QligFEP.py

import argparse
import re
import glob
import os
import shutil
import stat
import shlex
from subprocess import check_output

import functions as f
import settings as s
import IO

class Run(object):
    """
    Create dual topology FEP files based on two ligands
    """
    def __init__(self, 
                 lig1, 
                 lig2, 
                 FF, 
                 system, 
                 cluster, 
                 sphereradius, 
                 cysbond, 
                 start, 
                 temperature, 
                 replicates,
                 sampling,
                 *args, 
                 **kwargs):
        
        self.lig1 = lig1
        self.lig2 = lig2
        self.FF = FF
        self.system = system
        self.rootdir = os.getcwd()
        self.cluster = cluster
        self.sphereradius = sphereradius
        self.cysbond = cysbond
        self.start = start
        self.include = ['ATOM', 'HETATM']
        self.temperature = temperature
        self.replicates = replicates
        self.sampling = sampling
        #Temporary until flag is here
        self.ABS = False #True
        self.ABS_waters = []
        
        if self.system == 'protein':
            # Get last atom and residue from complexfile!
            with open('protein.pdb') as infile:
                for line in infile:
                    try:
                        resnr = int(line[22:26])
                        atnr = int(line[6:11])
                        
                    except:
                        continue

                self.residueoffset = resnr
                self.atomoffset = atnr
                
        else:
            self.atomoffset = 0
            self.residueoffset = 0
        
    def makedir(self):
        lignames = self.lig1 + '-' +self.lig2
        directory = self.rootdir + '/FEP_' + lignames
        if not os.path.exists(directory):
            os.makedirs(directory)
            
        if not os.path.exists(directory + '/inputfiles'):
            os.makedirs(directory + '/inputfiles')

        return directory
    
    def replace(self, string, replacements):
        pattern = re.compile(r'\b(' + '|'.join(replacements.keys()) + r')\b')
        replaced_string = pattern.sub(lambda x: replacements[x.group()], string)
        return replaced_string
        
    def read_files(self):
        changes_1 = {}
        changes_2 = {}
        charges = []
        atomtypes = []
        merged_molsize = 0
        
        with open(self.lig1 + '.lib') as infile:
            block = 0
            for line in infile:
                line = line.split()
                if len(line) > 0:
                    if line[0] == '[atoms]':
                        block = 1
                        continue
                    if line[0] == '[bonds]':
                        block = 2
                        
                if block == 1 and len(line) > 0:
                    #construct for FEP file
                    merged_molsize = merged_molsize + 1
                    charges.append([merged_molsize, line[3], '0.000'])
                    atomtypes.append([merged_molsize, line[2], 'DUM'])
                
                if block == 2:
                    break
                    
            molsize_lig1 = len(atomtypes)
            
        with open(self.lig2 + '.lib') as infile:
            block = 0
            for line in infile:
                line = line.split()
                if len(line) > 0:
                    if line[0] == '[atoms]':
                        block = 1
                        continue
                    if line[0] == '[bonds]':
                        block = 2
                        
                if block == 1 and len(line) > 0:
                    #construct for FEP file
                    merged_molsize = merged_molsize + 1
                    charges.append([merged_molsize, '0.000', line[3]])
                    
                    
                    #adjustments to be made for lib and prm files
                    cnt = 0
                    for i in [line[1], line[2]]:
                        cnt = cnt + 1
                        if self.FF == 'AMBER14sb' or self.FF == 'CHARMM36':
                            j = 'X' + i
                        else:
                            match = re.match(r"([a-z]+)([0-9]+)", i, re.I)
                            if match:
                                items = match.groups()
                                j = str(items[0]) + str(int(items[1]) + int(molsize_lig1))
                        
                        if self.FF == 'CHARMM_TEST':
                            j = 'X_' + i
                        
                        if cnt == 1:
                            changes_1[i] = j
                        if cnt == 2:
                            changes_2[i] = j
                            atomtypes.append([merged_molsize ,'DUM', j])
        
        molsize_lig2 = merged_molsize - molsize_lig1
        return [changes_1, changes_2],                      \
               [charges, atomtypes],                        \
               [molsize_lig1, molsize_lig2]
        

        
    def change_lib(self, replacements, writedir):
        replacements['LIG'] = 'LID'
        pattern = re.compile(r'\b(' + '|'.join(replacements.keys()) + r')\b')
        
        with open(self.lig2 + '.lib', 'r') as infile:
            file_replaced = []
            for line in infile:
                line2 = pattern.sub(lambda x: replacements[x.group()], line)
                file_replaced.append(line2)
                
