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FMC_1.py
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FMC_1.py
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#!/usr/bin/python
### ### ### ### ###
### ### ### ### ###
#####b. ####b. ###### .d##b. #####b. ### ####b. #####b. ###
### ### "##b "##b ### d##""##b ### "##b ### "##b ### "##b ###
### ### ### .d###### ### ### ### ### ### ### .d###### ### ###
### ### d##P ### ### Y##b. Y##..##P ### ### ### ### ### ### d##P ###
### #####P" "Y###### "Y### "Y##P" ### ### ### "Y###### #####P" ###
###
###
# THIS SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
# Comments and/or additions are welcome (send e-mail to:
###############################################################
# FMC_1.py #
# Monte Carlo Conformational Search #
# Dr Robert S Paton, University of Oxford 2010 #
###############################################################
####### Written by: Rob Paton ###############################
####### Last modified: Mar 20, 2013 #########################
###############################################################
# Python Libraries ############################################
import glob, subprocess, sys, os, random, math, tarfile
from numpy import *
###############################################################
# Full Monte Libaries #########################################
from FMTools import *
###############################################################
if __name__ == "__main__":
# An input file must be specified #############################
instruct = "default"
interactivemode = 1
if len(sys.argv)>1:
for arg in sys.argv:
if arg == "-setup": SETUPEXE(MOPAC_EXEC)
if arg == "-background": interactivemode = 0
filein = sys.argv[1].split(".")[0]
if len(sys.argv[1].split("."))>1:
if sys.argv[1].split(".")[1] == "com": filetype = "com"
if sys.argv[1].split(".")[1] == "pdb": filetype = "pdb"
if len(sys.argv)>2 and sys.argv[2] != "-background": instruct = sys.argv[2]
else: print "\nWrong number of arguments used. Correct format: FullMonte struc.com [params] \n"; sys.exit()
###############################################################
# Check if MOPAC.EXEC is defined ##############################
if not os.path.exists(MOPAC_EXEC): print "\no Mopac executable cannot be found. Rerun Full Monte with -setup as one of the arguments\n"; sys.exit()
###############################################################
# Initialize the logfile for all text output ##################
if os.path.exists(filein+"_fm.log") and interactivemode == 1:
var = raw_input("\no Log file already exists! OK to overwrite this file ? (Y/N) ")
if var.lower() == "y" or var.lower() == "": print " Overwriting ..."
else: print "\nExiting\n"; sys.exit(1)
log = FMLog(filein,"log", "fm")
###############################################################
# See if there are any remaining files from a previous run ####
if os.path.exists(filein+"_fm.tgz") and interactivemode == 1:
var = raw_input("\no Tarfile already exists! OK to overwrite these structures ? (Y/N) ")
if var.lower() == "y" or var.lower() == "": os.remove(filein+"_fm.tgz")
else: print "\nExiting\n"; sys.exit(1)
if len(glob.glob(filein+"*step*"))>0:
if interactivemode == 1:
print glob.glob(filein+"*step*")
var = raw_input("\no Some optimization ouput files already exist! OK to overwrite these structures ? (Y/N) ")
if var.lower() == "y" or var.lower() == "":
for file in glob.glob(filein+"*step*"): os.remove(file)
else: print "\nExiting\n"; sys.exit(1)
else:
for file in glob.glob(filein+"*step*"): os.remove(file)
###############################################################
# Open the structure file #####################################
log.Write("\no Extracting molecule from "+filein+"."+filetype+" ...")
MOLSPEC = getinData(filein,log)
###############################################################
# Open the specified parameter file for Monte Carlo parameters
# (default values will be used if not supplied) ###############
if instruct!="default": log.Write("\no Extracting conformational search parameters from "+instruct+" ...")
else: log.Write("\no No FullMonte parameters specified! Using default values ...")
