Metadata-Version: 2.1
Name: SimFRET
Version: 0.0.1
Summary: A Python package to simulate FRET experiments.
Home-page: https://github.com/diegoeduardok/SimFRET
Author: Diego Kleiman
Author-email: diegokleiman@hotmail.com
License: UNKNOWN
Description: # 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
        ```
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.7.6
Description-Content-Type: text/markdown