        with open(writedir + '/' + self.lig2 +'_renumber.lib', 'w') as outfile:
            block = 0
            for line in file_replaced:
                outfile.write(line)
                
        shutil.copy(self.lig1 + '.lib', writedir + '/' + self.lig1 + '.lib')
                                
            
    def change_prm(self, replacements, writedir):
        pattern = re.compile(r'\b(' + '|'.join(replacements.keys()) + r')\b')
        file1 = glob.glob(self.lig1 + '.prm')[0]
        file2 = glob.glob(self.lig2 + '.prm')[0]
        prm_file = s.FF_DIR + '/' + self.FF + '.prm'
        prm_merged = {'vdw':[],
                       'bonds':[],
                       'angle':[],
                       'torsion':[],
                       'improper':[]
                       }
        
        for file in [file1, file2]:
            with open(file) as infile:
                block = 0
                for line in infile:
                    if file == file2:
                        line = pattern.sub(lambda x: replacements[x.group()], line)
                    if line == '[atom_types]\n':
                        block = 1
                        continue
                    elif line == '[bonds]\n':
                        block = 2
                        continue
                    elif line == '[angles]\n':
                        block = 3
                        continue
                    elif line == '[torsions]\n':
                        block = 4
                        continue
                    if line == '[impropers]\n':
                        block = 5
                        continue

                    if block == 1:
                        prm_merged['vdw'].append(line)

                    elif block == 2:
                        prm_merged['bonds'].append(line)                

                    elif block == 3:
                        prm_merged['angle'].append(line)                

                    elif block == 4:
                        prm_merged['torsion'].append(line)                

                    elif block == 5:
                        prm_merged['improper'].append(line)
                        
        with open(prm_file) as infile, open(writedir + 
                                            '/' + 
                                            self.FF + 
                                            '_' + 
                                            self.lig1 +  
                                            '_' + 
                                            self.lig2 
                                            +'_merged.prm', 'w') as outfile:
            for line in infile:
                block = 0
                outfile.write(line)
                if len(line) > 1:
                    if line == "! Ligand vdW parameters\n":
                        block = 1
                    if line == "! Ligand bond parameters\n":
                        block = 2     
                    if line == "! Ligand angle parameters\n":
                        block = 3
                    if line == "! Ligand torsion parameters\n":
                        block = 4
                    if line == "! Ligand improper parameters\n":
                        block = 5
                # Read the parameters in from file and store them
                if block == 1: 
                    for line in prm_merged['vdw']:
                        outfile.write(line)

                if block == 2:
                    for line in prm_merged['bonds']:
                        outfile.write(line)

                if block == 3:
                    for line in prm_merged['angle']:
                        outfile.write(line)

                if block == 4:
                    for line in prm_merged['torsion']:
                        outfile.write(line)

                if block == 5:
                    for line in prm_merged['improper']:
                        outfile.write(line)                  
        
        #AND return the vdW list for the FEP file
        FEP_vdw = []
        for line in prm_merged['vdw']:
            if len(line) > 1 and line[0] != '!' and line[0:1]:
                line = line.split()
                line2 = "{:10}{:10}{:10}{:10}{:10}{:10}{:10}{:10}".format(line[0],
                                                                      line[1],
                                                                      line[3],
                                                                      str(0),
                                                                      str(0),
                                                                      line[4],
                                                                      line[5],
                                                                      line[6]
                                                                      )
                FEP_vdw.append(line2)
        return FEP_vdw
        
    def write_FEP_file(self, change_charges, change_vdw, FEP_vdw, writedir, lig_size1, lig_size2):
        lig_size1 = int(lig_size1)
        lig_size2 = int(lig_size2)
        lig_tot = lig_size1 + lig_size2
        
        
        with open(writedir + '/FEP1.fep', 'w') as outfile:
            total_atoms = len(change_charges)
            outfile.write('!info: ' + self.lig1 + ' --> ' + self.lig2 + '\n')
            outfile.write('[FEP]\n')
            outfile.write('states 2\n')
            outfile.write('softcore_use_max_potential on\n\n')

            # defining the atom order taken user given offset into account
            outfile.write('[atoms]\n')
            for i in range(1, total_atoms + 1):
                outfile.write("{:5}{:5}\n".format(str(i),
                                                  str(i + self.atomoffset)))
            outfile.write('\n\n')
            
            # changing charges
            outfile.write('[change_charges]\n')

            for line in change_charges:
                outfile.write("{:<5}{:>10}{:>10}\n".format(line[0],
                                                        line[1],
                                                        line[2]))
            outfile.write('\n\n')
            
