def run(configx):
"""
Entry point for the plugin manager
:param configx: plugin manager instance
:return: None
"""
global config, data
config = configx
printer = config.setup()
pdbiop = PDBIOP('test.test')
pdbiop.setup(new=True)
data = config.get_variable()
pdbiop.set(['cart', 'serial_numbers', 'name_prefixes', 'occupancies',
'adp_cart', 'residue_numbers', 'vdw_radii', 'point_charges'],
provide, new=True)
printer(pdbiop.export('PQR'))
with open(config.arg('write'), 'w') as fp:
fp.write(pdbiop.export('PQR'))
printer('\nPQR formatted output written to {}.'.format(config.arg('write')))
def report(accumulator):
"""
Compiles a table representing the data analysis results and
prints it to the output.
"""
printer('\n')
length = int(config.arg('list'))
gt = float(config.arg('gt'))
resi = config.arg('residue')
rtype = config.arg('type')
sigma = float(config.arg('sigma'))
sorted_atoms = sorted(accumulator.atoms(), key=lambda atom: atom.get_error_dist(), reverse=True)
printer.table(['Type', 'ID', 'Resi', '#', 'ESD', 'ESD: X Y Z', 'Average Position'], head=True)
counter = 0
for atom in sorted_atoms:
errors = '{:3.1f}'.format(atom.get_error_dist())
if gt:
if not float(errors) >= gt:
continue
if resi:
if not atom.get_residue() == resi:
continue
if rtype:
if not atom.get_type() == rtype:
continue
xyz_err = '{:3.1f} {:3.1f} {:3.1f}'.format(*atom.get_error_cart())
position = '{:5.1f} {:5.1f} {:5.1f}'.format(*atom.get_cart())
printer.table([atom.get_type(),
atom.get_serial_number(),
atom.get_residue(),
atom.get_residue_number(),
errors,
xyz_err,
position])
counter += 1
if counter == length:
break
printer.table(done=True)
def provideNew():
"""
Generator providing data to a PDB file.
"""
for thisatom in sorted_atoms:
if thisatom.get_error_dist() < cutoff:
yield [thisatom.get_name(),
thisatom.get_serial_number(),
thisatom.get_type(),
thisatom.get_residue(),
thisatom.get_residue_number(),
thisatom.get_cart(),
thisatom.get_occupancy(),
thisatom.get_adp_cart()]
# printer('\n\n{} atoms removed.'.format(ko))
_mask = config.arg('mask')
if not _mask:
_mask = 'all'
crosspdb = PDBIOP('{}_crosscheck.pdb'.format(_mask))
crosspdb.setup(new=True)
crosspdb.set(['serial_numbers', 'name_prefixes', 'residues',
'residue_numbers', 'cart', 'occupancies', 'adp_cart'],
provideNew, new=True)
crosspdb.complete_rebuild()
crosspdb.write()
printer('\n\nAveraged PDB file without atoms with ESDs larger than {} written to:\n{}'.format(cutoff,
'{}_crosscheck.pdb'.format(_mask)))
def run(conf):
global config
config = conf
printer = config.setup()
printer('\nThe resp_pqr_plugin has been successfully started.\n' \
'Now, resp-charges are assigned according to their invariom name.' \
'\nIn order to do this a file called chargeDABA.txt \ncontaining all invariomnames with' \
'the correcponding resp charges is needed.\n')
printer('\nAsking config for value of option \'load\': {}'.format(config.arg('load')))
printer('Asking config for value of option \'x\': {}'.format(config.arg('x')))
import lauescript.invstring2 as invstring
config.call('applyhdist')
###--------reading chargeDABA.txt into dictionary chargedict ---------------#
path_string = conf.get_databasepath()
global chargedict
chargedict = {}
f = open(path_string + '/chargeDABA.txt', 'r')
for line in f.readlines():
line = line[:-1].split()
chargedict[line[0]] = float(line[1])
f.close()
###----------------------
###--------molecule identifier ---------------#
global molcount
molcount=0
global chargedicts
chargedicts = {}
global resp_arrays
resp_arrays = {}
global atomcounts
atomcounts = {}
global average_charges
average_charges = {}
data = config.get_variable()
for atom in data['exp'].atoms:
if atom.molecule_id > molcount:
molcount = atom.molecule_id
resp_arrays[atom.molecule_id]= []
molcount=molcount+1
printer('{} molecule(s) detected.'.format(molcount))
for j in range(0,molcount):
resp_arrays[j] = []
atomcounts[j] = 0
average_charges[j] = 0.0
chargedicts[j]={}
for atom in data['exp'].atoms:
atomcounts[atom.molecule_id] = atomcounts[atom.molecule_id] + 1
###----------------------
global average_corrections
average_corrections = {}
overallcharges = {}
resp = 0.0
charged=config.arg("charged")
import charge_lib
for j in range(0,molcount):
overallcharges[j]=0.0
overallcharges[j]=charge_lib.check_charges(j, atomcounts, charged, printer )
### Electroneutrality correction
###-------------collecting charges for the molecule
