BFEE2.commonTools¶

BFEE2.commonTools.commonSlots¶

BFEE2.commonTools.commonSlots.openFileDialog(fileType, lineEdit)[source]¶

return a openFile function that opens special type of files: the openFile dialog is connected with a lineEdit widget

Parameters

fileType (str) – the file type for opening
lineEdit (QLineEdit) – the QLineEdit that connects to the QFileDialog

Returns

slot function opening special type of files

Return type

function obj

BFEE2.commonTools.commonSlots.openFilesDialog(fileType, listWidget)[source]¶

return a openFile function that opens a series of files: the openFile dialog is connected with a QListWidget

Parameters

fileType (str) – the file type for opening
listWidget (QListWidget) – the QListWidget that connects to the QFileDialog

Returns

slot function opening a series of files

Return type

function obj

BFEE2.commonTools.fileParser¶

exception BFEE2.commonTools.fileParser.SelectionError(arg)[source]¶: Bases: RuntimeError

class BFEE2.commonTools.fileParser.fileParser(topFile, coorFile='')[source]¶

Bases: object

topology and coordinate parser, this class implements basic method for the topology and coordinate file, used by BFEE

centerSystem()[source]¶: move all the atoms in the loaded file, such that the center of system be (0,0,0)

getResid(selection)[source]¶

return a string listing the resid of the selection: may be used to generate amber masks

Parameters: selection (str) – MDAnalysis selection
Raises: SelectionError – if the selection corresponds to nothing
Returns: a list of resid, e.g. (4,5,6,7,8,9,10)
Return type: str

measureCenter(selection)[source]¶

mimic vmd measure center

Parameters: selection (str) – selection of atoms
Raises: SelectionError – if the selection corresponds to nothing
Returns: (x, y, z)
Return type: np.array (3, float)

measureDistance(selection1, selection2)[source]¶

measure the distance between the center of mass: of two atom groups

Parameters

selection1 (str) – selection of atom group 1
selection2 (str) – selection of atom group 2

Returns

distance between the center of mass of the two atom groups

Return type

float

measureMinmax(selection)[source]¶

mimic VMD measure minmax

Parameters: selection (str) – selection of atoms
Raises: SelectionError – if the selection corresponds to nothing
Returns: ((minX, minY, minZ), (maxX, maxY, maxZ))
Return type: np.array (2*3, float)

measurePBC()[source]¶

measure periodic boundary condition of the file

Returns: ((lengthX, lengthY, lengthZ), (centerX, centerY, centerZ))
Return type: np.array (2*3, float)

measurePolarAngles(selectionPro, selectionLig)[source]¶

calculation the polar angles based on selectionPro and selectionLig

Parameters

selectionPro (str) – selection of the host molecule
selectionLig (str) – selection of the ligand molecule

Returns

(theta, phi) in degrees

Return type

np.array (2, float)

moveSystem(moveVector)[source]¶

move all the atoms in the loaded file

Parameters: moveVector (np.array, 3, float) – the vector of moving

rotateSystem(axis, degrees)[source]¶

rotate all the atoms in the loaded file

Parameters

axis (str) – ‘x’ or ‘y’ or ‘z’
degrees (float) – degrees to move by

saveFile(selection, targetPath, targetType, saveTop=False, topPath='')[source]¶

save the coordinate file to the target type: this function cannot really ‘save’ the topology file, it can only copy the original topology to the target path

Parameters

selection (str) – selection of atoms to save
targetPath (str) – path for the coor file to be saved
targetType (str) – type of the coor file (pdb, xyz)
saveTop (bool) – whether the topology file will be saved. Defaults to False.
topPath (str, optional) – path for the topology file to be saved. Defaults to ‘’.

Raises

SelectionError – if the selection corresponds to nothing

saveNDX(selections, names, targetPath, nonHydrogen=True)[source]¶

save an ndx file, including the selections

Parameters

selections (list of str) – the selections for the ndx file
names (list of str) – the name in ndx of each selection
targetPath (str) – path for the file to be saved
nonHydrogen (bool, optional) – whether only non-H atoms are considered. Defaults to True.

Raises

SelectionError – if the selection corresponds to nothing

setBeta(selection, beta)[source]¶

set beta for the selected atoms

Parameters

selection (str) – selection of atoms to change beta
beta (int) – beta value

Raises

SelectionError – if the selection corresponds to nothing

BFEE2.commonTools.ploter¶

BFEE2.commonTools.ploter.calcRMSD(inputArray)[source]¶

calculate RMSD of a np.array with respect to (0,0,0,…0)

Parameters: inputArray (1D np.array) – the input array
Returns: RMSD of a np.array with respect to (0,0,0,…0)
Return type: float

BFEE2.commonTools.ploter.mergePMF(pmfFiles)[source]¶

merge several PMF files

Parameters: pmfFiles (list of np.arrays) – list of 1D pmfs
Returns: merged PMF if the PMFs overlap, pmfFiles[0] otherwise
Return type: np.array (N * 2)

BFEE2.commonTools.ploter.parseHistFile(histPath)[source]¶

parse a hist.czar.pmf file and return frame-RMSD list

Parameters: histPath (str) – path to a hist.czar.pmf file
Returns: time evolution of RMSD with respect to zero array
Return type: 1D np.array

BFEE2.commonTools.ploter.plotConvergence(rmsdList)[source]¶

plot the time evolution of PMF rmsd

Parameters: rmsdList (list or 1D np.array, float) – time evolution of RMSD with respect to zero array

BFEE2.commonTools.ploter.plotPMF(pmf)[source]¶

plot a pmf

Parameters: np.array (pmf) – pmf to be plotted

BFEE2.commonTools.ploter.readFrame(input)[source]¶

read a frame of Colvars hist file and calculate its RMSD with respect to zero array

Parameters: input (python file object) – input object
Returns: RMSD with respect to zero array
Return type: float

BFEE2.commonTools.ploter.readPMF(pmfFile)[source]¶

read a 1D namd PMF file

Parameters: pmfFile (str) – path to the pmf File
Returns: 1D PMF
Return type: np.array (N * 2)

BFEE2.commonTools.ploter.writePMF(pmfFile, pmf)[source]¶

write a 1D namd PMF file

Parameters

pmfFile (str) – path to the pmf File
np.array (pmf) – pmf to be written