def center_at_protein_chain_groups(atomistic_protein_input, cg_com,
protein_mass, cg_backbone_masses):
for chain in atomistic_protein_input:
for part_val, part in enumerate(atomistic_protein_input[chain]):
sls, sle = int(part.split(':')[0]), int(part.split(':')[1])
if chain in g_var.group_chains:
atomistic_protein_mass = at_mod.COM(
protein_mass[g_var.group_chains[chain]],
'AT protein chain: ' + str(chain))
cg_com[chain].append(
at_mod.COM(cg_backbone_masses[g_var.group_chains[chain]],
'CG protein chain: ' + str(chain)))
else:
protein_mass = fetch_backbone_mass(
atomistic_protein_input[chain][part], [])
atomistic_protein_mass = at_mod.COM(
protein_mass, 'protein at: ' + str(chain) + ' ' +
part) #### add center of mass of CG_proteins
cg_com[chain].append(
at_mod.COM(g_var.backbone_coords[chain][sls:sle],
'protein cg: ' + str(chain) + ' ' + part))
atomistic_protein_input[chain][part] = update_part_coordinate(
atomistic_protein_input[chain][part], atomistic_protein_mass,
cg_com[chain][part_val])
return atomistic_protein_input, cg_com
def center_at_protein_all_chains(atomistic_protein_input, cg_com, protein_mass,
cg_backbone_masses):
atomistic_protein_mass = at_mod.COM(protein_mass, 'All AT protein chains')
for chain in atomistic_protein_input:
for part_val, part in enumerate(atomistic_protein_input[chain]):
cg_com[chain].append(
at_mod.COM(cg_backbone_masses['all'], 'All CG protein chains'))
atomistic_protein_input[chain][part] = update_part_coordinate(
atomistic_protein_input[chain][part], atomistic_protein_mass,
cg_com[chain][part_val])
return atomistic_protein_input, cg_com
def center_atomistic(atomistic_protein_input, backbone_coords):
cg_com={}
#### for each protein chain center on cg representation
for chain in atomistic_protein_input:
cg_com[chain]=[]
for part_val, part in enumerate(atomistic_protein_input[chain]):
sls, sle= int(part.split(':')[0]),int(part.split(':')[1])
protein_mass=[]
for residue in atomistic_protein_input[chain][part]:
#### creates a list of all coordinates and masses [[coord, mass],[coord, mass]]
for atom in atomistic_protein_input[chain][part][residue]:
short_line=atomistic_protein_input[chain][part][residue][atom]
protein_mass.append([short_line['coord'][0],short_line['coord'][1],short_line['coord'][2],short_line['frag_mass']])
#### returns the COM of the atomistic protein
atomistic_protein_mass = at_mod.COM(protein_mass, 'protein at: '+str(chain)+' '+part)#### add center of mass of CG_proteins
cg_com[chain].append(at_mod.COM(backbone_coords[chain][sls:sle], 'protein cg: '+str(chain)+' '+part))
#### each atoms coord is updated so the monomer COM is the same as the CG
for residue in atomistic_protein_input[chain][part]:
for atom in atomistic_protein_input[chain][part][residue]:
atomistic_protein_input[chain][part][residue][atom]['coord']=atomistic_protein_input[chain][part][residue][atom]['coord']-(atomistic_protein_mass-cg_com[chain][part_val])
return atomistic_protein_input, cg_com
def center_atomistic():
cg_com = {}
#### for each protein chain center on cg representation
for chain in g_var.atomistic_protein_input_aligned:
cg_com[chain] = []
for part_val, part in enumerate(
g_var.atomistic_protein_input_aligned[chain]):
sls, sle = int(part.split(':')[0]), int(part.split(':')[1])
if g_var.group_chains is None:
protein_mass = fetch_backbone_mass(
g_var.atomistic_protein_input_aligned[chain][part], [])
atomistic_protein_mass = at_mod.COM(
protein_mass, 'protein at: ' + str(chain) + ' ' +
part) #### add center of mass of CG_proteins
cg_com[chain].append(
at_mod.COM(g_var.backbone_coords[chain][sls:sle],
'protein cg: ' + str(chain) + ' ' + part))
g_var.atomistic_protein_input_aligned[chain][
part] = update_part_coordinate(
g_var.atomistic_protein_input_aligned[chain][part],
atomistic_protein_mass, cg_com[chain][part_val])
elif g_var.group_chains == 'all':
if 'protein_mass' not in locals():
protein_mass = []
protein_mass = fetch_backbone_mass(
g_var.atomistic_protein_input_aligned[chain][part],
protein_mass)
if 'cg_backbone_masses' not in locals():
cg_backbone_masses = {}
cg_backbone_masses['all'] = g_var.backbone_coords[chain][
sls:sle]
else:
cg_backbone_masses['all'] += g_var.backbone_coords[chain][
sls:sle]
else:
if 'protein_mass' not in locals():
protein_mass = {}
if chain in g_var.group_chains:
if g_var.group_chains[chain] not in protein_mass:
protein_mass[
g_var.group_chains[chain]] = fetch_backbone_mass(
g_var.atomistic_protein_input_aligned[chain]
[part], [])
else:
protein_mass[
g_var.group_chains[chain]] = fetch_backbone_mass(
g_var.atomistic_protein_input_aligned[chain]
[part], protein_mass[group_chain[chain]])
if 'cg_backbone_masses' not in locals():
cg_backbone_masses = {}
if g_var.group_chains[chain] not in cg_backbone_masses:
cg_backbone_masses[g_var.group_chains[
chain]] = g_var.backbone_coords[chain][sls:sle]
else:
cg_backbone_masses[g_var.group_chains[
chain]] += g_var.backbone_coords[chain][sls:sle]
if g_var.group_chains == 'all':
g_var.atomistic_protein_input_aligned, cg_com = center_at_protein_all_chains(
g_var.atomistic_protein_input_aligned, cg_com, protein_mass,
cg_backbone_masses)
if g_var.group_chains not in ['all', None]:
g_var.atomistic_protein_input_aligned, cg_com = center_at_protein_chain_groups(
g_var.atomistic_protein_input_aligned, cg_com, protein_mass,
cg_backbone_masses)
return g_var.atomistic_protein_input_aligned, cg_com