diff --git a/CHANGELOG b/CHANGELOG
index d9a954345652cb563d9261c50444ca44bdb5dec2..b55f179828bf98b9ca00232a969ccc30e12cd6fe 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -12,7 +12,7 @@ Release X
This simplifies the addition of other scoring functions in the future.
Be aware of breaking changes introduced in the process!
(SCWRLRotamerConstructor -> SCWRL4RotamerConstructor, changed interface of
- Particle class).
+ Particle and RotamerConstructor classes).
* Several minor bug fixes, improvements, and speed-ups
diff --git a/doc/tests/scripts/sidechain_steps.py b/doc/tests/scripts/sidechain_steps.py
index d73a626dd775fd254e62cd1e085f355a278f7d01..6f66e5ee139ae5a9148b33146fd5dd4ea3d4a0ba 100644
--- a/doc/tests/scripts/sidechain_steps.py
+++ b/doc/tests/scripts/sidechain_steps.py
@@ -37,7 +37,9 @@ frame_residues = list()
for i,r in enumerate(prot.residues):
frame_residue = rot_constructor.ConstructBackboneFrameResidue(
r, rotamer_ids[i], i,
- torsion_angles[i][0], i == 0,
+ torsion_angles[i][0],
+ torsion_angles[i][1],
+ i == 0,
i == (len(rotamer_ids)-1))
frame_residues.append(frame_residue)
@@ -54,7 +56,8 @@ for i,r in enumerate(prot.residues):
rot_group = rot_constructor.ConstructFRMRotamerGroup(
r, rotamer_ids[i], i, library,
- torsion_angles[i][0], torsion_angles[i][1])
+ torsion_angles[i][0], torsion_angles[i][1],
+ i == 0, i == (len(rotamer_ids)-1), 0.98)
# calculate pairwise energies towards the rigid frame
# the values will be stored and used by the solving algorithm
diff --git a/modelling/pymod/_reconstruct_sidechains.py b/modelling/pymod/_reconstruct_sidechains.py
index 969df78d40bcda96d881abf800892d8de6a0fd3a..b94c37c93c389fb54b3d8661777e7f720c58dced 100644
--- a/modelling/pymod/_reconstruct_sidechains.py
+++ b/modelling/pymod/_reconstruct_sidechains.py
@@ -84,14 +84,14 @@ def _GetDihedrals(res_list):
return phi_angles, psi_angles
def _AddBackboneFrameResidues(frame_residues, res_list, rotamer_ids,
- rotamer_constructor, phi_angles):
+ rotamer_constructor, phi_angles, psi_angles):
'''Update frame_residues (list) with BackboneFrameResidues for res_list.'''
for i,r in enumerate(res_list):
try:
frame_residue = rotamer_constructor.ConstructBackboneFrameResidue(\
r.handle, rotamer_ids[i], i,
- phi_angles[i], r.HasProp("n_ter"),
- r.HasProp("c_ter"))
+ phi_angles[i], psi_angles[i],
+ r.HasProp("n_ter"), r.HasProp("c_ter"))
frame_residues.append(frame_residue)
except:
continue
@@ -110,6 +110,7 @@ def _AddLigandFrameResidues(frame_residues, ent_lig, rotamer_constructor, offset
if rot_id != sidechain.XXX:
# get more info
phi = _GetPhiAngle(res)
+ psi = _GetPsiAngle(res)
r_prev = res.handle.prev
n_ter = not r_prev.IsValid() \
or not mol.InSequence(r_prev, res.handle)
@@ -120,10 +121,10 @@ def _AddLigandFrameResidues(frame_residues, ent_lig, rotamer_constructor, offset
try:
fr1 = rotamer_constructor.ConstructBackboneFrameResidue(\
res.handle, rot_id, res_idx,
- phi, n_ter, c_ter)
+ phi, psi, n_ter, c_ter)
fr2 = rotamer_constructor.ConstructSidechainFrameResidue(\
- res.handle, rot_id, res_idx)
+ res.handle, rot_id, res_idx, phi, psi, n_ter, c_ter)
frame_residues.extend([fr1,fr2])
except:
@@ -137,7 +138,7 @@ def _AddLigandFrameResidues(frame_residues, ent_lig, rotamer_constructor, offset
# NOTES:
# - ConstructFrameResidueHeuristic has fall back if res unknown
# - it only deals with few possible ligand cases and has not
- # been tested extensively!
+ # been tested extensively!
comp_lib = conop.GetDefaultLib()
fr = rotamer_constructor.ConstructFrameResidueHeuristic(\
res.handle, res_idx, comp_lib)
@@ -147,6 +148,7 @@ def _AddLigandFrameResidues(frame_residues, ent_lig, rotamer_constructor, offset
def _AddSidechainFrameResidues(frame_residues, incomplete_sidechains,
keep_sidechains, res_list, rotamer_ids,
+ phi_angles, psi_angles,
rotamer_constructor, cystein_indices=None):
'''Update frame_residues (list) with SidechainFrameResidues for res_list,
incomplete_sidechains (list of indices) with sidechains to be constructed,
@@ -165,7 +167,8 @@ def _AddSidechainFrameResidues(frame_residues, incomplete_sidechains,
try:
frame_residue = rotamer_constructor.ConstructSidechainFrameResidue(\
- r.handle, rotamer_ids[i], i)
+ r.handle, rotamer_ids[i], i, phi_angles[i],
+ psi_angles[i], r.HasProp("n_ter"), r.HasProp("c_ter"))
frame_residues.append(frame_residue)
except:
incomplete_sidechains.append(i)
@@ -182,6 +185,7 @@ def _AddSidechainFrameResidues(frame_residues, incomplete_sidechains,
def _AddCysteinFrameResidues(frame_residues, incomplete_sidechains,
keep_sidechains, res_list, rotamer_ids,
+ phi_angles, psi_angles,
rot_constructor, cystein_indices,
disulfid_indices, disulfid_rotamers):
'''Update frame_residues (list) with cysteins.
@@ -206,7 +210,9 @@ def _AddCysteinFrameResidues(frame_residues, incomplete_sidechains,
try:
frame_residue = rot_constructor.ConstructSidechainFrameResidue(\
res_list[idx].handle, rotamer_ids[idx],
- idx)
+ idx, phi_angles[idx], psi_angles[idx],
+ res_list[idx].handle.HasProp("n_ter"),
+ res_list[idx].handle.HasProp("c_ter"))
frame_residues.append(frame_residue)
except:
incomplete_sidechains.append(idx)
@@ -214,27 +220,24 @@ def _AddCysteinFrameResidues(frame_residues, incomplete_sidechains,
incomplete_sidechains.append(idx)
def _GetRotamerGroup(res_handle, rot_id, res_idx, rot_lib, rot_constructor,
- phi, psi, use_frm, bbdep, probability_cutoff = 0.98):
+ phi, psi, use_frm, bbdep,
+ probability_cutoff = 0.98):
+
if use_frm:
- if bbdep:
- return rot_constructor.ConstructFRMRotamerGroup(res_handle, rot_id,
- res_idx, rot_lib,
- phi, psi,
- probability_cutoff)
- else:
- return rot_constructor.ConstructFRMRotamerGroup(res_handle, rot_id,
- res_idx, rot_lib,
- probability_cutoff)
- else:
- if bbdep:
- return rot_constructor.ConstructRRMRotamerGroup(res_handle, rot_id,
- res_idx, rot_lib,
- phi, psi,
- probability_cutoff)
- else:
- return rot_constructor.ConstructRRMRotamerGroup(res_handle, rot_id,
- res_idx, rot_lib,
- probability_cutoff)
+ return rot_constructor.ConstructFRMRotamerGroup(res_handle, rot_id,
+ res_idx, rot_lib,
+ phi, psi,
+ res_handle.HasProp("n_ter"),
+ res_handle.HasProp("c_ter"),
+ probability_cutoff)
+ else:
+ return rot_constructor.ConstructRRMRotamerGroup(res_handle, rot_id,
+ res_idx, rot_lib,
+ phi, psi,
+ res_handle.HasProp("n_ter"),
+ res_handle.HasProp("c_ter"),
+ probability_cutoff)
+
def _GetRotamerGroups(res_list, rot_ids, indices, rot_lib, rot_constructor,
phi_angles, psi_angles, use_frm, bbdep, frame_residues):
@@ -341,10 +344,14 @@ def _GetDisulfidBridges(frame_residues, keep_sidechains, cystein_indices,
if sg.IsValid():
# we're constructing the required particle through a frame
# residue in the rotamer constructor
+ phi = _GetPhiAngle(r)
+ psi = _GetPsiAngle(r)
cys_frame_res = \
rotamer_constructor.ConstructSidechainFrameResidue(r.handle,
sidechain.CYD,
- 0)
+ 0, phi, psi,
+ r.HasProp("n_ter"),
+ r.HasProp("c_ter"))
for j in range(len(cys_frame_res)):
if cys_frame_res[j].GetName() == "SG":
particle_list = [cys_frame_res[j]]
@@ -474,7 +481,7 @@ def ReconstructSidechains(ent, keep_sidechains=False, build_disulfids=True,
frame_residues = list() # list of frame residues connected to frame
incomplete_sidechains = list() # residue indices
_AddBackboneFrameResidues(frame_residues, prot.residues, rotamer_ids,
- rotamer_constructor, phi_angles)
+ rotamer_constructor, phi_angles, psi_angles)
