def main():
root = '/Users/iwelsh/GitHub/ShortScripts/proteinStructures'
coords = gromos_cnf_parse(load_file(root + '/1d66_ss-dna_54a8.gch'))[1]
#pdb = pdb_parse(load_file(root + '/3blg.pdb'))
topo = gromos_topology_parse(load_file(root + '/1d66_ss-dna_54a8.top'))
mol = Molecule('3BLG', cnf=coords, topo=topo)
print(len(mol.atoms))
#for atm in mol.atoms:
# print(atm.data['residue_name'])
#unite_atoms(mol)
conect_graph = mol.labeled_graph
for atm in mol.atoms:
atm.hcount = united_h_count(atm)
with open(root + '/1d66_gch.pdb', 'w') as fh:
fh.write(print_pdb(mol))
with open(root + '/1d66_aa.pdb', 'w') as fh:
fh.write(print_pdb(convert_to_aa(mol)))
def main():
root = '/Users/iwelsh/GitHub/ShortScripts/proteinStructures'
coords = gromos_cnf_parse(load_file(root + '/1d66_ss-dna_54a8.gch'))[1]
#pdb = pdb_parse(load_file(root + '/3blg.pdb'))
topo = gromos_topology_parse(load_file(root + '/1d66_ss-dna_54a8.top'))
mol = Molecule('3BLG', cnf=coords, topo=topo)
print(len(mol.atoms))
#for atm in mol.atoms:
# print(atm.data['residue_name'])
#unite_atoms(mol)
conect_graph = mol.labeled_graph
for atm in mol.atoms:
atm.hcount = united_h_count(atm)
with open(root + '/1d66_gch.pdb','w') as fh:
fh.write(print_pdb(mol))
with open(root +'/1d66_aa.pdb','w') as fh:
fh.write(print_pdb(convert_to_aa(mol)))
def run_md_jobs(root, mols, descrips):
molecules = {
'AMINO-1': {'rigid':{'aa':[16,13,7,9],
'ua':[8,7,5,6],
'gamess':[2,1,8,9],
},
'name':'G564',
},
'AMINO0': {'rigid':{'aa':[2,5,8,13],
'ua':[1,2,3,8],
'gamess':[2,1,8,9],
},
'name':'N0GW',
},
'AMINO1': {'rigid':{'aa':[2,5,8,16],
'ua':[1,2,3,8],
'gamess':[2,1,8,9],
},
'name':'SHJ0',
},
'AMINO2': {'rigid':{'aa':[7,10,12,15],
'ua':[5,6,7,8],
'gamess':[2,1,8,9],
},
'name':'6AT1',
},
'CHLORO-1': {'rigid':{'aa':[2,5,8,14],
'ua':[1,2,3,6],
'gamess':[2,1,8,9],
},
'name':'PCRN',
},
'CHLORO0': {'rigid':{'aa':[2,5,8,11],
'ua':[1,2,3,5],
'gamess':[2,1,8,9],
},
'name':'682F',
},
'CHLORO1': {'rigid':{'aa':[2,5,8,14],
'ua':[1,2,3,6],
'gamess':[2,1,8,9],
},
'name':'ZB0H',
},
'CHLORO2': {'rigid':{'aa':[10,8,17,20],
'ua':[5,4,7,8],
'gamess':[2,1,8,9],
},
'name':'35MG',
},
'HYDRO-1': {'rigid':{'aa':[15,12,6,8],
'ua':[7,6,4,5],
'gamess':[2,1,8,9],
},
'name':'H5JT',
},
'HYDRO0': {'rigid':{'aa':[2,5,8,12],
'ua':[1,2,3,7],
'gamess':[2,1,8,9],
},
'name':'G096',
},
'HYDRO1': {'rigid':{'aa':[2,5,8,15],
'ua':[1,2,3,7],
'gamess':[2,1,8,9],
},
'name':'W6KL',
},
'HYDRO2': {'rigid':{'aa':[2,5,8,10],
'ua':[1,2,3,4],
'gamess':[2,1,8,9],
},
'name':'5KRK',
},
'METH-1': {'rigid':{'aa':[2,5,8,14],
'ua':[1,2,3,5],
'gamess':[2,1,8,9],
},
'name':'G011',
},
'METH0': {'rigid':{'aa':[2,5,8,14],
'ua':[1,2,3,5],
'gamess':[2,1,8,9],
},
'name':'G011',
},
'METH1': {'rigid':{'aa':[2,5,8,10],
'ua':[1,2,3,4],
'gamess':[2,1,8,9],
},
'name':'4MUW',
},
