From 5d0e63d9670f46c335aaf42fdebc41330fd9e8c4 Mon Sep 17 00:00:00 2001 From: luchini18 Date: Fri, 16 Apr 2021 11:36:32 -0700 Subject: [PATCH 1/2] Added default dependency to compute Sterimol parameters to DBSTEP --- README.md | 8 ++ wsterimol/sterimol.py | 10 +- wsterimol/sterimoltools.py | 281 ++++++++++++++++++++++--------------- wsterimol/wSterimol.py | 6 +- 4 files changed, 183 insertions(+), 122 deletions(-) diff --git a/README.md b/README.md index 3e378e9..7fba998 100644 --- a/README.md +++ b/README.md @@ -8,6 +8,14 @@ [![DOI](https://zenodo.org/badge/143098770.svg)](https://zenodo.org/badge/latestdoi/143098770) +This code is no longer actively supported. We recommend using the updated [DBSTEP](https://github.com/bobbypaton/DBSTEP) as an alternative Python project to measure Sterimol parameters through the command line or with Python scripting. The current version of wSterimol currently depends on DBSTEP to obtain Sterimol parameters. +To install the DBSTEP package into PyMOL, enter the following lines into the PyMol console + +``` +import pip +pip.main(['install', 'dbstep']) +``` + wSterimol is an automated computational workflow which computes multidimensional [Sterimol](http://doi.org/10.1021/bk-1984-0255.ch016) parameters. For flexible molecules or substituents, the program will generate & optimize a conformational ensemble, and produce Boltzmann-weighted Sterimol parameters. It has been developed as a [PyMol](https://pymol.org/2) plugin. All code is written in Python and was developed by [Alexandre Brethomé](http://www.oxfordsynthesiscdt.ox.ac.uk/people/students/2015cohort.html) at the University of Oxford and [Robert Paton](http://wwww.patonlab.com) at Colorado State University. The underlying python implementation of Sterimol parameters was written by Kelvin Jackson and Robert Paton and is available as a [command-line tool](https://github.com/bobbypaton/Sterimol) diff --git a/wsterimol/sterimol.py b/wsterimol/sterimol.py index 5304c01..a18303c 100644 --- a/wsterimol/sterimol.py +++ b/wsterimol/sterimol.py @@ -22,7 +22,7 @@ # run sterimol.py # sterimol atomid1, atomid2, (directory, setup_path, verbose) -def Sterimol(atomid1 = "id 1", atomid2 = "id 2", directory = "temp", setup_path = "default", verbose = "False"): +def Sterimol(atomid1 = "id 1", atomid2 = "id 2", directory = "temp", setup_path = "default", verbose = "False", classic = "False"): # If the directory exists if os.path.exists(directory): # Log generation @@ -33,6 +33,10 @@ def Sterimol(atomid1 = "id 1", atomid2 = "id 2", directory = "temp", setup_path verbose = True else: verbose = False + if classic.lower() in ['true', '1', 't', 'y', 'yes']: + classic = True + else: + classic = False try: atomid1 = int(atomid1.strip().strip('id ')) atomid2 = int(atomid2.strip().strip('id ')) @@ -63,10 +67,12 @@ def Sterimol(atomid1 = "id 1", atomid2 = "id 2", directory = "temp", setup_path filesplit = filename.split(".") #prepare the job try: - file_Params = calcSterimol(join(directory, filename), setup.radii, atomid1, atomid2, verbose) + file_Params = calcSterimol(join(directory, filename), setup.radii, atomid1, atomid2, verbose, classic) except ValueError: log.write("FATAL ERROR: An error occured in Sterimol calculation.