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import config 

from formats import * 

import os 

from copy import copy 

from log import reportWarning 

 

from titsite import Titsite as Site 

from tautomer import Tautomer 

from concurrency import startPoolProcesses, runInteractionCalcs 

import mc 

 

class Molecule: 

"""Molecule with more than one titrable sites 

""" 

def __init__(self): 

""" 

# DelPhi Parameters 

self._delphi_refparams (list): input DelPhi parameters 

 

# Sites 

self._sites (dict): key is residue number  

value is site object instance 

 

self._sites_order (list): values are site object instances 

order respects .sites 

 

# Atoms 

self._natoms (int): number of atoms in the molecule 

self._atoms (dict): key is atom id number 

value is atom name 

self._atoms_array_position (dict): 

key is atom number 

value is atom position in pqr 

Example: if the first atom in pqr is number 541 

then self._atoms_array_position[541] = 1 

 

# Offset of the first site 

This is only used because the membrane part is not finished 

and uses a pqr input of the first site 

self._InputPQRoffSet (list):  

x, y, z coordinates of the offset in the input pqr 

 

# Site Interactions 

self._site_interactions (list):  

contains tuples with pairs of site objects 

""" 

self._delphi_refparams = '' 

self._sites = {} 

self._sites_order = [] 

self._natoms = -1 

self._atoms = {} 

self._atoms_array_position = {} 

self._InputPQRoffSet = [] 

self._site_interactions = [] 

self.box = [] 

self._dat_to_write = '' 

self._correct_names = {} 

self._correct_atoms = {} 

 

self._NTR = None 

self._CTR = None 

 

self.readTermini() 

 

def readTermini(self): 

NTR_atoms = [] 

with open("{0}/{1}/sts/NTRtau1.st".format(config.script_dir, 

config.params['ffID'])) as f: 

for line in f: 

parts = line.split() 

if len(parts) > 1: 

NTR_atoms.append(parts[1].strip()) 

 

CTR_atoms = [] 

with open("{0}/{1}/sts/CTRtau1.st".format(config.script_dir, 

config.params['ffID'])) as f: 

for line in f: 

parts = line.split() 

if len(parts) > 1: 

CTR_atoms.append(parts[1].strip()) 

 

self._NTR_atoms = NTR_atoms 

self._CTR_atoms = CTR_atoms 

 

 

# Set Methods 

def addAtom(self, aname, anumb, position): 

self._atoms[anumb] = aname 

self._atoms_array_position[anumb] = position 

 

def loadParams(self, params): 

self._delphi_refparams = params 

 

def loadDelPhiParams(self, delphimol): 

if delphimol != 'reload': 

self._delphimol = delphimol 

else: 

delphimol = self._delphimol 

self.p_atpos = copy(delphimol.get_atpos()) 

self.p_rad3 = copy(delphimol.get_rad3()) 

self.p_chrgv4 = copy(delphimol.get_chrgv4()) 

self.atinf = copy(delphimol.get_atinf()) 

self.p_iatmed = copy(delphimol.get_iatmed()) 

 

# Get Methods 

def getSites(self): 

return self._sites 

 

def getSitesOrdered(self): 

return self._sites_order 

 

def getDelPhi(self): 

return self._delphimol 

 

def getArrayPosition(self, atom_id): 

"""Returns the index of the atom in DelPhi position array 

Disclamer: used only in testing""" 

return self._atoms_array_position[atom_id] 

 

def getAtomsList(self): 

"""Returns a list of atoms details  

(id, instance, atom index in DelPhi data structures) 

sorted by atom id number""" 

atom_list = [] 

for atom in sorted(self._atoms.keys()): 

atom_list.append((self._atoms[atom], atom, 

self._atoms_array_position[atom])) 

return atom_list 

 

def getDelPhiParams(self): 

return self._delphi_refparams 

 

def getTautomerNumber(self, t_index): 

"""Uncodes the tautomer index t_index needed for multiprocessing 

and returns the corresponding tautomer instance""" 

i = -1 

for site in self._sites_order: 

i += 1 

if i == t_index: 

return site._ref_tautomer 

for tautomer in sorted(site._tautomers.values()): 

i += 1 

if i == t_index: 

return tautomer 

raise Exception('Something is wrong') 

 

def getTautomerInstance(self, tautname, site_resnum): 

"""Return the tautomer instance named tautname  

existent in the site of the residue number site_resnum""" 

site = self._sites[site_resnum] 

if tautname in site._tautomers.keys(): 

return site._tautomers[tautname] 

elif tautname == site._ref_tautomer._name: 

return site._ref_tautomer 

raise Exception('Something is very wrong!!!') 