SEARCHPARAMS = getParams(MOLSPEC, instruct,log)
###############################################################
# Model Chemistry to be used ##################################
for level in ["AM1", "PM3", "PM6", "PM7", "PM6-DH2"]:
if SEARCHPARAMS.LEVL.upper() == level: JOB = JobSpec("Mopac")
for level in ["UFF", "AMBER", "PDDG"]:
if SEARCHPARAMS.LEVL.upper() == level: JOB = JobSpec("Gaussian")
if JOB.PROGRAM != "Mopac" and JOB.PROGRAM != "Gaussian": log.Fatal("\no "+SEARCHPARAMS.LEVL+" Level of Theory Not Yet Supported ... ")
JOB.JOBTYPE = SEARCHPARAMS.LEVL
log.Write("\no Using "+JOB.JOBTYPE+" level of theory ... ")
###############################################################
# For PM6, a dispersion/H-bond correction is available ########
if JOB.PROGRAM == "Mopac" and JOB.JOBTYPE.upper() == "PM6" and interactivemode == 1:
var = raw_input("\no Use dispersion and H-bonding correction ? (Y/N) ")
if var.lower() == "y" or var.lower() == "": JOB.JOBTYPE = "PM6-DH2"; log.Write(" Dispersion and H-bond correction on ... ")
###############################################################
# Solvation with CPCM #########################################
if JOB.PROGRAM == "Gaussian" and interactivemode == 1:
var = raw_input("\no Use CPCM solvation ? (Y/N) ")
if var.lower() == "y" or var.lower() == "":
EPS = raw_input("\n Enter solvent name (default=diethylether) ")
if EPS == "": EPS = "(cpcm,solvent=diethylether)"
JOB.JOBTYPE = JOB.JOBTYPE+" scrf"+EPS; log.Write(" CPCM solvation correction on ... ")
###############################################################
# Solvation with COSMO ########################################
if JOB.PROGRAM == "Mopac" and interactivemode == 1:
var = raw_input("\no Use COSMO solvation ? (Y/N) ")
if var.lower() == "y" or var.lower() == "":
EPS = raw_input("\n Enter solvent dielectric constant (default = 78.4) ")
if EPS == "": EPS = "78.4"
JOB.JOBTYPE = JOB.JOBTYPE+" EPS="+EPS; log.Write(" COSMO solvation correction on ... ")
###############################################################
# MM correction for N planarity? ##############################
if JOB.PROGRAM == "Mopac":
for atom in MOLSPEC.ATOMTYPES:
if atom == "N":
if interactivemode == 1:
var = raw_input("\no Use molecular mechanics correction for planar nitrogen atoms ? (Y/N) ")
if var.lower() == "y" or var.lower() == "": JOB.JOBTYPE = JOB.JOBTYPE+" mmok"; log.Write(" MM correction on ... ")
else: log.Write(" No MM correction ... ")
break
else:
JOB.JOBTYPE = JOB.JOBTYPE+" mmok"; log.Write(" MM correction on ... ")
###############################################################
# Check for any constraints specified #########################
if hasattr(MOLSPEC, "CONSTRAINED"):
JOB.CONSTRAINED = MOLSPEC.CONSTRAINED
#print MOLSPEC.CONSTRAINED
for const in MOLSPEC.CONSTRAINED:
if len(const) == 1: log.Write("\no The Cartesian position of "+str(const[0]+1)+" will be constrained ...")
if len(const) == 2: log.Write("\no The distance "+str(const[0]+1)+"-"+str(const[1]+1)+" will be constrained ...")
if len(const) == 3: log.Write("\no The angle "+str(const[0]+1)+"-"+str(const[1]+1)+"-"+str(const[2]+1)+" will be constrained ...")
if len(const) == 4: log.Write("\no The dihedral "+str(const[0]+1)+"-"+str(const[1]+1)+"-"+str(const[2]+1)+"-"+str(const[3]+1)+" will be constrained ...")
if JOB.PROGRAM == "Gaussian":
if len(MOLSPEC.CONSTRAINED)!=0: JOB.JOBTYPE = "opt(small,modredundant,loose) "+JOB.JOBTYPE
else: JOB.JOBTYPE = "opt(loose) "+JOB.JOBTYPE
###############################################################
if JOB.PROGRAM == "Gaussian":
JOB.JOBTYPE = "# geom=connectivity "+JOB.JOBTYPE
JOB.NPROC = SEARCHPARAMS.POOL
# Monte Carlo or Systematic (for comparison) ##################
if interactivemode == 1:
var = raw_input("\no MCMM (Y) or SUMM (N) ? (Y/N) ")
if var.lower() == "y" or var.lower() == "": SEARCHPARAMS.CSEARCH = "MCMM"
if var.lower() == "n": SEARCHPARAMS.CSEARCH = "SUMM"
###############################################################