            #add the Q atomtypes
            outfile.write('[atom_types]\n')
            for line in FEP_vdw:
                outfile.write(line + '\n')
                
            outfile.write('DUM       0.0000    0.0000    0         0         0.0000    0.0000    1.0080')
            outfile.write('\n\n')
            
            outfile.write('[softcore]\n')
            # ADD softcore
            for i in range(1, lig_size1 + 1):
                outfile.write("{:<5}{:>10}{:>10}\n".format(str(i),'0', '20'))
                
            for i in range(1 + lig_size1, lig_tot + 1):
                outfile.write("{:<5}{:>10}{:>10}\n".format(str(i),'20', '0'))
            
            outfile.write('\n\n')
            
            # changing atom types
            outfile.write('[change_atoms]\n')
            for line in change_vdw:
                outfile.write('{:<5}{:>10}{:>10}\n'.format(line[0],
                                                        line[1],
                                                        line[2]))
            
            
    def merge_pdbs(self, writedir):
        replacements = {}
        replacements['LIG'] = 'LID'
        pattern = re.compile(r'\b(' + '|'.join(replacements.keys()) + r')\b')
        file_replaced = []
        atnr = self.atomoffset
        with open(self.lig2 + '.pdb') as infile:
            for line in infile:
                if line.split()[0].strip() in self.include:
                    atom1 = IO.pdb_parse_in(line)
                    atom1[4] = 'LID'
                    #line2 = pattern.sub(lambda x: replacements[x.group()], line)
                    line = IO.pdb_parse_out(atom1) + '\n'
                    file_replaced.append(line)
                                            
        with open(self.lig1 + '.pdb') as infile,                                            \
             open(writedir + '/' + self.lig1 + '_' + self.lig2 + '.pdb', 'w') as outfile:

            if self.system == 'protein':
                with open('protein.pdb') as protfile:
                    for line in protfile:
                        outfile.write(line)
                        
            for line in infile:
                if line.split()[0].strip() in self.include:
                    resnr = int(line[22:26])
                    # The atoms are not allowed to overlap in Q
                    atnr += 1
                    atom1 = IO.pdb_parse_in(line)
                    atom1[1] = atom1[1] + self.atomoffset
                    atom1[6] = atom1[6] + self.residueoffset
                    atom1[8] = float(atom1[8]) + 0.001
                    atom1[9] = float(atom1[9]) + 0.001
                    atom1[10] = float(atom1[10]) + 0.001
                    line = IO.pdb_parse_out(atom1) + '\n'
              
                    outfile.write(line)
                    
            self.residueoffset = self.residueoffset + 2
            resnr = '{:4}'.format(self.residueoffset)
            for line in file_replaced:
                atnr = atnr + 1
                atchange = '{:5}'.format(atnr)
                line = line[0:6] + atchange + line[11:22] + resnr + line[26:]
                outfile.write(line)
    
    def write_water_pdb(self, writedir):
        header = self.sphereradius + '.0 SPHERE\n'
        with open('water.pdb') as infile, open(writedir + '/water.pdb', 'w') as outfile:
            outfile.write(header)
            for line in infile:
                outfile.write(line)
        
        
    def get_lambdas(self, windows, sampling):
        # Constructing the lambda partition scheme
        windows = int(windows)
        step = int(windows/2)
        lambdas = []
        lmbda_1 = []
        lmbda_2 = []
        k_dic = {'sigmoidal':-1.1, 
                 'linear':1000,
                 'exponential':-1.1,
                 'reverse_exponential':1.1
                }
        k = k_dic[sampling]

        if sampling == 'sigmoidal': 
            for i in range(0, step + 1):
                lmbda1 = '{:.3f}'.format(0.5 * (f.sigmoid(float(i)/float(step), k) + 1))
                lmbda2 = '{:.3f}'.format(0.5 * (-f.sigmoid(float(i)/float(step), k) + 1))
                lmbda_1.append(lmbda1)
                lmbda_2.append(lmbda2)

            lmbda_2 = lmbda_2[1:]

            for i in reversed(lmbda_2):
                lambdas.append(i)

            for i in lmbda_1:
                lambdas.append(i)

        else:
            for i in range(0, windows + 1):
                lmbda = '{:.3f}'.format(f.sigmoid(float(i)/float(windows), k))
                lambdas.append(lmbda)
        
        lambdas = lambdas[::-1]
        return lambdas            
    
    def overlapping_atoms(self, writedir):
        pdbfile = writedir + '/inputfiles/' + self.lig1 + '_' + self.lig2 + '.pdb'
        reslist = ['LIG', 'LID']
        overlap_list = f.overlapping_pairs(pdbfile, reslist)
        
