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 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))