BFEE2.inputGenerator

exception BFEE2.inputGenerator.DirectoryExistError(arg)

Bases: RuntimeError

exception BFEE2.inputGenerator.FileTypeUnknownError(arg)

Bases: RuntimeError

class BFEE2.inputGenerator.inputGenerator

Bases: object

generate all the inputs and define corresponding slots

generateGromacsGeometricFiles(path, topFile, pdbFile, ligandOnlyTopFile, ligandOnlyPdbFile, selectionPro, selectionLig, selectionSol='resname TIP3* or resname SPC*', temperature=300.0)

generate all the input files for Gromacs Geometric simulation

This function is based on BFEEGromacs.py contributed by Haochuan Chen (yjcoshc_at_mail.nankai.edu.cn)

Parameters

• path (str) – the directory for generation of all the files

• topFile (str) – the path of the topology (top) file

• pdbFile (str) – the path of the coordinate (pdb) file

• ligandOnlyTopFile (str) – the path of the ligand-only topology (top) file

• ligandOnlyPdbFile (str) – the path of the ligand-only coordinate (pdb) file

• selectionPro (str) – MDAnalysis-style selection of the protein

• selectionLig (str) – MDAnalysis-style selection of the ligand

• selectionSol (str, optional) – MDAnalysis-style selection of the solvent. Defaults to ‘resname TIP3* or resname SPC*’.

• temperature (float, optional) – Temperature of the simulation. Defaults to 300.0.

Raises

DirectoryExistError – when {path}/BFEE exists

generateNAMDAlchemicalFiles(path, topFile, coorFile, forceFieldType, forceFieldFiles, temperature, selectionPro, selectionLig, stratification=[1, 1, 1, 1], doubleWide=False, minBeforeSample=False, membraneProtein=False, neutralizeLigOnly='NaCl', pinDownPro=True, vmdPath='')

generate all the input files for NAMD alchemical simulation

Parameters

• path (str) – the directory for generation of all the files

• topFile (str) – the path of the topology (psf, parm) file

• coorFile (str) – the path of the coordinate (pdb, rst7) file

• forceFieldType (str) – ‘charmm’ or ‘amber’

• forceFieldFiles (list of str) – list of CHARMM force field files

• temperature (float) – temperature of the simulation

• selectionPro (str) – MDAnalysis-style selection of the protein

• selectionLig (str) – MDAnalysis-style selection of the ligand

• stratification (list of int, 8, optional) – number of windows for each simulation. Defaults to [1,1,1,1].

• doubleWide (bool, optional) – whether double-wide simulations are carried out. Defaults to False.

• minBeforeSample (bool, optional) – minimization before sampling in each FEP window. Defaults to False.

• membraneProtein (bool, optional) – whether simulating a membrane protein. Defaults to False.

• neutralizeLigOnly (str or None, optional) – ‘NaCl’, ‘KCl’, ‘CaCl2’ or None. neutralize the lig-only system using the salt. Defaluts to NaCl.

• pinDownPro (bool, optional) – whether pinning down the protien. Defaults to True.

• vmdPath (str, optional) – path to vmd. Defaults to ‘’.

generateNAMDGeometricFiles(path, topFile, coorFile, forceFieldType, forceFieldFiles, temperature, selectionPro, selectionLig, selectionRef='', userProvidedPullingTop='', userProvidedPullingCoor='', stratification=[1, 1, 1, 1, 1, 1, 1, 1], membraneProtein=False, neutralizeLigOnly='NaCl', pinDownPro=True, parallelRuns=1, vmdPath='')

generate all the input files for NAMD geometric simulation

Parameters

• path (str) – the directory for generation of all the files

• topFile (str) – the path of the topology (psf, parm) file

• coorFile (str) – the path of the coordinate (pdb, rst7) file

• forceFieldType (str) – ‘charmm’ or ‘amber’

• forceFieldFiles (list of str) – list of CHARMM force field files

• temperature (float) – temperature of the simulation

• selectionPro (str) – MDAnalysis-style selection of the protein

• selectionLig (str) – MDAnalysis-style selection of the ligand

• selectionRef (str, optional) – MDAnalysis-style selection of the reference group for pulling simulation, by default, this is the protein. Defaults to ‘’.

• userProvidedPullingTop (str, optional) – user-provided large solvation box for pulling simulation. Defaults to ‘’.

• userProvidedPullingCoor (str, optional) – user-provided large solvation box for pulling simulation. Defaults to ‘’.

• stratification (list, optional) – number of windows for each simulation. Defaults to [1,1,1,1,1,1,1,1].

• membraneProtein (bool, optional) – whether simulation a membrane protein. Defaults to False.

• neutralizeLigOnly (str or None, optional) – ‘NaCl’, ‘KCl’, ‘CaCl2’ or None. neutralize the lig-only system using the salt. Defaluts to NaCl.

• pinDownPro (bool, optional) – whether pinning down the protien. Defaults to True.

• parallelRuns (int, optional) – generate files for duplicate runs. Defaults to 1.

• vmdPath (str, optional) – path to vmd. Defaults to ‘’.