# add ligands?
if consider_ligands:
@@ -489,6 +496,7 @@ def ReconstructSidechains(ent, keep_sidechains=False, build_disulfids=True,
# update frame_residues, incomplete_sidechains, cystein_indices
_AddSidechainFrameResidues(frame_residues, incomplete_sidechains,
keep_sidechains, prot.residues, rotamer_ids,
+ phi_angles, psi_angles,
rotamer_constructor, cystein_indices)
# update frame_residues, incomplete_sidechains with cysteins (if needed)
if len(cystein_indices) > 0:
@@ -501,12 +509,14 @@ def ReconstructSidechains(ent, keep_sidechains=False, build_disulfids=True,
# update frame_residues, incomplete_sidechains
_AddCysteinFrameResidues(frame_residues, incomplete_sidechains,
keep_sidechains, prot.residues, rotamer_ids,
+ phi_angles, psi_angles,
rotamer_constructor, cystein_indices,
disulfid_indices, disulfid_rotamers)
else:
# update frame_residues, incomplete_sidechains
_AddSidechainFrameResidues(frame_residues, incomplete_sidechains,
keep_sidechains, prot.residues, rotamer_ids,
+ phi_angles, psi_angles,
rotamer_constructor)
# get rotamer groups and residues they're linked to
diff --git a/modelling/src/sidechain_env_listener.cc b/modelling/src/sidechain_env_listener.cc
index 19d97aa12f345b8c6b81bc184457b9c7cb7e7226..160a06755b141872796f646b2e808b0c7ee8f76f 100644
--- a/modelling/src/sidechain_env_listener.cc
+++ b/modelling/src/sidechain_env_listener.cc
@@ -193,6 +193,7 @@ void SidechainEnvListener::SetResidue_(loop::ConstAllAtomPositionsPtr all_pos,
= rot_constructor_.ConstructBackboneFrameResidue(*all_pos, res_idx,
r_id, res_idx,
phi_angle_[res_idx],
+ psi_angle_[res_idx],
n_ter_[res_idx],
c_ter_[res_idx]);
@@ -200,7 +201,11 @@ void SidechainEnvListener::SetResidue_(loop::ConstAllAtomPositionsPtr all_pos,
if (all_set) {
sc_frame_residue_[res_idx]
= rot_constructor_.ConstructSidechainFrameResidue(*all_pos, res_idx,
- r_id, res_idx);
+ r_id, res_idx,
+ phi_angle_[res_idx],
+ psi_angle_[res_idx],
+ n_ter_[res_idx],
+ c_ter_[res_idx]);
} else {
sc_frame_residue_[res_idx].reset();
}
diff --git a/modelling/src/sidechain_env_listener.hh b/modelling/src/sidechain_env_listener.hh
index cc8c2709a42e01b56f41cabd54a994460acd5de5..8c919cc298bd61b9435dcf24fa9345cbbd8d330d 100644
--- a/modelling/src/sidechain_env_listener.hh
+++ b/modelling/src/sidechain_env_listener.hh
@@ -142,13 +142,19 @@ public:
r_id, res_idx,
bbdep_library_,
phi_angle_[res_idx],
- psi_angle_[res_idx]);
+ psi_angle_[res_idx],
+ n_ter_[res_idx],
+ c_ter_[res_idx]);
} else {
rot_group = rot_constructor_.ConstructFRMRotamerGroup(*all_pos, res_idx,
r_id, res_idx,
- library_);
+ library_,
+ phi_angle_[res_idx],
+ psi_angle_[res_idx],
+ n_ter_[res_idx],
+ c_ter_[res_idx]);
}
- rot_constructor_.AssignInternalEnergies(rot_group);
+ rot_constructor_.AssignInternalEnergies(rot_group, r_id, res_idx);
}
void CreateRotamerGroup(sidechain::RRMRotamerGroupPtr& rot_group,
loop::ConstAllAtomPositionsPtr all_pos,
@@ -158,13 +164,19 @@ public:
r_id, res_idx,
bbdep_library_,
phi_angle_[res_idx],
- psi_angle_[res_idx]);
+ psi_angle_[res_idx],
+ n_ter_[res_idx],
+ c_ter_[res_idx]);
} else {
rot_group = rot_constructor_.ConstructRRMRotamerGroup(*all_pos, res_idx,
r_id, res_idx,
- library_);
+ library_,
+ phi_angle_[res_idx],
+ psi_angle_[res_idx],
+ n_ter_[res_idx],
+ c_ter_[res_idx]);
}
- rot_constructor_.AssignInternalEnergies(rot_group);
+ rot_constructor_.AssignInternalEnergies(rot_group, r_id, res_idx);
}
private:
diff --git a/sidechain/doc/rotamer_constructor.rst b/sidechain/doc/rotamer_constructor.rst
index b36d7d88619892d046e8ebe09aeaca7f71713046..3a297d5d0846dd0808cad22419dad15add0bf11b 100644
--- a/sidechain/doc/rotamer_constructor.rst
+++ b/sidechain/doc/rotamer_constructor.rst
@@ -34,22 +34,23 @@ Constructing Rotamers and Frame Residues
(e.g. :class:`SCWRL4RotamerConstructor`).
.. method:: ConstructRRMRotamerGroup(res, id, residue_index, rot_lib,\
- [probability_cutoff = 0.98])
- .. method:: ConstructRRMRotamerGroup(all_atom_pos, aa_res_idx, id,\
- residue_index, rot_lib,\
- [probability_cutoff = 0.98])
- .. method:: ConstructRRMRotamerGroup(res, id, residue_index, rot_lib,\
- [phi = -1.0472, psi = -0.7854,\
+ [phi = -1.0472, psi = -0.7854, \
+ n_ter = False, c_ter = False, \
probability_cutoff = 0.98])
.. method:: ConstructRRMRotamerGroup(all_atom_pos, aa_res_idx, id,\
residue_index, rot_lib,\
- [phi = -1.0472, psi = -0.7854,\
+ [phi = -1.0472, psi = -0.7854, \
+ n_ter = False, c_ter = False, \
probability_cutoff = 0.98])
.. method:: ConstructRRMRotamerGroup(res, id, residue_index, rot_lib_entries,\
- [probability_cutoff = 0.98])
+ [phi = -1.0472, psi = -0.7854, \
+ n_ter = False, c_ter = False, \
+ probability_cutoff = 0.98])
.. method:: ConstructRRMRotamerGroup(all_atom_pos, aa_res_idx, id,\
residue_index, rot_lib_entries,\
- [probability_cutoff = 0.98])
+ [phi = -1.0472, psi = -0.7854, \
+ n_ter = False, c_ter = False, \
+ probability_cutoff = 0.98])
All functions are also avaible for their flexible rotamer model counterpart.
=>ConstructFRMRotamerGroup(...) with the same parameters.
