BFEE2.commonTools

BFEE2.commonTools.commonSlots

BFEE2.commonTools.commonSlots.openFileDialog(fileType, lineEdit)

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)

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)

Bases: RuntimeError

BFEE2.commonTools.fileParser.amberToGromacs(parmFile, rstFile, PBC, outputPrefix)

convert a set of Amber files (parm7 + rst7) into the Gromacs format

Parameters:

• parmFile (str) – path of the parm7 file

• rstFile (str) – path of the rst7 file

• PBC (list of flost) – pbc information

• outputPrefix (str) – path + prefix of the output file

BFEE2.commonTools.fileParser.charmmToGromacs(psfFile, pdbFile, prmFiles, PBC, outputPrefix)

convert a set of CHARMM files (psf + pdb + prm + pbc) into the Gromacs format

Parameters:

• psfFile (str) – path of the psf file

• pdbFile (str) – path of the pdb file

• prmFiles (list of str) – pathes of the prm files

• PBC (list of flost) – pbc information

• outputPrefix (str) – path + prefix of the output file

class BFEE2.commonTools.fileParser.fileParser(topFile, coorFile='')

Bases: object

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

centerSystem()

move all the atoms in the loaded file, such that the center of system be (0,0,0)

getResid(selection)

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)

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)

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)

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()

measure periodic boundary condition of the file

Returns:

((lengthX, lengthY, lengthZ), (centerX, centerY, centerZ))

Return type:

np.array (2*3, float)

measurePolarAngles(selectionPro, selectionLig)

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)

move all the atoms in the loaded file

Parameters:

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

rotateSystem(axis, degrees)

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='')

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)

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)

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.fileParser.gromacsToAmber(topFile, groFile, PBC, outputPrefix)

convert a set of Gromacs files (top + gro/pdb) into the Amber format

Parameters:

• topFile (str) – path of the top file

• groFile (str) – path of the gro file

• PBC (list of flost) – pbc information

• outputPrefix (str) – path + prefix of the output file

BFEE2.commonTools.ploter

exception BFEE2.commonTools.ploter.NoCorrectionFileError(arg)

Bases: RuntimeError

BFEE2.commonTools.ploter.calcRMSD(inputArray)

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.correctGaWTM(pmfFile, correctionFile=None)

read a 1D namd PMF file and correct it using cumulant.pmf file

Parameters:

• pmfFile (str) – path to the pmf File

• correctionFile (str, optional) – path to the correction file. If None, will try to find it in the same directory (legacy behavior).

Returns:

1D PMF

Return type:

np.array (N*2)

BFEE2.commonTools.ploter.correctGaWTMHist(histPmfFile, correctionFile, is_hist_correction=True)

Apply GaWTM correction to a History PMF file.

Parameters:

• histPmfFile (str) – path to the history PMF file (.hist.czar.pmf)

• correctionFile (str) – path to the correction file

• is_hist_correction (bool) – True if correction file is history format (.hist.pmf), False if single-frame format (.pmf)

Returns:

list of corrected PMF frames

Return type:

list[np.array]

BFEE2.commonTools.ploter.getGaWTMBaseName(filePath)

Extract the base name from a GaWTM PMF file or its correction file.

For example:

‘path/to/001.czar.pmf’ -> ‘001’ ‘path/to/001.reweightamd1.cumulant.pmf’ -> ‘001’ ‘path/to/step1.czar.pmf’ -> ‘step1’

Parameters:

filePath (str) – path to the file

Returns:

base name of the file (without extensions)

Return type:

str

BFEE2.commonTools.ploter.getGaWTMBaseNames(filePath)

Extract all possible base names from a GaWTM PMF file for flexible matching.

This function returns a list of candidate base names to support flexible pairing. For example:

'path/to/abf_1.abf1.czar.pmf' -> ['abf_1.abf1', 'abf_1']
'path/to/001.czar.pmf' -> ['001']
'path/to/step1.abf2.czar.pmf' -> ['step1.abf2', 'step1']

Parameters:

filePath (str) – path to the file

Returns:

list of possible base names (primary first, then alternatives)

Return type:

list[str]

BFEE2.commonTools.ploter.getGaWTMHistBaseName(filePath)

Extract the base name from a GaWTM History PMF file or its correction file.

For example:

‘path/to/001.hist.czar.pmf’ -> ‘001’ ‘path/to/001.reweightamd1.cumulant.hist.pmf’ -> ‘001’ ‘path/to/001.reweightamd1.cumulant.pmf’ -> ‘001’ ‘path/to/step1.hist.czar.pmf’ -> ‘step1’

Parameters:

filePath (str) – path to the file

Returns:

base name of the file (without extensions)

Return type:

str

BFEE2.commonTools.ploter.getGaWTMHistBaseNames(filePath)

Extract all possible base names from a GaWTM History PMF file for flexible matching.

This function returns a list of candidate base names to support flexible pairing. For example:

'path/to/abf_1.abf1.hist.czar.pmf' -> ['abf_1.abf1', 'abf_1']
'path/to/001.hist.czar.pmf' -> ['001']

Parameters:

filePath (str) – path to the file

Returns:

list of possible base names (primary first, then alternatives)

Return type:

list[str]

BFEE2.commonTools.ploter.interpolateHistPMFFrames(all_hist_pmfs, target_num_frames)

Interpolate history PMF frames to a target number of frames.