 

def getNAtoms(self): 

"""Return number of atoms of the Site""" 

return self._natoms 

 

def getTautNAtoms(self, taut_name): 

"""Return number of atoms of the tautomer named taut_name 

Disclamer: it was used for testing""" 

for site in self._sites.values(): 

for tautomer in site.getTautomers(): 

if tautomer._name == taut_name: 

return tautomer._natoms 

 

def getPQROffset(self): 

return self._InputPQRoffSet 

 

# Iter Methods 

def iterAtoms(self): 

"""Generator that iterates through all atoms details (name, id, 

position) in the Site""" 

for atom in sorted(self._atoms.keys()): 

yield (self._atoms[atom], atom, 

self._atoms_array_position[atom]) 

 

def iterAllSitesTautomers(self): 

"""Generator that iterates through all Tautomer instances. 

The iteration is sorted by site and within each site the first 

to be yielded is the reference tautomer and then the rest of 

the tautomers by order""" 

for site in self._sites_order: 

yield site._ref_tautomer 

for tautomer in sorted(site._tautomers.values()): 

yield tautomer 

 

def iterNonRefSitesTautomers(self): 

"""Generator that iterates through all Tautomer instances except 

the reference ones""" 

for site in self._sites_order: 

for tautomer in sorted(site._tautomers.values()): 

yield tautomer 

def iterAllSites(self): 

for site in self._sites_order: 

yield site 

 

# Printing Methods 

def printAllSites(self): 

"""Prints all Site names""" 

for site in self._sites_order: 

print site.getName() 

 

def printAllTautomers(self): 

"""Prints all Tautomer details""" 

for site in self._sites_order: 

print site.getName() 

for tautomer in site.iterTautomers(): 

print tautomer 

print site._ref_tautomer 

 

# Input Files Manipulation Methods 

def makeSimpleSites(self): 

def SitesFileLine(resnumb, resname): 

for res in config.REGULARTITRATINGRES: 

if res[0:2] == resname[0:2]: 

resname = res 

 

if resname in config.TITRABLETAUTOMERS: 

ntautomers = config.TITRABLETAUTOMERS[resname] 

else: 

for res in config.REGULARTITRATINGRES: 

if res[0:2] == resname[0:2]: 

ntautomers = config.TITRABLETAUTOMERS[res] 

text = '{0} '.format(resnumb) 

for i in range(ntautomers): 

text += '{0}tau{1} '.format(resname, i + 1) 

 

if resname in ('NTR', 'CTR'): 

resnumb += config.terminal_offset 

 

sID = self.addSite(resnumb) 

self.addTautomers(sID, ntautomers, resname) 

 

return text + '\n' 

 

def add2chain(chain, chain_res, resnumb, resname): 

if chain in chain_res: 

chain_res[chain][resnumb] = resname 

else: 

chain_res[chain] = {} 

chain_res[chain][resnumb] = resname 

 

sites_file = '' 

 

sites = [] 

chain_res = {} 

with open(config.f_in) as f: 

nline = 0 

maxnlines = 0 

resnumb = None 

resname = None 

for line in f: 

nline += 1 

if 'ATOM ' == line[0:5]: 

(aname, anumb, resname, chain, resnumb, x, y, z) = read_pdb_line(line) 

if chain == ' ': 

chain = 'A' 

 

if resnumb not in sites: 

if len(sites) == 0 and 'NTR' not in sites: 

sites.append('NTR') 

sites_file += SitesFileLine(resnumb, 'NTR') 

self._NTR = resnumb 

if resname in config.TITRABLERESIDUES and \ 

resname != 'NTR' and resname != 'CTR': 

sites.append(resnumb) 

sites_file += SitesFileLine(resnumb, resname) 

add2chain(chain, chain_res, resnumb, resname) 

 

if 'CTR' not in sites and \ 

aname in ('CT', 'OT', 'OT1', 'OT2', 'O1', 'O2'): 

sites.append('CTR') 

sites_file += SitesFileLine(resnumb, 'CTR') 

self._CTR = resnumb 

add2chain(chain, chain_res, resnumb, 'CTR') 

 

# Adding the reference tautomer to each site 

self.addReferenceTautomers() 

# Assigning a charge set to each tautomer 

self.addTautomersChargeSets() 

 

with open('tmp.sites', 'w') as f_new: 

f_new.write(sites_file) 

 

return chain_res, sites 

 

def makeSites(self, useTMPgro=None, sites=None): 

"""Identifies titrable residues and checks integrity of the residue blocks 

(excluding Hydrogens) 

""" 

def correctResName(resname): 

for res in config.REGULARTITRATINGRES: 

if res[0:2] == resname[0:2]: 

return res 

return resname 

 

def makeSite(resnumb, resname): 

if resname in config.TITRABLETAUTOMERS: 

ntautomers = config.TITRABLETAUTOMERS[resname] 

else: 

for res in config.REGULARTITRATINGRES: 

if res[0:2] == resname[0:2]: 

ntautomers = config.TITRABLETAUTOMERS[res] 

 

 

sID = self.addSite(resnumb) 

self.addTautomers(sID, ntautomers, resname) 

 

def warning(resnumb, resname, res_atoms, mode=None): 

if mode == 'CYS' or resname == 'CYS': 

CYS_atoms = ['N', 'CA', 'CB', 'SG', 'C', 'O', 'H'] 

if (set(res_atoms).issubset(CYS_atoms) and 

set(CYS_atoms).issubset(res_atoms)): 