'METH2': {'rigid':{'aa':[2,5,8,10],
'ua':[1,2,3,4],
'gamess':[2,1,8,9],
},
'name':'YE4E',
},
'THIO-1': {'rigid':{'aa':[2,5,8,15],
'ua':[1,2,3,7],
'gamess':[2,1,8,9],
},
'name':'ZK6W',
},
'THIO0': {'rigid':{'aa':[2,5,8,12],
'ua':[1,2,3,7],
'gamess':[2,1,8,9],
},
'name':'1QIU',
},
'THIO1': {'rigid':{'aa':[2,5,8,15],
'ua':[1,2,3,7],
'gamess':[2,1,8,9],
},
'name':'5G2Q',
},
'THIO2': {'rigid':{'aa':[6,9,18,21],
'ua':[4,5,8,9],
'gamess':[2,1,8,9],
},
'name':'PJLY',
},
}
descriptors = {'Original': ['rigid']}
#'AMINO-1' : {'gamess':[2,1,8,9], 'aa' : [16,13,7,9], 'ua' : [8,7,5,6], }
#for m in sorted(molecules):
# print("'{}' : {},".format(m, molecules[m]['rigid']))
#return
with open(root + '/Parameters/Templates/dihedral.template','r') as fh:
imd_temp_1 = fh.read()
with open(root + '/Parameters/Templates/dihedral2.template','r') as fh:
imd_temp_2 = fh.read()
with open(root + '/Parameters/Templates/dihedral3.template','r') as fh:
imd_temp_3 = fh.read()
with open(root + '/Parameters/Templates/dihedral_constraint.template','r') as fh:
constraint_temp = fh.read()
for m in mols:
forms = dict(mol=m, root=root)
aa_mtb = inlib.gromos_mtb_parse(genlib.load_file('{root}/Parameters/{mol}/{mol}.aa.mtb'.format(**forms)))
ua_mtb = inlib.gromos_mtb_parse(genlib.load_file('{root}/Parameters/{mol}/{mol}.ua.mtb'.format(**forms)))
aa_work_mol = storage.Molecule(molecules[m]['name'], mtb=aa_mtb)
ua_work_mol = storage.Molecule(molecules[m]['name'], mtb=ua_mtb)
for d in descrips:
forms['des'] = d
forms['outdir'] = '{root}/{des}/{mol}/MD_data'.format(**forms)
forms['name'] = molecules[m]['name']
if not os.path.exists('{outdir}'.format(**forms)):
os.makedirs('{outdir}'.format(**forms))
with open('{outdir}/{mol}.aa.1.imd'.format(**forms),'w') as fh:
fh.write(imd_temp_1.format(**{'numberOfAtoms':aa_work_mol.atom_count}))
with open('{outdir}/{mol}.ua.1.imd'.format(**forms),'w') as fh:
fh.write(imd_temp_1.format(**{'numberOfAtoms':ua_work_mol.atom_count}))
with open('{outdir}/{mol}.aa.2.imd'.format(**forms),'w') as fh:
fh.write(imd_temp_2.format(**{'numberOfAtoms':aa_work_mol.atom_count}))
with open('{outdir}/{mol}.ua.2.imd'.format(**forms),'w') as fh:
fh.write(imd_temp_2.format(**{'numberOfAtoms':ua_work_mol.atom_count}))
with open('{outdir}/{mol}.aa.3.imd'.format(**forms),'w') as fh:
fh.write(imd_temp_3.format(**{'numberOfAtoms':aa_work_mol.atom_count}))
with open('{outdir}/{mol}.ua.3.imd'.format(**forms),'w') as fh:
fh.write(imd_temp_3.format(**{'numberOfAtoms':ua_work_mol.atom_count}))
os.chdir('{root}'.format(**forms))
os.system(('/usr/local/gromos++/bin/make_top @build Parameters/{mol}/{mol}.aa.mtb Parameters/54A7.mtb '
'@param Parameters/54A7.ifp @seq {name} @solv H2O > {outdir}/{mol}.aa.top'.format(**forms)))
os.system(('/usr/local/gromos++/bin/make_top @build Parameters/{mol}/{mol}.ua.mtb Parameters/54A7.mtb '
