def _indexGenerator(self):
frame = self.dsim.getFrame(0)
# atom and global indices of all atoms in the system
self.all_atom_ids = np.arange(len(self.dsim.cst.atom)) + 1
self.all_atom_gids = np.arange(
len(self.dsim.cst.atom) + self.dsim.cst._pseudo_total)
# obtain oxygen atom and global indices for all water molecules
oxygen_sel = FAS('atom.ele O')
all_oxygen_atoms = oxygen_sel.getAtomIndices(frame)
water_sel = select_component(self.dsim.cst, ['solvent'])
solvent_atoms = water_sel.getAtomIndices(frame)
solvent_oxygen_atoms = list(
set(solvent_atoms).intersection(set(all_oxygen_atoms)))
solvent_oxygen_atoms.sort()
self.wat_oxygen_atom_ids = np.array(solvent_oxygen_atoms, dtype=np.int)
self.wat_oxygen_atom_gids = self.wat_oxygen_atom_ids - 1
# obtain atom indices for all water atoms
self.wat_atom_ids = self.getWaterIndices(self.wat_oxygen_atom_ids)
# obtain atom and global indices for all water atoms
#wat_id_list = self.getWaterIndices(self.wat_oxygen_atom_ids)
#self.wat_atom_ids = wat_id_list[0]
#self.wat_atom_gids = wat_id_list[1]
# obtain all non-water atom and global indices
self.non_water_atom_ids = np.setxor1d(self.all_atom_ids,
self.wat_atom_ids).astype(int)
def _indexGenerator(self, ligand_file):
frame = self.dsim.getFrame(0)
# atom and global indices of all atoms in the system
self.all_atom_ids = np.arange(len(self.dsim.cst.atom))+1
self.all_atom_gids = np.arange(len(self.dsim.cst.atom)+self.dsim.cst._pseudo_total)
# obtain oxygen atom and global indices for all water molecules
oxygen_sel = FAS('atom.ele O')
all_oxygen_atoms = oxygen_sel.getAtomIndices(frame)
water_sel = select_component(self.dsim.cst, ['solvent'])
solvent_atoms = water_sel.getAtomIndices(frame)
solvent_oxygen_atoms = list(set(solvent_atoms).intersection(set(all_oxygen_atoms)))
solvent_oxygen_atoms.sort()
self.wat_oxygen_atom_ids = np.array(solvent_oxygen_atoms, dtype=np.int)
self.wat_oxygen_atom_gids = self.wat_oxygen_atom_ids - 1
# obtain atom indices for all water atoms
self.wat_atom_ids = self.getWaterIndices(self.wat_oxygen_atom_ids)
# obtain atom and global indices for all water atoms
#wat_id_list = self.getWaterIndices(self.wat_oxygen_atom_ids)
#self.wat_atom_ids = wat_id_list[0]
#self.wat_atom_gids = wat_id_list[1]
# obtain all non-water atom and global indices
self.non_water_atom_ids = np.setxor1d(self.all_atom_ids, self.wat_atom_ids).astype(int)
# here add commands to restrict non-water atom ids to within 5.0A of ligand
#***************************************************************
# Tag protein atoms that are near ligand
solute_indices_near_lig = []
ligand = structure.StructureReader(ligand_file).next()
self.ligand = ligand
lig_atom_coords = ligand.getXYZ()
solute_pos = frame.position[self.non_water_atom_ids-1]
d_solute_nbrs = _DistanceCell(solute_pos, 5)
for coord in lig_atom_coords:
solute_nbr_indices = d_solute_nbrs.query_nbrs(coord)
for solute_nbr_index in solute_nbr_indices:
if solute_nbr_index not in solute_indices_near_lig:
solute_indices_near_lig.append(solute_nbr_index)
#print self.non_water_atom_ids
self.non_water_atom_ids_near_lig = [self.non_water_atom_ids[nbr_index] for nbr_index in solute_indices_near_lig]
#self.non_water_atom_ids_near_lig = self.non_water_atom_ids
#***************************************************************
# Type protein atoms
acc_list = []
don_list = []
acc_don_list = []
# To speed up calculations, we will pre-create donor atom, hydrogen pairs
self.don_H_pair_dict = {}
if self.non_water_atom_ids.size != 0:
frame_st = self.dsim.getFrameStructure(0)
for solute_at_id in self.non_water_atom_ids:
solute_atom = frame_st.atom[solute_at_id]
solute_atom_type = solute_atom.pdbres.strip(" ") + " " + solute_atom.pdbname.strip(" ")