# no need to correct residue name 

warn = '{0} {1} is assumed to be participating '\ 

'in a SS-bond'.format(resnumb, resname) 

reportWarning(warn) 

return 

 

CY0_atoms = ['N', 'CA', 'CB', 'SG', 'C', 'O', 'H', 'HG1'] 

if (set(res_atoms).issubset(CY0_atoms) and 

set(CY0_atoms).issubset(res_atoms)): 

self._correct_names[resnumb] = 'CY0' 

return 

 

CY0_atoms = ['N', 'CA', 'CB', 'SG', 'C', 'O', 'H', 'HG'] 

if (set(res_atoms).issubset(CY0_atoms) and 

set(CY0_atoms).issubset(res_atoms)): 

self._correct_names[resnumb] = 'CY0' 

self._correct_atoms[resnumb] = {'HG': 'HG1'} 

return 

else: 

warn = '{0} {1} failed integrity check'.format(resnumb, 

resname) 

reportWarning(warn) 

 

elif resname not in config.TITRABLERESIDUES: 

return 

else: 

warn = '{0} {1} failed integrity check'.format(resnumb, 

resname) 

reportWarning(warn) 

 

if config.f_in and not useTMPgro: 

filename = config.f_in 

filetype = 'pdb' 

else: 

filename = "TMP.gro" 

filetype = 'gro' 

 

resnumb = None 

cur_atoms = [] 

prev_resnumb = None 

prev_resname = None 

first_res = None 

with open(filename) as f: 

nline = 0 

maxnlines = 0 

for line in f: 

resname = None 

nline += 1 

if 'ATOM ' == line[0:5]: 

(aname, anumb, resname, chain, resnumb, x, y, z) = read_pdb_line(line) 

elif filetype == 'gro': 

if nline > 2 and nline < maxnlines: 

(aname, anumb, resname, resnumb, x, y, z) = read_gro_line(line) 

elif nline == 2: 

natoms = int(line.strip()) 

maxnlines = natoms + 3 

 

if line == 'TER\n': 

resnumb += 1 

if (prev_resnumb != resnumb or nline == maxnlines) and \ 

prev_resnumb: 

if nline == maxnlines: 

prev_resnumb = copy(resnumb) 

resnumb = 'None' 

 

if prev_resname in config.TITRABLERESIDUES or \ 

(prev_resnumb == self._NTR or resnumb == self._NTR) or \ 

(prev_resnumb == self._CTR or resnumb == self._CTR): 

if prev_resnumb == self._NTR and resnumb != self._NTR: 

prev_resname = correctResName(prev_resname) 

 

if prev_resname in config.TITRABLERESIDUES: 

res_tits = True 

else: 

res_tits = False 

 

integrity_nter, integrity_site = self.check_integrity(prev_resname, 

cur_atoms, 

nter=True, 

site=res_tits) 

if integrity_nter: 

nter_resnumb = prev_resnumb + config.terminal_offset 

makeSite(nter_resnumb, 'NTR') 

self._NTR = prev_resnumb 

else: 

warning(prev_resnumb, 'NTR', '') 

 

if sites and prev_resnumb in sites: 

if integrity_site: 

makeSite(prev_resnumb, prev_resname) 

else: 

warning(prev_resnumb, prev_resname, cur_atoms) 

 

prev_resnumb = None 

 

# Dealing with the last residue and CTR 

elif prev_resnumb == self._CTR and resnumb != self._CTR: 

prev_resname = correctResName(prev_resname) 

 

if prev_resname in config.TITRABLERESIDUES: 

res_tits = True 

else: 

res_tits = False 

 

integrity_cter, integrity_site = self.check_integrity(prev_resname, 

cur_atoms, 

cter=True, 

site=res_tits) 

if integrity_cter: 

cter_resnumb = prev_resnumb + config.terminal_offset 

makeSite(cter_resnumb, 'CTR') 

self._CTR = prev_resnumb 

else: 

warning(prev_resnumb, 'CTR', '') 

 

if sites and prev_resnumb in sites: 

if integrity_site: 

makeSite(prev_resnumb, prev_resname) 

else: 

warning(prev_resnumb, prev_resname, cur_atoms) 

 

# Dealing with the previous residue 

elif prev_resnumb: 

if sites and prev_resnumb in sites: 

prev_resname = correctResName(prev_resname) 

res_atoms = copy(cur_atoms) 

integrity_site = self.check_integrity(prev_resname, 

cur_atoms) 

 

if integrity_site: 

makeSite(prev_resnumb, prev_resname) 

else: 

prev_resname = warning(prev_resnumb, prev_resname, res_atoms) 

elif prev_resname == 'CYS': 

# dealing with a CYS that is not in sites 

res_atoms = copy(cur_atoms) 

integrity_site = self.check_integrity(prev_resname, 

cur_atoms) 

 

if not integrity_site: 

prev_resname = warning(prev_resnumb, prev_resname, 

res_atoms, mode='CYS') 

elif prev_resname == 'ALA': 