'@param Parameters/54A7.ifp @seq {name} @solv H2O > {outdir}/{mol}.ua.top'.format(**forms)))
for a in range(0,360,5):
skip_angle = False
forms['ang2'] = a
if a == 180:
a = 179
forms['ang'] = a
try:
with open('{root}/{des}/{mol}/{mol}.{ang:03}.log'.format(**forms), 'r') as fh:
gamess = extract_conformation(fh.readlines(), scale=1, key='name', optimised=False)
except FileNotFoundError:
with open('{root}/{des}/{mol}/{mol}.{ang2:03}.log'.format(**forms), 'r') as fh:
gamess = extract_conformation(fh.readlines(), scale=1, key='name', optimised=False)
for atm in aa_work_mol.atoms:
try:
atm.xyz = gamess[atm.atm_name.upper()]['vec']
except TypeError:
print('TypeError', atm.atm_name, d, m, a)
skip_angle = True
break
except KeyError:
print('KeyError', atm.atm_name, d, m, a)
raise
if skip_angle:
continue
for atm in ua_work_mol.atoms:
atm.xyz = gamess[atm.atm_name.upper()]['vec']
with open('{outdir}/{mol}.{ang:03}.aa.cnf'.format(**forms), 'w') as fh:
fh.write(outlib.print_gromos_cnf(aa_work_mol))
with open('{outdir}/{mol}.{ang:03}.ua.cnf'.format(**forms), 'w') as fh:
fh.write(outlib.print_gromos_cnf(ua_work_mol))
#with open('{outdir}/{mol}.{ang:03}.aa.pdb'.format(**forms), 'w') as fh:
# fh.write(outlib.print_pdb(aa_work_mol))
#with open('{outdir}/{mol}.{ang:03}.ua.pdb'.format(**forms), 'w') as fh:
# fh.write(outlib.print_pdb(ua_work_mol))
angs_aa, angs_ua = [], []
for des in descriptors[d]:
atm_a = aa_work_mol.atom(molecules[m][des]['aa'][0]).xyz
atm_b = aa_work_mol.atom(molecules[m][des]['aa'][1]).xyz
atm_c = aa_work_mol.atom(molecules[m][des]['aa'][2]).xyz
atm_d = aa_work_mol.atom(molecules[m][des]['aa'][3]).xyz
ang = dihedral_angle(atm_a,atm_b,atm_c,atm_d,scale='deg')
angs_aa.append(' {1} {2} {3} {4} 1.0 {0:.3f} 0.0 0.0001'.format(ang, *molecules[m][des]['aa']))
angs_ua.append(' {1} {2} {3} {4} 1.0 {0:.3f} 0.0 0.0001'.format(ang, *molecules[m][des]['ua']))
with open('{outdir}/{mol}.{ang:03}.aa.constraints.dat'.format(**forms), 'w') as fh:
fh.write(constraint_temp.format(**{'constraints':'\n'.join(angs_aa)}))
with open('{outdir}/{mol}.{ang:03}.ua.constraints.dat'.format(**forms), 'w') as fh:
fh.write(constraint_temp.format(**{'constraints':'\n'.join(angs_ua)}))
# first pass
os.system(('/opt/local/gromosXX-1773/bin/md @topo {outdir}/{mol}.aa.top @conf {outdir}/{mol}.{ang:03}.aa.cnf '
'@input {outdir}/{mol}.aa.1.imd @fin {outdir}/{mol}.{ang:03}.aa.min.1.cnf @develop '
'@dihrest {outdir}/{mol}.{ang:03}.aa.constraints.dat > {outdir}/{mol}.{ang:03}.aa.1.log'.format(**forms) ))
os.system(('/opt/local/gromosXX-1773/bin/md @topo {outdir}/{mol}.ua.top @conf {outdir}/{mol}.{ang:03}.ua.cnf '
'@input {outdir}/{mol}.ua.1.imd @fin {outdir}/{mol}.{ang:03}.ua.min.1.cnf @develop '
'@dihrest {outdir}/{mol}.{ang:03}.ua.constraints.dat > {outdir}/{mol}.{ang:03}.ua.1.log'.format(**forms) ))