        if self.ABS == True:
            with open(pdbfile) as infile:
                for line in infile:
                    if line[13].strip() == 'O': 
                        line = IO.pdb_parse_in(line)
                        self.ABS_waters.append(int(line[1])+self.atomoffset)
                            
        return overlap_list
        
    def write_MD_05(self, lambdas, writedir, lig_size1, lig_size2):
        lambda_tot = len(lambdas)
        replacements = {}
        file_list1 = []
        file_list2 = []
        file_list3 = []
        lig_total = lig_size1 + lig_size2
        lambda_1 = []
        lambda_2 = []
        block = 0
        index = 0
        cnt = -1
        restlist = []
        
        for line in lambdas:
            if line == '0.500':
                block = 1
                
            if block == 0:
                lambda_1.append(line)
                
            if block == 1:
                lambda_2.append(line)

        lambda_1 = lambda_1[::-1]
        lambda_2 = lambda_2[1:]
        replacements['ATOM_START_LIG1'] =   '{:<6}'.format(self.atomoffset + 1)
        replacements['ATOM_END_LIG1']   =   '{:<7}'.format(self.atomoffset + lig_size1)           
        replacements['ATOM_START_LIG2'] =   '{:<6}'.format(self.atomoffset + lig_size1 + 1)
        replacements['ATOM_END_LIG2']   =   '{:<7}'.format(self.atomoffset + lig_size1 + lig_size2)
        replacements['SPHERE']          =   self.sphereradius
        replacements['ATOM_END']        =   '{:<6}'.format(self.atomoffset + lig_total)
        replacements['EQ_LAMBDA']       =   '0.500 0.500'
        
        if self.system == 'water' or self.system == 'vacuum':
            if self.ABS == False:
                replacements['WATER_RESTRAINT'] = '{:<7}{:<7} 1.0 0 1   \n'.format(self.atomoffset + 1, 
                                                                              self.atomoffset + lig_size1 + 
                                                                              lig_size2
                                                                             )
            
            else:
                replacements['WATER_RESTRAINT'] = '{:<7}{:<7} 1.0 0 1   \n'.format(self.atomoffset + 1, 
                                                                              self.atomoffset + lig_size1
                                                                             )
                

                for i in range(self.atomoffset + 1+ lig_size1,
                               self.atomoffset + 2+ lig_size1 + lig_size2):
                    cnt += 1
                    if cnt == 0:
                        rest = '{:<7}{:<7} 1.0 0 1   \n'.format(i,i)
                        restlist.append(rest)
                        
                    if cnt == 2:
                        cnt = -1

        elif self.system == 'protein':
            replacements['WATER_RESTRAINT'] = ''
                    
        for eq_file_in in sorted(glob.glob(s.ROOT_DIR + '/INPUTS/eq*.inp')):
            eq_file = eq_file_in.split('/')[-1:][0]
            eq_file_out = writedir + '/' + eq_file

            with open(eq_file_in) as infile, open(eq_file_out, 'w') as outfile:
                for line in infile:
                    line = run.replace(line, replacements)
                    outfile.write(line)
                    if line == '[distance_restraints]\n':
                        for line in overlapping_atoms:
                            outfile.write('{:d} {:d} 0.0 0.1 1.5 0\n'.format(line[0], line[1]))  
                            
                    if line == '[sequence_restraints]\n':
                        for line in restlist:
                            outfile.write(line)
                        
                file_list1.append(eq_file)
                
        file_in = s.INPUT_DIR + '/md_0500_0500.inp'
        file_out = writedir + '/md_0500_0500.inp' 
        with open(file_in) as infile, open(file_out, 'w') as outfile:
            for line in infile:
                line = run.replace(line, replacements)
                outfile.write(line)
                if line == '[distance_restraints]\n':
                    for line in overlapping_atoms:
                        outfile.write('{:d} {:d} 0.0 0.1 1.5 0\n'.format(line[0], line[1]))

                if line == '[sequence_restraints]\n':
                    for line in restlist:
                        outfile.write(line)                        
                        
                        
        file_list1.append('md_0500_0500.inp')
        
        for lambdas in [lambda_1, lambda_2]:
            index += 1
            filename_N = 'md_0500_0500'
            filenr = -1

            for line in lambdas:
                filenr += 1
                if index == 1:
                    lambda1 = lambda_1[filenr]
                    lambda2 = lambda_2[filenr]
                    
                elif index == 2:
                    lambda1 = lambda_2[filenr]
                    lambda2 = lambda_1[filenr]
                    
                filename = 'md_' + lambda1.replace('.', '') + '_' + lambda2.replace('.', '')
                replacements['FLOAT_LAMBDA1']   =   lambda1 
                replacements['FLOAT_LAMBDA2']   =   lambda2
                replacements['FILE']          =   filename
                replacements['FILE_N'] = filename_N

