bfee2 2.5.0__py3-none-any.whl

BFEE2/templates_namd/updateCenters.py

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+# Read eq.histogramX.dat and update Centers in *.in files
+# This step is optional but may improve the convergence
+
+import os, sys, re
+import numpy as np
+
+def isGeometric():
+    """Check the route of the simulation, True for geometric,
+       False for alchemical.
+       
+    Returns:
+        bool: the route of the free-energy calculation. True for geometric,
+              False for alchemical
+    """
+    
+    if os.path.exists('../fep.tcl'):
+        return False
+    else:
+        return True
+    
+    
+def parseDat(filename):
+    """Parse a dat (histogram) file and return the most probable CV value
+
+    Args:
+        filename (str): the dat file to be parsed with
+        
+    Returns:
+        float: the most probable CV value
+    """
+    
+    data = np.loadtxt(filename)
+    CVs = data[:,0]
+    counts = data[:,1]
+    
+    maxCV = -1
+    maxCount = -1
+    for i, j in zip(CVs, counts):
+        if j > maxCount:
+            maxCV = i
+            maxCount = j
+    return maxCV
+
+def findOptimalCVs():
+    """ read *.dat files generated through equilibration
+        and find out the most probable values of CVs
+        
+    Returns:
+        list[Float]: the most probable values of RMSD, eulerTheta, eulerPhi, eulerPsi, polarTheta, polarPhi, r
+    """
+    
+    optimalCVs = []
+    files = [
+        'output/eq.histogram1.dat',
+        'output/eq.histogram2.dat',
+        'output/eq.histogram3.dat',
+        'output/eq.histogram4.dat',
+        'output/eq.histogram5.dat',
+        'output/eq.histogram6.dat',
+        'output/eq.histogram7.dat'
+    ]
+    
+    for file in files:
+        optimalCVs.append(parseDat(file))
+    
+    return optimalCVs
+ 
+def readCenters(filename, CVs):
+    """ find the value of centers of provided CVs in a *.in file
+
+    Args:
+        filename (str): a Colvars config file
+        CVs (List[str]): a list, showing the CVs whose centers are to be get
+        
+    Returns:
+        List[float]: centers of the provided CVs
+    """
+    
+    # whether parsing a harmonic block
+    # either None or the index of the corresponding CV
+    inBlock = None
+    
+    # the CV values
+    CVValues = [0 for i in range(len(CVs))]
+    
+    with open(filename, 'r') as colvarsFile:
+        for line in colvarsFile.readlines():
+            splitedLine = line.strip().split()
+                
+            if inBlock is not None:
+                if line.strip().lower().startswith('centers'):
+                    if inBlock != -1:
+                        CVValues[inBlock] = float(splitedLine[1])
+                    
+                    if splitedLine[0] == '}':
+                        inBlock = None
+                        
+            if line.strip().lower().startswith('harmonic'):
+                inBlock = -1
+                        
+            if line.strip().lower().startswith('colvars'):
+                for index, CV in enumerate(CVs):
+                    if splitedLine[1].lower() == CV.lower():
+                        inBlock = index
+    
+    return CVValues
+ 
+def changeCenters(filename, CVs, newCenters):
+    """ change Centers of harmonic restraints in a *.in file
+
+    Args:
+        filename (str): a Colvars config file
+        CVs (List[str]): a list, showing the Centers of which harmonic blocks are to be replaced
+        newCenters (List[float]): a list, containing the new values of Centers
+    """
+    
+    # whether parsing a harmonic block
+    # either None or the index of the corresponding CV
+    inBlock = None
+    with open(filename, 'r') as oldColvarsFile:
+        # Python cannot modify text file in place
+        with open(filename + '.tmp', 'w') as newColvarsFile:
+            for line in oldColvarsFile.readlines():
+                splitedLine = line.strip().split()
+                
+                if inBlock is None:
+                    newColvarsFile.write(line)
+                else:
+                    if not line.strip().lower().startswith('centers'):
+                        newColvarsFile.write(line)
+                    else:
+                        # 'colvars' not in CVs
+                        if inBlock == -1:
+                            newColvarsFile.write(line)
+                        else:
+                            newColvarsFile.write(f'    Centers    {newCenters[inBlock]}\n')
+                    
+                    if len(splitedLine) > 0:
+                        if splitedLine[0] == '}':
+                            inBlock = None
+                        
+                if line.strip().lower().startswith('harmonic'):
+                    inBlock = -1
+                        
+                if line.strip().lower().startswith('colvars'):
+                    for index, CV in enumerate(CVs):
+                        if splitedLine[1].lower() == CV.lower():
+                            inBlock = index
+    
+    os.remove(filename)
+    os.rename(filename + '.tmp', filename)
+    
+def changeABFRange(filename, CVs, newCenters, originalCenters):
+    """ change lowerboundary, upperboundary, lowerWalls, upperWalls of ABF in a *.in file
+
+    Args:
+        filename (str): a Colvars config file
+        CVs (List[str]): a list, showing the corresponding options of which CV blocks are to be replaced
+        newCenters (List[float]): a list, containing the new values of Centers of these CVs
+        originalCenters (List[float]): a list, containing the original values of Centers of these CVs
+    """
+    
+    # whether parsing a harmonic block
+    # either None or the index of the corresponding CV
+    inBlock = None
+    with open(filename, 'r') as oldColvarsFile:
+        # Python cannot modify text file in place
+        with open(filename + '.tmp', 'w') as newColvarsFile:
+            for line in oldColvarsFile.readlines():
+                splitedLine = line.strip().split()