def run_md_jobs(root, mols, descrips):
molecules = {
'AMINO-1': {
'rigid': {
'aa': [16, 13, 7, 9],
'ua': [8, 7, 5, 6],
'gamess': [2, 1, 8, 9],
},
'name': 'G564',
},
'AMINO0': {
'rigid': {
'aa': [2, 5, 8, 13],
'ua': [1, 2, 3, 8],
'gamess': [2, 1, 8, 9],
},
'name': 'N0GW',
},
'AMINO1': {
'rigid': {
'aa': [2, 5, 8, 16],
'ua': [1, 2, 3, 8],
'gamess': [2, 1, 8, 9],
},
'name': 'SHJ0',
},
'AMINO2': {
'rigid': {
'aa': [7, 10, 12, 15],
'ua': [5, 6, 7, 8],
'gamess': [2, 1, 8, 9],
},
'name': '6AT1',
},
'CHLORO-1': {
'rigid': {
'aa': [2, 5, 8, 14],
'ua': [1, 2, 3, 6],
'gamess': [2, 1, 8, 9],
},
'name': 'PCRN',
},
'CHLORO0': {
'rigid': {
'aa': [2, 5, 8, 11],
'ua': [1, 2, 3, 5],
'gamess': [2, 1, 8, 9],
},
'name': '682F',
},
'CHLORO1': {
'rigid': {
'aa': [2, 5, 8, 14],
'ua': [1, 2, 3, 6],
'gamess': [2, 1, 8, 9],
},
'name': 'ZB0H',
},
'CHLORO2': {
'rigid': {
'aa': [10, 8, 17, 20],
'ua': [5, 4, 7, 8],
'gamess': [2, 1, 8, 9],
},
'name': '35MG',
},
'HYDRO-1': {
'rigid': {
'aa': [15, 12, 6, 8],
'ua': [7, 6, 4, 5],
'gamess': [2, 1, 8, 9],
},
'name': 'H5JT',
},
'HYDRO0': {
'rigid': {
'aa': [2, 5, 8, 12],
'ua': [1, 2, 3, 7],
'gamess': [2, 1, 8, 9],
},
'name': 'G096',
},
'HYDRO1': {
'rigid': {
'aa': [2, 5, 8, 15],
'ua': [1, 2, 3, 7],
'gamess': [2, 1, 8, 9],
},
'name': 'W6KL',
},
'HYDRO2': {
'rigid': {
'aa': [2, 5, 8, 10],
'ua': [1, 2, 3, 4],
'gamess': [2, 1, 8, 9],
},
'name': '5KRK',
},
'METH-1': {
'rigid': {
'aa': [2, 5, 8, 14],
'ua': [1, 2, 3, 5],
'gamess': [2, 1, 8, 9],
},
'name': 'G011',
},
'METH0': {
'rigid': {
'aa': [2, 5, 8, 14],
'ua': [1, 2, 3, 5],
'gamess': [2, 1, 8, 9],
},
'name': 'G011',
},
'METH1': {
'rigid': {
'aa': [2, 5, 8, 10],
'ua': [1, 2, 3, 4],
'gamess': [2, 1, 8, 9],
},
'name': '4MUW',
},
'METH2': {
'rigid': {
'aa': [2, 5, 8, 10],
'ua': [1, 2, 3, 4],
'gamess': [2, 1, 8, 9],
},
'name': 'YE4E',
},
'THIO-1': {
'rigid': {
'aa': [2, 5, 8, 15],
'ua': [1, 2, 3, 7],
'gamess': [2, 1, 8, 9],
},
'name': 'ZK6W',
},
'THIO0': {
'rigid': {
'aa': [2, 5, 8, 12],
'ua': [1, 2, 3, 7],
'gamess': [2, 1, 8, 9],
},
'name': '1QIU',
},
'THIO1': {
'rigid': {
'aa': [2, 5, 8, 15],
'ua': [1, 2, 3, 7],
'gamess': [2, 1, 8, 9],
},
'name': '5G2Q',
},
'THIO2': {
'rigid': {
'aa': [6, 9, 18, 21],
'ua': [4, 5, 8, 9],
'gamess': [2, 1, 8, 9],
},
'name': 'PJLY',
},
}
descriptors = {'Original': ['rigid']}
#'AMINO-1' : {'gamess':[2,1,8,9], 'aa' : [16,13,7,9], 'ua' : [8,7,5,6], }
#for m in sorted(molecules):
# print("'{}' : {},".format(m, molecules[m]['rigid']))
#return
with open(root + '/Parameters/Templates/dihedral.template', 'r') as fh:
imd_temp_1 = fh.read()
with open(root + '/Parameters/Templates/dihedral2.template', 'r') as fh:
imd_temp_2 = fh.read()
with open(root + '/Parameters/Templates/dihedral3.template', 'r') as fh:
imd_temp_3 = fh.read()