#TODO: check residue block integrity for other non titrating residues 

pass 

 

# Dealing with the new residue 

if prev_resnumb != resnumb: 

cur_atoms = [aname] 

prev_resnumb = resnumb 

prev_resname = resname 

 

elif resnumb: 

cur_atoms.append(aname) 

if prev_resname in ('NTR', 'CTR') and \ 

prev_resname != resname: 

prev_resname = resname 

 

 

# Adding the reference tautomer to each site 

self.addReferenceTautomers() 

# Assigning a charge set to each tautomer 

self.addTautomersChargeSets() 

 

#TODO: report blocks that failed the check (in .log file with 

#numbering reference to stepwise scheme) 

 

#TODO: add lipid residues 

 

if config.debug: 

print 'exiting makeSites' 

 

def check_integrity(self, resname, res_atoms, nter=False, cter=False, site=True): 

def read_anames(filename): 

res_atoms_st = [] 

with open(filename) as f: 

for line in f.readlines()[1:]: 

cols = line.strip().split() 

aname = cols[1] 

res_atoms_st.append(aname) 

return res_atoms_st 

 

def pop_atoms(anames1, anames2): 

trigger = False 

for aname in anames1: 

if aname not in anames2: 

trigger = True 

if config.debug: 

print aname, 'not in', resname 

else: 

anames2.remove(aname) 

if trigger: 

return anames2, False 

else: 

return anames2, True 

 

if config.debug: 

print '###### INTEGRITY CHECK ######' 

print res_atoms 

integrity = None 

 

if nter: 

res_atoms_st = read_anames('{0}/{1}/sts/NTRtau1.st'.format(config.script_dir, 

config.params['ffID'])) 

res_atoms, integrity_nter = pop_atoms(res_atoms_st, res_atoms) 

elif cter: 

res_atoms_st = read_anames('{0}/{1}/sts/CTRtau1.st'.format(config.script_dir, 

config.params['ffID'])) 

res_atoms, integrity_cter = pop_atoms(res_atoms_st, res_atoms) 

 

if site: 

main_chain = ('N', 'H', 'CA', 'C', 'O') 

if nter: 

main_chain = () 

if cter: 

main_chain = ('N', 'H') 

 

for aname in main_chain: 

if aname in res_atoms: 

res_atoms.remove(aname) 

elif not nter and not cter: 

integrity = False 

 

if config.debug: 

print 'i', integrity 

 

if integrity != False: 

filename = '{0}/{1}/sts/{2}tau1.st'.format(config.script_dir, 

config.params['ffID'], resname) 

res_atoms_st = read_anames(filename) 

res_atoms, integrity = pop_atoms(res_atoms_st, res_atoms) 

if config.debug: 

print res_atoms_st, res_atoms 

print 'i', integrity 

 

if len(res_atoms) != 0 and integrity: 

raise Exception('Something is wrong') 

 

if nter: 

return integrity_nter, integrity 

elif cter: 

return integrity_cter, integrity 

else: 

return integrity 

 

 

def addSite(self, resnum): 

sID = Site(resnum, self) 

self._sites[resnum] = sID 

self._sites_order.append(sID) 

 

return sID 

 

def addTautomers(self, sID, ntautomers, resname): 

rootname = resname[0:2] 

sID._res_name = resname 

for itautomer in range(ntautomers): 

tautomer = rootname + str(itautomer) 

tID = Tautomer(tautomer, sID, sID._molecule) 

sID._tautomers[tautomer] = tID 

return sID._tautomers 

 

def loadSites(self, chains_length, chains_res): 

def siteHasNTautomers(chain, resnum): 

if resnum in chains_res[chain]: 

resname = chains_res[chain][resnum] 

if resname in config.TITRABLETAUTOMERS: 

ntauts = config.TITRABLETAUTOMERS[resname] 

return ntauts, resname 

else: 

for res in config.TITRABLETAUTOMERS: 

if res[:-1] == resname[:-1]: 

ntauts = config.TITRABLETAUTOMERS[res] 

return ntauts, res 

raise Exception('Something is wrong.') 

 

for chain in config.sites: 

sites = config.sites[chain] 

for site in sites: 

if 'N' in site: 

resnum = int(site[:-1]) 

self._NTR = resnum 

resnum += config.terminal_offset 

res_ntauts = 3 

res_name = 'NTR' 

elif 'C' in site: 

resnum = int(site[:-1]) 

self._CTR = resnum 

resnum += config.terminal_offset 

res_ntauts = 4 

res_name = 'CTR' 

else: 

resnum = int(site) 

res_ntauts, res_name = siteHasNTautomers(chain, resnum) 

 

sID = self.addSite(resnum) 

sID.setTautomers(res_ntauts, res_name) 

 

self.addReferenceTautomers() 

self.addTautomersChargeSets() 

 

 

def addReferenceTautomers(self): 

for site in self._sites.values(): 

site.addReferenceTautomer() 