###-------------to get a correction factor for electroneutrality
### ----Option a
###-------------via a correction averaged over the whole molecule
neutral = config.arg("neutral")
if not neutral or neutral == "a":
printer(neutral)
for atom in data['exp'].atoms:
import charge_lib
charge_lib.build_resp_arrays( atom, resp_arrays, chargedict, average_charges)
for key in resp_arrays:
printer('\nMolecule number {}:'.format(key))
printer('Number of atoms read: {}'.format(atomcounts[key]))
#printer('\nCharges of the invarioms')
#printer(resp_array)
printer('Charge of molecule if uncorrected: {:5.3f}'.format(sum(resp_arrays[key])))
printer('Deviation from charge of {:5.3f}: {:5.3f}'.format(overallcharges[key],sum(resp_arrays[key])-overallcharges[key]))
average_corrections[key] = float(float((sum(resp_arrays[key])-overallcharges[key])) / float(atomcounts[key]))
printer('Correction for every atom: {:5.3f}'.format(average_corrections[key]))
printer('Average charge per atom: {:5.3f}, correction in percent: {:5.2f}%'.format(average_charges[key]/atomcounts[key],100*average_corrections[key]/(average_charges[key]/atomcounts[key])))
### Assigning charge
#print '\natom elec val_elec invariom resp_charge corr_charge\n'
#i = 0
already_corrected_inv_list = []
data = config.get_variable()
for atom in data['exp'].atoms:
if atom.molecule_id == key :
#i = i + 1
resp = chargedict[atom.invariom_name]
if atom.invariom_name not in already_corrected_inv_list:
charge = resp - average_corrections[key]
#chargedict[atom.invariom_name] = charge
already_corrected_inv_list.append(atom.invariom_name)
chargedicts[key][atom.invariom_name] = charge
else:
charge = resp- average_corrections[key]
#resp = charge + average_corrections[key]
#print atom.name, atom.invariom_name, resp, charge
### ----Option b
###-------------via a correction averaged all hydrogen atoms only
elif neutral == "b":
printer(neutral)
data = config.get_variable()
Hatomcounts = {}
for j in range(0,molcount):
Hatomcounts[j] = 0
for atom in data['exp'].atoms:
if atom.element == "H":
Hatomcounts[atom.molecule_id] = Hatomcounts[atom.molecule_id] + 1
import charge_lib
charge_lib.build_resp_arrays( atom, resp_arrays, chargedict, average_charges)
for key in resp_arrays:
printer(key)
printer('\nNumber of H atoms read:')
printer(Hatomcounts[key])
printer('Charges of the invarioms')
printer(resp_arrays[key])
printer('\nCharge of molecule if uncorrected:')
printer(sum(resp_arrays[key]))
printer('Deviation from charge of {}:'.format(overallcharges[key]))
printer(sum(resp_arrays[key])-overallcharges[key])
average_corrections[key] = float(float((sum(resp_arrays[key])-overallcharges[key])) / float(Hatomcounts[key]))
printer('Correction for every H atom:')
printer(average_corrections[key])
printer('\nAverage charge per atom, correction in percent:')
printer(average_charges[key]/Hatomcounts[key])
printer(average_corrections[key]/(average_charges[key]/Hatomcounts[key]))
### Assigning charge
#print '\natom elec val_elec invariom resp_charge corr_charge\n'
i = 0
already_corrected_inv_list = []
data = config.get_variable()
for atom in data['exp'].atoms:
if atom.molecule_id == key :
i = i + 1
resp = chargedict[atom.invariom_name]
if atom.element == "H":
if atom.invariom_name not in already_corrected_inv_list:
charge = resp - average_corrections[key]
chargedicts[key][atom.invariom_name] = charge
already_corrected_inv_list.append(atom.invariom_name)
else:
charge = resp - average_corrections[key]
resp = charge
else:
charge = resp
chargedicts[key][atom.invariom_name] = charge
#print atom.name, atom.invariom_name, resp, charge
### -----------------------------------
###
### Writing the charges into a pqr file
###
### -----------------------------------
from lauescript.laueio.pdb_iop import PDBIOP
global data
pdbiop = PDBIOP('test.test')
pdbiop.setup(new=True)
pdb_data = config.get_variable()
pdbiop.set(['cart', 'serial_numbers', 'name_prefixes', 'occupancies',
'adp_cart', 'residue_numbers', 'vdw_radii', 'point_charges'],
provide_pdb, new=True)
#print pdbiop.export('PQR')
text_file = open("resp.pqr", "w")
## ADD THE CRYST INSTRUCTUINS HERE
text_file.write("CRYST1 {:6.4f} {:6.4f} {:6.4f} {:6.4f} {:6.4f} {:6.4f} \n".format(*data["exp"].get_cell()))
text_file.write("%s" % pdbiop.export('PQR'))
text_file.close()
printer(
'\n resp.pqr has been written, with the assigned resp charges and vdw radii according to J Phys Chem, 2009, p. 5806-5812.\n')