+                
+                if inBlock is None:
+                    newColvarsFile.write(line)
+                else:
+                    if (not line.strip().lower().startswith('lowerboundary')) and \
+                        (not line.strip().lower().startswith('upperboundary')) and \
+                        (not line.strip().lower().startswith('lowerwalls')) and \
+                        (not line.strip().lower().startswith('upperwalls')):
+                        newColvarsFile.write(line)
+                    else:
+                        # 'name' not in CVs
+                        if inBlock == -1:
+                            newColvarsFile.write(line)
+                        else:
+                            if line.strip().lower().startswith('lowerboundary'):
+                                newColvarsFile.write(
+                                    f'    Lowerboundary    {float(splitedLine[1]) + newCenters[inBlock] - originalCenters[inBlock]}\n'
+                                )
+                            elif line.strip().lower().startswith('upperboundary'):
+                                newColvarsFile.write(
+                                    f'    Upperboundary    {float(splitedLine[1]) + newCenters[inBlock] - originalCenters[inBlock]}\n'
+                                    )
+                            elif line.strip().lower().startswith('lowerwalls'):
+                                newColvarsFile.write(
+                                    f'    LowerWalls    {float(splitedLine[1]) + newCenters[inBlock] - originalCenters[inBlock]}\n'
+                                    )
+                            elif line.strip().lower().startswith('upperwalls'):
+                                newColvarsFile.write(
+                                    f'    UpperWalls    {float(splitedLine[1]) + newCenters[inBlock] - originalCenters[inBlock]}\n'
+                                    )
+                            else:
+                                print("Selected CV(s) not for free-energy calculation!")
+                    
+                    if len(splitedLine) > 0:
+                        if splitedLine[0] == '}':
+                            inBlock = None
+                
+                if len(splitedLine) > 0:
+                    if splitedLine[0].lower() == 'colvar' or line.strip().lower().startswith('harmonicwalls'):
+                        inBlock = -1
+                    
+                    if line.strip().lower().startswith('name') or splitedLine[0].lower() == 'colvars':
+                        for index, CV in enumerate(CVs):
+                            if splitedLine[1].lower() == CV.lower():
+                                inBlock = index
+    
+    os.remove(filename)
+    os.rename(filename + '.tmp', filename)
+
+def updateAlchemicalFiles():
+    """Update the Centers of *.in files based on equilibration
+    """
+    
+    files = [
+        './colvars2.in',
+        '../001_MoleculeBound/colvars.in',
+        '../002_RestraintBound/colvars_forward.in',
+        '../002_RestraintBound/colvars_backward.in'
+    ]
+    
+    for file in files:
+        if not os.path.exists(file):
+            print(f'File {file} does not exist!')
+            continue
+        changeCenters(
+            file, 
+            [
+                'eulerTheta', 'eulerPhi', 'eulerPsi', 'polarTheta', 'polarPhi', 'r'
+            ], 
+            findOptimalCVs()[1:]
+        )
+        print(f'File {file} updated!')
+
+    # if re-eqilibrated
+    if os.path.exists('./000.1_eq2_re-eq.conf'):
+        confFiles = [
+            '../001_MoleculeBound/001.1_fep_backward.conf',
+            '../001_MoleculeBound/001_fep_doubleWide.conf',
+            '../002_RestraintBound/002.1_ti_backward.conf',
+        ]
+        for confFile in confFiles:
+            if not os.path.exists(confFile):
+                print(f'File {confFile} does not exist!')
+                continue
+            with open(confFile,'r') as readFile:
+                data=readFile.read()
+            data = re.sub('../000_eq/output/eq.coor', '../000_eq/output/eq2.coor', data)
+            data = re.sub('../000_eq/output/eq.vel', '../000_eq/output/eq2.vel', data)
+            data = re.sub('../000_eq/output/eq.xsc', '../000_eq/output/eq2.xsc', data)
+            with open(confFile,'w') as writeFile:
+                writeFile.write(data)
+            print(f'File {confFile} updated!')
+        
+def updateGeometricFiles():
+    """Update the Centers of *.in files based on equilibration
+    """
+    
+    CVNames = ['eulerTheta', 'eulerPhi', 'eulerPsi', 'polarTheta', 'polarPhi']
+    optimalCVValues = findOptimalCVs()[1:6]
+    originalCVValues = readCenters('../007_r/colvars_eq.in', CVNames)
+    
+    # in geometrical route, there may be many windows
+    folders = [
+        '../002_EulerTheta',
+        '../003_EulerPhi',
+        '../004_EulerPsi',
+        '../005_PolarTheta',
+        '../006_PolarPhi',
+        '../007_r'
+    ]
+    
+    for fIndex, folder in enumerate(folders):
+        # *.in in folder 
+        files = []
+        for file in os.listdir(folder):
+            if file.endswith('.in') or file.endswith('.in.amd'):
+                files.append(os.path.join(folder, file))
+                
+        for inFile in files:
+            changeCenters(
+                inFile, 
+                CVNames[:fIndex], 
+                optimalCVValues[:fIndex]
+            )
+            
+            changeABFRange(
+                inFile,
+                CVNames[:fIndex+1],
+                optimalCVValues[:fIndex+1],
+                originalCVValues[:fIndex+1]
+            )
+            print(f'File {inFile} updated!')
+        
+if __name__ == '__main__':
+    
+    if isGeometric():
+        updateGeometricFiles()
+        print('All the *.in files updated for the Geometrical route!')
+    else:
+        updateAlchemicalFiles()
+        print('All the *.in files updated for the Alchemical route!')