                # Consider putting this in a function seeing as it is called multiple times
                pattern = re.compile(r'\b(' + '|'.join(replacements.keys()) + r')\b')
                file_in = s.INPUT_DIR + '/md_XXXX_XXXX.inp'
                file_out = writedir + '/' + filename + '.inp'

                with open(file_in) as infile, open(file_out, 'w') as outfile:
                    for line in infile:
                        line = pattern.sub(lambda x: replacements[x.group()], line)
                        outfile.write(line)
                        if line == '[distance_restraints]\n':
                            for line in overlapping_atoms:
                                outfile.write('{:d} {:d} 0.0 0.2 0.5 0\n'.format(line[0], line[1]))
                                
                                
                        if line == '[sequence_restraints]\n':
                            for line in restlist:
                                outfile.write(line)                

                filename_N = filename
                
                if index == 1:
                    file_list2.append(filename + '.inp')
                    
                elif index == 2:
                    file_list3.append(filename + '.inp')
        return [file_list1, file_list2, file_list3]
    
    
    def write_MD_1(self, lambdas, writedir, lig_size1, lig_size2, overlapping_atoms):
        totallambda = len(lambdas)
        file_list_1 = []
        file_list_2 = []
        file_list_3 = []
        replacements = {}
        lig_total = lig_size1 + lig_size2
        lambda_1 = []
        lambda_2 = []
        
        replacements['ATOM_START_LIG1'] =   '{:<6}'.format(self.atomoffset + 1)
        replacements['ATOM_END_LIG1']   =   '{:<7}'.format(self.atomoffset + lig_size1)           
        replacements['ATOM_START_LIG2'] =   '{:<6}'.format(self.atomoffset + lig_size1 + 1)
        replacements['ATOM_END_LIG2']   =   '{:<7}'.format(self.atomoffset + lig_size1 + lig_size2)
        replacements['SPHERE']          =   self.sphereradius
        replacements['ATOM_END']        =   '{:<6}'.format(self.atomoffset + lig_total)        
        replacements['EQ_LAMBDA']       =   '1.000 0.000'

        if self.system == 'water' or self.system == 'vacuum':
            replacements['WATER_RESTRAINT'] = '{:<7}{:<7} 1.0 0 1   '.format(self.atomoffset + 1, 
                                                                          self.atomoffset + lig_size1 + 
                                                                          lig_size2
                                                                         )
            
            
        elif self.system == 'protein':
            replacements['WATER_RESTRAINT'] = ''
        
        for eq_file_in in sorted(glob.glob(s.ROOT_DIR + '/INPUTS/eq*.inp')):
            eq_file = eq_file_in.split('/')[-1:][0]
            eq_file_out = writedir + '/' + eq_file

            with open(eq_file_in) as infile, open(eq_file_out, 'w') as outfile:
                for line in infile:
                    line = run.replace(line, replacements)
                    outfile.write(line)
                    if line == '[distance_restraints]\n':
                        for line in overlapping_atoms:
                            outfile.write('{:d} {:d} 0.0 0.2 0.5 0\n'.format(line[0], line[1]))

                file_list_1.append(eq_file)
                
        file_in = s.INPUT_DIR + '/md_1000_0000.inp'
        file_out = writedir + '/md_1000_0000.inp' 
        with open(file_in) as infile, open(file_out, 'w') as outfile:
            for line in infile:
                line = run.replace(line, replacements)
                outfile.write(line)
                if line == '[distance_restraints]\n':
                    for line in overlapping_atoms:
                        outfile.write('{:d} {:d} 0.0 0.2 0.5 0\n'.format(line[0], line[1]))
                
        file_list_1.append('md_1000_0000.inp')
        filenr = 0

        for l in lambdas:
            if l == '1.000':
                filename_N = 'md_1000_0000'
                continue
            else:
                step_n = totallambda - filenr - 2

                lambda1 = l
                lambda2 = lambdas[step_n]
                filename = 'md_' + lambda1.replace('.', '') + '_' + lambda2.replace('.', '')
                replacements['FLOAT_LAMBDA1']   =   lambda1 
                replacements['FLOAT_LAMBDA2']   =   lambda2
                replacements['FILE']          =   filename
                replacements['FILE_N'] = filename_N

