4 Command line arguments

4.1 Synopsis

Usage: RunSadic [options] [--] [entity]

entity can be either a file name, a fully qualified URL or a pdbId code. The URL protocol can be file, http or ftp. If a pdbId is specified, the entity is searched by mangling the id with the URL schema specified in the file pdblist.conf. If entity is missing, data are read from stdin. The entity can be compressed in the compress format: in this case it must present a .Z or .z extension.

4.2 Options

--version

show program's version number and exit

-h, --help

show this help message and exit

-d S1 [S2 [...]

, --data S1 [S2 [...]]]
Output the data streams SN. Each SN can be one of the strings:

hv (Hidden volume)
ev (Exposed volume)
hs (Hidden surface)
es (Exposed surface)
di (Depth index)
adi (Average depth index per residue)

Default: di.

--models M1 [M2 [...]

]
Select the models to query. Useful if the entity contains more than one model (MODEL/ENDMDL blocks). Each MN is an integer or an integers range in N1-N2 format. If not specified, query all the models.

-o [PATH]FILENAME.EXT, --output [PATH]FILENAME.EXT

Base name for output files. Many files may be written: one for each model in the entity and for each data stream (option --data). Generate files FILENAME_SN.EXT (if the entity contains one model) or FILENAME_mMN_SN.EXT (if the entity contains many models), where SN is replaced by the symbol of the data stream, and MN by the model serial. By default FILENAME is the entity name, EXT depends from the output format. If PATH is not specified, store files in the current directory.

-f FORMAT, --format FORMAT

Output format. Currently table and pdb are implemented. If FORMAT is table, store a table with the output values, with a sampling point in each row and a column for each sampling radius. If FORMAT is pdb, store a PDB entity with the required data in the tempFactor field. Default: table.

--quiet

Don't emit info messages. If not specified, print info messages on stdout.

4.3 Query options

These options control the points where to sample. At most one of the options --atom-name (default), --serials, --all-atoms and --point can be specified.

--atom-name ATOM: Process every atom with name field ATOM. Default: CA.
--residues R1 [R2 [...]: ]
Only useful with --atom-name: process only atoms named ATOM with resSeq field RN. Each RN is an integer or an integers range in N1-N2 format. If not specified, sample all the residues.
--chains C1 [C2 [...]: ]
Only useful with --atom-name or --all-atoms: process only atoms named ATOM with chainID field CN. Each CN is a letter. If not specified, sample all the chains.
--serials S1 [S2 [...]: ]
Process only atoms with serial field SN. If the entity contains many models, only one model must be selected (through the --models option) and the atoms must be in the selected model.
--all-atoms: Process all the structure atoms. Only ATOM records are processed.
--point X Y Z: Process the point X Y Z in the entity space. Many points can be sampled by selecting this option more than once.

4.4 Sampling options

These options control how the sampling is performed on the selected points.

-r RADIUS, --radius RADIUS: Sampling radius. If not specified, automatically select a radius such that no atom has depth index = 0.
--step STEP: The sampling step size, in Angstroms. If the --cstep is specified, the sampling step in radial direction. If --radius is used too, the program may reduce the step to exactly fit the chosen radius. Default: 1.0.
--cstep STEP: Sampling step along directions orthogonal to the radius, in Angstroms. If not specified, use the value selected with --step.

4.5 Entity options

These options control the entity details.

--probe-radius RADIUS

Approximate the probe with a sphere of radius RADIUS. The approximation is performed by adding RADIUS to the radius of every atom in the model. Default: 1.4.

--atom-radii A1 R1 [A2 R2 [...]

]
Radii for ATOM records. AN is an atom name and RN its radius. User defined values replace or are added to the default mapping. Every atom name in the entity must be specified. Default:

H: 1.000
O: 1.480
N: 1.625
C: 1.700
S: 1.782
P: 1.871

--hetatm

Include HETATM atoms in sampling. A radius for each atom name in the entity HET group must be provided through the --hetatm-radii option.

--hetatm-radii A1 R1 [A2 R2 [...]

]
Radii for HETATM records. AN is an atom name and RN its radius. If a name is not found in this list, its radius is looked for in the --atom-radii list. Every atom name in the entity must be specified. Default:

F: 1.560
CL: 1.735
BR: 1.978
I: 2.094

--solvent S1 [S2 [...]

]
HETATM records with resName SN is a solvent and must not be sampled. Default: H2O WAT SOL HOH DIS.

4.6 Output options

These options control the output details.

--no-totals: If the entity contains more models, don't compute totals. If not specified, store the average and standard deviation of the --data stream SN in files named respectively FILENAME_avg_SN.EXT and FILENAME_std_SN.EXT.
--table-bare: Don't save column and row headers in the output files for --format table. If not specified, the first column will contain the atom serial (or point coordinates) and the first row the sampling radius.
--table-fmt FMT: The format of numbers in output for --format table. Must be a proper floating point placeholder. Default: %.3f.
--table-sep SEP: The separator of numbers in output for --format table. Enter /t for a tab character, // for a single /. Default: /t.