with open(root + '/Parameters/Templates/dihedral_constraint.template',
'r') as fh:
constraint_temp = fh.read()
for m in mols:
forms = dict(mol=m, root=root)
aa_mtb = inlib.gromos_mtb_parse(
genlib.load_file(
'{root}/Parameters/{mol}/{mol}.aa.mtb'.format(**forms)))
ua_mtb = inlib.gromos_mtb_parse(
genlib.load_file(
'{root}/Parameters/{mol}/{mol}.ua.mtb'.format(**forms)))
aa_work_mol = storage.Molecule(molecules[m]['name'], mtb=aa_mtb)
ua_work_mol = storage.Molecule(molecules[m]['name'], mtb=ua_mtb)
for d in descrips:
forms['des'] = d
forms['outdir'] = '{root}/{des}/{mol}/MD_data'.format(**forms)
forms['name'] = molecules[m]['name']
if not os.path.exists('{outdir}'.format(**forms)):
os.makedirs('{outdir}'.format(**forms))
with open('{outdir}/{mol}.aa.1.imd'.format(**forms), 'w') as fh:
fh.write(
imd_temp_1.format(
**{'numberOfAtoms': aa_work_mol.atom_count}))
with open('{outdir}/{mol}.ua.1.imd'.format(**forms), 'w') as fh:
fh.write(
imd_temp_1.format(
**{'numberOfAtoms': ua_work_mol.atom_count}))
with open('{outdir}/{mol}.aa.2.imd'.format(**forms), 'w') as fh:
fh.write(
imd_temp_2.format(
**{'numberOfAtoms': aa_work_mol.atom_count}))
with open('{outdir}/{mol}.ua.2.imd'.format(**forms), 'w') as fh:
fh.write(
imd_temp_2.format(
**{'numberOfAtoms': ua_work_mol.atom_count}))
with open('{outdir}/{mol}.aa.3.imd'.format(**forms), 'w') as fh:
fh.write(
imd_temp_3.format(
**{'numberOfAtoms': aa_work_mol.atom_count}))
with open('{outdir}/{mol}.ua.3.imd'.format(**forms), 'w') as fh:
fh.write(
imd_temp_3.format(
**{'numberOfAtoms': ua_work_mol.atom_count}))
os.chdir('{root}'.format(**forms))
os.system((
'/usr/local/gromos++/bin/make_top @build Parameters/{mol}/{mol}.aa.mtb Parameters/54A7.mtb '
'@param Parameters/54A7.ifp @seq {name} @solv H2O > {outdir}/{mol}.aa.top'
.format(**forms)))
os.system((
'/usr/local/gromos++/bin/make_top @build Parameters/{mol}/{mol}.ua.mtb Parameters/54A7.mtb '
'@param Parameters/54A7.ifp @seq {name} @solv H2O > {outdir}/{mol}.ua.top'
.format(**forms)))
for a in range(0, 360, 5):
skip_angle = False
forms['ang2'] = a
if a == 180:
a = 179
forms['ang'] = a
try:
with open(
'{root}/{des}/{mol}/{mol}.{ang:03}.log'.format(
**forms), 'r') as fh:
gamess = extract_conformation(fh.readlines(),
scale=1,
key='name',
optimised=False)
except FileNotFoundError:
with open(
'{root}/{des}/{mol}/{mol}.{ang2:03}.log'.format(
**forms), 'r') as fh:
gamess = extract_conformation(fh.readlines(),
scale=1,
key='name',
optimised=False)
for atm in aa_work_mol.atoms:
try:
atm.xyz = gamess[atm.atm_name.upper()]['vec']
except TypeError:
print('TypeError', atm.atm_name, d, m, a)
skip_angle = True
break
except KeyError:
print('KeyError', atm.atm_name, d, m, a)
raise
if skip_angle:
continue
for atm in ua_work_mol.atoms:
atm.xyz = gamess[atm.atm_name.upper()]['vec']