\n\n%s\n\n" % ValueError) return False + if file_Params.lval == None and file_Params.B1 == None and file_Params.newB5 == None: + return False lval = file_Params.lval; B1 = file_Params.B1; B5 = file_Params.newB5 message = " %-31s " % filename+" %8.2f" % lval+ " %8.2f" % B1+ " %8.2f" % B5 log.write(message, verbose) diff --git a/wsterimol/sterimoltools.py b/wsterimol/sterimoltools.py index 5bec874..0465637 100644 --- a/wsterimol/sterimoltools.py +++ b/wsterimol/sterimoltools.py @@ -546,123 +546,170 @@ def linearcheck(carts): return ans class calcSterimol: - def __init__(self, file, radii, atomA, atomB,verbose): - - if len(file.split(".com"))>1 or len(file.split(".gjf"))>1: fileData = getinData(file) - if len(file.split(".out"))>1 or len(file.split(".log"))>1: fileData = getoutData(file) - - # initialize the array of atomic vdw radii - molcart = fileData.CARTESIANS; atomtype = fileData.ATOMTYPES; natoms = len(molcart); vdw_radii = [] - - if radii == "cpk": - atomic_co_no = ncoord(natoms, rcov, atomtype, molcart) - sterimol_types = generate_atom_types(atomtype, atomic_co_no) - #print sterimol_types - for i in range(0,natoms): - for j in range(0,len(sterimol_atomtypes)): - if sterimol_types[i] == sterimol_atomtypes[j]: vdw_radii.append(cpk_radii[j]/100.00) - - if radii == "bondi": - for i in range(0,natoms): vdw_radii.append(bondiRadius(periodictable.index(fileData.ATOMTYPES[i].lower().capitalize()))) - -# Define vector along the L-axis connecting base atom and the next attached atom -# subtract one since the array starts from zero not one - atomA = atomA - 1; atomB = atomB - 1 - next_atom = molcart[atomB] - vect1=np.subtract(getcoords(atomA,molcart),next_atom) - if verbose == True: - print(" Atoms", atomA, "and", atomB, "define the L-axis and direction", vect1) - print("\n", " Atom ".ljust(9), " Xco/A".rjust(9), " Yco/A".rjust(9), " Zco/A".rjust(9), " VdW/pm".rjust(9)) - print(" ##############################################") - # Remove the base atom from the list of atoms to be considered for sterics (after printing all) - atomlist = list(range(0,natoms)) - if verbose == True: - for atom in atomlist: - if radii == "cpk": print(" ", sterimol_types[atom].ljust(6), end=' ') - if radii == "bondi": print(" ", atomtype[atom].ljust(6), end=' ') - for coord in molcart[atom]: - if coord < 0.0: print(" %.3f".rjust(6) % coord, end=' ') - else: print(" %.3f".rjust(6) % coord, end=' ') - print(" %.1f" % round(vdw_radii[atom]*100)) - atomlist.remove(atomA) - - adjlist=[]; opplist=[]; theta=[] - for i in atomlist: - vect2=np.subtract(getcoords(atomA,molcart),getcoords(i,molcart)) - oppdist=calcopposite(atomA,i,angle(vect1,vect2),molcart) - opplist.append(oppdist+vdw_radii[i]) - adjdist=calcadj(atomA,i,angle(vect1,vect2),molcart) - #minadjlist.append(adjdist-vdw_radii[i]) - adjlist.append(adjdist+vdw_radii[i]) - - B5=max(opplist) - #self.lval=max(adjlist)-minval - # A bit weird, but seems like original sterimol adds on the difference between the bond length and vdw radius of atom B. For a C-H bond this is 1.50 - 1.10 = 0.40 Angstrom) - self.lval=max(adjlist)+0.40 - - ###Useful - do not delete! - #print " B5 atom", atomlist[opplist.index(max(opplist))]+1, "distance", max(opplist) - #print " Highest atom", atomlist[adjlist.index(max(adjlist))]+1,"distance", max(adjlist),"\n Lowest atom", atomlist[minadjlist.index(min(minadjlist))]+1,"distance", min(minadjlist) - - zcarts=[]#zeroed carts - for i in atomlist: zcarts.append(np.subtract(molcart[i],molcart[atomA])) - zvect=[0,0,1] - zcent=np.subtract(next_atom,molcart[atomA]) - for cart in range(len(zcarts)): - zcoord= rotrel(zcent,zvect,zcarts[cart]) - zcarts[cart]=zcoord - twodcarts=[] - for row in zcarts: twodcarts.append([row[0],row[1]]) - fragrad=[]#radii of fragment atoms - for t in atomlist: fragrad.append(vdw_radii[t]) - singledist=[] - for t in range(len(fragrad)): - d=np.linalg.norm(twodcarts[t])#;print d - d=d+fragrad[t] - singledist.append(d) - self.newB5=max(singledist) #This is the same as the 3D calculated value from above - - center=[0,0] - vlist=[]#list of distances from the origin to the tangential vectors - alist=[]#list of atoms between which the tangential vectors pass through no other atoms - iav=[]#interatomic vectors - sym=symcheck(twodcarts) - for x in range(len(twodcarts)): - if sym==1: - twodcarts[x][0]=twodcarts[x][0]+0.000001 - twodcarts[x][1]=twodcarts[x][1]+0.000001 - for y in range(len(twodcarts)): - if x!