 

def addTautomersChargeSets(self): 

for site in self._sites.values(): 

# reads .st files 

site.addChargeSets() 

 

def readIndexFile(self): 

protein_trigger = False 

protein_atoms = [] 

with open(f_ndx) as f: 

for line in f: 

if "[ protein ]" in line.lower(): 

protein_trigger = True 

elif protein_trigger: 

for atom in line.split(): 

protein_atoms.append(int(atom)) 

return protein_atoms 

 

def deleteAllSites(self): 

for site in self._sites.values(): 

site._tautomers = {} 

site._ref_tautomer = '' 

self._sites = {} 

self._sites_order = [] 

 

def readGROFile(self, groname): 

"""  

""" 

#TODO: For CpHMD read the index file: 

#self.readIndexFile() 

 

# Getting the "protein" with trjconv PBC mol 

#os.system('echo "Protein" | {GroDIR}/trjconv ' 

# '-f TMP_{config.sysname}.gro -s TMP_CpHMD.tpr ' 

# '-n TMP_CpHMD.ndx -o TMP_auxD1.gro ' 

# '-pbc mol -quiet'.format(GroDIR=paths['GroDIR'], sysname=config.sysname)) 

 

new_pdb_content = """TITLE Protein in water 

REMARK THIS IS A SIMULATION BOX 

CRYST1 000.000 000.000 000.000 60.00 60.00 90.00 P 1 1 

MODEL 1 

""" 

new_pdb_content = "" 

site_positions = {} 

site_Hs = {} 

with open(groname) as f: 

line_counter = 0 

natoms_left = 0 

natoms = 0 

 

lines = f.read().splitlines() 

penul_line = lines[-2] 

last_line = lines[-1] 

final_res_numb = int(penul_line[:5].strip()) 

final_atom_numb = int(penul_line[15:20].strip()) 

self.box = [float(i) for i in last_line.split()[:3]] 

 

if config.params['pbc_dim'] == 2: 

scaleP = (config.params['gsize'] - 1) / (self.box[0] * 10) 

scaleM = int(4 / scaleP + 0.5) * scaleP 

 

config.params['scaleP'] = scaleP 

config.params['scaleM'] = scaleM 

 

for line in lines: 

line_counter += 1 

if natoms_left > 0: 

 

natoms_left -= 1 

natoms += 1 

aposition = natoms - 1 

 

(aname, anumb, resname, \ 

resnumb, x, y, z) = read_gro_line(line) 

x, y, z = x*10, y*10, z *10 

 

#print resnumb, resname, aname, anumb, aposition, x, y, z 

 

if resnumb == self._NTR and aname in self._NTR_atoms: 

resname = 'NTR' 

resnumb += config.terminal_offset 

elif resnumb == self._CTR and aname in self._CTR_atoms: 

resname = 'CTR' 

resnumb += config.terminal_offset 

if aname == 'C': 

aname = 'CT' 

elif aname in ('O1', 'O2'): 

aname = aname[0] + 'T' + aname[1] 

 

if resnumb in self._correct_names.keys(): 

resname = self._correct_names[resnumb] 

if resnumb in self._correct_atoms.keys() and \ 

aname in self._correct_atoms[resnumb]: 

aname = self._correct_atoms[resnumb][aname] 

 

self.addAtom(aname, anumb, aposition) 

ref_tau_name = resname 

 

if resnumb in self._sites.keys() and \ 

aname in self._sites[resnumb]._ref_tautomer._charge_set.keys(): 

#( aname not in ('N', 'H', 'C', 'O', 'CA') or  

#(aname in ('N', 'H', 'C', 'O', 'CA') and resname == 'NTR')): 

# change res name to reference tautomer 

ref_tau_name = self._sites[resnumb].getRefTautomerName() 

 

# add atom to corresponding site 

self._sites[resnumb].addAtom(aname, anumb) 

if resnumb in site_positions: 

site_positions[resnumb].append((x, y, z)) 

if aname[0] == 'H': 

site_Hs[resnumb].append((x, y, z)) 

else: 

site_positions[resnumb] = [(x, y, z)] 

if aname[0] == 'H': 

site_Hs[resnumb] = [(x, y, z)] 

else: 

site_Hs[resnumb] = [] 

 

#if len(aname) == 4: 

# aname = aname[-1] + aname[0:3]  

new_pdb_content += new_pdb_line(aposition, aname, ref_tau_name, resnumb, x, y, z) 

 

#more_pdb_content, final_res_numb, final_atom_numb = add_pbc(aposition, aname, ref_tau_name, x, y, z, self.box[0], final_res_numb, final_atom_numb) 

#new_pdb_content += more_pdb_content 

 

elif line_counter == 2: 

natoms_left = int(line.strip()) 

self._natoms = natoms_left 

 

new_pdb_content += 'TER\nENDMDL\n' 

with open('delphi_in_stmod.pdb', 'w') as f_new: 

f_new.write(new_pdb_content) 

 

#TODO: check Terminal_offset has to be bigger than the total number of residues 

#TODO: delete terminal_offset and use another approach to distinguish between N- and C-ter 