@@ -66,10 +67,10 @@ Constructing Rotamers and Frame Residues
:param rot_lib: To search for rotamers
:param rot_lib_entries: :class:`RotamerLibEntry` objects to circumvent the
direct use of a rotamer library
- :param phi: Phi dihedral angle used to search for rotamers if a
- :class:`BBDepRotamerLib` is given as input
- :param psi: Psi dihedral angle used to search for rotamers if a
- :class:`BBDepRotamerLib` is given as input
+ :param phi: Phi dihedral angle
+ :param psi: Psi dihedral angle
+ :param n_ter: Whether the residue is n-terminal
+ :param c_ter: Whether the residue is c-terminal
:param probability_cutoff: For some rotamers, there might be many low
probability entries in the library.
The function adds single rotamers to the group until
@@ -77,8 +78,7 @@ Constructing Rotamers and Frame Residues
larger or equal **probability_cutoff**.
:returns: The rotamer group containing all constructed rotamers
- with internal energies assigned based on the
- probabilities extracted from the rotamer library.
+ with internal energies assigned.
:type res: :class:`ost.mol.ResidueHandle`
:type all_atom_pos: :class:`promod3.loop.AllAtomPositions`
@@ -87,6 +87,10 @@ Constructing Rotamers and Frame Residues
:type residue_index: :class:`int`
:type rot_lib: :class:`RotamerLib` / :class:`BBDepRotamerLib`
:type rot_lib_entries: :class:`list`
+ :type phi: :class:`float`
+ :type psi: :class:`float`
+ :type n_ter: :class:`bool`
+ :type c_ter: :class:`bool`
:type probability_cutoff: :class:`float`
:rtype: :class:`RRMRotamerGroup`
@@ -96,12 +100,13 @@ Constructing Rotamers and Frame Residues
.. method:: ConstructBackboneFrameResidue(res, id, residue_index, \
- [ phi = -1.0472, n_ter = False, \
- c_ter = False])
+ [phi = -1.0472, psi = -0.7854, \
+ n_ter = False, c_ter = False])
.. method:: ConstructBackboneFrameResidue(all_atom_pos, aa_res_idx, id,\
- residue_index, [phi = -1.0472,\
- n_ter = False, c_ter = False])
+ residue_index, \
+ [phi = -1.0472, psi = -0.7854\
+ n_ter = False, c_ter = False])
Constructs frame residues only containing backbone atoms (the ones that
don't show up in a rotamer).
@@ -115,19 +120,17 @@ Constructing Rotamers and Frame Residues
:class:`Frame` you don't want to calculate a pairwise
energy of the sidechain particles towards particles
representing the own backbone...
- :param phi: The dihedral angle of the current residue, required to
- construct the polar nitrogen hydrogen
- :param n_ter: Whether to add additional hydrogens at the nitrogen
- to represent a proper n-terminus
- :param c_ter: Whether to add an additional oxygen at the carbon to
- represent a proper c-terminus
-
+ :param phi: The dihedral angle of the current residue
+ :param psi: The dihedral angle of the current residue
+ :param n_ter: Whether the residue is n-terminal
+ :param c_ter: Whether the residue is c-terminal
:type res: :class:`ost.mol.ResidueHandle`
:type all_atom_pos: :class:`promod3.loop.AllAtomPositions`
:type aa_res_idx: :class:`int`
:type id: :class:`RotamerID`
:type residue_index: :class:`int`
:type phi: :class:`float`
+ :type psi: :class:`float`
:type n_ter: :class:`bool`
:type c_ter: :class:`bool`
@@ -139,26 +142,40 @@ Constructing Rotamers and Frame Residues
positions are set in **all_atom_pos**.
- .. method:: ConstructSidechainFrameResidue(res, id, residue_index)
+ .. method:: ConstructSidechainFrameResidue(res, id, residue_index, \
+ [phi = -1.0472, psi = -0.7854, \
+ n_ter = False, c_ter = False])
- .. method:: ConstructSidechainFrameResidue(all_atom, aa_res_idx, id,\
- residue_index)
+ .. method:: ConstructSidechainFrameResidue(all_atom_pos, aa_res_idx, id,\
+ residue_index, \
+ [phi = -1.0472, psi = -0.7854\
+ n_ter = False, c_ter = False])
Constructs frame residues only containing sidechain atoms (the ones that
you observe in a rotamer).
- :param res: Residue from which to extract the sidechain positions
- :param all_atom_pos: To extract the sidechain positions
+ :param res: Residue from which to extract the backbone positions
+ :param all_atom_pos: To extract the backbone positions
:param aa_res_idx: Index of residue in **all_atom_pos** from which to
- extract the sidechain positions
+ extract the backbone positions
:param id: Identifies the sidechain
- :param residue_index: idenfifies residue in frame
-
+ :param residue_index: Important for the energy calculations towards the
+ :class:`Frame` you don't want to calculate a pairwise
+ energy of the sidechain particles towards particles
+ representing the own backbone...
+ :param phi: The dihedral angle of the current residue
+ :param psi: The dihedral angle of the current residue
+ :param n_ter: Whether the residue is n-terminal
+ :param c_ter: Whether the residue is c-terminal
:type res: :class:`ost.mol.ResidueHandle`
:type all_atom_pos: :class:`promod3.loop.AllAtomPositions`
:type aa_res_idx: :class:`int`
:type id: :class:`RotamerID`
:type residue_index: :class:`int`
+ :type phi: :class:`float`
+ :type psi: :class:`float`
+ :type n_ter: :class:`bool`
+ :type c_ter: :class:`bool`
:rtype: :class:`FrameResidue`
@@ -167,7 +184,9 @@ Constructing Rotamers and Frame Residues
atoms are present in **residue** or not all required sidechain
atom positions are set in **all_atom_pos**.
- .. method:: AssignInternalEnergies(rot_group)
+ .. method:: AssignInternalEnergies(rot_group, id, residue_index, \
+ [phi = -1.0472, psi = -0.7854, \
+ n_ter = False, c_ter = False])
Assigns an internal energy to every rotamer in *rot_group*, i.e. an energy
value before looking at any structural component of the energy function.
@@ -176,8 +195,21 @@ Constructing Rotamers and Frame Residues
:param rot_group: containing all rotamers for which internal energies have
to be assigned
+ :param id: Identifies the sidechain
+ :param residue_index: The index of the residue which is represented by
+ *rot_group*
+ :param phi: The dihedral angle of the current residue
+ :param psi: The dihedral angle of the current residue
+ :param n_ter: Whether the residue is n-terminal
+ :param c_ter: Whether the residue is c-terminal
:type rot_group: :class:`RRMRotamerGroup` / :class:`FRMRotamerGroup`
+ :type id: :class:`RotamerID`
+ :type residue_index: :class:`int`
+ :type phi: :class:`float`
+ :type psi: :class:`float`
+ :type n_ter: :class:`bool`
+ :type c_ter: :class:`bool`
@@ -244,7 +276,9 @@ Constructing Rotamers and Frame Residues
:returns: :class:`FrameResidue`
- .. method:: AssignInternalEnergies(rot_group)
+ .. method:: AssignInternalEnergies(rot_group, id, residue_index, \
+ [phi = -1.0472, psi = -0.7854, \
+ n_ter = False, c_ter = False])
Overrides the method defined in :class:`RotamerConstructor`.