with open('{outdir}/{mol}.{ang:03}.aa.cnf'.format(**forms),
'w') as fh:
fh.write(outlib.print_gromos_cnf(aa_work_mol))
with open('{outdir}/{mol}.{ang:03}.ua.cnf'.format(**forms),
'w') as fh:
fh.write(outlib.print_gromos_cnf(ua_work_mol))
#with open('{outdir}/{mol}.{ang:03}.aa.pdb'.format(**forms), 'w') as fh:
# fh.write(outlib.print_pdb(aa_work_mol))
#with open('{outdir}/{mol}.{ang:03}.ua.pdb'.format(**forms), 'w') as fh:
# fh.write(outlib.print_pdb(ua_work_mol))
angs_aa, angs_ua = [], []
for des in descriptors[d]:
atm_a = aa_work_mol.atom(molecules[m][des]['aa'][0]).xyz
atm_b = aa_work_mol.atom(molecules[m][des]['aa'][1]).xyz
atm_c = aa_work_mol.atom(molecules[m][des]['aa'][2]).xyz
atm_d = aa_work_mol.atom(molecules[m][des]['aa'][3]).xyz
ang = dihedral_angle(atm_a,
atm_b,
atm_c,
atm_d,
scale='deg')
angs_aa.append(
' {1} {2} {3} {4} 1.0 {0:.3f} 0.0 0.0001'.
format(ang, *molecules[m][des]['aa']))
angs_ua.append(
' {1} {2} {3} {4} 1.0 {0:.3f} 0.0 0.0001'.
format(ang, *molecules[m][des]['ua']))
with open(
'{outdir}/{mol}.{ang:03}.aa.constraints.dat'.format(
**forms), 'w') as fh:
fh.write(
constraint_temp.format(
**{'constraints': '\n'.join(angs_aa)}))
with open(
'{outdir}/{mol}.{ang:03}.ua.constraints.dat'.format(
**forms), 'w') as fh:
fh.write(
constraint_temp.format(
**{'constraints': '\n'.join(angs_ua)}))
# first pass
os.system((
'/opt/local/gromosXX-1773/bin/md @topo {outdir}/{mol}.aa.top @conf {outdir}/{mol}.{ang:03}.aa.cnf '
'@input {outdir}/{mol}.aa.1.imd @fin {outdir}/{mol}.{ang:03}.aa.min.1.cnf @develop '
'@dihrest {outdir}/{mol}.{ang:03}.aa.constraints.dat > {outdir}/{mol}.{ang:03}.aa.1.log'
.format(**forms)))
os.system((
'/opt/local/gromosXX-1773/bin/md @topo {outdir}/{mol}.ua.top @conf {outdir}/{mol}.{ang:03}.ua.cnf '
'@input {outdir}/{mol}.ua.1.imd @fin {outdir}/{mol}.{ang:03}.ua.min.1.cnf @develop '
'@dihrest {outdir}/{mol}.{ang:03}.ua.constraints.dat > {outdir}/{mol}.{ang:03}.ua.1.log'
.format(**forms)))
def main():
root = '/Users/iwelsh/GitHub/ExtractedData/Torsions/AdditionalFixedTorsions'
for mol, data in mol_data():
if not os.path.isdir(root + '/AlignedStructures/' + mol +
'/EM_Changes'):
os.makedirs(root + '/AlignedStructures/' + mol + '/EM_Changes')
formatting = dict(root=root + '/Original', mol=mol, root2=root)
topo = gromos_topology_parse(
load_file(
'{root}/{mol}/MD_data/{mol}.ua.top'.format(**formatting)))
cnf = gromos_cnf_parse(
load_file('{root}/{mol}/MD_data/{mol}.000.ua'
'.min.1.cnf'.format(**formatting)))
cnf_initial = gromos_cnf_parse(
load_file(
'{root}/{mol}/MD_data/{mol}.000.ua.cnf'.format(**formatting)))
mol_ob = Molecule(mol, cnf=cnf[1], topo=topo)
mol_ob_initial = Molecule(mol, cnf=cnf_initial[1], topo=topo)
previous, previous_initial = [], []
mol_ob.centre_molecule(data['ua'][1])
