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# $Id: rdkpympi.py 1272 2009-10-31 06:09:20Z glandrum $
#
# Copyright (C) 2009 Greg Landrum
# All rights reserved
#
# Demo for using boost.mpi with the RDKit
#
# run this with : mpirun -n 4 python rdkpympi.py
#
from boost import mpi
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.RDLogger import logger
logger = logger()
def dividetask(data,task,silent=True):
data=mpi.broadcast(mpi.world,data,0)
nProcs = mpi.world.size
chunkSize=len(data)//nProcs
extraBits =len(data)%nProcs
res=[]
allRes=[]
# the root node handles the extra pieces:
if mpi.world.rank == 0:
for i in range(extraBits):
elem=data[i]
res.append(task(elem))
if not silent:
logger.info('task(%d) done %d'%(mpi.world.rank,i+1))
pos=extraBits+mpi.world.rank*chunkSize;
for i in range(chunkSize):
elem=data[pos]
pos += 1
res.append(task(elem))
if not silent:
logger.info('task(%d) done %d'%(mpi.world.rank,i+1))
if mpi.world.rank==0:
tmp=mpi.gather(mpi.world,res,0)
for res in tmp: allRes.extend(res)
else:
mpi.gather(mpi.world,res,0)
return allRes
if __name__=='__main__':
from rdkit import RDConfig
import os
fName = os.path.join(RDConfig.RDBaseDir,'Projects','DbCLI','testData','bzr.sdf')
if mpi.world.rank==0:
data = [x for x in Chem.SDMolSupplier(fName)][:50]
else:
data=None
def generateconformations(m):
m = Chem.AddHs(m)
ids=AllChem.EmbedMultipleConfs(m,numConfs=10)
for id in ids:
AllChem.UFFOptimizeMolecule(m,confId=id)
return m
cms=dividetask(data,generateconformations,silent=False)
# report:
if mpi.world.rank==0:
for i,mol in enumerate(cms):
print i,mol.GetNumConformers()
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