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Chapter 9. Command line options
The following command line options are legal:
volsurf [-o filename.vol | -c commandfile] [-q]
VolSurf program can be started simply typing its named in any shell window with no argument.
volsurf |
This will start the GUI (Graphic User Interface) of VolSurf. This GUI contains menu panes, dialog windows, etc... which can be used to access all the VolSurf functionality.
Advanced Users can use the command line options to accelerate the opening of data files:
volsurf -o filename.vol |
VolSurf offers the possibility to run the program without GUI, by providing a command file that describes the structures or fields to import and the computations to be done. The syntax to run VolSurf using a command file is as follows:
volsurf -c commandfile -q |
The optional -q argument produces VolSurf to run in quiet mode, without producing any output on the screen. Otherwise, the program dumps to the standard output the messages that are usually presented in the screen when the GUI is activated.
The syntax of the command file is described in the next section.
9.1. Command file syntax
Command files are plain ASCII text organised in lines. Lines starting with the dash (#) character and empty lines are ignored. The order of the lines is irrelevant.
The command file must provide at least the name and type of the input structures or fields used for the computations and the name and type of the output written to disk. For all the rest of the information, VolSurf has default values defined, that can be changed with the appropriate commands.
Correct commands in VolSurf command files are:
common
input file <filename> input list <listname> output GOLPE <filename> output ASCII <filename> probes [OH2 |DRY |BOTH|O |O:: |N1 |N:= |N3+ |O- ] scaling [raw|auto]
applicable to structures
grid spacing [REAL_VALUE] import series [mmol2|mol2|kout|sdf] save KONT [yes|no]
applicable to fields
import fields [kont|dat]
special
activity file <filename> <pKno|pKmilli|pKmicro|pKnano> [names] model library <path> project [INTEGER_VALUE] [REAL_VALUE] [pca|pls] sdflabel [TEXT_STRING] volsurf <filename>
Commands should appear as written above. Capitalisation do matters. There should be just one space in between the command and the arguments and in between the different words composing the name of the command. The use of tabs is discouraged.
Note that probes identifiers have to be made of exactly four characters using spaces as filling characters. An extra space has to be used as separator if you have more than one probe.
Defaults are:
import series mol2 probes OH2 DRY save KONT no grid spacing 0.5 scaling auto volsurf output.vol |
9.2. Command file examples
In the following, there are some examples of command files and the explanation of their mode of action. The commented examples, the molecules and the activity files needed are fully reported in the tutor/command_line_tutorial distribution directory.
import series mol2 save KONT yes scaling raw grid spacing 0.5 output GOLPE set00.dat input list set00.lst volsurf set00.vol |
This command file will read the mol2 files, whose names are listed in file set00.lst and process all of them, running first GRID with probes OH2 and DRY (the default) and a grid spacing of 0.5 Å and then processing the output in VolSurf. The kont files will be kept in disk. The resulting descriptors will be saved both in VolSurf format as set00.vol and in GOLPE format in file set00.dat. The scaling will be RAW.
import fields kont probes OH2 DRY N1 input file file00.kont output ASCII file00.txt |
This command file will read the kont file file00.kont. The fields described inside are assumed to be of type OH2 DRY and N1, as defined by command probe. The file will be processed and the resulting VolSurf variables will be written in ASCII format to file file00.txt
import series sdf sdflabel MOLNAME probes OH2 DRY input file cpd32.sdf output ASCII cpd32.txt |
This command file will read the file in format SDFile cpd32.sdf. The structures described inside will be read one by one and processed by GRID, using probes OH and DRY, and the default 0.5 Å grid spacing. The file will be processed and the resulting VolSurf variables will be written in ASCII format to file cpd32.txt
input list l20.lst import series mol2 output GOLPE l20.dat scaling raw volfurf l20.vol model library /usr/volsurf/models save KONT no project 4 0.7 pls activity file l20.txt pKno names |
This command file will generate VolSurf descriptors for mol2 structures listed in l20.lst. The GOLPE output will be in RAW format. The structures will be projected on the fourth model (a pls model) in the library directory (i.e. /usr/volsurf/models). The activity file will be l20.txt and no transformations on the activity scale will be performed. Structure names are present in the activity file.