Takes the rotamer group and assigns every single rotamer its internal
@@ -257,6 +291,18 @@ Constructing Rotamers and Frame Residues
:param rot_group: containing all rotamers for which internal energies have
to be assigned
+ :param id: Identifies the sidechain
+ :param residue_index: The index of the residue which is represented by
+ *rot_group*
+ :param phi: The dihedral angle of the current residue
+ :param psi: The dihedral angle of the current residue
+ :param n_ter: Whether the residue is n-terminal
+ :param c_ter: Whether the residue is c-terminal
:type rot_group: :class:`RRMRotamerGroup` / :class:`FRMRotamerGroup`
-
+ :type id: :class:`RotamerID`
+ :type residue_index: :class:`int`
+ :type phi: :class:`float`
+ :type psi: :class:`float`
+ :type n_ter: :class:`bool`
+ :type c_ter: :class:`bool`
diff --git a/sidechain/pymod/export_rotamer_constructor.cc b/sidechain/pymod/export_rotamer_constructor.cc
index 8b6b6890e0a65cda168fc55e89001f8e95ac6fe6..cf28f603746dd64ab52ecb8a238057ee7081f05f 100644
--- a/sidechain/pymod/export_rotamer_constructor.cc
+++ b/sidechain/pymod/export_rotamer_constructor.cc
@@ -39,9 +39,11 @@ RRMRotamerGroupPtr WrapRRMGroup_res(RotamerConstructorPtr constructor,
RotamerID id,
uint residue_idx,
RotamerLibPtr rot_lib,
+ Real phi, Real psi, bool n_ter, bool c_ter,
Real probability_cutoff){
return constructor->ConstructRRMRotamerGroup(res, id, residue_idx,
- rot_lib, probability_cutoff);
+ rot_lib, phi, psi, n_ter, c_ter,
+ probability_cutoff);
}
RRMRotamerGroupPtr WrapRRMGroup_aa(RotamerConstructorPtr constructor,
@@ -50,20 +52,27 @@ RRMRotamerGroupPtr WrapRRMGroup_aa(RotamerConstructorPtr constructor,
RotamerID rotamer_id,
uint residue_idx,
RotamerLibPtr rot_lib,
+ Real phi, Real psi,
+ bool n_ter, bool c_ter,
Real probability_cutoff){
return constructor->ConstructRRMRotamerGroup(all_atom_pos, all_atom_pos_idx,
rotamer_id, residue_idx,
- rot_lib, probability_cutoff);
+ rot_lib, phi, psi, n_ter, c_ter,
+ probability_cutoff);
}
FRMRotamerGroupPtr WrapFRMGroup_res(RotamerConstructorPtr constructor,
const ost::mol::ResidueHandle& res,
RotamerID id,
uint residue_idx,
- RotamerLibPtr rot_lib,
+ RotamerLibPtr rot_lib,
+ Real phi, Real psi,
+ bool n_ter, bool c_ter,
Real probability_cutoff){
return constructor->ConstructFRMRotamerGroup(res, id, residue_idx,
- rot_lib, probability_cutoff);
+ rot_lib, phi, psi,
+ n_ter, c_ter,
+ probability_cutoff);
}
FRMRotamerGroupPtr WrapFRMGroup_aa(RotamerConstructorPtr constructor,
@@ -72,10 +81,12 @@ FRMRotamerGroupPtr WrapFRMGroup_aa(RotamerConstructorPtr constructor,
RotamerID rotamer_id,
uint residue_idx,
RotamerLibPtr rot_lib,
+ Real phi, Real psi, bool n_ter, bool c_ter,
Real probability_cutoff){
return constructor->ConstructFRMRotamerGroup(all_atom_pos, all_atom_pos_idx,
rotamer_id, residue_idx,
- rot_lib, probability_cutoff);
+ rot_lib, phi, psi, n_ter, c_ter,
+ probability_cutoff);
}
RRMRotamerGroupPtr WrapRRMGroup_bbdep_res(RotamerConstructorPtr constructor,
@@ -84,9 +95,10 @@ RRMRotamerGroupPtr WrapRRMGroup_bbdep_res(RotamerConstructorPtr constructor,
uint residue_idx,
BBDepRotamerLibPtr rot_lib,
Real phi, Real psi,
+ bool n_ter, bool c_ter,
Real probability_cutoff){
return constructor->ConstructRRMRotamerGroup(res, id, residue_idx,
- rot_lib, phi, psi,
+ rot_lib, phi, psi, n_ter, c_ter,
probability_cutoff);
}
@@ -97,6 +109,7 @@ RRMRotamerGroupPtr WrapRRMGroup_bbdep_aa(RotamerConstructorPtr constructor,
uint residue_idx,
BBDepRotamerLibPtr rot_lib,
Real phi, Real psi,
+ bool n_ter, bool c_ter,
Real probability_cutoff){
return constructor->ConstructRRMRotamerGroup(all_atom_pos, all_atom_pos_idx,
rotamer_id, residue_idx,
@@ -110,9 +123,10 @@ FRMRotamerGroupPtr WrapFRMGroup_bbdep_res(RotamerConstructorPtr constructor,
uint residue_idx,
BBDepRotamerLibPtr rot_lib,
Real phi, Real psi,
+ bool n_ter, bool c_ter,
Real probability_cutoff){
return constructor->ConstructFRMRotamerGroup(res, id, residue_idx,
- rot_lib, phi, psi,
+ rot_lib, phi, psi, n_ter, c_ter,
probability_cutoff);
}
@@ -123,10 +137,11 @@ FRMRotamerGroupPtr WrapFRMGroup_bbdep_aa(RotamerConstructorPtr constructor,
uint residue_idx,
BBDepRotamerLibPtr rot_lib,
Real phi, Real psi,
+ bool n_ter, bool c_ter,
Real probability_cutoff){
return constructor->ConstructFRMRotamerGroup(all_atom_pos, all_atom_pos_idx,
rotamer_id, residue_idx,
- rot_lib, phi, psi,
+ rot_lib, phi, psi, n_ter, c_ter,
probability_cutoff);
}
@@ -135,11 +150,14 @@ RRMRotamerGroupPtr WrapRRMGroup_entries_res(RotamerConstructorPtr constructor,
RotamerID id,
uint residue_idx,
const boost::python::list& entries,
+ Real phi, Real psi,
+ bool n_ter, bool c_ter,
Real probability_cutoff){
std::vector<RotamerLibEntry> v_entries;
core::ConvertListToVector(entries, v_entries);
return constructor->ConstructRRMRotamerGroup(res, id, residue_idx,
- v_entries,
+ v_entries, phi, psi,
+ n_ter, c_ter,
probability_cutoff);
}
@@ -149,12 +167,14 @@ RRMRotamerGroupPtr WrapRRMGroup_entries_aa(RotamerConstructorPtr constructor,
RotamerID rotamer_id,
uint residue_idx,
const boost::python::list& entries,
+ Real phi, Real psi,
+ bool n_ter, bool c_ter,
Real probability_cutoff){
std::vector<RotamerLibEntry> v_entries;
core::ConvertListToVector(entries, v_entries);
return constructor->ConstructRRMRotamerGroup(all_atom_pos, all_atom_pos_idx,
rotamer_id, residue_idx,
- v_entries,
+ v_entries, phi, psi, n_ter, c_ter,
probability_cutoff);
}
@@ -163,11 +183,14 @@ FRMRotamerGroupPtr WrapFRMGroup_entries_res(RotamerConstructorPtr constructor,
RotamerID id,
uint residue_idx,
const boost::python::list& entries,
+ Real phi, Real psi,
+ bool n_ter, bool c_ter,
Real probability_cutoff){
std::vector<RotamerLibEntry> v_entries;
core::ConvertListToVector(entries, v_entries);
return constructor->ConstructFRMRotamerGroup(res, id, residue_idx,
v_entries,
+ phi, psi, n_ter, c_ter,
probability_cutoff);
}
@@ -177,56 +200,68 @@ FRMRotamerGroupPtr WrapFRMGroup_entries_aa(RotamerConstructorPtr constructor,
RotamerID rotamer_id,
uint residue_idx,
const boost::python::list& entries,
+ Real phi, Real psi, bool n_ter,
+ bool c_ter,