# Perform an optimization of the starting geometry ############
MOLSPEC.NAME = MOLSPEC.NAME+"_step_0"
writeInput(JOB, MOLSPEC)
submitJob(JOB, MOLSPEC,log)
while isJobFinished(JOB, MOLSPEC) == 0: time.sleep(0.1)
if isJobFinished(JOB, MOLSPEC) == -1: log.Fatal("\nFATAL ERROR: Optimization of [ %s ] stuck"%file)
if isJobFinished(JOB, MOLSPEC) == 2: log.Fatal("\nFATAL ERROR: Optimization of [ %s ] failed"%file)
###############################################################
# Read the output from the optimization then clean up #########
MOLSPEC.CARTESIANS = getoutData(MOLSPEC).CARTESIANS
MOLSPEC.ENERGY = getoutData(MOLSPEC).ENERGY
for suffix in [".com", ".csh", ".mop", ".arc", ".aux", ".joblog", ".errlog", ".chk"]:
if os.path.exists(MOLSPEC.NAME+suffix): os.remove(MOLSPEC.NAME+suffix)
###############################################################
# Assign variable torsions, number of separate molecules and ##
# (eventually when I get round to it) rings ###################
# If number of steps is not assigned use 3^rotatable torsions #
FMVAR = Assign_Variables(MOLSPEC, SEARCHPARAMS, log)
if SEARCHPARAMS.CSEARCH == "MCMM" and SEARCHPARAMS.STEP == 0:
SEARCHPARAMS.STEP = int(math.pow(3,FMVAR.MCNV))
if SEARCHPARAMS.FLEX == "ON": SEARCHPARAMS.STEP = SEARCHPARAMS.STEP + int(math.pow(3,len(FMVAR.RING)-1))
if SEARCHPARAMS.CSEARCH == "SUMM":
if interactivemode == 1:
SEARCHPARAMS.ITVL = raw_input("\no Required Interval (degrees) for systematic rotations ? ")
if SEARCHPARAMS.ITVL == "": SEARCHPARAMS.ITVL = "60"
SEARCHPARAMS.ITVL = int(SEARCHPARAMS.ITVL)
interval = SEARCHPARAMS.ITVL; ninterval = 360.0/interval
SEARCHPARAMS.STEP = int(math.pow(ninterval,FMVAR.MCNV))-1
###############################################################
# MONTE CARLO SEARCH ##########################################
start = time.strftime("%Y/%m/%d %H:%M:%S", time.localtime())
asciiArt(start); Writeintro(MOLSPEC, SEARCHPARAMS, FMVAR, start, log)
CONFSPEC = MOLSPEC
CSEARCH.NAME.append(MOLSPEC.NAME)
CSEARCH.CARTESIANS.append(MOLSPEC.CARTESIANS)
CSEARCH.TORVAL = [getTorsion(MOLSPEC)]
CSEARCH.CONNECTIVITY.append(MOLSPEC.CONNECTIVITY)
CSEARCH.ENERGY = [MOLSPEC.ENERGY]
CSEARCH.GLOBMIN = MOLSPEC.ENERGY
CSEARCH.CPU = [getoutData(MOLSPEC).CPU]
CSEARCH.ALLCPU = [getoutData(MOLSPEC).CPU]
CSEARCH.LASTFOUND = 0
CSEARCH.CLASH = [0]
# Stop once number of steps exceeded or no new conformers found
while CSEARCH.STEP*SEARCHPARAMS.POOL <= SEARCHPARAMS.STEP:
log.Write("o STEP "+str(CSEARCH.STEP)+": Generating "+str(SEARCHPARAMS.POOL)+" structures ...")
# Setting the geometry that will be altered to generate new conformers - only relevant to MCMM
if SEARCHPARAMS.CSEARCH == "MCMM":
for i in range(0, CSEARCH.NSAVED):
if CSEARCH.ENERGY[i] - CSEARCH.GLOBMIN == 0.0: startgeom = i
# Generate new geometries
for i in range(((CSEARCH.STEP-1)*SEARCHPARAMS.POOL+1),((CSEARCH.STEP)*SEARCHPARAMS.POOL)+1):
CONFSPEC.NAME = filein+"_step_"+str(i)
if SEARCHPARAMS.CSEARCH == "MCMM":
if SEARCHPARAMS.MCSS == "Uniform Usage Directed":
for j in range(0, CSEARCH.NSAVED):
if (CSEARCH.ENERGY[j] - CSEARCH.GLOBMIN) * 2625.5 < SEARCHPARAMS.EWIN:
if CSEARCH.USED[j] < CSEARCH.USED[startgeom]: startgeom = j
if CSEARCH.USED[j] == CSEARCH.USED[startgeom] and CSEARCH.ENERGY[j] < CSEARCH.ENERGY[startgeom]: startgeom = j
CSEARCH.USED[startgeom] = CSEARCH.USED[startgeom] + 1
NBcontacts = 1
if SEARCHPARAMS.CSEARCH == "SUMM":
attempts = 0
torsiontwist = [0]* len(FMVAR.TORSION)
for j in range(0,len(FMVAR.TORSION)-1):
#print i, math.pow(ninterval, (len(torsiontwist)-j-1))
#print int(i)/int(math.pow(ninterval, (len(torsiontwist)-j-1))), int(i)%int(math.pow(ninterval, (len(torsiontwist)-j-1)))
torsiontwist[j] = int(i)/int(math.pow(ninterval, (len(torsiontwist)-j-1))) * interval
while torsiontwist[j] >= 360.0: torsiontwist[j] = torsiontwist[j] - 360.0
torsiontwist[len(FMVAR.TORSION)-1] = int(i)%int(math.pow(ninterval, (len(torsiontwist)-j-1))) * interval
print " Dihedral twists in degrees:", torsiontwist