                # Move to functio
                pattern = re.compile(r'\b(' + '|'.join(replacements.keys()) + r')\b')
                file_in = s.INPUT_DIR + '/md_XXXX_XXXX.inp'
                file_out = writedir + '/' + filename + '.inp'

                with open(file_in) as infile, open(file_out, 'w') as outfile:
                    for line in infile:
                        line = pattern.sub(lambda x: replacements[x.group()], line)
                        outfile.write(line)
                        if line == '[distance_restraints]\n':
                            for line in overlapping_atoms:
                                outfile.write('{:d} {:d} 0.0 0.2 0.5 0\n'.format(line[0], line[1]))

                filename_N = filename
                filenr += 1
                file_list_2.append(filename + '.inp')

        return [file_list_1, file_list_2, file_list_3]
    
    def write_submitfile(self, writedir):
        replacements = {}
        replacements['TEMP_VAR']    = self.temperature
        replacements['RUN_VAR']     = self.replicates
        replacements['RUNFILE']     = 'run' + self.cluster + '.sh'
        submit_in = s.ROOT_DIR + '/INPUTS/FEP_submit.sh'
        submit_out = writedir + ('/FEP_submit.sh')
        with open(submit_in) as infile, open (submit_out, 'w') as outfile:
            for line in infile:
                line = run.replace(line, replacements)
                outfile.write(line)
        
        try:
            st = os.stat(submit_out)
            os.chmod(submit_out, st.st_mode | stat.S_IEXEC)
        
        except:
            print("WARNING: Could not change permission for " + submit_out)

        
    def write_runfile(self, writedir, file_list):
        ntasks = getattr(s, self.cluster)['NTASKS']
        src = s.INPUT_DIR + '/run.sh'
        tgt = writedir + '/run' + self.cluster + '.sh'
        EQ_files = sorted(glob.glob(writedir + '/eq*.inp'))
        
        if self.start == '1':
            MD_files = reversed(sorted(glob.glob(writedir + '/md*.inp')))
            
        elif self.start == '0.5':
            md_1 = file_list[1]
            md_2 = file_list[2]
        
        replacements = getattr(s, self.cluster)
        replacements['FEPS']='FEP1.fep'
        run_threads = '{}'.format(int(replacements['NTASKS']))
        
        with open(src) as infile, open(tgt, 'w') as outfile:
            if self.cluster=='CSB':

                for line in infile:
                    if line.strip() == '#SBATCH -A ACCOUNT':
                        try:
                            replacements['ACCOUNT']
                            
                        except:
                            line = ''
                    outline = IO.replace(line, replacements)
                    outfile.write(outline)
                    
                    if line.strip() == '#EQ_FILES':
                        for line in EQ_files:
                            file_base = line.split('/')[-1][:-4]
                            outline = 'time mpirun -np {} $qdyn {}.inp' \
                                    ' > {}.log\n'.format(ntasks,
                                                        file_base,
                                                        file_base)
                            outfile.write(outline)
                            
                    if line.strip() == '#RUN_FILES':
                        if self.start == '1':
                            for line in MD_files:
                                file_base = line.split('/')[-1][:-4]
                                outline = 'time mpirun -np {} $qdyn {}.inp'  \
                                        ' > {}.log\n'.format(ntasks,
                                                            file_base,
                                                            file_base)
                                outfile.write(outline)
                                
                        elif self.start == '0.5':
                            outline = 'time mpirun -np {} $qdyn {}.inp' \
                                    ' > {}.log\n\n'.format(ntasks,
                                                        'md_0500_0500',
                                                        'md_0500_0500')
                            outfile.write(outline)
                            for i, md in enumerate(md_1):
                                outline1 = 'time mpirun -np {:d} $qdyn {}.inp'  \
                                        ' > {}.log &\n'.format(int(int(ntasks)/2),
                                                            md_1[i][:-4],
                                                            md_1[i][:-4])

                                outline2 = 'time mpirun -np {:d} $qdyn {}.inp'  \
                                        ' > {}.log\n'.format(int(int(ntasks)/2),
                                                            md_2[i][:-4],
                                                            md_2[i][:-4])

                                outfile.write(outline1)
                                outfile.write(outline2)
                                outfile.write('\n')
            elif self.cluster=='TETRA':

                for line in infile:
                    if line.strip() == '#SBATCH -A ACCOUNT':
                        try:
                            replacements['ACCOUNT']
                            
                        except:
                            line = ''
                    outline = IO.replace(line, replacements)
                    outfile.write(outline)
                    
                    if line.strip() == '#EQ_FILES':
                        for line in EQ_files:
                            file_base = line.split('/')[-1][:-4]
                            outline = 'time mpprun -np {} $qdyn {}.inp' \
                                    ' > {}.log\n'.format(ntasks,
                                                        file_base,
                                                        file_base)
                            outfile.write(outline)
                            
                    if line.strip() == '#RUN_FILES':
                        if self.start == '1':
                            for line in MD_files:
                                file_base = line.split('/')[-1][:-4]
                                outline = 'time mpprun -np {} $qdyn {}.inp'  \
                                        ' > {}.log\n'.format(ntasks,
                                                            file_base,
                                                            file_base)
                                outfile.write(outline)
                                