Real probability_cutoff){
std::vector<RotamerLibEntry> v_entries;
core::ConvertListToVector(entries, v_entries);
return constructor->ConstructFRMRotamerGroup(all_atom_pos, all_atom_pos_idx,
rotamer_id, residue_idx,
- v_entries,
+ v_entries, phi, psi, n_ter, c_ter,
probability_cutoff);
}
FrameResiduePtr WrapBBFrame_res(RotamerConstructorPtr constructor,
const ost::mol::ResidueHandle& residue,
RotamerID id, uint residue_index,
- Real phi, bool n_ter, bool c_ter){
+ Real phi, Real psi, bool n_ter, bool c_ter){
return constructor->ConstructBackboneFrameResidue(residue, id, residue_index,
- phi, n_ter, c_ter);
+ phi, psi, n_ter, c_ter);
}
FrameResiduePtr WrapBBFrame_aa(RotamerConstructorPtr constructor,
const promod3::loop::AllAtomPositions& all_atom_pos,
uint all_atom_pos_idx,
RotamerID id, uint residue_index,
- Real phi, bool n_ter, bool c_ter){
+ Real phi, Real psi, bool n_ter, bool c_ter){
return constructor->ConstructBackboneFrameResidue(all_atom_pos, all_atom_pos_idx,
id, residue_index,
- phi, n_ter, c_ter);
+ phi, psi, n_ter, c_ter);
}
FrameResiduePtr WrapSCFrame_res(RotamerConstructorPtr constructor,
const ost::mol::ResidueHandle& residue,
- RotamerID id, uint residue_index){
- return constructor->ConstructSidechainFrameResidue(residue, id, residue_index);
+ RotamerID id, uint residue_index,
+ Real phi, Real psi, bool n_ter, bool c_ter){
+ return constructor->ConstructSidechainFrameResidue(residue, id, residue_index,
+ phi, psi, n_ter, c_ter);
}
FrameResiduePtr WrapSCFrame_aa(RotamerConstructorPtr constructor,
const promod3::loop::AllAtomPositions& all_atom_pos,
uint all_atom_pos_idx,
- RotamerID id, uint residue_index){
+ RotamerID id, uint residue_index,
+ Real phi, Real psi, bool n_ter, bool c_ter){
return constructor->ConstructSidechainFrameResidue(all_atom_pos, all_atom_pos_idx,
- id, residue_index);
+ id, residue_index, phi, psi,
+ n_ter, c_ter);
}
void AssignInternalEnergiesRRM(RotamerConstructorPtr constructor,
- RRMRotamerGroupPtr group){
- constructor->AssignInternalEnergies(group);
+ RRMRotamerGroupPtr group, RotamerID id,
+ uint residue_index,
+ Real phi, Real psi, bool n_ter, bool c_ter){
+ constructor->AssignInternalEnergies(group, id, residue_index, phi, psi,
+ n_ter, c_ter);
}
void AssignInternalEnergiesFRM(RotamerConstructorPtr constructor,
- FRMRotamerGroupPtr group){
- constructor->AssignInternalEnergies(group);
+ FRMRotamerGroupPtr group, RotamerID id,
+ uint residue_index,
+ Real phi, Real psi, bool n_ter, bool c_ter){
+ constructor->AssignInternalEnergies(group, id, residue_index, phi, psi,
+ n_ter, c_ter);
}
} // anon ns
@@ -240,23 +275,39 @@ void export_RotamerConstructor(){
arg("rotamer_id"),
arg("residue_idx"),
arg("rot_lib"),
+ arg("phi") = -1.0472,
+ arg("psi") = -0.7854,
+ arg("n_ter") = false,
+ arg("c_ter") = false,
arg("probability_cutoff") = 0.98))
.def("ConstructRRMRotamerGroup", &WrapRRMGroup_aa,(arg("all_atom_pos"),
arg("all_atom_pos_idx"),
arg("rotamer_id"),
arg("residue_idx"),
arg("rot_lib"),
+ arg("phi") = -1.0472,
+ arg("psi") = -0.7854,
+ arg("n_ter") = false,
+ arg("c_ter") = false,
arg("probability_cutoff") = 0.98))
.def("ConstructFRMRotamerGroup", &WrapFRMGroup_res,(arg("residue"),
arg("rotamer_id"),
arg("residue_idx"),
arg("rot_lib"),
+ arg("phi") = -1.0472,
+ arg("psi") = -0.7854,
+ arg("n_ter") = false,
+ arg("c_ter") = false,
arg("probability_cutoff") = 0.98))
.def("ConstructFRMRotamerGroup", &WrapFRMGroup_aa,(arg("all_atom_pos"),
arg("all_atom_pos_idx"),
arg("rotamer_id"),
arg("residue_idx"),
arg("rot_lib"),
+ arg("phi") = -1.0472,
+ arg("psi") = -0.7854,
+ arg("n_ter") = false,
+ arg("c_ter") = false,
arg("probability_cutoff") = 0.98))
.def("ConstructRRMRotamerGroup", &WrapRRMGroup_bbdep_res,(arg("residue"),
arg("rotamer_id"),
@@ -264,6 +315,8 @@ void export_RotamerConstructor(){
arg("rot_lib"),
arg("phi") = -1.0472,
arg("psi") = -0.7854,
+ arg("n_ter") = false,
+ arg("c_ter") = false,
arg("probability_cutoff") = 0.98))
.def("ConstructRRMRotamerGroup", &WrapRRMGroup_bbdep_aa,(arg("all_atom_pos"),
arg("all_atom_pos_idx"),
@@ -272,6 +325,8 @@ void export_RotamerConstructor(){
arg("rot_lib"),
arg("phi") = -1.0472,
arg("psi") = -0.7854,
+ arg("n_ter") = false,
+ arg("c_ter") = false,
arg("probability_cutoff") = 0.98))
.def("ConstructFRMRotamerGroup", &WrapFRMGroup_bbdep_res,(arg("residue"),
arg("rotamer_id"),
@@ -279,6 +334,8 @@ void export_RotamerConstructor(){
arg("rot_lib"),
arg("phi") = -1.0472,
arg("psi") = -0.7854,
+ arg("n_ter") = false,
+ arg("c_ter") = false,
arg("probability_cutoff") = 0.98))
.def("ConstructFRMRotamerGroup", &WrapFRMGroup_bbdep_aa,(arg("all_atom_pos"),
arg("all_atom_pos_idx"),
@@ -287,33 +344,52 @@ void export_RotamerConstructor(){
arg("rot_lib"),
arg("phi") = -1.0472,
arg("psi") = -0.7854,
+ arg("phi") = false,
+ arg("psi") = false,
arg("probability_cutoff") = 0.98))
.def("ConstructRRMRotamerGroup", &WrapRRMGroup_entries_res,(arg("residue"),
arg("rotamer_id"),
arg("residue_idx"),
arg("entries"),
+ arg("phi") = -1.0472,
+ arg("psi") = -0.7854,
+ arg("n_ter") = false,
+ arg("c_ter") = false,
arg("probability_cutoff") = 0.98))
.def("ConstructRRMRotamerGroup", &WrapRRMGroup_entries_aa,(arg("all_atom_pos"),
arg("all_atom_pos_idx"),
arg("rotamer_id"),
arg("residue_idx"),
arg("entries"),
+ arg("phi") = -1.0472,
+ arg("psi") = -0.7854,
+ arg("n_ter") = false,
+ arg("c_ter") = false,
arg("probability_cutoff") = 0.98))
.def("ConstructFRMRotamerGroup", &WrapFRMGroup_entries_res,(arg("residue"),
arg("rotamer_id"),
arg("residue_idx"),
arg("entries"),
+ arg("phi") = -1.0472,
+ arg("psi") = -0.7854,
+ arg("n_ter") = false,
+ arg("c_ter") = false,
arg("probability_cutoff") = 0.98))
.def("ConstructFRMRotamerGroup", &WrapFRMGroup_entries_aa,(arg("all_atom_pos"),
arg("all_atom_pos_idx"),
arg("rotamer_id"),
arg("residue_idx"),
arg("entries"),
+ arg("phi") = -1.0472,
+ arg("psi") = -0.7854,
+ arg("n_ter") = false,
+ arg("c_ter") = false,
arg("probability_cutoff") = 0.98))
.def("ConstructBackboneFrameResidue", &WrapBBFrame_res,(arg("residue"),
arg("rotamer_id"),
arg("residue_index"),
arg("phi") = -1.0472,
