def GenerateContactMap(TimeStep,protocol):
"""Read a frame and compute the contactMap between two groups of atom given a ContactMapProtocol
NOTE: if protocol.byres=True, then we report the number of atomic contacts for a given
residue pair in contact
Numbering of atoms and residues is the one given by the PSF file"""
rowNS = AtomNeighborSearch(protocol.rowGroup) #KDE-tree object for rowGroup
colNS = AtomNeighborSearch(protocol.colGroup) #KDE-tree object for colGroup
rowClose = rowNS.search_list(protocol.colGroup,protocol.cutOff) #atoms of rowGroup in contact with colGroup
if not rowClose: #no contacts
shape=(TimeStep.numatoms,TimeStep.numatoms) #all atoms in the system
if protocol.byres: shape=(protocol.numberOfResidues,protocol.numberOfResidues)
csr=csr_matrix( ([],([],[])), shape, dtype='int32') #empty map
cma=CMA.csr_ContactMap(csr)
cma.setDistanceCutOff(protocol.cutOff)
return cma
colClose = colNS.search_list(rowClose,protocol.cutOff) #atoms of colGroup in contact with rowClose/rowGroup
dd=distance_array(rowClose.coordinates(),colClose.coordinates(),TimeStep.dimensions[0:3])
(rowIndices,colIndices) = numpy.where(dd<protocol.cutOff)
rowIndices=rowClose.indices()[rowIndices]
colIndices=colClose.indices()[colIndices]
if protocol.byres:
#switch from atomic indices to residue numbers
rowIndices=protocol.atom2res[rowIndices]
colIndices=protocol.atom2res[colIndices]
shape=(protocol.numberOfResidues,protocol.numberOfResidues)
else:
#Take into account if the first atomic index was zero
rowIndices += protocol.shift
colIndices += protocol.shift
shape=(TimeStep.numatoms,TimeStep.numatoms) #all atoms in the system
#create sparse matrix for the contact map.
data=numpy.ones( len(rowIndices) ) #just signaling a contact map
csr=csr_matrix( (data, (rowIndices,colIndices)), shape, dtype='int32')
if protocol.byres: csr.data[:]=1 #overwrite number of atomic contacts per residue pair with 1 only
#trace()
if protocol.filter: csr=protocol.filter(csr) #Filtering
cma=CMA.csr_ContactMap(csr)
cma.setDistanceCutOff(protocol.cutOff)
return cma
import sys
sys.path.append('/home/jbq/repositories/ContactMapAnalysis')
import ContactMapAnalysis as CMA
import argparse
from pdb import set_trace as tr
if __name__=='__main__':
parser = argparse.ArgumentParser(description='save all residence times as a single column file')
parser.add_argument('hdf5',help='HDF5 file containing the residence times')
parser.add_argument('--outfile',help='save to file. Otherwise print to standard output"')
args = parser.parse_args()
rtl = CMA.loadResidenceTimesListFromFile(args.hdf5)
buf=''
for ires in range(1,rtl.n):
if rtl.data[ires]:
L=rtl.data[ires] #list of isopropanol residence times to this particular residue
buf+='\n'.join([str(x) for x in L])+'\n'
if args.outfile:
open(args.outfile,'w').write(buf)
else:
print buf
