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SimFRET-0.0.1
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مشاهده بیشترتوضیحات
A Python package to simulate FRET experiments.
| ویژگی | مقدار |
|---|---|
| سیستم عامل | OS Independent |
| نام فایل | SimFRET-0.0.1 |
| نام | SimFRET |
| نسخه کتابخانه | 0.0.1 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Diego Kleiman |
| ایمیل نویسنده | diegokleiman@hotmail.com |
| آدرس صفحه اصلی | https://github.com/diegoeduardok/SimFRET |
| آدرس اینترنتی | https://pypi.org/project/SimFRET/ |
| مجوز | - |
# SimFRET
A Python package to simulate FRET experiments.
## Installation
The easiest way is through conda:
```
$ conda create --name SimFRET --file simfret.yml
```
## Usage
There are four modules (`simulate.py`, `suggest.py`, `overlap.py`, `compute.py`). <br>
- `simulate.py` runs a quick simulation using the SMOG potential. Input files for this module can be obtained through the [SMOG Webtool](http://smog-server.org/cgi-bin/GenTopGro.pl). <br>
- `suggest.py` suggests pairs of residues for FRET dye attachment. <br>
- `overlap.py` overlaps the dyes to the macromolecule (some dye molecules are already available under the folder dyes). <br>
- `compute.py` computes the FRET efficiency (ignoring frames where dye atoms are superimposed with the macromolecule). <br>
Note: `simulate.py` and `suggest.py` are not necessary if the molecule under study has already been simulated and the places where FRET dyes are attached are known. <br>
### simulate.py
```
usage: simulate.py [-h] -ref REF -top TOP [-p PREFIX] [-dt TIMESTEP]
[--nsteps NSTEPS] [--nstxout NSTXOUT] [--nstlog NSTLOG]
[--nstdcdout NSTDCDOUT] [--gamma GAMMA] [-t TEMP]
[--rcutoff RCUTOFF]
Run fast simulations with the SMOG potential.
optional arguments:
-h, --help show this help message and exit
-ref REF Structure file (.gro) from SMOG/SOMG2.
-top TOP Topology file (.top) from SMOG/SOMG2.
-p PREFIX, --prefix PREFIX
Output files' prefix (default SMOG).
-dt TIMESTEP, --timestep TIMESTEP
Simulation timestep in ps (default 2 fs).
--nsteps NSTEPS Number of simulation steps (defaul 50000).
--nstxout NSTXOUT Interval to save checkpoint (default 10000 steps).
--nstlog NSTLOG Interval to save energy information (default 1000
steps).
--nstdcdout NSTDCDOUT
Interval to save simulation frames (default 1000
steps).
--gamma GAMMA Friction factor for Langeving integrator in ps^-1
(default 1/ps).
-t TEMP, --temperature TEMP
Simulation temperature. Not physical temperature
(default 75 K).
--rcutoff RCUTOFF Cutoff for nonbonded interactions in nm (default 1.5
nm).
Output: <prefix>_settings.txt, <prefix>_traj.dcd, <prefix>_checkpoint.chk,
<prefix>_energy.log
```
### suggest.py
```
usage: suggest.py [-h] -r REF -t TRAJ [-c CONSTRAINT] [-p PREFIX]
Suggest residues to place FRET dyes.
optional arguments:
-h, --help show this help message and exit
-r REF, --ref REF Structure file (any format accepted by MDAnalysis).
-t TRAJ, --traj TRAJ Trajectory file (any format accepted by MDAnalysis).
-c CONSTRAINT, --constraint CONSTRAINT
Maximum distance admitted for the dyes (Å).
-p PREFIX, --prefix PREFIX
Output files' prefix.
Output: <prefix>_residues.txt
```
### overlap.py
```
usage: overlap.py [-h] -r REFERENCE -d DONOR STRUCTURE -dt DONOR TRAJ -a
ACCEPTOR STRUCTURE -at ACCEPTOR TRAJ [-rd DONOR RES]
[-ra ACCEPTOR RES] [-p PREFIX]
Anchor FRET dyes to reference molecule. (This script is intended to visualize
dye docking only.)
optional arguments:
-h, --help show this help message and exit
-r REFERENCE, --ref REFERENCE
Structure file for reference molecule.