+ arg("psi") = -0.7854,
arg("n_ter")=false,
arg("c_ter")=false))
.def("ConstructBackboneFrameResidue", &WrapBBFrame_aa,(arg("all_atom_pos"),
@@ -321,17 +397,38 @@ void export_RotamerConstructor(){
arg("rotamer_id"),
arg("residue_index"),
arg("phi") = -1.0472,
+ arg("psi") = -0.7854,
arg("n_ter")=false,
arg("c_ter")=false))
.def("ConstructSidechainFrameResidue", &WrapSCFrame_res,(arg("residue"),
arg("rotamer_id"),
- arg("residue_index")))
+ arg("residue_index"),
+ arg("phi") = -1.0472,
+ arg("psi") = -0.7854,
+ arg("n_ter")=false,
+ arg("c_ter")=false))
.def("ConstructSidechainFrameResidue", &WrapSCFrame_aa,(arg("all_atom_pos"),
arg("all_atom_pos_idx"),
arg("rotamer_id"),
- arg("residue_index")))
- .def("AssignInternalEnergies", &AssignInternalEnergiesRRM)
- .def("AssignInternalEnergies", &AssignInternalEnergiesFRM)
+ arg("residue_index"),
+ arg("phi") = -1.0472,
+ arg("psi") = -0.7854,
+ arg("n_ter")=false,
+ arg("c_ter")=false))
+ .def("AssignInternalEnergies", &AssignInternalEnergiesRRM, (arg("rot_group"),
+ arg("rotamer_id"),
+ arg("residue_index"),
+ arg("phi")=-1.0472,
+ arg("psi")=-0.7854,
+ arg("n_ter")=false,
+ arg("c_ter")=false))
+ .def("AssignInternalEnergies", &AssignInternalEnergiesFRM, (arg("rot_group"),
+ arg("rotamer_id"),
+ arg("residue_index"),
+ arg("phi")=-1.0472,
+ arg("psi")=-0.7854,
+ arg("n_ter")=false,
+ arg("c_ter")=false))
;
diff --git a/sidechain/src/CMakeLists.txt b/sidechain/src/CMakeLists.txt
index ac3b4ed867e19ba8c82c75c02dbc454206686938..953b809ad3108aa9ae82d9431483ecdc8e6eaedc 100644
--- a/sidechain/src/CMakeLists.txt
+++ b/sidechain/src/CMakeLists.txt
@@ -18,6 +18,7 @@ set(SIDECHAIN_HEADERS
sidechain_connector.hh
sidechain_object_loader.hh
rotamer_constructor.hh
+ rotamer_lookup.hh
scwrl4_rotamer_constructor.hh
subrotamer_optimizer.hh
)
@@ -39,6 +40,7 @@ set(SIDECHAIN_SOURCES
sidechain_connector.cc
sidechain_object_loader.cc
rotamer_constructor.cc
+ rotamer_lookup.cc
scwrl4_rotamer_constructor.cc
subrotamer_optimizer.cc
)
diff --git a/sidechain/src/disulfid.cc b/sidechain/src/disulfid.cc
index 5cdb808cf97ab4b6dcba60b7d88b16419d51f00d..bfa4c682e95769d0a8ce303aab584698519e21c0 100644
--- a/sidechain/src/disulfid.cc
+++ b/sidechain/src/disulfid.cc
@@ -433,8 +433,8 @@ void ResolveCysteins(const std::vector<FRMRotamerGroupPtr>& rot_groups,
std::vector<std::pair<uint, uint> >& rotamer_indices) {
CysteinResolve<FRMRotamerGroupPtr>(rot_groups, ca_pos, cb_pos,
- disulfid_score_thresh, disulfid_indices,
- rotamer_indices);
+ disulfid_score_thresh, disulfid_indices,
+ rotamer_indices);
if(optimize_subrotamers) {
diff --git a/sidechain/src/rotamer_constructor.cc b/sidechain/src/rotamer_constructor.cc
index 3dfe130fcb331240a44ae2ab2b691af6dd4a95af..354e2c4b22b199c632d7f8ffa9536476c98ea320 100644
--- a/sidechain/src/rotamer_constructor.cc
+++ b/sidechain/src/rotamer_constructor.cc
@@ -14,239 +14,957 @@
// limitations under the License.
#include <promod3/sidechain/rotamer_constructor.hh>
+#include <promod3/loop/amino_acid_atoms.hh>
+#include <promod3/loop/sidechain_atom_constructor.hh>
+#include <promod3/sidechain/scwrl4_particle_scoring.hh>
+
namespace promod3 { namespace sidechain{
-RotamerConstructor::RotamerConstructor() {
+RotamerConstructor::RotamerConstructor(bool cb_in_sidechain,
+ RotamerLookupMode mode,
+ const RotamerLookupParam& param):
+ rotamer_lookup_(cb_in_sidechain, mode, param),
+ mode_(mode) {
+
String s(XXX,'X');
for(uint i = 0; i < XXX; ++i){
s[i] = RotIDToOLC(RotamerID(i));
}
pos_buffer_ = boost::make_shared<promod3::loop::AllAtomPositions>(s);
+ hydrogen_buffer_ = boost::make_shared<promod3::loop::HydrogenStorage>();
}
-
// PUBLICLY ACCESSIBLE QUERY FUNCTIONS
RRMRotamerGroupPtr RotamerConstructor::ConstructRRMRotamerGroup(
const ost::mol::ResidueHandle& res, RotamerID id,
- uint residue_index, RotamerLibPtr rot_lib,
- Real probability_cutoff) {
+ uint residue_idx, RotamerLibPtr rot_lib, Real phi,
+ Real psi, bool n_ter, bool c_ter, Real probability_cutoff) {
if(id == XXX) {
throw promod3::Error("Cannot construct RRMRotamerGroup for unknown "
"rotamer id!");
}
+ id_ = id;
+ residue_idx_ = residue_idx;
+ phi_ = phi;
+ psi_ = psi;
+ n_ter_ = n_ter;
+ c_ter_ = c_ter;
std::pair<RotamerLibEntry*,uint> lib_entries = rot_lib->QueryLib(id);
- this->SetPosBuffer(res, id);
- return this->ConstructRRMGroup(id, residue_index, lib_entries,
- probability_cutoff);
+ this->SetPosBuffer(res);
+ return this->ConstructRRMGroup(lib_entries, probability_cutoff);
}
+
RRMRotamerGroupPtr RotamerConstructor::ConstructRRMRotamerGroup(
const promod3::loop::AllAtomPositions& all_atom,
- uint aa_res_idx, RotamerID id, uint residue_index,
- RotamerLibPtr rot_lib, Real probability_cutoff) {
+ uint aa_res_idx, RotamerID id, uint residue_idx,
+ RotamerLibPtr rot_lib, Real phi, Real psi, bool n_ter, bool c_ter,
+ Real probability_cutoff) {
if(id == XXX) {
throw promod3::Error("Cannot construct RRMRotamerGroup for unknown "
"rotamer id!");
}
+ id_ = id;
+ residue_idx_ = residue_idx;
+ phi_ = phi;
+ psi_ = psi;
+ n_ter_ = n_ter;
+ c_ter_ = c_ter;
std::pair<RotamerLibEntry*,uint> lib_entries = rot_lib->QueryLib(id);
- this->SetPosBuffer(all_atom, aa_res_idx, id);
- return this->ConstructRRMGroup(id, residue_index, lib_entries,
- probability_cutoff);
+ this->SetPosBuffer(all_atom, aa_res_idx);
+ return this->ConstructRRMGroup(lib_entries, probability_cutoff);
}
+
FRMRotamerGroupPtr RotamerConstructor::ConstructFRMRotamerGroup(
const ost::mol::ResidueHandle& res, RotamerID id,
- uint residue_index, RotamerLibPtr rot_lib,
- Real probability_cutoff) {
+ uint residue_idx, RotamerLibPtr rot_lib, Real phi, Real psi,
+ bool n_ter, bool c_ter, Real probability_cutoff) {
if(id == XXX) {
throw promod3::Error("Cannot construct FRMRotamerGroup for unknown "
"rotamer id!");
}
+ id_ = id;
+ residue_idx_ = residue_idx;
+ phi_ = phi;
+ psi_ = psi;
+ n_ter_ = n_ter;
+ c_ter_ = c_ter;
std::pair<RotamerLibEntry*,uint> lib_entries = rot_lib->QueryLib(id);
- this->SetPosBuffer(res, id);
- return this->ConstructFRMGroup(id, residue_index, lib_entries,
- probability_cutoff);