CONFSPEC.CONNECTIVITY = MOLSPEC.CONNECTIVITY
CONFSPEC.ATOMTYPES = MOLSPEC.ATOMTYPES
CONFSPEC.CHARGE = MOLSPEC.CHARGE
CONFSPEC.MULT = MOLSPEC.MULT
CONFSPEC.MMTYPES = MOLSPEC.MMTYPES
CONFSPEC.CARTESIANS = []
for i in range (0,len(CSEARCH.CARTESIANS[0])):
CONFSPEC.CARTESIANS.append([])
for cart in (CSEARCH.CARTESIANS[0][i]):
CONFSPEC.CARTESIANS[i].append(cart)
print CONFSPEC.CARTESIANS
if FMVAR.MCNV != 0: FMVAR.ADJUST = []
for j in range(0,len(FMVAR.TORSION)): FMVAR.ADJUST.append([int(FMVAR.TORSION[j][0])+1, int(FMVAR.TORSION[j][1])+1, int(torsiontwist[j])])
if hasattr(FMVAR, "ADJUST"):
#print FMVAR.ADJUST
for torsion in FMVAR.ADJUST:
if torsion[2] != 0: CONFSPEC.CARTESIANS = AtomRot(MOLSPEC, torsion, CONFSPEC.CARTESIANS)
NBcontacts = checkDists(CONFSPEC, SEARCHPARAMS)
CSEARCH.CLASH.append(NBcontacts)
if SEARCHPARAMS.CSEARCH == "MCMM":
attempts = 0
while NBcontacts > 0 and attempts < 100:
CONFSPEC.CARTESIANS = []
# The coordinates of the lowest energy, least used structure will be altered
print " STARTING FROM GEOMETRY OF", CSEARCH.NAME[startgeom]
#print CSEARCH.CARTESIANS[startgeom]
#print "SUM1", sum(CSEARCH.CARTESIANS[startgeom])
for i in range (0,len(CSEARCH.CARTESIANS[startgeom])):
CONFSPEC.CARTESIANS.append([])
#print (CSEARCH.CARTESIANS[startgeom][i])
for cart in (CSEARCH.CARTESIANS[startgeom][i]):
#print i, cart
CONFSPEC.CARTESIANS[i].append(cart)
CONFSPEC.CONNECTIVITY = CSEARCH.CONNECTIVITY[startgeom]
CONFSPEC.ATOMTYPES = MOLSPEC.ATOMTYPES
CONFSPEC.CHARGE = MOLSPEC.CHARGE
CONFSPEC.MULT = MOLSPEC.MULT
CONFSPEC.MMTYPES = MOLSPEC.MMTYPES
nrandom = random.randint(FMVAR.MCNVmin, FMVAR.MCNVmax)
#print CONFSPEC.CARTESIANS
#print getTorsion(CONFSPEC)
if FMVAR.MCNV != 0:
FMVAR.ADJUST = []
for dihedral in random.sample(FMVAR.TORSION, nrandom):
FMVAR.ADJUST.append([int(dihedral[0])+1, int(dihedral[1])+1, random.randint(0,360)])
if len(FMVAR.ETOZ) > 0:
ezisomerize = random.choice([0,1])
for dihedral in random.sample(FMVAR.ETOZ,ezisomerize):
#print "ETOZ",dihedral,ezisomerize
FMVAR.ADJUST.append([int(dihedral[0]), int(dihedral[1]), 180])
# Take input geometry and apply specified torsional changes
if hasattr(FMVAR, "ADJUST"):
#print FMVAR.ADJUST
for torsion in FMVAR.ADJUST: CONFSPEC.CARTESIANS = AtomRot(MOLSPEC, torsion, CONFSPEC.CARTESIANS)
#print "AFTER ADJUSTMENT:"
#print getTorsion(CONFSPEC)
# For separate molecules, alter the distances and orientations between a random number of them
if FMVAR.NMOLS > 1:
CONFSPEC.CARTESIANS = translateMol(FMVAR, CONFSPEC)
CONFSPEC.CARTESIANS = rotateMol(FMVAR, CONFSPEC)
if FMVAR.MCRI > 0 and SEARCHPARAMS.FLEX == "ON":
print " Detected a ring substructure: atoms", FMVAR.RING, "are connected"
rcom = find_centroid(FMVAR.RING,CONFSPEC)[3:]
coeffplane, xav, yav, zav, rotated = find_coeffplane(FMVAR.RING,CONFSPEC)
xcoeff= coeffplane.tolist()[0][0]; ycoeff= coeffplane.tolist()[1][0]; cval= coeffplane.tolist()[2][0]
#print "Equation of best-fit plane:","z="+str(xcoeff)+"x+"+str(ycoeff)+"y+"+str(cval) #This gives the equation for the plane of best-fit
####################Make unit vector
rawvector=array([xcoeff,ycoeff,-1]) #Need to make into unit vector
x=float(rawvector[0]); y=float(rawvector[1]); z=float(rawvector[2])
normfactor=1/(x**2+y**2+z**2)**0.5
x=x*normfactor; y=y*normfactor; z=z*normfactor
if z<0: z=-z;y=-y;x=-x #Sign flip if z is negative
#print " Unit vector:", x, y, z #The length of this vector is 1
if rotated == 1:
print "************ coordinated system was rotated! ***********"
old_x = z; old_y = x; old_z = y
if old_z<0: old_z=-old_z;old_y=-old_y;old_x=-old_x
print "Unit vector:", old_x, old_y, old_z
x = old_x; y = old_y; z = old_z
if rotated == 2:
print "************ coordinated system was rotated! ***********"
old_x = y; old_y = z; old_z = x
if old_z<0: old_z=-old_z;old_y=-old_y;old_x=-old_x
print "Unit vector:", old_x, old_y, old_z
x = old_x; y = old_y; z = old_z
if rotated == 3:
print "didn't I tell you this was a bad idea?"
