continuousflex.protocols.protocol_genesis module

class continuousflex.protocols.protocol_genesis.ProtGenesis(**kwargs)

Bases: pwem.protocols.protocol.EMProtocol

Protocol to perform MD simulation using GENESIS.

convertInputEMStep()

Convert EM data step :return None:

convertInputPDBStep()

Convert input PDB step. Generate topology files and copy input PDB files :return None:

convertInputVol(fnInput, volPrefix)

Convert input volume data :param str fnInput: input volume file name :param str volPrefix: ouput volume prefix :return None:

convertReusOutputDcd()

createGenesisInputFile(inputPDB, outputPrefix, indexFit)

Create INP input file for GENESIS :param str inputPDB: input PDB file name :param str outputPrefix: output prefix :param int indexFit: index of the simulation :return None:

createOutputStep()

Create output PDB or set of PDBs :return None:

getForceField()

Get simulation forcefield :return int: forcefield

getGenesisCmd(prefix)

Get GENESIS cmd to run :param str prefix: prefix of the simulation :return str : GENESIS commadn to run

getGenesisEnv()

Get environnement for running GENESIS :return Environ: environnement

getInputEMfn()

Get the input EM data file names :return list: list of input EM data file names

getInputEMprefix(index=0)

Get the input EM data prefix of the specified index :param int index: index of the EM data :return str: Input EM data prefix

getInputPDBfn()

Get the input PDB file names :return list : list of input PDB file names

getInputPDBprefix(index=0)

Get the input PDB prefix of the specified index :param int index: index of input PDB :return str: Input PDB prefix

getMPIParams()

Get mpi parameters for the simulation :return tuple: numberOfMpiPerFit, numberOfLinearFit, numberOfParallelFit, numberOflastIter

getNumberOfInputEM()

Get the number of input EM data to analyze :return int : number of input EM data

getNumberOfInputPDB()

Get the number of input PDBs :return int: number of input PDBs

getNumberOfSimulation()

Get the number of simulations to perform :return int: Number of simulations

getOutputPrefix(index=0)

Output prefix of the specified index :param int index: index of the simulation to get :return string : Output prefix of the specified index

getOutputPrefixAll(index=0)

All output prefix of the specified index including multiple replicas in case of REUS :param int index: index of the simulation to get :return list: list of all output prefix of the specified index

getRestartFile(index=0)

Get input restart file :param int index: Index of the simulation :return str: restart file

getRigidBodyParams(index=0)

Get the current rigid body parameters for the specified index in case of EMFIT with iamges :param int index: Index of the simulation :return list: angle_rot, angle_tilt, angle_psi, shift_x, shift_y

runGenesisStep()

Run GENESIS simulations step :return None:

runParallelGenesis()

Run multiple GENESIS simulations in parallel :return None:

runParallelGenesisRBFitting()