(exit) Alias for quit.

2.1.3 quit-on-error

(quit-on-error t-or-f)

/t-or-f/: boolean

Indicate that the program should end after any error.

2.2 Flow Control

2.2.1 begin

(begin s-expressions)

/s-expressions/: ...

Evaluate one more more statements. Return the return-value of the last one.

2.2.2 wait-for-click

(wait-for-click) Stop the script until the user clicks on the main window of the GUI.

2.3 Selection

2.3.1 select-all

(select-all) Select all atoms in the scratch area.

2.3.2 unselect-all

(unselect-all) Unselect all atoms in the scratch area.

2.3.3 select-by-atomic-number

(select-by-atomic-number atomic-number)

atomic-number/: integer Select all atoms with atomic number of /atomic-number in the scratch area.

2.4 Deleting

2.4.1 delete-selected

(delete-selected) Delete selected atoms from the scratch area.

2.4.2 clear

(clear) Delete all atoms and bonds in the scratch area.

2.5 Conversion

2.5.1 sexp->mol

(sexp->mol molecule)

/molecule/: (molecule ...)

Interpret an s-expression molecule and place it in the scratch area.

2.5.2 mol->sexp

(mol->sexp) Turn the molecule in the scratch area into an s-expression.

2.5.3 sexp->format

(sexp->format molecule format)

/molecule/: (molecule ...)
format/: "string" Convert an s-expression molecule into an external format. /format should be a string that will be recognized by Open Babel's /obConversion.FindFormat/, such as "cml" or "smiles". format can also be "dia".

2.5.4 format->sexp

(format->sexp data format)

/data/: "string"
format/: "string" Convert an external format into an s-expression molecule. /format should be a string that will be recognized by Open Babel's /obConversion.FindFormat/.

2.5.5 sexp->name

(sexp->name molecule)

/molecule/: (molecule ...)

Run smormo-namer on an s-expression molecule, return a list of possible names for the molecule.

2.6 Hydrogens

2.6.1 strip-hydrogens

(strip-hydrogens molecule selected-only)

/molecule/: (molecule ...)
selected-only/: boolean Remove Hydrogen atoms from an s-expression molecule. If /selected-only is #t, only remove Hydrogen atoms that are bonded to atoms that are selected.

2.6.2 add-hydrogens

(add-hydrogens molecule selected-only)

/molecule/: (molecule ...)
selected-only/: boolean Add Hydrogen atoms to an s-expression molecule. The number of Hydrogens added depends on the valence of the other atoms. If /selected-only is #t, only bond Hydrogens to atoms that are selected.

2.7 Input and Output

2.7.1 read

(read) Read and return an s-expression from stdin.

2.7.2 display

(display s-expressions)

/s-expressions/: ...

Print one or more s-expressions to stdout.

2.7.3 newline

(newline) Send a newline character to stdout.

2.7.4 load-molecule-file

(load-molecule-file filename)

/filename/: "string"

Read a molecule from a file on disk. The format will be determined by the extension on the filename. This procedure is disabled in cgi mode.

2.7.5 save-molecule-file

(save-molecule-file molecule filename)

/molecule/: (molecule ...)
/filename/: "string"

Save an s-expression molecule to a file on disk. The format will be determined by the extension on the filename. This procedure is disabled in cgi mode.

display-style/: "string" Set the display style of selected atoms in the scratch area. /display-style should be one of "normal" (draw letters), "condensed" (CH), "implied" (lines only) or "nonring" (lines for Carbons in a ring, letters for the rest).

2.9.2 set-electron-display-style

(set-electron-display-style electron-display-style)

electron-display-style/: "string" Set the electron display style for selected atoms in the scratch area. /electron-display-style should be one of "normal" (use default), "show" or "hide".