from molsysmt._private.digestion import digest
from molsysmt import pyunitwizard as puw
from molsysmt.element.atom import get_atom_type_from_atom_name
from molsysmt.element.group import get_group_type_from_group_name
import numpy as np
[docs]
@digest(form='file:crd')
def to_molsysmt_Topology(item, atom_indices='all', structure_indices='all', skip_digestion=False):
# EXT:
# (i10,2x,a) natoms,'EXT'
# (2I10,2X,A8,2X,A8,3F20.10,2X,A8,2X,A8,F20.10)
# iatom,ires,resn,typr,x,y,z,segid,rid,wmain
# standard:
# (i5) natoms
# (2I5,1X,A4,1X,A4,3F10.5,1X,A4,1X,A4,F10.5)
# iatom,ires,resn,typr,x,y,z,segid,orig_resid,wmain
from molsysmt.native.topology import Topology
tmp_item = Topology()
atom_id = []
atom_name = []
atom_type = []
group_index = []
group_id = []
group_name = []
group_type = []
chain_index = []
chain_name = []
extended = False
former_group_id = -1
former_chain_name = ''
aux_group_index = -1
aux_chain_index = -1
with open(item) as fff:
for line in fff:
if line.strip().startswith('*') or line.strip() == "":
continue
field = line.split()
if len(field)==1:
n_atoms = int(field[0])
elif len(field)==2:
n_atoms = int(field[0])
extended = True
else:
atom_id.append(int(field[0]))
atom_name.append(field[3])
aux_group_id = int(field[1])
aux_chain_name = field[7]
if former_group_id!=aux_group_id:
former_group_id=aux_group_id
group_id.append(aux_group_id)
group_name.append(field[2])
aux_group_index += 1
if former_chain_name!=aux_chain_name:
former_chain_name=aux_chain_name
chain_name.append(aux_chain_name)
aux_chain_index += 1
group_index.append(aux_group_index)
chain_index.append(aux_chain_index)
if len(atom_id)!=n_atoms:
raise ValueError
for ii in atom_name:
atom_type.append(get_atom_type_from_atom_name(ii))
for ii in group_name:
group_type.append(get_group_type_from_group_name(ii))
n_groups = len(group_name)
n_chains = len(chain_name)
tmp_item.reset_atoms(n_atoms=n_atoms)
tmp_item.reset_groups(n_groups=n_groups)
tmp_item.reset_chains(n_chains=n_chains)
tmp_item.atoms.atom_id = np.array(atom_id, dtype=int)
tmp_item.atoms.atom_name = np.array(atom_name, dtype=object)
tmp_item.atoms.atom_type = np.array(atom_type, dtype=object)
tmp_item.atoms.group_index = np.array(group_index, dtype=int)
tmp_item.atoms.chain_index = np.array(chain_index, dtype=int)
tmp_item.groups.group_id = np.array(group_id, dtype=int)
tmp_item.groups.group_name = np.array(group_name, dtype=object)
tmp_item.groups.group_type = np.array(group_type, dtype=object)
tmp_item.chains.chain_id = np.arange(n_chains, dtype=int)
tmp_item.chains.chain_name = np.array(chain_name, dtype=object)
del(atom_id, atom_name, atom_type,
group_index, group_id, group_name, group_type,
chain_index, chain_name)
return tmp_item