-d DONOR STRUCTURE, --donor DONOR STRUCTURE
Structure file for donor dye.
-dt DONOR TRAJ, --donor_traj DONOR TRAJ
Trajectory file for donor dye.
-a ACCEPTOR STRUCTURE, --acceptor ACCEPTOR STRUCTURE
Structure file for acceptor dye.
-at ACCEPTOR TRAJ, --acceptor_traj ACCEPTOR TRAJ
Trajectory file for acceptor dye.
-rd DONOR RES, --residue_donor DONOR RES
Residue index to attach donor dye. If this flag is
set, --residue_acceptor must also be set.
-ra ACCEPTOR RES, --residue_acceptor ACCEPTOR RES
Residue index to attach acceptor dye. If this flag is
set, --residue_donor must also be set.
-p PREFIX, --prefix PREFIX
Output files' prefix.
Output: <prefix>_donor_fitted.pdb, <prefix>_acceptor_fitted.pdb,
<prefix>_alignment_donor.dcd, <prefix>_alignment_acceptor.dcd
```
### compute.py
```
usage: compute.py [-h] -r REF STRUCTURE [-rt REF TRAJ] [-s N] -d DONOR
STRUCTURE -dt DONOR TRAJ -a ACCEPTOR STRUCTURE -at ACCEPTOR
TRAJ -rd DONOR RES -ra ACCEPTOR RES -R0 R0
[-avg {static,isotropic,dynamic}] [--burst {0,1}]
[--burst_threshold BURST_THRESHOLD]
[--burst_decay BURST_DECAY] [-p PREFIX]
Compute FRET efficiency.
optional arguments:
-h, --help show this help message and exit
-r REF STRUCTURE, --ref REF STRUCTURE
Structure file for reference.
-rt REF TRAJ, --ref_traj REF TRAJ
If provided, output will be averaged over trajectory.
All frames are used unless --sample is set.
-s N, --sample N If provided, pick frames from REF TRAJ every N frames.
-d DONOR STRUCTURE, --donor DONOR STRUCTURE
Structure file for donor dye.
-dt DONOR TRAJ, --donor_traj DONOR TRAJ
Trajectory file for donor dye.
-a ACCEPTOR STRUCTURE, --acceptor ACCEPTOR STRUCTURE
Structure file for acceptor dye.
-at ACCEPTOR TRAJ, --acceptor_traj ACCEPTOR TRAJ
Trajectory file for acceptor dye.
-rd DONOR RES, --residue_donor DONOR RES
Residue index to attach donor dye. If this flag is
set, --residue_acceptor must also be set.
-ra ACCEPTOR RES, --residue_acceptor ACCEPTOR RES
Residue index to attach acceptor dye. If this flag is
set, --residue_donor must also be set.
-R0 R0 R0 (Å) for the FRET dyes pair.
-avg {static,isotropic,dynamic}, --averaging_regime {static,isotropic,dynamic}
Averaging regime. Default 'isotropic'.
--burst {0,1} Turn on burst averaging: 0 = no (default), 1 = yes.
--burst_threshold BURST_THRESHOLD
Burst size threshold to use with burst averaging
(default 30).
--burst_decay BURST_DECAY
Burst size decay constant to use with burst averaging
(default 3).
-p PREFIX, --prefix PREFIX
Output files' prefix.
Output: <prefix>_dist.txt, <prefix>_kappa2.txt, <prefix>_insteff.txt
```
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.7.6 | Python |
نحوه نصب
نصب پکیج whl SimFRET-0.0.1:
pip install SimFRET-0.0.1.whl
نصب پکیج tar.gz SimFRET-0.0.1:
pip install SimFRET-0.0.1.tar.gz