9.3. Commands description
- input file <filename>, input list <listname>
These two commands define the input. The input can be either a file containing the actual structure/field (input file) or a file containing a list of files names (input list). The argument should be the name of an existing file of the type specified.
- output GOLPE <filename>, output ASCII <filename>
These two commands define the output. The VolSurf variables can be written in either GOLPE or ASCII format as defined by the name of the command. The argument should be a correct file name, according to UNIX syntax rules.
- probes [OH2 | DRY | BOTH| O | O:: | N1 | N:= | N3+ | O- ]
When importing structures, this command defines the probes used to run GRID. When importing fields, this command describes the probes used by GRID when these fields were generated. In the latter case, VolSurf will not check the correctness of the information provided. For example, if the number of fields included in the file are smaller than the number of probes, results can be undefined.
The arguments of the command are any number of probe names from the above list. The command should have at least one argument and a maximum of five. No other probe names should be used. The probes names should be written in capitals, separated by a single space and made of exactly four characters (i.e. "DRY " has to be used instead of "DRY").
The default is:
probes OH2 DRY
- scaling [auto|raw]
This directive tells VolSurf whether to apply AUTO or RAW scaling to VolSurf descriptors.
Use RAW scaling if your output is intended to be projected on an external model or, in general, when you want to export the VolSurf descriptors as is
AUTO scaling is the default setting.
- grid spacing [REAL_VALUE]
This command defines the grid spacing to apply in the GRID calculations performed by VolSurf. It is not required when importing fields.
The argument is a single real number larger than 0.0 and preferably in between 0.1 and 1.0 Å.
The default is:
grid spacing 0.5
- import series [mmol2 | mol2 | kout | sdf], import fields [kont | dat]
These commands informs VolSurf that the input file or list contains structures (import series) of type multi-mol2, mol2, kout or SDFile, or fields (import fields) of type kont or GOLPE. VolSurf will not check for the correctness of the information provided, and therefore, if the format of the input file does not correspond an error will be obtained.
Please notice that mol2 and kout file describe one single structure, while SDFiles can describe one or, more often, many structures. While it is possible to import lists with many mol2 or kout files, it is not possible to import lists of SDFiles or multi-mol2 files.
The argument is one of the keywords provided, separated from the command name by a single space.
The default is:
import series mol2
- save KONT [yes|no]
This command determines if the the kont files obtained during GRID computations have to be removed from disk or not. It is not required when importing fields.
The default is:
save KONT no
- activity file <filename> [pKno | pKmilli | pKmicro | pKnano] [names]
This command imports activity values from the specified file; logaritmic transformations may be applied using one of the pKs modifiers; is molecules names are present in the file the "names" directive has to be used.
- model library <path>
This command set the path for the models library you will use with the project command.
- project [INTEGER_VALUE] [REAL_VALUE] [pca|pls]
This command will select the n-th model (specified by the integer value) in the current model library directory (remember to use the command model library to set the path), then it will compute VolSurf descriptors using the same probes of the selected model with the grid spacing supplied by the real value. It will produce three output files, namely TMPRED0000.dat, TMPRED0000.dat.VarNames, TMPRED0000.dat.VarType
- sdflabel [TEXT_STRING]
When importing series from SDFiles, the name given to the objects is expected to be provided under a field labelled appropriately. The name of this label can be provided using this command, i.e. the command
sdflabel MOLNAME
will make VolSurf to look for the object name in a field called "<MOLNAME>" within the SDFile.
If no sdflabel command is present, the program will assume the first line of the SDFile, for each structure, to be the name of the object. If not found VolSurf will, in any case, provide a object name based in sequential numbers.
This command is ignored if the format of the input file is other than SDFile format.
- volsurf <filename>
This command defines the name given to the VolSurf .vol file generated during computations. This file is always written and can be opened after the computations were completed using the GUI, in order to review or process the results.
The argument can be any correct file name, according to UNIX syntax rules, but it is advisable to use the extension .vol.
The default is:
volsurf output.vol
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