#TODO: check size xy > config.cutoff * 2 

# if so, raise Exception, and ask to change cutoff value 

 

#TODO: check if pbc_dim -> set gsizes from pdb size xy and ignore perfil 

 

site_centers = {} 

for site in site_positions: 

if site in self._sites.keys(): 

pos_max = [-9999990, -999999, -999999] 

pos_min = [999999, 999999, 999999] 

focus_center = [0, 0, 0] 

for atom in site_positions[site]: 

for i in range(3): 

if pos_max[i] < atom[i]: 

pos_max[i] = atom[i] 

if pos_min[i] > atom[i]: 

pos_min[i] = atom[i] 

focus_center[0] = (pos_max[0] + pos_min[0] ) / 2 

focus_center[1] = (pos_max[1] + pos_min[1] ) / 2 

focus_center[2] = (pos_max[2] + pos_min[2] ) / 2 

if config.params['pbc_dim'] == 2: 

self._sites[site].addCenter(focus_center, 

boxsize=self.box[0], 

box_z=self.box[2]) 

else: 

self._sites[site].addCenter(focus_center) 

hx, hy, hz = 0, 0, 0 

nHs = len(site_Hs[site]) 

if nHs == 0: 

sitename = self._sites[site].getName() 

raise Exception('Site {1}{0} appears ' 

'to have no Hydrogen atoms'.format(site, 

sitename)) 

for h in site_Hs[site]: 

hx += h[0] 

hy += h[1] 

hz += h[2] 

hx /= nHs 

hy /= nHs 

hz /= nHs 

Hcenter = (round(hx, 2), round(hy, 2), round(hz, 2)) 

self._sites[site].addCenterH(Hcenter) 

 

with open('cent', 'w') as f_new: 

text = '' 

for site in site_positions: 

if site in self._sites.keys(): 

text += str(self._sites[site]._center) + '\n' 

f_new.write(text) 

if config.params['pbc_dim'] == 2: 

with open('centHs', 'w') as f_new: 

text = '' 

for site in site_positions: 

if site in self._sites.keys(): 

text += '{0} {1}'.format(site, self._sites[site]._centerH) + '\n' 

f_new.write(text) 

with open('cent_original', 'w') as f_new: 

text = '' 

for site in site_positions: 

if site in self._sites.keys(): 

text += '{0} {1}'.format(site, self._sites[site]._center_original) + '\n' 

f_new.write(text) 

 

def readCenters(self, f_cent, boxsize=False): 

"""Opens cent file  

Stores centers of sites 

""" 

with open(f_cent) as f: 

nsites = 0 

for line in f: 

nsites += 1 

cols = line.split() 

res_number = cols[0] 

x = float(cols[1]) * 10 

y = float(cols[2]) * 10 

z = float(cols[3]) * 10 

if nsites == 1: 

x = truncate(x, 3) 

y = truncate(y, 3) 

z = truncate(z, 3) 

self._InputPQRoffSet = [x, y, z] 

if res_number in self._sites: 

if boxsize: 

self._sites[res_number].addCenter([x, y, z], boxsize=boxsize) 

else: 

self._sites[res_number].addCenter([x, y, z]) 

else: 

raise Exception('Something is wrong... Site in Centers ' 

'not defined in cent file') 

 

def calcSiteInteractionsParallel(self, ncpus): 

"""Calculates the pairwise interaction energies  

and writes them in a formatted .dat file 

Interactions are calculated using a pool of processes 

 

Args: 

ncpus (int): number of cpus to be used 

""" 

self.writeDatHeader() 

counter = 0 

for site1 in self.getSitesOrdered()[:-1]: 

counter += 1 

for site2 in self.getSitesOrdered()[counter:]: 

self._site_interactions.append((site1, site2)) 

 

sites = self.getSitesOrdered() 

self._npossible_states = [len(site._tautomers) + 1 for site in sites] 

 

self._interactions = [] 

for nstate1 in range(sum(self._npossible_states)): 

self._interactions.append([]) 

for nstate2 in range(sum(self._npossible_states)): 

self._interactions[nstate1].append(-999999) 

 

self._interactions_look = [] 

aux = -1 

site = -1 

for nstates in self._npossible_states: 

site += 1 

self._interactions_look.append([]) 

for state in range(nstates): 

aux += 1 

self._interactions_look[site].append(aux) 

 

ncpus = min(len(self._site_interactions), ncpus) 

if ncpus > 0: 

results = startPoolProcesses(runInteractionCalcs, 

self._site_interactions, ncpus, 

assign='ordered', merged_results=True) 

else: 

results = [] 

to_write = '' 

T = float(config.params['temp']) 

for interaction in results: 

site1i = interaction[0] 

site2i = interaction[1] 

if self._interactions[site1i][site2i] != -999999: 

self._interactions[site1i][site2i] += interaction[2] 

self._interactions[site2i][site1i] += interaction[2] 

self._interactions[site1i][site2i] /= 2 

self._interactions[site2i][site1i] /= 2 

 

to_write += interaction[3][6:18] + interaction[3][:6] + ' {0:13.6e}\n'.format(self._interactions[site1i][site2i] * (config.kBoltz * T)) 

else: 

self._interactions[site1i][site2i] = interaction[2] 

self._interactions[site2i][site1i] = interaction[2] 