nrandom = random.randint(1, len(FMVAR.RING)/2)
for atomid in random.sample(FMVAR.RING, nrandom):
count = 0; stop=0; currentatom=[]; nextlot=[]
currentatom.append([atomid])
#print currentatom
while count<100 and stop==0:
nextlot=[]; ringneighbour = []
for onecurrentatom in currentatom[count]:
#print "onecurrentatom", (onecurrentatom+1)
for partners in CONFSPEC.CONNECTIVITY[onecurrentatom]:
#print "partners", partners
inf = partners.split("__")
for n in range(0,len(inf)/2):
noback=0
for onepreviousatom in currentatom[count-1]:
if (int(inf[2*n])-1)==onepreviousatom: noback=noback+1
for onepreviousatom in currentatom[count]:
if (int(inf[2*n])-1)==onepreviousatom: noback=noback+1
for ringatom in FMVAR.RING:
if (int(inf[2*n])-1)==ringatom:
#ringneighbour.append(int(inf[2*n])-1)
noback=noback+1
if noback==0: nextlot.append(int(inf[2*n])-1)
count=count+1
#print count
if len(nextlot) == 0:stop=stop+1
currentatom.append(nextlot)
for partners in CONFSPEC.CONNECTIVITY[atomid]:
inf = partners.split("__")
for ringatom in FMVAR.RING:
if (int(inf[2*n])-1)==ringatom:
ringneighbour.append(int(inf[2*n])-1)
print " Neighbours in the ring", ringneighbour
oldvecA = [CONFSPEC.CARTESIANS[atomid][0] - CONFSPEC.CARTESIANS[ringneighbour[0]][0], CONFSPEC.CARTESIANS[atomid][1] - CONFSPEC.CARTESIANS[ringneighbour[0]][1], CONFSPEC.CARTESIANS[atomid][2] - CONFSPEC.CARTESIANS[ringneighbour[0]][2]]
oldvecB = [CONFSPEC.CARTESIANS[atomid][0] - CONFSPEC.CARTESIANS[ringneighbour[1]][0], CONFSPEC.CARTESIANS[atomid][1] - CONFSPEC.CARTESIANS[ringneighbour[1]][1], CONFSPEC.CARTESIANS[atomid][2] - CONFSPEC.CARTESIANS[ringneighbour[1]][2]]
oldnorm = [oldvecA[1]*oldvecB[2]-oldvecA[2]*oldvecB[1], oldvecA[2]*oldvecB[0]-oldvecA[0]*oldvecB[2], oldvecA[0]*oldvecB[1]-oldvecA[1]*oldvecB[0]]
oldmag = (oldnorm[0]**2 + oldnorm[1]**2 + oldnorm[2]**2) ** 0.5
oldnorm = [oldnorm[0]/oldmag, oldnorm[1]/oldmag, oldnorm[2]/oldmag]
mag = 1.0; magnitude = random.uniform(-1*mag,mag)
print CONFSPEC.CARTESIANS[atomid]
CONFSPEC.CARTESIANS[atomid][0] = CONFSPEC.CARTESIANS[atomid][0] + x * magnitude
CONFSPEC.CARTESIANS[atomid][1] = CONFSPEC.CARTESIANS[atomid][1] + y * magnitude
CONFSPEC.CARTESIANS[atomid][2] = CONFSPEC.CARTESIANS[atomid][2] + z * magnitude
print " TRANSLATING ATOM", (atomid+1), "BY ", [magnitude*x,magnitude*y,magnitude*z]
print CONFSPEC.CARTESIANS[atomid]
newvecA = [CONFSPEC.CARTESIANS[atomid][0] - CONFSPEC.CARTESIANS[ringneighbour[0]][0], CONFSPEC.CARTESIANS[atomid][1] - CONFSPEC.CARTESIANS[ringneighbour[0]][1], CONFSPEC.CARTESIANS[atomid][2] - CONFSPEC.CARTESIANS[ringneighbour[0]][2]]
newvecB = [CONFSPEC.CARTESIANS[atomid][0] - CONFSPEC.CARTESIANS[ringneighbour[1]][0], CONFSPEC.CARTESIANS[atomid][1] - CONFSPEC.CARTESIANS[ringneighbour[1]][1], CONFSPEC.CARTESIANS[atomid][2] - CONFSPEC.CARTESIANS[ringneighbour[1]][2]]
newnorm = [newvecA[1]*newvecB[2]-newvecA[2]*newvecB[1], newvecA[2]*newvecB[0]-newvecA[0]*newvecB[2], newvecA[0]*newvecB[1]-newvecA[1]*newvecB[0]]
newmag = (newnorm[0]**2 + newnorm[1]**2 + newnorm[2]**2) ** 0.5
