.\" Man page for FressSASA
.TH freesasa 1 "2017" "2.1.2" "FreeSASA man page"
.SH NAME
FreeSASA \- calculate Solvent Accessible Surface Areas from PDB files
.SH SYNOPSIS
.B freesasa \fIPDB\-FILE\fR ... [ \-\-\fBshrake\-rupley\fR | \-\-\fBlee\-richards\fR
    \fB\-\-probe\-radius=\fR\fINUMBER\fR
    \fB\-\-resolution=\fR\fIINTEGER\fR \fB\-\-n\-threads=\fR\fIINTEGER\fR
    \fB\-\-radius\-from\-occupancy\fR | \fB\-\-config\-file=\fR\fIFILE\fR | \fB\-\-radii=\fR\fBprotor\fR|\fBnaccess\fR
    \fB\-\-separate\-models\fR | \fB\-\-join\-models\fR
    \fB\-\-hetatm\fR \fB\-\-hydrogen\fR
    \fB\-\-separate\-chains\fR | \fB\-\-chain\-groups=\fR\fISTRING\fR ...
    \fB\-\-unknown=\fR\fBguess\fR|\fBskip\fR|\fBhalt\fR
    \fB\-\-cif
    \fB\-\-output=\fR\fIFILE\fR \fB\-\-error-file=\fR\fIFILE\fR \fB\-\-no\-warnings\fR
    \fB\-\-select=\fR\fISTRING\fR ...
    \fB\-\-format=\fR\fBlog\fR|\fBres\fR|\fBseq\fR|\fBpdb\fR|\fBrsa\fR|\fBxml\fR|\fBjson\fR ...
    \fB\-\-depth\fR=\fBstructure\fR|\fBchain\fR|\fBresidue\fR|\fBatom\fR ]
.sp
.B freesasa
[\fIoptions\fR] < \fIPDB-FILE\fR
.sp
.B freesasa
(\fB\-\-help\fR | \fB\-\-version\fR | \fB\-\-deprecated\fR)
.sp

.SH DESCRIPTION
Calculate the Solvent Accessible Surface Area (SASA) of biomolecules from PDB files using either Lee & Richards' or Shrake & Rupley's algorithms.

Report bugs to:
.UR
https://github.com/mittinatten/freesasa/issues
.UE

Home page:
.UR
http://freesasa.github.io
.UE


.SH OPTIONS

.SS Parameters
.TP
.BR  \-S ", " \-\-shrake-rupley
Use Shrake & Rupley algorithm
.TP
.BR  \-L ", " \-\-lee-richards
Use Lee & Richards algorithm [default]
.TP
.BR \-p ", " \-\-probe\-radius " " \fINUMBER\fR
Set probe radius in Angstroms [default: 1.40 Å]
.TP
.BR -n ", " \-\-resolution " " \fIINTEGER\fR
Set resolution for calculation.
  S&R: number of test points/atom [default: 100],
  L&R: slices/atom [default: 20].
.TP
.BR -t ", " \-\-n\-threads " " \fIINTEGER\fR
Number of threads to use [default: 2]

.SS Atom radii and classes (maximum one of the following)
.TP
.BR \-O ", " \-\-radius\-from\-occupancy
Read atomic radii from Occupancy in PDB input
.TP
.BR \-c ", " \-\-config\-file " " \fIFILE\fR
Clasifier to determine radii and classes. Example files in 'share/'
.TP
.BR \-\-radii " " protor|naccess
Use either ProtOr or NACCESS radii and classes [defatul: protor]

.SS Input options
.TP
.BR \-\-cif
Input is in mmCIF format
.TP
.BR \-H ", " \-\-hetatm
Include HETATM entries from input
.TP
.BR \-Y ", " \-\-hydrogen
Include hydrogen atoms, suppress warnings with -w
.TP
.BR \-m ", " \-\-join\-models
Join all MODELs in input into one structure
.TP
.BR \-C ", " \-\-separate-chains
Calculate SASA for each chain separately
.TP
.BR \-M ", " \-\-separate-models
Calculate SASA for each MODEL separately
.TP
.BR \-\-unknown " " guess|skip|halt
When unknown atom is encountered, either guess its radius/class, skip it, or halt. [default: guess]
.TP
.BR \-g ", " \-\-chain\-groups " " \fILIST\fR
Each group will be treated separately.
.IP
Examples:
  '-g A', '-g A+B', '-g A -g B', '-g AB+CD'

.SS Output options
.TP
.BR \-w ", " \-\-no\-warnings
Skip most warnings
.TP
.BR \-o ", " \-\-output " " \fIFILE\fR
Output file
.TP
.BR \-e ", " \-\-error\-file " " \fIFILE\fR
Redirect errors and warnings to file
.TP
.BR -f ", " \-\-format " " log|res|seq|pdb|rsa|cif|xml|json
Output format, can be repeated. [default: log]
.TP
.BR -d ", " \-\-depth " " structure|chain|residue|atom
Depth of JSON and XML output [default: chain]
.TP
.BR \-\-select " " \fICOMMAND\fR
Select atoms using Pymol select syntax, can be repeated.
.IP
Examples:
  \-\-select "AR, resn ala+arg", \-\-select "chain_A, chain A"
.SS Deprecated
.PP
These options have been replaced and will disappear in later versions
.TP
.BR  \-\-rsa
Equivalent to \-\-format=rsa
.TP
.BR \-B  ", " \-\-print\-as\-B\-values
Equivalent to \-\-format=pdb
.TP
.BR \-r ", " \-\-foreach\-residue\-type
Equivalent to \-\-format=res
.TP
.BR \-R ", " \-\-foreach\-residue
Equivalent to \-\-format=seq
.TP
.BR \-l ", "  \-\-no\-log
Log suppressed if other format selected. Option has no effect.