 

#if site1i == 0 or site2i == 0: 

# print site1i, site2i, interaction[2] * (config.kBoltz * T) 

# print interaction[3] 

 

 

with open('interactions.dat', 'a') as f_new: 

f_new.write(to_write) 

 

def calcInteractionNumber(self, inumber): 

"""Calculates the pairwise interaction energies 

related to the two sites specified in inumber 

 

Args: 

inumber (int): site interaction pair code 

 

Ensures:  

to_write (str): site interaction energies formatted 

to be written in .dat file 

""" 

to_write = '' 

sites = self._site_interactions[inumber] 

site1 = sites[0] 

site2 = sites[1] 

pairs = ((site1, site2), (site2, site1)) 

 

iterAtomsList = self.getAtomsList() 

 

T = float(config.params['temp']) 

interactions = [] 

for pair in pairs: 

site1 = pair[0] 

site2 = pair[1] 

ordered_tautomers_site1 = site1.getOrderedTautomersList() 

ordered_tautomers_site2 = site2.getOrderedTautomersList() 

for taut1 in ordered_tautomers_site1: 

site_atom_list = taut1._site.getAtomNumbersList() 

for taut2 in ordered_tautomers_site2: 

interaction = taut1.calcInteractionWith(taut2, 

site_atom_list, 

iterAtomsList) 

 

gg = interaction / (config.kBoltz * T) 

 

nsite1 = self.getSitesOrdered().index(taut1._site) 

nsite2 = self.getSitesOrdered().index(taut2._site) 

 

state1 = int(taut1._name[-1]) 

state2 = int(taut2._name[-1]) 

 

if config.debug: 

print nsite1, nsite2, state1, state2, taut1._name, taut2._name, gg 

site1i = self._interactions_look[nsite1][state1] 

site2i = self._interactions_look[nsite2][state2] 

 

interactions.append((site1i, site2i, gg, 

self.convertIntoDatFormat(taut1, taut2, interaction))) 

 

return interactions 

 

def convertIntoDatFormat(self, tau1, tau2, interaction): 

"""Returns a .dat format interaction line 

 

Args: 

tau1 (Tautomer): first tautomer of the pair 

tau2 (Tautomer): second tautomer of the pair 

interaction (float): interaction energy of the tautomers pair 

 

Ensures: 

line (str): .dat formatted interaction line 

""" 

site1_index = self._sites_order.index(tau1._site) 

tau1_index = tau1._name[-1] 

tau1_dat = '{0:>3} {1:>2}'.format(site1_index, tau1_index) 

site2_index = self._sites_order.index(tau2._site) 

tau2_index = tau2._name[-1] 

tau2_dat = '{0:>3} {1:>2}'.format(site2_index, tau2_index) 

line = '{0} {1} {2:13.6e}\n'.format(tau1_dat, tau2_dat, interaction) 

return line 

 

def writeDatHeader(self): 

"""Writes pKint energies in .dat file header""" 

to_write = '{0}\n'.format(len(self._sites)) 

for site in self._sites_order: 

to_write += '{0:3s}-{1:<7}{2:>2} P *\n'.format(site._res_name, 

site._res_number, 

len(site._tautomers) + 1) 

if site._type == 'c': 

tau_prot_state = 0 

ref_prot_state = 1 

elif site._type == 'a': 

tau_prot_state = 1 

ref_prot_state = 0 

 

for tautomer in site.iterOrderedTautomersWithoutRef(): 

to_write += '{0:1d} {1:13.6e}\n'.format(tau_prot_state, tautomer._dg) 

to_write += '{0:1d} 0.000000e+00\n'.format(ref_prot_state) 

with open('interactions.dat', 'w') as f_new: 

f_new.write(to_write) 

 

 

def calcpKint(self, unpacked_results): 

"""Calculation the pKint of all tautomers 

""" 

i = -1 

if config.debug: 

print '############ results ############' 

pkints = '' 

contributions = '' 

for tautomer in config.tit_mole.iterAllSitesTautomers(): 

i += 1 

core_index = i % config.params['ncpus'] 

job_index = i / config.params['ncpus'] 

result = unpacked_results[core_index][job_index] 

 

tautname = result[0] 

tautresnumb = result[1] 

 

esolvationM = result[2] 

sitpotM = result[3] 

esolvationS = result[4] 

sitpotS = result[5] 

 

tautomer = config.tit_mole.getTautomerInstance(tautname, tautresnumb) 

 

tautomer.saveDelPhiResults(esolvationS, sitpotS, esolvationM, 

sitpotM) 

if config.debug: 

print '### new tautomer ###' 

print (i, core_index, job_index, tautname, 

tautomer._name, esolvationM, esolvationS) 

print (tautomer._name, tautomer._esolvationS, 

len(tautomer._sitpotS), tautomer._esolvationM, 

len(tautomer._sitpotM)) 