BFEE2/templates_readme/Readme_Gromacs_Geometrical.txt

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+To calculate the binding free energy:
+
+1.1.  run 000_eq/000_generate_tpr.sh
+1.2.  run 000_eq/000_eq.tpr
+2.1.  run 001_RMSD_bound/001_generate_tpr.sh
+2.2.  run 001_RMSD_bound/001_RMSD_bound.tpr
+3.1.  run 002_euler_theta/002_generate_tpr.sh
+3.2.  run 002_euler_theta/002_euler_theta.tpr
+4.1.  run 003_euler_phi/003_generate_tpr.sh
+4.2.  run 003_euler_phi/003_euler_phi.tpr
+5.1.  run 004_euler_psi/004_generate_tpr.sh
+5.2.  run 004_euler_psi/004_euler_psi.tpr
+6.1.  run 005_polar_theta/005_generate_tpr.sh
+6.2.  run 005_polar_theta/005_polar_theta.tpr
+7.1.  run 006_polar_phi/006_generate_tpr.sh
+7.2.  run 006_polar_phi/006_polar_phi.tpr
+8.1.  run 007_r/007.1_generate_eq_tpr.sh
+8.2.  run 007_r/007_r.eq.tpr
+8.3.  run 007_r/007.2_generate_tpr.sh
+8.4   run 007_r/007_r.tpr
+9.1.  run 008_RMSD_unbound/008.1_generate_eq_tpr.sh
+9.2.  run 008_RMSD_unbound/008_RMSD_unbound.eq.tpr
+9.3.  run 008_RMSD_unbound/008.2_generate_tpr.sh
+9.4.  run 008_RMSD_unbound/008_RMSD_unbound.tpr
+10.   do post-treatment using BFEE