newnorm = [newnorm[0]/newmag, newnorm[1]/newmag, newnorm[2]/newmag]
rotang = 180.0/math.pi*math.acos(oldnorm[0]*newnorm[0]+oldnorm[1]*newnorm[1]+oldnorm[2]*newnorm[2])
print " A ROTATION THROUGH", rotang
#newvec = [CONFSPEC.CARTESIANS[atomid][0] - rcom[0], CONFSPEC.CARTESIANS[atomid][1] - rcom[1], CONFSPEC.CARTESIANS[atomid][2] - rcom[2]]
#coords = [oldvec, [0.0,0.0,0.0],newvec]
#rotang = calcangle(0,1,2,coords)
#vectorAB = [oldvec[1]*z-oldvec[2]*y, oldvec[2]*x -oldvec[0]*y, oldvec[0]*y-oldvec[1]*x]
#print " OLD VECTOR FROM COM", oldvec
#print " NEW VECTOR FROM COM", newvec
#print " A ROTATION OF",rotang
#print " ABOUT", vectorAB
#distAB = math.sqrt(vectorAB[0]*vectorAB[0]+vectorAB[1]*vectorAB[1]+vectorAB[2]*vectorAB[2])
#unitAB = [vectorAB[0]/distAB,vectorAB[1]/distAB,vectorAB[2]/distAB]
for subst in currentatom[1:]:
for nextatomid in subst:
print " ALSO TRANSLATING ATOM", (nextatomid+1), "BY ", [magnitude*x,magnitude*y,magnitude*z]
CONFSPEC.CARTESIANS[nextatomid][0] = CONFSPEC.CARTESIANS[nextatomid][0] + x * magnitude
CONFSPEC.CARTESIANS[nextatomid][1] = CONFSPEC.CARTESIANS[nextatomid][1] + y * magnitude
CONFSPEC.CARTESIANS[nextatomid][2] = CONFSPEC.CARTESIANS[nextatomid][2] + z * magnitude
print " ALSO ROTATING ATOM", (nextatomid+1), "THROUGH ANGLE", rotang, "ABOUT THE AXIS", ringneighbour
print CONFSPEC.CARTESIANS[nextatomid]
atomA = ringneighbour[0]; atomB = ringneighbour[1]
vectorAB = [CONFSPEC.CARTESIANS[atomB][0]-CONFSPEC.CARTESIANS[atomA][0],CONFSPEC.CARTESIANS[atomB][1]-CONFSPEC.CARTESIANS[atomA][1],CONFSPEC.CARTESIANS[atomB][2]-CONFSPEC.CARTESIANS[atomA][2]]
distAB = (vectorAB[0]**2+vectorAB[1]**2+vectorAB[2]**2) ** 0.5
unitAB = [vectorAB[0]/distAB,vectorAB[1]/distAB,vectorAB[2]/distAB]
dotproduct = unitAB[0]*(CONFSPEC.CARTESIANS[nextatomid][0] - CONFSPEC.CARTESIANS[atomid][0]) + unitAB[1]*(CONFSPEC.CARTESIANS[nextatomid][1] - CONFSPEC.CARTESIANS[atomid][1]) + unitAB[2]*(CONFSPEC.CARTESIANS[nextatomid][2] - CONFSPEC.CARTESIANS[atomid][2])
centre = [CONFSPEC.CARTESIANS[atomid][0] + dotproduct*unitAB[0], CONFSPEC.CARTESIANS[atomid][1] + dotproduct*unitAB[1], CONFSPEC.CARTESIANS[atomid][2] + dotproduct*unitAB[2]]
v = [CONFSPEC.CARTESIANS[nextatomid][0] - centre[0], CONFSPEC.CARTESIANS[nextatomid][1] - centre[1], CONFSPEC.CARTESIANS[nextatomid][2] - centre[2]]
theta = -float(rotang)/180.0*math.pi
d = (v[0]**2+v[1]**2+v[2]**2) ** 0.5
px = v[0]*math.cos(theta) + v[1]*math.sin(theta)*unitAB[2] - v[2]*math.sin(theta)*unitAB[1]
py = v[1]*math.cos(theta) + v[2]*math.sin(theta)*unitAB[0] - v[0]*math.sin(theta)*unitAB[2]
pz = v[2]*math.cos(theta) + v[0]*math.sin(theta)*unitAB[1] - v[1]*math.sin(theta)*unitAB[0]
CONFSPEC.CARTESIANS[nextatomid] = [px + centre[0], py + centre[1], pz + centre[2]]
print CONFSPEC.CARTESIANS[nextatomid]
# Check for any VDW contacts smaller than specified limits
NBcontacts = checkDists(CONFSPEC, SEARCHPARAMS)
if NBcontacts != 0:
attempts = attempts + 1
print " EXTREME CONTACTS: TRYING AGAIN..."
