PocketFEATURE Library
Teague Sterling, Tianyun Liu 2013-2014
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pyFEATURE: Wrappers for calling FEATURE binaries from Python
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PocketFEATURE: Implementations of PocketFEATURE scripts and utilities in Python
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FEATUREdb: FEATUREDB Implementation (currently empty)
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data: Includes default background data for PocketFEATURE
- Python 2.7
- BioPython [1.58 or higher]
- Numpy [1.62 or higher]
- SciPy (For BioPython) [0.11.0 or higher]
- sh (For subprocess calling)
- Munkres (for experimental alignment)
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Install Python 2.7 (If needed)
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Install pyFEATURE (Dependencies will be installed)
$ cd pyFEATURE $ python setup.py install $ cd .. -
Install PocketFEATURE (Dependencies will be installed)
$ cd PocketFEATURE $ python setup.py install $ cd ..
Once the installation is complete, the following will give you a quick introduction to using PocketFEAUTRE.
$ cd <pocketfeaturedb directory>
$ run_pf data/1qhx.pdb data/1qrd.pdb \
-b data/background.ff -n data/background.coeffs\
--pymolA=/tmp/1qhx.py --pymolB=/tmp/1qrd.py
$ pymol -l /tmp/1qhx.py &
$ pymol -l /tmp/1qrd.py &
Find or list pockets around ligands and write as either a Pointfile or list of Residues.
Examples:
# List ligands found in PDB
$ pf_extract 1fo4.pdb -l
# Generate pocket around "best" (biggest) ligand with specified PDB
$ pf_extract somepdb.pdb -i 1fo4 -o somepdb.ptf
# Generate pocket around ATP (Full Ligand ID and short)
$ pf_extract 1qhx.pdb 1qhx/0/A/501/ATP
$ pf_extract 1qhx.pdb ATP -o 1qhx-ATP.ptf
Command Usage:
usage: Identify and extract pockets around ligands in a PDB file
[-h] [-i PDBID] [-o PTF] [--log LOG] [-d CUTOFF] [-P] [-R] [-L]
[PDB] [LIG]
positional arguments:
PDB Path to PDB file [default: STDIN]
LIG Ligand ID to build pocket around [default: <largest>]
optional arguments:
-h, --help show this help message and exit
-i PDBID, --pdbid PDBID
PDB ID to use for input structure [default: BEST
GUESS]
-o PTF, --output PTF Path to output file [default: STDOUT]
--log LOG Path to log errors [default: <open file '<stderr>',
mode 'w' at 0x7f05d94f4270>]
-d CUTOFF, --distance CUTOFF
Residue active site distance threshold [default: 6.0]
-P, --print-pointfile
Print point file (default behavior)
-R, --print-residues Print residue ID list instead of point file
-L, --list-only List residues instead of creating pocket
A wrapper around featurize that allows command line arguments to set or override environmental variables
Examples:
$ pf_featurize -P 1qhx-ATP.ptf \
--feature-dir=~/FEATURE/trunk \
--feature-bin=~/FEATURE/trunk \
--pdb-dir=~/db/pdb \
--dssp-dir=~/db/dssp > 1qhx-ATP.ff
Command Usage:
usage: Call featurize in a custom environment [-h] [-P [POINTILE]]
[-n [SHELLS]] [-w [WIDTH]]
[-x [HETATMS]]
[-l [PROPERTYFILE]]
[-s [SEARCH_DIR]]
[--feature-root [FEATURE_ROOT]]
[--feature-dir [FEATURE_DIR]]
[--feature-bin [FEATURE_BIN]]
[--pdb-dir [PDB_DIR]]
[--dssp-dir [DSSP_DIR]]
[PDB]
positional arguments:
PDB
optional arguments:
-h, --help show this help message and exit
-P [POINTILE]
-n [SHELLS]
-w [WIDTH]
-x [HETATMS]
-l [PROPERTYFILE]
-s [SEARCH_DIR]
--feature-root [FEATURE_ROOT]
--feature-dir [FEATURE_DIR]
--feature-bin [FEATURE_BIN]
--pdb-dir [PDB_DIR]
--dssp-dir [DSSP_DIR]
Compute pairwise tanimoto similarities for two FEATURE files based on provided background files.
Examples:
$ pf_compare 1qhx-ATP.ff 1qrd-FAD.ff -b data/background.ff -n data/background.coeffs -o scores
# Default background files are ./background.ff and ./background.coeffs
$ pf_compare1qhx-ATP.ff 1qrd-FAD.ff > 1qhx-ATP-1qrd-FAD.scores
Command Usage:
usage: Compute tanimoto matrix for two FEATURE vectors with a background and score normalizations
[-h] [-b FEATURESTATS] [-n COEFFICIENTS] [-o VALUES] [--log LOG]
FEATUREFILE1 FEATUREFILE2
positional arguments:
FEATUREFILE1 Path to first FEATURE file
FEATUREFILE2 Path to second FEATURE file
optional arguments:
-h, --help show this help message and exit
-b FEATURESTATS, --background FEATURESTATS
FEATURE file containing standard devations of
background [default: background.ff]
-n COEFFICIENTS, --normalization COEFFICIENTS
Map of normalization coefficients for residue type
pairs [default: background.coeffs
-o VALUES, --output VALUES
Path to output file [default: STDOUT]
--log LOG Path to log errors [default: STDERR]
Compute the best alignment of a scores file.