                        elif self.start == '0.5':
                            outline = 'time mpprun -np {} $qdyn {}.inp' \
                                    ' > {}.log\n\n'.format(ntasks,
                                                        'md_0500_0500',
                                                        'md_0500_0500')
                            outfile.write(outline)
                            for i, md in enumerate(md_1):
                                outline1 = 'time mpprun -np {:d} $qdyn {}.inp'  \
                                        ' > {}.log &\n'.format(int(int(ntasks)/2),
                                                            md_1[i][:-4],
                                                            md_1[i][:-4])

                                outline2 = 'time mpprun -np {:d} $qdyn {}.inp'  \
                                        ' > {}.log\n'.format(int(int(ntasks)/2),
                                                            md_2[i][:-4],
                                                            md_2[i][:-4])

                                outfile.write(outline1)
                                outfile.write(outline2)
                                outfile.write('\n')   
            elif self.cluster == 'ALICE':
                outfile.write('rm *.dcd\n')
                outfile.write('rm *.en\n')
                outfile.write('rm *.re\n')
            else:
                raise ValueError(f"Unknown cluster: {self.cluster}")
            
    def write_qfep(self, inputdir, windows, lambdas):
        qfep_in = s.ROOT_DIR + '/INPUTS/qfep.inp' 
        qfep_out = writedir + '/inputfiles/qfep.inp'
        i = 0
        total_l = len(lambdas)
        
        # TO DO: multiple files will need to be written out for temperature range
        kT = f.kT(float(self.temperature))
        replacements = {}
        replacements['kT']=kT
        replacements['WINDOWS']=windows
        replacements['TOTAL_L']=str(total_l)
        with open(qfep_in) as infile, open(qfep_out, 'w') as outfile:
            for line in infile:
                line = run.replace(line, replacements)
                outfile.write(line)
            
            if line == '!ENERGY_FILES\n':
                for i in range(0, total_l):
                    j = -(i + 1)
                    lambda1 = lambdas[i]
                    lambda2 = lambdas[j]
                    filename = 'md_' +                          \
                                lambda1.replace('.', '') +      \
                                '_' +                           \
                                lambda2.replace('.', '') +      \
                                '.en\n'
                                
                    outfile.write(filename)

    def write_qprep(self, writedir):
        replacements = {}
        center = f.COG(self.lig1 + '.pdb')
        center = '{:} {:} {:}'.format(center[0], center[1], center[2])
        qprep_in = s.ROOT_DIR + '/INPUTS/qprep.inp'
        qprep_out = writedir + '/qprep.inp'
        replacements['FF_LIB'] = s.ROOT_DIR + '/FF/' + self.FF + '.lib'
        replacements['LIG1']   = self.lig1 + '.lib'
        replacements['LIG2']   = self.lig2 + '_renumber.lib'
        replacements['LIGPRM'] = self.FF + '_' + self.lig1 + '_' + self.lig2 + '_merged.prm'
        replacements['LIGPDB'] = self.lig1 + '_' + self.lig2 + '.pdb'
        replacements['CENTER'] = center
        replacements['SPHERE'] = self.sphereradius
        if self.system =='vacuum':
            replacements['solvate'] = '!solvate'
        if self.system == 'water':
            replacements['SOLVENT']  = '1 HOH'
        if self.system == 'protein':
            replacements['SOLVENT']  = '4 water.pdb'            
        
        with open(qprep_in) as infile, open(qprep_out, 'w') as outfile:
            for line in infile:
                line = run.replace(line, replacements)
                if line == '!addbond at1 at2 y\n' and self.cysbond != None:
                    cysbond = self.cysbond.split(',')
                    for cys in cysbond:
                        at1 = cys.split('_')[0]
                        at2 = cys.split('_')[1]
                        outfile.write('addbond ' + at1 + ' ' + at2 + ' y \n' )
                    continue
                outfile.write(line)
        
    def qprep(self, writedir):
        os.chdir(writedir)
        cluster_options = getattr(s, self.cluster)
        qprep = cluster_options['QPREP']
        options = ' < qprep.inp > qprep.out'
        # Somehow Q is very annoying with this < > input style so had to implement
        # another function that just calls os.system instead of using the preferred
        # subprocess module....
        IO.run_command(qprep, options, string = True)
        os.chdir('../../')


def parseargs(args: list[str] = []) -> argparse.Namespace:
    """Return a Namespace after parsing an argument string.