 

tautomer.calcBackEnergy() 

if not tautomer.isRefTautomer(): 

tautomer.calcpKint() 

if config.debug: 

print ('pkint', tautomer._name, tautomer._dg, 

id(tautomer)) 

pkints += '{} {} {}\n'.format(tautomer._name, 

tautomer._dg, tautomer.pKint) 

contributions += '{}{} {} {} {} {}\n'.format(tautomer._site._res_number, 

tautomer._name, 

tautomer.dG_solvationM, 

tautomer.dG_solvationS, 

tautomer.dG_solvationM - tautomer.dG_solvationS, 

tautomer.dG_back) 

with open('pkint', 'w') as f_new: 

f_new.write(pkints) 

with open('contributions', 'w') as f_new: 

f_new.write(contributions) 

 

def runMC(self): 

def resize_list_of_lists(listn, maxsize, filler=None): 

for i in range(len(listn)): 

diff = maxsize - len(listn[i]) 

for ii in range(diff): 

listn[i].append(filler) 

 

print '\nStart MC' 

 

sites = self.getSitesOrdered() 

nsites = len(sites) 

self._possible_states = [[] for site in sites] 

self._possible_states_g = [[] for site in sites] 

self._possible_states_occ = [[] for site in sites] 

 

T = float(config.params['temp']) 

isite = -1 

for site in sites: 

isite += 1 

itaut = 0 

for tautomer in site.iterOrderedTautomersWithoutRef(): 

dg = tautomer._dg / (config.kBoltz * T) 

self._possible_states_g[isite].append(dg) 

self._possible_states[isite].append(itaut) 

if site._type == 'c': 

prot_state = 0 

elif site._type == 'a': 

prot_state = 1 

 

self._possible_states_occ[isite].append(prot_state) 

itaut += 1 

 

if site._type == 'c': 

prot_state = 1 

elif site._type == 'a': 

prot_state = 0 

self._possible_states_occ[isite].append(prot_state) 

self._possible_states_g[isite].append(0.0) 

 

 

maxstates = max(self._npossible_states) 

resize_list_of_lists(self._possible_states, maxstates) 

resize_list_of_lists(self._possible_states_g, maxstates) 

resize_list_of_lists(self._possible_states_occ, maxstates, filler=-500) 

resize_list_of_lists(self._interactions_look, maxstates, filler=-500) 

 

pHmin, pHmax = config.params['pHmin'], config.params['pHmax'] 

dpH = config.params['pHstep'] 

couple_min = config.params['couple_min'] 

mcsteps = config.params['mcsteps'] 

eqsteps = config.params['eqsteps'] 

seed = config.params['seed'] 

 

pHsteps = int(round(1 + (pHmax - pHmin) / dpH, 0)) 

 

pKas, pmeans_raw = mc.MCrun(nsites, self._npossible_states, 

self._possible_states_g, self._possible_states_occ, 

self._interactions, self._interactions_look, 

pHsteps, mcsteps, eqsteps, seed, pHmin, dpH, 

couple_min) 

 

print '\n\nResults' 

text_pks = '' 

text_prots = '# pH total' 

c = -1 

for i in pKas: 

c += 1 

site = self.getSitesOrdered()[c] 

sitename = site.getName() 

if sitename in ('NTR', 'CTR'): 

resnumb = site.getResNumber() - config.terminal_offset 

text_prots += ' {0:3}'.format(sitename) 

else: 

resnumb = site.getResNumber() 

text_prots += '{0:5d}{1:3s}'.format(resnumb, sitename) 

text_pks += '{0} {1} {2}\n'.format(resnumb, sitename, i[0]) 

if i[0] != 100.0: 

print '{0} {1} {2}'.format(resnumb, sitename, round(i[0], 2)) 

else: 

print '{0} {1} Not in range'.format(resnumb, sitename) 

print '' 

 

if config.f_out: 

with open(config.f_out, 'w') as f: 

f.write(text_pks) 

 

pmeans = {} 

for pHstep in range(pHsteps): 

pH = pHmin + pHstep * dpH 

c = -1 

pmeans[pH] = {} 

text_prots += '\n{0:5.2f}'.format(pH) 

 

# total protonation 

pmean = pmeans_raw[pHstep][c] 

pmeans[pH]['total'] = pmean 

text_prots += '\t{0:7.4f}'.format(pmean) 

 

for site in self.getSitesOrdered(): 

c += 1 

sitename = site.getName() 

sitenumb = site.getResNumber() 

pmean = pmeans_raw[pHstep][c] 

pmeans[pH][sitenumb] = pmean 

if pmean != 100.0: 

text_prots += '\t{0:7.4f}'.format(pmean) 

else: 

text_prots += '\t-' 

 

if config.f_prot_out: 

with open(config.f_prot_out, 'w') as f: 

f.write(text_prots) 

 

 

return pKas, pmeans