BFEE2/templates_readme/Readme_NAMD_Alchemical.txt

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+To calculate the binding free energy:
+
+1.1.  run 000_eq/000.1_eq.conf
+1.2.  (optionally) run 000_eq/000.3_updateCenters.py
+2.1.  run 001_MoleculeBound/001.1_fep_backward.conf
+2.2.  run 001_MoleculeBound/001.2_fep_forward.conf
+3.1.  run 002_RestraintBound/002.1_ti_backward.conf
+3.2.  run 002_RestraintBound/002.2_ti_forward.conf
+4.1.  CHARMM user:
+        (if you didn't link BFEE with VMD before generating inputs)
+        run 002.3_removeProtein.tcl using VMD
+      Amber user:
+        run 002.3_removeProtein.cpptraj using cpptraj
+4.2   run 000_eq/000.2_eq_ligandOnly.conf
+4.3.  run 003_MoleculeUnbound/003.1_fep_backward.conf
+4.4.  run 003_MoleculeUnbound/003.2_fep_forward.conf
+5.1.  run 004_RestraintUnbound/004.1_ti_backward.conf
+5.2.  run 004_RestraintUnbound/004.2_ti_forward.conf
+(steps 2-5 can be done in parallel)
+6.    do post-treatment using BFEE

BFEE2/templates_readme/Readme_NAMD_Geometrical.txt

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+To calculate the binding free energy:
+
+1.1   run 000_eq/000.1_eq.conf
+1.2.  (optionally) run 000_eq/000.2_updateCenters.py
+      (If this is done, then there is usually no need to change restraining centers
+       after steps 3.x.)
+2.    run 001_RMSDBound/001_abf_1.conf
+3.1.  run 002_EulerTheta/002_abf_1.conf
+3.2.  change restraining center of "eulerTheta" in
+      003_EulerPhi/colvars_1.in to
+      the CV value corresponding to dG=0 in 
+      002_EulerTheta/output/abf_1.czar.pmf,
+3.3.  run 003_EulerPhi/003_abf_1.conf
+3.4.  similarly, change "eulerTheta" and "eulerPhi" in 
+      004_EulerPsi/colvars_1.in
+3.5.  run 004_EulerPsi/004_abf_1.conf
+3.6.  change 005_PolarTheta/colvars_1.in correspondingly
+3.7.  run 005_PolarTheta/005_abf_1.conf
+3.8.  change 006_PolarPhi/colvars_1.in correspondingly
+3.9.  run 006_PolarPhi/006_abf_1.conf
+3.10. change 007_r/colvars_eq.in and 007_r/colvars_1.in correspondingly
+3.11. (if you didn't link BFEE with VMD before generating inputs)
+      run 007_r/007.0_solvate.tcl using VMD
+3.12. run 007_r/007.1_eq.conf
+3.13. run 007_r/007.2_abf_1.conf
+4.1.  CHARMM user:
+        (if you didn't link BFEE with VMD before generating inputs)
+        run 008_RMSDUnbound/008.0_removeProtein.tcl using VMD
+      Amber user:
+        run 008.0_removeProtein.cpptraj using cpptraj
+4.2.  run 008_RMSDUnbound/008.1_eq.conf
+4.3.  run 008_RMSDUnbound/008.2_abf_1.conf
+(steps 2-4 can be done in parallel)
+5.    do post-treatment using BFEE

BFEE2/templates_readme/__init__.py

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+