def densper_res(where,residueArray,minresnum,sideormain,densmet,pdbname):
# plots a boxplot for each residue detailing the electron density
# distn.
# 'minresnum' is the threshold for the min number of residues of a
# given type that need to be present in structure to be included in
# the end plot
# 'sideormain' specifies whether 'sidechain' only, 'mainchain' only,
# or ['sidechain','mainchain'] are selected
# 'densmet' specifies the density metric to be used ('mean','median',
# 'max','min')
residue_label = []
# The next section of code plots a boxplot for each residue/base
# type in structure
densitylist = []
for res in residueArray:
# only residue types with more than a specified frequency will be
# included in the plot
if res.frequency > minresnum:
print str(res.name) + ' -----> '\
+ str(res.frequency)
# need to merge 2d list res_obj of atoms by atom type into 1d list
merged_atms = sum(res.atms_bytype,[])
# determine the density metric to use and create list of densities
# from merged_atms
if densmet in ('mean'):
merged_dens = [atom.meandensity for atom in merged_atms
if (atom.side_or_main() in sideormain)]
elif densmet in ('median'):
merged_dens = [atom.mediandensity for atom in merged_atms
if (atom.side_or_main() in sideormain)]
elif densmet in ('min'):
merged_dens = [atom.mindensity for atom in merged_atms
if (atom.side_or_main() in sideormain)]
elif densmet in ('max'):
merged_dens = [atom.maxdensity for atom in merged_atms
if (atom.side_or_main() in sideormain)]
else:
print 'Unknown electron density metric specified'
sys.exit()
densitylist.append(merged_dens)
# get list of residue names for boxplot x-axis label
residue_label.append(res.name)
print 'Plotting all present residues now......'
residue_violinplotter(where,densitylist,
residue_label,
densmet,
'ALL'+str(sideormain),
pdbname,
densmet)
def densper_resatom_NOresidueclass(where = '',
PDBarray = [],
plot = True,
densMet = 'mean',
pdbName = ''):
# this function plots violin plots of atom density for each residue
# type, and also outputs a list of residue objects (see residuetype
# class)
# KEY:
# 'PDBarray' is list of atoms of structure
# 'plot' (boolian) determines whether individual boxplots plotted
# 'densmet' takes values 'mean','median','max','min' to determine
# metric of electron density
# first ensure PDB list ordered by atom number
PDBarray.sort(key=lambda x: (x.basetype,x.atomnum))
# find list of protein residues and nucleic acids
# present in structure (with repeated names removed)
resi_list = [atom.basetype for atom in PDBarray]
restype_list = []
appendres = restype_list.append
for res in resi_list:
if res not in restype_list:
appendres(res)
restype_list.sort()
residueArray = []
for res in restype_list:
#create an object for the residue type (in residuetype class)
res_obj = res2atomsbytype(PDBarray,res)
print '------------SUMMARY---------------'
print 'Total number of residues of type {}: {}'.format(res_obj.name,str(res_obj.frequency))
print 'Maximum size of residue calculated to be: {}'.format(res_obj.atm_names)
# determine the density metric to use and create list of densities
# from 'atms_bytype' attribute for the residue object
dens_list = []
if densmet in ('mean'):
for atmtype in res_obj.atms_bytype:
dens_list.append([atm.meandensity for atm in atmtype])
elif densmet in ('median'):
for atmtype in res_obj.atms_bytype:
dens_list.append([atm.mediandensity for atm in atmtype])
elif densmet in ('min'):
for atmtype in res_obj.atms_bytype:
dens_list.append([atm.mindensity for atm in atmtype])
elif densmet in ('max'):
for atmtype in res_obj.atms_bytype:
dens_list.append([atm.maxdensity for atm in atmtype])
else:
print 'Unknown electron density metric specified'
sys.exit()
# call the boxplotting function to plot boxplot of atom type
# against electron density change for given residue type
if plot is True:
print 'Plotting now...'
residue_violinplotter(where,dens_list,
res_obj.atm_names,
res_obj.name,
res_obj.frequency,
pdbname,
densmet)
residueArray.append(res_obj)
return residueArray