mol_ob_initial.centre_molecule(data['ua'][1])
for atm in data['ua'][:3]:
previous.append(np.asarray(mol_ob.atom(atm).xyz))
previous_initial.append(np.asarray(mol_ob_initial.atom(atm).xyz))
previous = np.asarray(previous)
previous_initial = np.asarray(previous_initial)
for level, atoms in data.items():
formatting = dict(root=root + '/Original',
level=level,
mol=mol,
root2=root)
if level in ['gamess', 'aa']:
topo = gromos_topology_parse(
load_file('{root}/{mol}/MD_data/{mol}.aa.top'.format(
**formatting)))
else:
topo = gromos_topology_parse(
load_file('{root}/{mol}/MD_data/{mol}.ua.top'.format(
**formatting)))
for i in range(360):
formatting['i'] = i
try:
if level == 'gamess':
gamess = gamess_log_parse(
load_file('{root}/{mol}/{mol}.{i:03}.log'.format(
**formatting),
blank_lines=True))
mol_ob2 = Molecule(mol,
gamess=gamess[max(gamess)],
topo=topo)
mol_ob2_initial = Molecule(mol,
gamess=gamess[min(gamess)],
topo=topo)
else:
cnf = gromos_cnf_parse(
load_file(
'{root}/{mol}/MD_data/{mol}.{i:03}.{level}'
'.min.1.cnf'.format(**formatting)))
cnf_initial = gromos_cnf_parse(
load_file(
'{root}/{mol}/MD_data/{mol}.{i:03}.{level}'
'.cnf'.format(**formatting)))
mol_ob2 = Molecule(mol, cnf=cnf[1], topo=topo)
mol_ob2_initial = Molecule(mol,
cnf=cnf_initial[1],
topo=topo)
except FileNotFoundError:
continue
current, current_initial = [], []
if level == 'gamess':
mol_ob2.centre_molecule(data['aa'][1])
mol_ob2_initial.centre_molecule(data['aa'][1])
atms = data['aa']
else:
try:
mol_ob2.centre_molecule(atoms[1])
except TypeError:
print(mol, level, i, atoms, len(mol_ob2.atoms))
print(mol_ob2.atom(atoms[1]).xyz)
for atm in mol_ob2.atoms:
print(atm.data)
raise
mol_ob2_initial.centre_molecule(atoms[1])
atms = atoms
for atm in atms[:3]:
current.append(np.asarray(mol_ob2.atom(atm).xyz))
current_initial.append(
np.asarray(mol_ob2_initial.atom(atm).xyz))
current = np.asarray(current)
current_initial = np.asarray(current_initial)
rot_mat = kabsch_alignment(current, previous)
rot_mat_initial = kabsch_alignment(current_initial, previous)
mol_ob2.rotate(rot_mat)
mol_ob2_initial.rotate(rot_mat_initial)
with open(
('{root2}/AlignedStructures/{mol}/EM_Changes/'
'{mol}.{i:03}.{level}.initial.pdb'.format(**formatting)),
'w') as fh:
fh.write(print_pdb(mol_ob2_initial))
with open(
'{root2}/AlignedStructures/{mol}/{mol}.{i:03}.{level}.pdb'
.format(**formatting), 'w') as fh:
fh.write(print_pdb(mol_ob2))
def main():
root = '/Users/iwelsh/GitHub/ExtractedData/Torsions/AdditionalFixedTorsions'
for mol, data in mol_data():
if not os.path.isdir(root + '/AlignedStructures/' + mol + '/EM_Changes'):
os.makedirs(root + '/AlignedStructures/' + mol + '/EM_Changes')
formatting = dict(root=root+'/Original', mol=mol, root2=root)
topo = gromos_topology_parse(load_file('{root}/{mol}/MD_data/{mol}.ua.top'.format(**formatting)))
