def makeIndexFile(self,
grofile,
ndxfile,
protein=True,
ions=True,
sol=True,
bath=True,
system=True,
debug=False):
"""Reads in the grofile, and make an *.ndx file with atom groups corresponding to a list of commmon-sense names
given in the groups=[] list.
REQUIRED
grofile - gromacs structure filename from which to compile the atom groups
ndxfile - filename to write the index file to
Supported group names so far:
protein All protein atoms
sol All solvent atoms. (protein + sol + ions) shouuld equal (system) !
ions All ions
bath (sol + ions)
system All atoms
Note: This subroutine assumes it's being called from the current working directory
OUTPUT
Writes an index file to the given filename.
"""
ndx = IndexFile()
all_indices = ndx.getAtomListFromGrofile(grofile)
ion_indices = ndx.getAtomListFromGrofile(
grofile, ResName=['Na', 'Cl', 'Na+', 'Cl-', 'Mg', 'Ca'])
sol_indices = ndx.getAtomListFromGrofile(grofile,
ResName=['SOL', 'HOH'])
# The protein indices are considered to be all the residues besides ions and solvent
protein_indices = [
i for i in all_indices
if (ion_indices.count(i) == 0 and sol_indices.count(i) == 0)
]
# The bath is just the ions plus the solvent
bath_indices = ion_indices + sol_indices
# Create the index file groups
ndx.addIndexGroup('protein', protein_indices)
ndx.addIndexGroup('sol', sol_indices)
ndx.addIndexGroup('ions', ion_indices)
ndx.addIndexGroup('bath', bath_indices)
ndx.addIndexGroup('system', all_indices)
# write the ndxfile
ndx.writeIndexFile(ndxfile)
def make_ndx(self, grofile, ndxfile, protein=True, ions=True, sol=True, bath=True, system=True, debug=False):
"""Make an *.ndx file with atom groups corresponding to a list of commmon-sense names
given in the groups=[] list. Supported group names so far:
protein All protein atoms
sol All solvent atoms. (protein + sol + ions) shouuld equal (system) !
ions All ions
bath (sol + ions)
system All atoms
Note: This subroutine assumes it's being called from the current working directory
"""
ndx = IndexFile()
all_indices = ndx.getAtomListFromGrofile(grofile)
ion_indices = ndx.getAtomListFromGrofile(grofile, ResName=['Na','Cl','Na+','Cl-','Mg','Ca'])
sol_indices = ndx.getAtomListFromGrofile(grofile, ResName=['SOL','HOH'])
# The protein indices are considered to be all the residues besides ions and solvent
protein_indices = [i for i in all_indices if (ion_indices.count(i) == 0 and sol_indices.count(i) == 0) ]
# The bath is just the ions plus the solvent
bath_indices = ion_indices + sol_indices
# Create the index file groups
ndx.addIndexGroup('protein', protein_indices)
ndx.addIndexGroup('sol', sol_indices)
ndx.addIndexGroup('ions', ion_indices)
ndx.addIndexGroup('bath', bath_indices)
ndx.addIndexGroup('system', all_indices)
# write the ndxfile
ndx.writeIndexFile(ndxfile)