=y: - try:nvect= (twod_vect(center,twodcarts[x],twodcarts[y]))#origin normal vector to connecting atomic centers vector - except ValueError:nvect=[0,0] - iav=np.subtract(twodcarts[x],twodcarts[y])#interatomic vector - iad=np.linalg.norm(iav)#interatomic distance - try:theta=math.asin((fragrad[y]-fragrad[x])/iad)#calculates angle by which to rotate vdw radii before adding - except ValueError: theta=np.pi/2 - try:unvect=nvect/np.linalg.norm(nvect) - except RuntimeWarning:pass#unvect=[0,0] - xradv=twod_rot(unvect*fragrad[x],theta) - yradv=twod_rot(unvect*fragrad[y],theta) - mvect= (twod_vect(center,twodcarts[x]-xradv,twodcarts[y]-yradv)) - nvect= (twod_vect(center,twodcarts[x]+xradv,twodcarts[y]+yradv))#origin normal vector to connecting atomic surfaces tangential vector - newx=twodcarts[x]+xradv - newy=twodcarts[y]+yradv - mewx=twodcarts[x]-xradv - mewy=twodcarts[y]-yradv - if np.cross(nvect,xradv)<0.000000001 and theta!=np.pi/2: - satpoint=[]#Satisfied points not within range of tangential vector - for z in range(len(twodcarts)): - pvdist=twod_dist(twodcarts[z],newx,newy) - if z!=x and z!=y and pvdist>(fragrad[z]-0.0001):satpoint.append(pvdist) - if len(satpoint)==len(atomlist)-2:vlist.append(np.linalg.norm(nvect));alist.append([x,y]);#print x,y - satpoint=[] - for z in range(len(twodcarts)): - pvdist=twod_dist(twodcarts[z],mewx,mewy) - if z!=x and z!=y and pvdist>(fragrad[z]-0.0001):satpoint.append(pvdist) - if len(satpoint)==len(atomlist)-2:vlist.append(np.linalg.norm(mvect));alist.append([x,y]) - if linearcheck(twodcarts)==1:self.B1 = max(fragrad) - elif len(vlist) > 0: self.B1=min(vlist) - else: self.B1 = max(fragrad) + def __init__(self, file, radii, atomA, atomB, verbose, classic): + if not classic: + try: + import dbstep.Dbstep as db + except ModuleNotFoundError as e: + print(e) + print("The DBSTEP Python package is used as the default method to compute Sterimol parameters for this package and can be found at https://www.github.com/bobbypaton/DBSTEP") + print("The package can be installed into PyMOL using the following lines in the PyMOL console:\n") + print(">import pip") + print(">pip.main(['install', 'dbstep'])") + print("\nThe previous method to compute Sterimol parameters can be invoked by calling 'wSterimol' with the 'classic=True' argument.") + self.lval = None + self.B1 = None + self.newB5 = None + return + #calc sterimol with DBSTEP + sterics = db.dbstep(file,atom1=atomA,atom2=atomB,verbose=verbose,sterimol=True,measure='classic',commandline=True,quiet=True) + self.lval = sterics.L + self.B1 = sterics.Bmin + self.newB5 = sterics.Bmax + else: + if len(file.split(".com"))>1 or len(file.split(".gjf"))>1: + fileData = getinData(file) + if len(file.split(".out"))>1 or len(file.split(".log"))>1: + fileData = getoutData(file) + + # initialize the array of atomic vdw radii + molcart = fileData.CARTESIANS; + atomtype = fileData.ATOMTYPES; + natoms = len(molcart); vdw_radii = [] + + if radii == "cpk": + atomic_co_no = ncoord(natoms, rcov, atomtype, molcart) + sterimol_types = generate_atom_types(atomtype, atomic_co_no) + #print sterimol_types + for i in range(0,natoms): + for j in range(0,len(sterimol_atomtypes)): + if sterimol_types[i] == sterimol_atomtypes[j]: + vdw_radii.append(cpk_radii[j]/100.00) + + if radii == "bondi": + for i in range(0,natoms): + vdw_radii.append(bondiRadius(periodictable.index(fileData.ATOMTYPES[i].lower().capitalize()))) + + # Define vector along the L-axis connecting base atom and the next attached atom + # subtract one since the array starts from zero not one + atomA = atomA - 1; atomB = atomB - 1 + next_atom = molcart[atomB] + vect1=np.subtract(getcoords(atomA,molcart),next_atom) + if verbose == True: + print(" Atoms", atomA, "and", atomB, "define the L-axis and direction", vect1) + print("\n", " Atom ".ljust(9), " Xco/A".rjust(9), " Yco/A".rjust(9), " Zco/A".rjust(9), " VdW/pm".rjust(9)) + print(" ##############################################") + # Remove the base atom from the list of atoms to be considered for sterics (after printing all) + atomlist = list(range(0,natoms)) + if verbose == True: + for atom in atomlist: + if radii == "cpk": + print(" ", sterimol_types[atom].ljust(6), end=' ') + if radii == "bondi": + print(" ", atomtype[atom].ljust(6), end=' ') + for coord in molcart[atom]: + if coord < 0.0: + print(" %.3f".rjust(6) % coord, end=' ') + else: + print(" %.3f".rjust(6) % coord, end=' ') + print(" %.1f" % round(vdw_radii[atom]*100)) + atomlist.remove(atomA) + + adjlist=[]; opplist=[]; theta=[] + for i in atomlist: + vect2=np.subtract(getcoords(atomA,molcart),getcoords(i,molcart)) + oppdist=calcopposite(atomA,i,angle(vect1,vect2),molcart) + opplist.append(oppdist+vdw_radii[i]) + adjdist=calcadj(atomA,i,angle(vect1,vect2),molcart) + #minadjlist.append(adjdist-vdw_radii[i]) + adjlist.append(adjdist+vdw_radii[i]) + + B5=max(opplist) + #self.lval=max(adjlist)-minval + # A bit weird, but seems like original sterimol adds on the difference between the bond length and vdw radius of atom B. For a C-H bond this is 1.50 - 1.10 = 0.40 Angstrom) + + self.lval=max(adjlist)+0.40 + + ###Useful - do not delete! + #print " B5 atom", atomlist[opplist.index(max(opplist))]+1, "distance", max(opplist) + #print " Highest atom", atomlist[adjlist.index(max(adjlist))]+1,"distance", max(adjlist),"\n Lowest atom", atomlist[minadjlist.index(min(minadjlist))]+1,"distance", min(minadjlist) + + zcarts=[]#zeroed carts + for i in atomlist: zcarts.append(np.subtract(molcart[i],molcart[atomA])) + zvect=[0,0,1] + zcent=np.subtract(next_atom,molcart[atomA]) + for cart in range(len(zcarts)): + zcoord= rotrel(zcent,zvect,zcarts[cart]) + zcarts[cart]=zcoord + twodcarts=[] + for row in zcarts: + twodcarts.append([row[0],row[1]]) + fragrad=[]#radii of fragment atoms + for t in atomlist: + fragrad.append(vdw_radii[t]) + singledist=[] + for t in range(len(fragrad)): + d=np.linalg.norm(twodcarts[t])#;print d + d=d+fragrad[t] + singledist.append(d) + + self.newB5=max(singledist) #This is the same as the 3D calculated value from above + + center=[0,0] + vlist=[]#list of distances from the origin to the tangential vectors + alist=[]#list of atoms between which the tangential vectors pass through no other atoms + iav=[]#interatomic vectors + sym=symcheck(twodcarts) + for x in range(len(twodcarts)): + if sym==1: + twodcarts[x][0]=twodcarts[x][0]+0.000001 + twodcarts[x][1]=twodcarts[x][1]+0.000001 + for y in range(len(twodcarts)): + if x!=y: + try: + nvect= (twod_vect(center,twodcarts[x],twodcarts[y]))#origin normal vector to connecting atomic centers vector + except ValueError: + nvect=[0,0] + iav=np.subtract(twodcarts[x],twodcarts[y])#interatomic vector + iad=np.linalg.norm(iav)#interatomic distance + try: + theta=math.asin((fragrad[y]-fragrad[x])/iad)#calculates angle by which to rotate vdw radii before adding + except ValueError: + theta=np.pi/2 + try: + unvect=nvect/np.linalg.norm(nvect) + except RuntimeWarning: + pass#unvect=[0,0] + xradv=twod_rot(unvect*fragrad[x],theta) + yradv=twod_rot(unvect*fragrad[y],theta) + mvect= (twod_vect(center,twodcarts[x]-xradv,twodcarts[y]-yradv)) + nvect= (twod_vect(center,twodcarts[x]+xradv,twodcarts[y]+yradv))#origin normal vector to connecting atomic surfaces tangential vector + newx=twodcarts[x]+xradv + newy=twodcarts[y]+yradv + mewx=twodcarts[x]-xradv + mewy=twodcarts[y]-yradv + if np.cross(nvect,xradv)<0.000000001 and theta!