if solute_atom.element in ["O", "S"]:
# if O/S atom is bonded to an H, type it as donor and an acceptor
if "H" in [bonded_atom.element for bonded_atom in solute_atom.bonded_atoms]:
#print "Found donor-acceptor atom type: %i %s" % (solute_at_id, solute_atom_type)
acc_don_list.append(solute_at_id)
# create a dictionary entry for this atom, that will hold all atom, H id pairs
self.don_H_pair_dict[solute_at_id] = []
for bonded_atom in solute_atom.bonded_atoms:
if bonded_atom.element == "H":
self.don_H_pair_dict[solute_at_id].append([solute_at_id, bonded_atom.index])
# if O/S atom is not bonded to an H, type it as an acceptor
else:
#print "Found acceptor atom type: %i %s" % (solute_at_id, solute_atom_type)
acc_list.append(solute_at_id)
if solute_atom.element in ["N"]:
# if N atom is bonded to an H, type it as a donor
if "H" in [bonded_atom.element for bonded_atom in solute_atom.bonded_atoms]:
#print "Found donor atom type: %i %s" % (solute_at_id, solute_atom_type)
don_list.append(solute_at_id)
# create a dictionary entry for this atom, that will hold all atom, H id pairs
self.don_H_pair_dict[solute_at_id] = []
for bonded_atom in solute_atom.bonded_atoms:
if bonded_atom.element == "H":
self.don_H_pair_dict[solute_at_id].append([solute_at_id, bonded_atom.index])
else:
#print "Found acceptor atom type: %i %s" % (solute_at_id, solute_atom_type)
acc_list.append(solute_at_id)
#print don_list
#print acc_list
#print acc_don_list
self.solute_acc_ids = np.array(acc_list, dtype=np.int)
self.solute_acc_don_ids = np.array(acc_don_list, dtype=np.int)
self.solute_don_ids = np.array(don_list, dtype=np.int)
self.prot_hbond_data = {}
for hb_group in np.concatenate((self.solute_acc_ids, self.solute_acc_don_ids, self.solute_don_ids)):
hb_group_name = self.dsim.cst.atom[hb_group].getResidue().pdbres.strip() + str(self.dsim.cst.atom[hb_group].getResidue().resnum) + " " + self.dsim.cst.atom[hb_group].pdbname.strip()
self.prot_hbond_data[hb_group] = [hb_group_name, np.zeros(10, dtype="float64")]
#print self.prot_hbond_data[hb_group]
#***************************************************************
# Type ligand atoms
lig_acc_list = []
lig_don_list = []
lig_acc_don_list = []
self.lig_don_H_pair_dict = {}
if len(ligand.atom) != 0:
for lig_at in ligand.atom:
lig_atom_type = lig_at.pdbres.strip(" ") + " " + lig_at.pdbname.strip(" ")
if lig_at.element in ["O", "S"]:
# if O/S atom is bonded to an H, type it as donor and an acceptor
if "H" in [bonded_atom.element for bonded_atom in lig_at.bonded_atoms]:
#print "Found donor-acceptor atom type: %i %s" % (lig_at.index, lig_atom_type)
lig_acc_don_list.append(lig_at.index)
# create a dictionary entry for this atom, that will hold all atom, H id pairs
self.lig_don_H_pair_dict[lig_at.index] = []
for bonded_atom in lig_at.bonded_atoms:
if bonded_atom.element == "H":
self.lig_don_H_pair_dict[lig_at.index].append([lig_at.index, bonded_atom.index])
# if O/S atom is not bonded to an H, type it as an acceptor
else:
#print "Found acceptor atom type: %i %s" % (lig_at.index, lig_atom_type)
lig_acc_list.append(lig_at.index)
if lig_at.element in ["N"]:
# if N atom is bonded to an H, type it as a donor
if "H" in [bonded_atom.element for bonded_atom in lig_at.bonded_atoms]:
#print "Found donor atom type: %i %s" % (lig_at.index, lig_atom_type)
lig_don_list.append(lig_at.index)
# create a dictionary entry for this atom, that will hold all atom, H id pairs
self.lig_don_H_pair_dict[lig_at.index] = []
for bonded_atom in lig_at.bonded_atoms:
if bonded_atom.element == "H":
self.lig_don_H_pair_dict[lig_at.index].append([lig_at.index, bonded_atom.index])
else:
#print "Found acceptor atom type: %i %s" % (lig_at.index, lig_atom_type)
lig_acc_list.append(lig_at.index)
self.ligand_acc_ids = np.array(lig_acc_list, dtype=np.int)
self.ligand_acc_don_ids = np.array(lig_acc_don_list, dtype=np.int)
self.ligand_don_ids = np.array(lig_don_list, dtype=np.int)
def _indexGenerator(self):
frame = self.dsim.getFrame(0)
# atom and global indices of all atoms in the system
self.all_atom_ids = np.arange(len(self.dsim.cst.atom)) + 1
self.all_atom_gids = np.arange(
len(self.dsim.cst.atom) + self.dsim.cst._pseudo_total)
# obtain oxygen atom and global indices for all water molecules
oxygen_sel = FAS('atom.ele O')
all_oxygen_atoms = oxygen_sel.getAtomIndices(frame)
water_sel = select_component(self.dsim.cst, ['solvent'])
solvent_atoms = water_sel.getAtomIndices(frame)
solvent_oxygen_atoms = list(
set(solvent_atoms).intersection(set(all_oxygen_atoms)))
solvent_oxygen_atoms.sort()
self.wat_oxygen_atom_ids = np.array(solvent_oxygen_atoms, dtype=np.int)
self.wat_oxygen_atom_gids = self.wat_oxygen_atom_ids - 1
# obtain atom indices for all water atoms
self.wat_atom_ids = self.getWaterIndices(self.wat_oxygen_atom_ids)
# obtain atom and global indices for all water atoms
#wat_id_list = self.getWaterIndices(self.wat_oxygen_atom_ids)
#self.wat_atom_ids = wat_id_list[0]
#self.wat_atom_gids = wat_id_list[1]
# obtain all non-water atom and global indices
self.non_water_atom_ids = np.setxor1d(self.all_atom_ids,
self.wat_atom_ids).astype(int)
#self.non_water_gids = np.setxor1d(self.all_atom_gids,self.wat_atom_gids)
# These lists define the search space for solute water Hbond calculation
acc_list = []
don_list = []
acc_don_list = []
# To speed up calculations, we will pre-create donor atom, hydrogen pairs
self.don_H_pair_dict = {}
if self.non_water_atom_ids.size != 0:
frame_st = self.dsim.getFrameStructure(0)
for solute_at_id in self.non_water_atom_ids:
solute_atom = frame_st.atom[solute_at_id]
solute_atom_type = solute_atom.pdbres.strip(
" ") + " " + solute_atom.pdbname.strip(" ")
if solute_atom.element in ["O", "S"]:
# if O/S atom is bonded to an H, type it as donor and an acceptor
if "H" in [
bonded_atom.element
for bonded_atom in solute_atom.bonded_atoms
]:
#print "Found donor-acceptor atom type: %i %s" % (solute_at_id, solute_atom_type)
acc_don_list.append(solute_at_id)
# create a dictionary entry for this atom, that will hold all atom, H id pairs
self.don_H_pair_dict[solute_at_id] = []
for bonded_atom in solute_atom.bonded_atoms:
if bonded_atom.element == "H":
self.don_H_pair_dict[solute_at_id].append(
[solute_at_id, bonded_atom.index])
# if O/S atom is not bonded to an H, type it as an acceptor
else:
#print "Found acceptor atom type: %i %s" % (solute_at_id, solute_atom_type)
acc_list.append(solute_at_id)
if solute_atom.element in ["N"]:
# if N atom is bonded to an H, type it as a donor
if "H" in [
bonded_atom.element
for bonded_atom in solute_atom.bonded_atoms
]:
#print "Found donor atom type: %i %s" % (solute_at_id, solute_atom_type)
don_list.append(solute_at_id)
# create a dictionary entry for this atom, that will hold all atom, H id pairs
self.don_H_pair_dict[solute_at_id] = []
for bonded_atom in solute_atom.bonded_atoms:
if bonded_atom.element == "H":
self.don_H_pair_dict[solute_at_id].append(
[solute_at_id, bonded_atom.index])
# if N atom is not bonded to an H, type it as an acceptor
else:
#print "Found acceptor atom type: %i %s" % (solute_at_id, solute_atom_type)
acc_list.append(solute_at_id)
#print don_list
#print acc_list
#print acc_don_list
self.solute_acc_ids = np.array(acc_list, dtype=np.int)
self.solute_acc_don_ids = np.array(acc_don_list, dtype=np.int)
self.solute_don_ids = np.array(don_list, dtype=np.int)