+ this->SetPosBuffer(res);
+ return this->ConstructFRMGroup(lib_entries, probability_cutoff);
}
+
FRMRotamerGroupPtr RotamerConstructor::ConstructFRMRotamerGroup(
const promod3::loop::AllAtomPositions& all_atom,
- uint aa_res_idx, RotamerID id, uint residue_index,
- RotamerLibPtr rot_lib, Real probability_cutoff) {
+ uint aa_res_idx, RotamerID id, uint residue_idx,
+ RotamerLibPtr rot_lib, Real phi, Real psi, bool n_ter, bool c_ter,
+ Real probability_cutoff) {
if(id == XXX) {
throw promod3::Error("Cannot construct FRMRotamerGroup for unknown "
"rotamer id!");
}
+ id_ = id;
+ residue_idx_ = residue_idx;
+ phi_ = phi;
+ psi_ = psi;
+ n_ter_ = n_ter;
+ c_ter_ = c_ter;
std::pair<RotamerLibEntry*,uint> lib_entries = rot_lib->QueryLib(id);
- this->SetPosBuffer(all_atom, aa_res_idx, id);
- return this->ConstructFRMGroup(id, residue_index, lib_entries,
- probability_cutoff);
+ this->SetPosBuffer(all_atom, aa_res_idx);
+ return this->ConstructFRMGroup(lib_entries, probability_cutoff);
}
+
RRMRotamerGroupPtr RotamerConstructor::ConstructRRMRotamerGroup(
const ost::mol::ResidueHandle& res, RotamerID id,
- uint residue_index, BBDepRotamerLibPtr rot_lib,
- Real phi, Real psi, Real probability_cutoff) {
+ uint residue_idx, BBDepRotamerLibPtr rot_lib,
+ Real phi, Real psi, bool n_ter, bool c_ter, Real probability_cutoff) {
if(id == XXX) {
throw promod3::Error("Cannot construct RRMRotamerGroup for unknown "
"rotamer id!");
}
+ id_ = id;
+ residue_idx_ = residue_idx;
+ phi_ = phi;
+ psi_ = psi;
+ n_ter_ = n_ter;
+ c_ter_ = c_ter;
std::pair<RotamerLibEntry*,uint> lib_entries = rot_lib->QueryLib(id, phi, psi);
- this->SetPosBuffer(res, id);
- return this->ConstructRRMGroup(id, residue_index, lib_entries,
- probability_cutoff);
+ this->SetPosBuffer(res);
+ return this->ConstructRRMGroup(lib_entries, probability_cutoff);
}
+
RRMRotamerGroupPtr RotamerConstructor::ConstructRRMRotamerGroup(
const promod3::loop::AllAtomPositions& all_atom,
- uint aa_res_idx, RotamerID id, uint residue_index,
+ uint aa_res_idx, RotamerID id, uint residue_idx,
BBDepRotamerLibPtr rot_lib,
- Real phi, Real psi, Real probability_cutoff) {
+ Real phi, Real psi, bool n_ter, bool c_ter, Real probability_cutoff) {
if(id == XXX) {
throw promod3::Error("Cannot construct RRMRotamerGroup for unknown "
"rotamer id!");
}
+ id_ = id;
+ residue_idx_ = residue_idx;
+ phi_ = phi;
+ psi_ = psi;
+ n_ter_ = n_ter;
+ c_ter_ = c_ter;
std::pair<RotamerLibEntry*,uint> lib_entries = rot_lib->QueryLib(id, phi, psi);
- this->SetPosBuffer(all_atom, aa_res_idx, id);
- return this->ConstructRRMGroup(id, residue_index, lib_entries,
- probability_cutoff);
+ this->SetPosBuffer(all_atom, aa_res_idx);
+ return this->ConstructRRMGroup(lib_entries, probability_cutoff);
}
+
FRMRotamerGroupPtr RotamerConstructor::ConstructFRMRotamerGroup(
const ost::mol::ResidueHandle& res, RotamerID id,
- uint residue_index, BBDepRotamerLibPtr rot_lib,
- Real phi, Real psi, Real probability_cutoff) {
+ uint residue_idx, BBDepRotamerLibPtr rot_lib,
+ Real phi, Real psi, bool n_ter, bool c_ter, Real probability_cutoff) {
if(id == XXX) {
throw promod3::Error("Cannot construct FRMRotamerGroup for unknown "
"rotamer id!");
}
+ id_ = id;
+ residue_idx_ = residue_idx;
+ phi_ = phi;
+ psi_ = psi;
+ n_ter_ = n_ter;
+ c_ter_ = c_ter;
std::pair<RotamerLibEntry*,uint> lib_entries = rot_lib->QueryLib(id, phi, psi);
- this->SetPosBuffer(res, id);
- return this->ConstructFRMGroup(id, residue_index, lib_entries,
- probability_cutoff);
+ this->SetPosBuffer(res);
+ return this->ConstructFRMGroup(lib_entries, probability_cutoff);
}
+
FRMRotamerGroupPtr RotamerConstructor::ConstructFRMRotamerGroup(
const promod3::loop::AllAtomPositions& all_atom,
- uint aa_res_idx, RotamerID id, uint residue_index,
+ uint aa_res_idx, RotamerID id, uint residue_idx,
BBDepRotamerLibPtr rot_lib,
- Real phi, Real psi, Real probability_cutoff) {
+ Real phi, Real psi, bool n_ter, bool c_ter, Real probability_cutoff) {
if(id == XXX) {
throw promod3::Error("Cannot construct FRMRotamerGroup for unknown "
"rotamer id!");
}
+ id_ = id;
+ residue_idx_ = residue_idx;
+ phi_ = phi;
+ psi_ = psi;
+ n_ter_ = n_ter;
+ c_ter_ = c_ter;
std::pair<RotamerLibEntry*,uint> lib_entries = rot_lib->QueryLib(id, phi, psi);
- this->SetPosBuffer(all_atom, aa_res_idx, id);
- return this->ConstructFRMGroup(id, residue_index, lib_entries,
- probability_cutoff);
+ this->SetPosBuffer(all_atom, aa_res_idx);
+ return this->ConstructFRMGroup(lib_entries, probability_cutoff);
}
+
RRMRotamerGroupPtr RotamerConstructor::ConstructRRMRotamerGroup(
const ost::mol::ResidueHandle& res, RotamerID id,
- uint residue_index,
+ uint residue_idx,
std::vector<RotamerLibEntry>& lib_entries,
- Real probability_cutoff) {
+ Real phi, Real psi, bool n_ter, bool c_ter, Real probability_cutoff) {
if(id == XXX) {
throw promod3::Error("Cannot construct RRMRotamerGroup for unknown "
"rotamer id!");
}
+ id_ = id;
+ residue_idx_ = residue_idx;
+ phi_ = phi;
+ psi_ = psi;
+ n_ter_ = n_ter;
+ c_ter_ = c_ter;
std::pair<RotamerLibEntry*,uint> I_LIKE_CHEESE =
std::make_pair(&lib_entries[0], lib_entries.size());
- this->SetPosBuffer(res, id);
- return this->ConstructRRMGroup(id, residue_index, I_LIKE_CHEESE,
- probability_cutoff);
+ this->SetPosBuffer(res);
+ return this->ConstructRRMGroup(I_LIKE_CHEESE, probability_cutoff);
}
+
RRMRotamerGroupPtr RotamerConstructor::ConstructRRMRotamerGroup(
const promod3::loop::AllAtomPositions& all_atom,
- uint aa_res_idx, RotamerID id, uint residue_index,
+ uint aa_res_idx, RotamerID id, uint residue_idx,
std::vector<RotamerLibEntry>& lib_entries,
- Real probability_cutoff) {
+ Real phi, Real psi, bool n_ter, bool c_ter, Real probability_cutoff) {
if(id == XXX) {
throw promod3::Error("Cannot construct RRMRotamerGroup for unknown "
"rotamer id!");
}
+ id_ = id;
+ residue_idx_ = residue_idx;
+ phi_ = phi;
+ psi_ = psi;
+ n_ter_ = n_ter;
+ c_ter_ = c_ter;
std::pair<RotamerLibEntry*,uint> I_LIKE_CHEESE =
std::make_pair(&lib_entries[0], lib_entries.size());
- this->SetPosBuffer(all_atom, aa_res_idx, id);