=np.pi/2: + satpoint=[]#Satisfied points not within range of tangential vector + for z in range(len(twodcarts)): + pvdist=twod_dist(twodcarts[z],newx,newy) + if z!=x and z!=y and pvdist>(fragrad[z]-0.0001): + satpoint.append(pvdist) + if len(satpoint)==len(atomlist)-2: + vlist.append(np.linalg.norm(nvect)) + alist.append([x,y]);#print x,y + satpoint=[] + for z in range(len(twodcarts)): + pvdist=twod_dist(twodcarts[z],mewx,mewy) + if z!=x and z!=y and pvdist>(fragrad[z]-0.0001): + satpoint.append(pvdist) + if len(satpoint)==len(atomlist)-2:vlist.append(np.linalg.norm(mvect));alist.append([x,y]) + + if linearcheck(twodcarts)==1: + self.B1 = max(fragrad) + elif len(vlist) > 0: + self.B1=min(vlist) + else: + self.B1 = max(fragrad) def symcheck(carts):#Add symmetry criteria center=[0,0] diff --git a/wsterimol/wSterimol.py b/wsterimol/wSterimol.py index 28cea01..4fde4d2 100644 --- a/wsterimol/wSterimol.py +++ b/wsterimol/wSterimol.py @@ -16,9 +16,9 @@ # Generate the wSterimol parameters from the optimised structures # Use in Pymol command prompt: # run wSterimol.py -# wSterimol dihedrals, atomid1, atomid2, (radii, walltime, directory, setup_path, verbose) +# wSterimol dihedrals, atomid1, atomid2, (radii, walltime, directory, setup_path, verbose, classic) -def wSterimol(dihedrals, atomid1 = "id 1", atomid2 = "id 2", directory = "temp", setup_path = '.', walltime = 300, verbose = "False"): +def wSterimol(dihedrals, atomid1 = "id 1", atomid2 = "id 2", directory = "temp", setup_path = '.', walltime = 300, verbose = "False", classic = "False"): # Log generation wlog = Log() # Do weighted Sterimol @@ -27,7 +27,7 @@ def wSterimol(dihedrals, atomid1 = "id 1", atomid2 = "id 2", directory = "temp", if prepare_file(directory, setup_path, verbose): if optimisation(directory, walltime, verbose, setup_path): if filter_opt(directory, setup_path, verbose): - if Sterimol(atomid1, atomid2, directory, setup_path, verbose): + if Sterimol(atomid1, atomid2, directory, setup_path, verbose, classic): if weight(setup_path, verbose): wlog.write("---- wSterimol finished ----\n") wlog.finalize() From cc48521f72ec2020638cdfaefec51a7c8f0f58f0 Mon Sep 17 00:00:00 2001 From: luchini18 Date: Fri, 16 Apr 2021 11:54:54 -0700 Subject: [PATCH 2/2] Updated ReadMe --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 7fba998..c472de7 100644 --- a/README.md +++ b/README.md @@ -9,12 +9,14 @@ [![DOI](https://zenodo.org/badge/143098770.svg)](https://zenodo.org/badge/latestdoi/143098770) This code is no longer actively supported. We recommend using the updated [DBSTEP](https://github.com/bobbypaton/DBSTEP) as an alternative Python project to measure Sterimol parameters through the command line or with Python scripting. The current version of wSterimol currently depends on DBSTEP to obtain Sterimol parameters. -To install the DBSTEP package into PyMOL, enter the following lines into the PyMol console +To install the DBSTEP package into PyMOL, enter the following lines into the PyMol console: ``` import pip pip.main(['install', 'dbstep']) ``` +Note that there will likely be differences in results computed by DBSTEP compared to the previous wSterimol method, as DBSTEP uses van der Waals radii, as opposed to CPK radii. +The previous method to compute Sterimol parameters can be invoked by calling 'wSterimol' with the 'classic=True' argument in PyMOL. wSterimol is an automated computational workflow which computes multidimensional [Sterimol](http://doi.org/10.1021/bk-1984-0255.ch016) parameters. For flexible molecules or substituents, the program will generate & optimize a conformational ensemble, and produce Boltzmann-weighted Sterimol parameters. It has been developed as a [PyMol](https://pymol.org/2) plugin.