CSEARCH.CLASH.append(NBcontacts)
# Write input and optimize geometry
#print CONFSPEC.CARTESIANS
if NBcontacts == 0 and attempts < 100: print " SUCCESSFULLY ALTERED GEOM..."
if attempts > 99 and NBcontacts != 0: print " EXCEEDED MAXIMUM ATTEMPTS TO ALTER GEOM..."
if NBcontacts == 0: writeInput(JOB, CONFSPEC); submitJob(JOB, CONFSPEC, log)
# Filter after optimization
for i in range(((CSEARCH.STEP-1)*SEARCHPARAMS.POOL+1),((CSEARCH.STEP)*SEARCHPARAMS.POOL)+1):
CONFSPEC.NAME = filein+"_step_"+str(i)
# Make sure optimization is complete
#print i, CSEARCH.CLASH
if CSEARCH.CLASH[i] == 0:
while isJobFinished(JOB, CONFSPEC) == 0: time.sleep(0.1)
# Successful termination - extract details
if isJobFinished(JOB, CONFSPEC) == 1:
CONFSPEC = getoutData(CONFSPEC)
CONFSPEC.ATOMTYPES = MOLSPEC.ATOMTYPES
CSEARCH.ALLCPU.append(CONFSPEC.CPU)
#Check whether the molecule has isomerized - usually this is undesirable so filter out structural isomers
concheck = checkconn(CONFSPEC, MOLSPEC, CSEARCH, SEARCHPARAMS)
if concheck[0] == 0: CONFSPEC.CONNECTIVITY = MOLSPEC.CONNECTIVITY; isomerize = 0
else: isomerize = 1; log.Write(" "+(CONFSPEC.NAME+" is rejected: "+concheck[1]+concheck[2]+" has broken from "+concheck[3]+concheck[4]).ljust(50))
#Check whether any stereogenic centres have been epimerized
chircheck = checkchir(CONFSPEC, MOLSPEC, CSEARCH, SEARCHPARAMS)
if chircheck[0] == 0: CONFSPEC.CONNECTIVITY = MOLSPEC.CONNECTIVITY; isomerize = 0
else: isomerize = 1; log.Write(" "+(CONFSPEC.NAME+" is rejected: atom "+str(chircheck[1])+" has been epimerized").ljust(50))
#Check whether the molecule has high energy
if ((CONFSPEC.ENERGY-CSEARCH.GLOBMIN)*2625.5) < SEARCHPARAMS.DEMX: toohigh = 0
else: toohigh = 1; log.Write(" "+(CONFSPEC.NAME+" is rejected due to high energy ... ").ljust(50))
samecheck=0
# Save or discard the optimized structure - reject if higher than global minimum by DEMX kJ/mol
if toohigh == 0 and isomerize == 0:
for j in range(0, CSEARCH.NSAVED):
#if (CONFSPEC.ENERGY-CSEARCH.GLOBMIN)*2625.5 < -0.1: break
if abs((CONFSPEC.ENERGY-CSEARCH.ENERGY[j])*2625.5) < ECOMP:
#print " COMPARING "+CONFSPEC.NAME+" "+str(CONFSPEC.ENERGY)+" cf "+CSEARCH.NAME[j]+" "+str(CSEARCH.ENERGY[j])+": ediff = "+str((CONFSPEC.ENERGY-CSEARCH.ENERGY[j])*2625.5)
if checkSame(CONFSPEC, CSEARCH, SEARCHPARAMS, j) > 0 or checkSame(makemirror(CONFSPEC), CSEARCH, SEARCHPARAMS, j) > 0:
log.Write(" "+(CONFSPEC.NAME+" is a duplicate of conformer "+CSEARCH.NAME[j]+" ... ").ljust(50))
CSEARCH.TIMESFOUND[j] = CSEARCH.TIMESFOUND[j] + 1
CSEARCH.NREJECT = CSEARCH.NREJECT + 1
samecheck = samecheck + 1
break
# Unique conformation with low energy! ########################
if samecheck == 0:
if CONFSPEC.ENERGY < CSEARCH.GLOBMIN:
CSEARCH.GLOBMIN = CONFSPEC.ENERGY
log.Write(" "+(CONFSPEC.NAME+" is a new Global Minimum!").ljust(80)+("E = "+str(CSEARCH.GLOBMIN)).rjust(rightcol))
else : log.Write(" "+(CONFSPEC.NAME+" is saved").ljust(80)+("E = "+str(CONFSPEC.ENERGY)).rjust(rightcol))
AddConformer(CSEARCH, CONFSPEC)
if (CONFSPEC.ENERGY-CSEARCH.GLOBMIN)*2625.5 < SEARCHPARAMS.EWIN: CSEARCH.LASTFOUND = CSEARCH.STEP*SEARCHPARAMS.POOL
###############################################################
# Rejection - discard #########################################
else: CSEARCH.NREJECT = CSEARCH.NREJECT + 1
else:
log.Write("\n Unsuccessful optimization of "+CONFSPEC.NAME+".out ...")