    If args is not provided, defaults to args from command line.
    """
    parser = argparse.ArgumentParser(
        prog='QligFEP',
        formatter_class=argparse.RawDescriptionHelpFormatter,
        description = '       == Generate FEP files for dual topology ligand FEP == ')

    parser.add_argument('-l1', '--lig_1',
                        dest = "lig1",
                        required = True,
                        help = "name of ligand 1")

    parser.add_argument('-l2', '--lig_2',
                        dest = "lig2",
                        required = True,
                        help = "name of ligand 2")

    parser.add_argument('-FF', '--forcefield',
                        dest = "FF",
                        required = True,
                        choices = ['OPLS2005', 'OPLS2015', 'AMBER14sb', 'CHARMM36', 'CHARMM22', 'CHARMM_TEST'],
                        help = "Forcefield to be used")

    parser.add_argument('-s', '--system',
                        dest = "system",
                        required = True,
                        choices = ['water', 'protein', 'vacuum'],
                        help = "what type of system we are setting up")

    parser.add_argument('-c', '--cluster',
                        dest = "cluster",
                        required = True,
                        help = "cluster you want to submit to, cluster specific parameters added to settings"
                       )

    parser.add_argument('-r', '--sphereradius',
                        dest = "sphereradius",
                        required = False,
                        default = '15',
                        help = "size of the simulation sphere"
                       )

    parser.add_argument('-b', '--cysbond',
                        dest = "cysbond",
                        default = None,
                        help = "Function to add cysbonds given as at1_at2,at3_at4,(...)"
                       )

    parser.add_argument('-l', '--start',
                        dest = "start",
                        default = '0.5',
                        choices = ['1', '0.5'],
                        help = "Starting FEP in the middle or endpoint"
                       )

    parser.add_argument('-T', '--temperature',
                        dest = "temperature",
                        default = '298',
                        help = "Temperature(s), mutliple tempereratures given as 'T1,T2,...,TN'"
                       )

    parser.add_argument('-R', '--replicates',
                        dest = "replicates",
                        default = '10',
                        help = "How many repeats should be run"
                       )

    parser.add_argument('-S', '--sampling',
                        dest = "sampling",
                        default = 'linear',
                        choices = ['linear', 'sigmoidal', 'exponential', 'reverse_exponential'],
                        help = "Lambda spacing type to be used"
                       )

    parser.add_argument('-w', '--windows',
                        dest = "windows",
                        default = '50',
                        help = "Total number of windows that will be run"
                       )

    if args:
        return parser.parse_args(args)
    else:
        return parser.parse_args()


if __name__ == "__main__":
    args = parseargs()
    run = Run(lig1 = args.lig1,
              lig2 = args.lig2,
              FF= args.FF,
              system = args.system,
              cluster = args.cluster,
              sphereradius = args.sphereradius,
              cysbond = args.cysbond,
              start = args.start,
              temperature = args.temperature,
              replicates = args.replicates,
              sampling = args.sampling
             )

    writedir = run.makedir()
    inputdir = writedir + '/inputfiles'
    a = run.read_files()
    changes_for_libfiles = a[0][1]
    changes_for_prmfiles = a[0][1]
    change_charges       = a[1][0]
    change_vdw           = a[1][1]
    changes_for_pdbfiles = a[0][0]
    lig_size1, lig_size2 = a[2][0], a[2][1]

    # Write the merged files
    run.change_lib(changes_for_libfiles, inputdir)
    FEP_vdw = run.change_prm(changes_for_prmfiles, inputdir)
    run.write_FEP_file(change_charges, change_vdw, FEP_vdw, inputdir, lig_size1, lig_size2)
    run.merge_pdbs(inputdir)
    if args.system == 'protein':
        run.write_water_pdb(inputdir)
    lambdas = run.get_lambdas(args.windows, args.sampling)
    overlapping_atoms = run.overlapping_atoms(writedir)
    
    # Handling the correct offset here
    if args.start == '0.5':
        file_list = run.write_MD_05(lambdas, inputdir, lig_size1, lig_size2)
        run.write_runfile(inputdir, file_list)    
        
    if args.start == '1':
        file_list = run.write_MD_1(lambdas, inputdir, lig_size1, lig_size2, overlapping_atoms)
        run.write_runfile(inputdir, file_list)    
    
    run.write_submitfile(writedir)
    run.write_qfep(inputdir, args.windows, lambdas)
    run.write_qprep(inputdir)
    run.qprep(inputdir)