Each PMF file may have different number of frames. This function interpolates the frame values to achieve a uniform frame count across all files.

Parameters:

• all_hist_pmfs (list[list[np.array]]) – list of history PMFs, each is a list of frames

• target_num_frames (int) – target number of frames to interpolate to

Returns:

interpolated history PMFs with uniform frame count

Return type:

list[list[np.array]]

BFEE2.commonTools.ploter.isGaWTM(pmfFiles)

determine whether the input PMFs indicate Ga-WTM simulations

Parameters:

pmfFiles (list[str]) – path to a set of PMFs (and pmf corrections)

Returns:

GaWTM simulation or not

Return type:

bool

BFEE2.commonTools.ploter.isGaWTMHist(pmfFiles)

determine whether the input History PMFs indicate Ga-WTM simulations

Parameters:

pmfFiles (list[str]) – path to a set of History PMFs (and pmf corrections)

Returns:

GaWTM simulation or not

Return type:

bool

BFEE2.commonTools.ploter.mergeHistPMF(all_hist_pmfs)

Merge multiple history PMF files frame-by-frame.

Each input is a list of frames (from different PMF windows). The function first interpolates all to have the same number of frames, then merges each frame using the standard mergePMF function.

Parameters:

all_hist_pmfs (list[list[np.array]]) – list of history PMFs, each is a list of frames from one window

Returns:

merged history PMF (list of merged frames)

Return type:

list[np.array]

BFEE2.commonTools.ploter.mergePMF(pmfFiles)

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.pairGaWTMFiles(pmfFiles)

Pair GaWTM PMF files with their corresponding correction files.

This function looks for files with matching base names: - xxx.czar.pmf paired with xxx.reweightamd1.cumulant.pmf

Files without a corresponding correction file are returned as unpaired. Orphan correction files (without matching czar.pmf) are also returned separately. Wrong correction files (.reweightamd1.reweight.pmf instead of .cumulant.pmf) are also detected.

Parameters:

pmfFiles (list[str]) – list of all PMF file paths (including correction files)

Returns:

(paired_list, unpaired_czar_list, orphan_correction_list, other_files, wrong_correction_files)

paired_list: list of tuples (pmf_file_path, correction_file_path) unpaired_czar_list: list of czar.pmf file paths without correction orphan_correction_list: list of correction file paths without matching czar.pmf other_files: list of other PMF files wrong_correction_files: list of .reweightamd1.reweight.pmf files (wrong type)

Return type:

tuple

BFEE2.commonTools.ploter.pairGaWTMHistFiles(pmfFiles)

Pair GaWTM History PMF files with their corresponding correction files.

This function looks for files with matching base names: - xxx.hist.czar.pmf paired with xxx.reweightamd1.cumulant.hist.pmf or xxx.reweightamd1.cumulant.pmf

Files without a corresponding correction file are returned as unpaired. Orphan correction files (without matching hist.czar.pmf) are also returned separately. Wrong correction files (.reweightamd1.reweight.pmf instead of .cumulant.pmf) are also detected.

Parameters:

pmfFiles (list[str]) – list of all History PMF file paths (including correction files)

Returns:

(paired_list, unpaired_czar_list, orphan_correction_list, other_files, wrong_correction_files)

paired_list is a list of tuples (pmf_file_path, correction_file_path, is_hist_correction). is_hist_correction is True if correction is .hist.pmf and False if it is a single-frame .pmf. Other returned lists contain unpaired hist.czar.pmf files, orphan correction files, other PMF files, and wrong .reweightamd1.reweight.pmf correction files.

Return type:

tuple

BFEE2.commonTools.ploter.parseHistFile(histPath)

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)

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.plotHysteresis(forwardProfile, backwardProfile)

plot the profile describing the hysteresis between forward and backward

simulations

Parameters:

• forwardProfile (np.array, N*2) – forward free-energy profile to be plotted

• backwardProfile (np.array, N*2) – backward free-energy profile to be plotted

BFEE2.commonTools.ploter.plotPMF(pmf)

plot a pmf

Parameters:

pmf (np.array, N*2) – pmf to be plotted

BFEE2.commonTools.ploter.readFrame(input)

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.readHistPMF(histPmfFile)

Read a History PMF file and return a list of PMF frames.

Each frame is a 2D numpy array with shape (N, 2) where N is the number of points.

Parameters:

histPmfFile (str) – path to the history PMF file

Returns:

list of PMF frames, each as (N, 2) array

Return type:

list[np.array]

BFEE2.commonTools.ploter.readPMF(pmfFile)

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.saveConvergence(rmsdList, filePath)

save the PMF RMSD convergence data to a text file

Parameters:

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

• filePath (str) – path to save the data file

BFEE2.commonTools.ploter.saveHysteresis(forwardProfile, backwardProfile, filePath)

save the hysteresis data to a text file

Parameters:

• forwardProfile (np.array, N*2) – forward free-energy profile data

• backwardProfile (np.array, N*2) – backward free-energy profile data

• filePath (str) – path to save the data file

BFEE2.commonTools.ploter.writeHistPMF(histPmfFile, frames)

Write a History PMF file.

Parameters:

• histPmfFile (str) – path to the output history PMF file

• frames (list[np.array]) – list of PMF frames to write

BFEE2.commonTools.ploter.writePMF(pmfFile, pmf)

write a 1D namd PMF file

Parameters:

• pmfFile (str) – path to the pmf File

• pmf (np.array, N*2) – pmf to be written