CSEARCH.NFAILED = CSEARCH.NFAILED + 1
CleanAfterJob(JOB, CONFSPEC, samecheck, toohigh, isomerize)
OrderConfs(CSEARCH, SEARCHPARAMS, start, log)
###############################################################
else: log.Write("\n "+CONFSPEC.NAME+" not run due to extreme steric crowding ...")
# End of step - update the search statistics ##################
if (CSEARCH.STEP*SEARCHPARAMS.POOL-CSEARCH.NFAILED) != 0: CSEARCH.AERATE = float(CSEARCH.STEP*SEARCHPARAMS.POOL-CSEARCH.NREJECT-CSEARCH.NFAILED)/float(CSEARCH.STEP*SEARCHPARAMS.POOL-CSEARCH.NFAILED)*100.0
else: CSEARCH.AERATE = 0.0
if len(CSEARCH.TIMESFOUND) > 0:
for dup in CSEARCH.TIMESFOUND:
if dup < CSEARCH.DMIN: CSEARCH.DMIN = dup
else: CSEARCH.DMIN = 0
###############################################################
#Tidy up the geometries and output the results ################
if CSEARCH.STEP % 100 == 0:
todel=[]
#print (CSEARCH.NAME)
for i in range(0,len(CSEARCH.NAME)):
if ((CSEARCH.ENERGY[i] - CSEARCH.GLOBMIN)*2625.5) > SEARCHPARAMS.DEMX or (i > 199):
#print CSEARCH.NAME[i], "earmarked for deletion"
todel.append(i)
if len(todel) !=0: RemoveConformer(CSEARCH, todel)
WriteSummary(CSEARCH, SEARCHPARAMS, start, log)
CleanUp(CSEARCH, SEARCHPARAMS, filein, log)
makeGVformat(filein, MOLSPEC, CSEARCH, SEARCHPARAMS, "fm"); makePDBformat(filein, MOLSPEC, CSEARCH, "fm")
#End of step - update step number
CSEARCH.STEP = CSEARCH.STEP + 1
###############################################################
#Summary of completed Full Monte search #######################
CSEARCH.COMPLETE = 1
if SEARCHPARAMS.CSEARCH == "MCMM":
if (CSEARCH.STEP*SEARCHPARAMS.POOL-CSEARCH.LASTFOUND) >100: log.Write("\no Full Monte stopped finding new conformers ...")
CSEARCH.STEP = SEARCHPARAMS.STEP
else:log.Write("\no Full Monte completed all "+str(SEARCHPARAMS.STEP)+" steps...")
WriteSummary(CSEARCH, SEARCHPARAMS, start, log)
CleanUp(CSEARCH, SEARCHPARAMS, filein, log)
makeGVformat(filein, MOLSPEC, CSEARCH, SEARCHPARAMS, "fm"); makePDBformat(filein, MOLSPEC, CSEARCH, "fm")
###############################################################
# Multiple Minimization with higher convergence criterion ####
if SEARCHPARAMS.MMIN >0:
log.Write("\no Reoptimizing conformers with strict convergence criteria ...")
if JOB.PROGRAM == "Mopac": JOB.JOBTYPE = JOB.JOBTYPE+" gnorm=0.0 "
if JOB.PROGRAM == "Gaussian": JOB.JOBTYPE = JOB.JOBTYPE.replace("loose", "")
MultMin(CSEARCH, SEARCHPARAMS,CONFSPEC, MOLSPEC, JOB, start, log)
#OrderConfs(CSEARCH, SEARCHPARAMS, start, log)
CSEARCH.GLOBMIN = CSEARCH.ENERGY[0]
###############################################################
# Final Summary of Full Monte search ##########################
WriteSummary(CSEARCH, SEARCHPARAMS, start, log)
if os.path.isfile(filein+"_fm.tgz") == 1: os.remove(filein+"_fm.tgz")
CleanUp(CSEARCH, SEARCHPARAMS, filein, log)
makeGVformat(filein, MOLSPEC, CSEARCH, SEARCHPARAMS, "fm"); makePDBformat(filein, MOLSPEC, CSEARCH, "fm")
end = time.strftime("%Y/%m/%d %H:%M:%S", time.localtime())
asciiArt(end); log.Write(normaltermination); log.Finalize()
###############################################################