cnf = gromos_cnf_parse(load_file('{root}/{mol}/MD_data/{mol}.000.ua'
'.min.1.cnf'.format(**formatting)))
cnf_initial = gromos_cnf_parse(load_file('{root}/{mol}/MD_data/{mol}.000.ua.cnf'.format(**formatting)))
mol_ob = Molecule(mol, cnf=cnf[1], topo=topo)
mol_ob_initial = Molecule(mol, cnf=cnf_initial[1], topo=topo)
previous, previous_initial = [], []
mol_ob.centre_molecule(data['ua'][1])
mol_ob_initial.centre_molecule(data['ua'][1])
for atm in data['ua'][:3]:
previous.append(np.asarray(mol_ob.atom(atm).xyz))
previous_initial.append(np.asarray(mol_ob_initial.atom(atm).xyz))
previous = np.asarray(previous)
previous_initial = np.asarray(previous_initial)
for level, atoms in data.items():
formatting = dict(root=root+'/Original', level=level, mol=mol, root2=root)
if level in ['gamess','aa']:
topo = gromos_topology_parse(load_file('{root}/{mol}/MD_data/{mol}.aa.top'.format(**formatting)))
else:
topo = gromos_topology_parse(load_file('{root}/{mol}/MD_data/{mol}.ua.top'.format(**formatting)))
for i in range(360):
formatting['i'] = i
try:
if level == 'gamess':
gamess = gamess_log_parse(load_file('{root}/{mol}/{mol}.{i:03}.log'.format(**formatting),
blank_lines=True))
mol_ob2 = Molecule(mol, gamess=gamess[max(gamess)], topo=topo)
mol_ob2_initial = Molecule(mol, gamess=gamess[min(gamess)], topo=topo)
else:
cnf = gromos_cnf_parse(load_file('{root}/{mol}/MD_data/{mol}.{i:03}.{level}'
'.min.1.cnf'.format(**formatting)))
cnf_initial = gromos_cnf_parse(load_file('{root}/{mol}/MD_data/{mol}.{i:03}.{level}'
'.cnf'.format(**formatting)))
mol_ob2 = Molecule(mol, cnf=cnf[1], topo=topo)
mol_ob2_initial = Molecule(mol, cnf=cnf_initial[1], topo=topo)
except FileNotFoundError:
continue
current, current_initial = [], []
if level == 'gamess':
mol_ob2.centre_molecule(data['aa'][1])
mol_ob2_initial.centre_molecule(data['aa'][1])
atms = data['aa']
else:
try:
mol_ob2.centre_molecule(atoms[1])
except TypeError:
print(mol, level, i, atoms, len(mol_ob2.atoms))
print(mol_ob2.atom(atoms[1]).xyz)
for atm in mol_ob2.atoms:
print(atm.data)
raise
mol_ob2_initial.centre_molecule(atoms[1])
atms = atoms
for atm in atms[:3]:
current.append(np.asarray(mol_ob2.atom(atm).xyz))
current_initial.append(np.asarray(mol_ob2_initial.atom(atm).xyz))
current = np.asarray(current)
current_initial = np.asarray(current_initial)
rot_mat = kabsch_alignment(current, previous)
rot_mat_initial = kabsch_alignment(current_initial, previous)
mol_ob2.rotate(rot_mat)
mol_ob2_initial.rotate(rot_mat_initial)
with open(('{root2}/AlignedStructures/{mol}/EM_Changes/'
'{mol}.{i:03}.{level}.initial.pdb'.format(**formatting)), 'w') as fh:
fh.write(print_pdb(mol_ob2_initial))
with open('{root2}/AlignedStructures/{mol}/{mol}.{i:03}.{level}.pdb'.format(**formatting), 'w') as fh:
fh.write(print_pdb(mol_ob2))