Examples:
# Using defaults (standard greedy alignment and cutoff of -0.15)
$ pf_align 1qhx-ATP-1qrd-FAD.scores -o 1qhx-ATP-1qrd-FAD.aligned
# Cutoff at 0.0
$ cat 1qhx-ATP-1qrd-FAD.scores | pf_align -c 0 > 1qhx-ATP-1qrd-FAD.aligned
Command Usage:
usage: Align scores from a PocketFEATURE score matrix [-h] [-c CUTOFF]
[-s COLINDEX]
[-m ALIGN_METHOD]
[-o VALUES] [--log LOG]
SCOREFILE
positional arguments:
SCOREFILE Path to score file [default: STDIN]
optional arguments:
-h, --help show this help message and exit
-c CUTOFF, --cutoff CUTOFF
Minium score (cutoff) to align [default: -0.15
-s COLINDEX, --score-column COLINDEX
Value column index in score file to use for aligning
[default: 1]
-m ALIGN_METHOD, --method ALIGN_METHOD
Alignment method to use (one of: munkres, greedy)
[default: greedy]
-o VALUES, --output VALUES
Path to output file [default: STDOUT]
--log LOG Path to log errors [default: STDERR]
Create a Pymol script to visualize the alignment.
Examples:
# Assuming default PDB file names, colors and radii
$ pf_vis 1qhx-ATP.ptf 1qrd-FAD.ptf 1qhx-ATP-1qrd-FAD.aligned
# Explictly specifying PDB names
$ pf_vis 1qhx-ATP.ptf 1qrd-FAD.ptf 1qhx-ATP-1qrd-FAD.aligned\
--pdbA=somepdb.pdb --pdbB=../1qrd.pdb
# Overriding colors
$ pf_vis 1qhx-ATP.ptf 1qrd-FAD.ptf 1qhx-ATP-1qrd-FAD.aligned\
--colors=reds.colors\
--A=somepdb.py --B=1qrd.py
# Viewing PyMol scripts
$ pymol -l somepdb.py &
$ pymol -l 1qrd.py &
Command Usage:
usage: Create PyMol scripts to visualize an alignment [-h] [-A CMD1] [-B CMD2]
[--pdbA [PDB1]]
[--pdbB [PDB2]]
[--colors [COLORFILE]]
[--radii [RADIIFILE]]
[--log LOG]
POINTS1 POINTS2
ALIGNMENT
positional arguments:
POINTS1 Path to FEATURE point file
POINTS2 Path to FEATURE point file
ALIGNMENT Path to PocketFEATURE alignment
optional arguments:
-h, --help show this help message and exit
-A CMD1, --outputA CMD1
Path to first command output file
-B CMD2, --outputB CMD2
Path to second command output file
--pdbA [PDB1] Path to first PDB file
--pdbB [PDB2] Path to second PDB file
--colors [COLORFILE] File of 0.0-1.0 RGB colors to use
--radii [RADIIFILE] File of point radii to use
--log LOG Path to log errors [default: <open file '<stderr>',
mode 'w' at 0x7f4e15f61270>]
Run an entire PocketFEATURE calculation, writing out desired intermediate files
Examples:
# Only View alignment and scores (using all defaults)
$ run_pf 1qrd.pdb 1qhx.pdb
# Produce visualization Scripts and override backgrounds
$ run_pf ../PDBA.pdb ../PDBB.pdb \
-b ../background.ff -n ../background.coeffs \
--pymolA=pdba.py --pymolb=pdbb.py
# Save Pointfiles
$ run_pf ../PDBA.pdb ../PDBB.pdb --ptfA=pdba.ptf --ptfB=pdbb.ptf
Command Usage:
usage: Identify and extract pockets around ligands in a PDB file
[-h] [--ligandA [LIGA]] [--ligandB [LIGB]] [-b FEATURESTATS]
[-n COEFFICIENTS] [-d CUTOFF] [-c CUTOFF] [-o ALIGNMENT]
[--ptfA [PTFA]] [--ptfB [PTFB]] [--ffA [FFA]] [--ffB [FFB]]
[--scores [SCORES]] [--pymolA [PYMOLA]] [--pymolB [PYMOLB]] [--log LOG]
PDBA PDBB
positional arguments:
PDBA Path to first PDB file
PDBB Path to second PDB file
optional arguments:
-h, --help show this help message and exit
--ligandA [LIGA] Ligand ID to build first pocket around [default:
<largest>]
--ligandB [LIGB] Ligand ID to build second pocket around [default:
<largest>]
-b FEATURESTATS, --background FEATURESTATS
FEATURE file containing standard devations of
background [default: background.ff]
-n COEFFICIENTS, --normalization COEFFICIENTS
Map of normalization coefficients for residue type
pairs [default: background.coeffs
-d CUTOFF, --distance CUTOFF
Residue active site distance threshold [default: 6.0]
-c CUTOFF, --cutoff CUTOFF
Minium score (cutoff) to align [default: -0.15
-o ALIGNMENT, --output ALIGNMENT
Path to alignment file [default: STDOUT]
--ptfA [PTFA] Path to first point file [default: None]
--ptfB [PTFB] Path to second point file [default: None]
--ffA [FFA] Path to first FEATURE file [default: None]
--ffB [FFB] Path to second FEATURE file [default: None]
--scores [SCORES] Path to scores file [default: None]
--pymolA [PYMOLA] Path to first PyMol script [default: None]
--pymolB [PYMOLB] Path to second PyMol script [default: None]
--log LOG Path to log errors [default: <open file '<stderr>',
mode 'w' at 0x7f5e988d9270>]