- return this->ConstructRRMGroup(id, residue_index, I_LIKE_CHEESE,
- probability_cutoff);
+ this->SetPosBuffer(all_atom, aa_res_idx);
+ return this->ConstructRRMGroup(I_LIKE_CHEESE, probability_cutoff);
}
+
FRMRotamerGroupPtr RotamerConstructor::ConstructFRMRotamerGroup(
const ost::mol::ResidueHandle& res, RotamerID id,
- uint residue_index, std::vector<RotamerLibEntry>& lib_entries,
- Real probability_cutoff) {
+ uint residue_idx, std::vector<RotamerLibEntry>& lib_entries,
+ Real phi, Real psi, bool n_ter, bool c_ter, Real probability_cutoff) {
if(id == XXX) {
throw promod3::Error("Cannot construct FRMRotamerGroup for unknown "
"rotamer id!");
}
+ id_ = id;
+ residue_idx_ = residue_idx;
+ phi_ = phi;
+ psi_ = psi;
+ n_ter_ = n_ter;
+ c_ter_ = c_ter;
std::pair<RotamerLibEntry*,uint> I_LIKE_CHEESE =
std::make_pair(&lib_entries[0], lib_entries.size());
- this->SetPosBuffer(res, id);
- return this->ConstructFRMGroup(id, residue_index, I_LIKE_CHEESE,
- probability_cutoff);
+ this->SetPosBuffer(res);
+ return this->ConstructFRMGroup(I_LIKE_CHEESE, probability_cutoff);
}
+
FRMRotamerGroupPtr RotamerConstructor::ConstructFRMRotamerGroup(
const promod3::loop::AllAtomPositions& all_atom,
- uint aa_res_idx, RotamerID id, uint residue_index,
+ uint aa_res_idx, RotamerID id, uint residue_idx,
std::vector<RotamerLibEntry>& lib_entries,
- Real probability_cutoff) {
+ Real phi, Real psi, bool n_ter, bool c_ter, Real probability_cutoff) {
if(id == XXX) {
throw promod3::Error("Cannot construct FRMRotamerGroup for unknown "
"rotamer id!");
}
+ id_ = id;
+ residue_idx_ = residue_idx;
+ phi_ = phi;
+ psi_ = psi;
+ n_ter_ = n_ter;
+ c_ter_ = c_ter;
std::pair<RotamerLibEntry*,uint> I_LIKE_CHEESE =
std::make_pair(&lib_entries[0], lib_entries.size());
- this->SetPosBuffer(all_atom, aa_res_idx, id);
- return this->ConstructFRMGroup(id, residue_index, I_LIKE_CHEESE,
- probability_cutoff);
+ this->SetPosBuffer(all_atom, aa_res_idx);
+ return this->ConstructFRMGroup(I_LIKE_CHEESE, probability_cutoff);
}
-void RotamerConstructor::AssignInternalEnergies(RRMRotamerGroupPtr group) {
+
+FrameResiduePtr RotamerConstructor::ConstructBackboneFrameResidue(
+ const ost::mol::ResidueHandle& res, RotamerID id, uint residue_idx,
+ Real phi, Real psi, bool n_ter, bool c_ter) {
+
+ core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "RotamerConstructor::ConstructBackboneFrameResidue", 2);
+
+ if(id == XXX) {
+ throw promod3::Error("Cannot construct FrameResidue for unknown "
+ "rotamer id!");
+ }
+
+ id_ = id;
+ residue_idx_ = residue_idx;
+ phi_ = phi;
+ psi_ = psi;
+ n_ter_ = n_ter;
+ c_ter_ = c_ter;
+
+ const RotamerInfo& info = rotamer_lookup_.GetBackboneInfo(id);
+
+ for(uint i = 0; i < info.particles.size(); ++i){
+ if(!info.particles[i].is_hydrogen){
+ ost::mol::AtomHandle a = res.FindAtom(info.particles[i].name);
+ if(!a.IsValid()){
+ throw promod3::Error("Expected atom " + info.particles[i].name +
+ " to be present in input residue!");
+ }
+ pos_buffer_->SetPos(id, info.particles[i].atom_idx, a.GetPos());
+ }
+ }
+
+ return this->ConstructBackboneFrameResidue();
+}
+
+
+FrameResiduePtr RotamerConstructor::ConstructBackboneFrameResidue(
+ const promod3::loop::AllAtomPositions& all_atom, uint aa_res_idx,
+ RotamerID id, uint residue_idx,
+ Real phi, Real psi, bool n_ter, bool c_ter) {
+
+ core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "RotamerConstructor::ConstructBackboneFrameResidue", 2);
+
+ if(id == XXX) {
+ throw promod3::Error("Cannot construct FrameResidue for unknown "
+ "rotamer id!");
+ }
+
+ id_ = id;
+ residue_idx_ = residue_idx;
+ phi_ = phi;
+ psi_ = psi;
+ n_ter_ = n_ter;
+ c_ter_ = c_ter;
+
+ const RotamerInfo& info = rotamer_lookup_.GetBackboneInfo(id);
+
+ for(uint i = 0; i < info.particles.size(); ++i){
+ if(!info.particles[i].is_hydrogen){
+
+ if(!all_atom.IsSet(aa_res_idx, info.particles[i].atom_idx)){
+ throw promod3::Error("Expected atom " + info.particles[i].name +
+ " to be set in all_atom");
+ }
+
+ pos_buffer_->SetPos(id, info.particles[i].atom_idx,
+ all_atom.GetPos(aa_res_idx, info.particles[i].atom_idx));
+ }
+ }
+
+ return this->ConstructBackboneFrameResidue();
+}
+
+
+FrameResiduePtr RotamerConstructor::ConstructSidechainFrameResidue(
+ const ost::mol::ResidueHandle& res, RotamerID id, uint residue_idx,
+ Real phi, Real psi, bool n_ter, bool c_ter) {
+
+ core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "RotamerConstructor::ConstructSidechainFrameResidue", 2);
+
+ if(id == XXX) {
+ throw promod3::Error("Cannot construct FrameResidue for unknown "
+ "rotamer id!");
+ }
+
+ id_ = id;
+ residue_idx_ = residue_idx;
+ phi_ = phi;
+ psi_ = psi;
+ n_ter_ = n_ter;
+ c_ter_ = c_ter;
+
+ const RotamerInfo& info = rotamer_lookup_.GetSidechainInfo(id);
+
+ for(uint i = 0; i < info.particles.size(); ++i){
+ if(!info.particles[i].is_hydrogen){
+ ost::mol::AtomHandle a = res.FindAtom(info.particles[i].name);
+ if(!a.IsValid()){
+ throw promod3::Error("Expected atom " + info.particles[i].name +
+ " to be present in input residue!");
+ }
+ pos_buffer_->SetPos(id, info.particles[i].atom_idx, a.GetPos());
+ }
+ }
+
+ //set bb hydrogen
+ if(info.has_hydrogens){
+ // to construct hydrogens, we might also need backbone atoms in the buffer
+ const RotamerInfo& bb_info = rotamer_lookup_.GetBackboneInfo(id);
+
+ for(uint i = 0; i < bb_info.particles.size(); ++i){
+ if(!bb_info.particles[i].is_hydrogen){
+ ost::mol::AtomHandle a = res.FindAtom(bb_info.particles[i].name);
+ if(!a.IsValid()){
+ throw promod3::Error("Expected atom " + bb_info.particles[i].name +
+ " to be present in input residue!");
+ }
+ pos_buffer_->SetPos(id, bb_info.particles[i].atom_idx, a.GetPos());
+ }
+ }
+
+ promod3::loop::ConstructHydrogens(*pos_buffer_, id, *hydrogen_buffer_,
+ mode_ == POLAR_HYDROGEN_MODE,
+ promod3::loop::PROT_STATE_HISH);
+ }
+
+ int num_particles = info.particles.size();
+ std::vector<Particle> particles(num_particles);
+
+ for(int i = 0; i < num_particles; ++i) {
+ const ParticleInfo& pi = info.particles[i];
+ particles[i].SetName(pi.name);
+ this->ParametrizeParticle(pi.atom_idx, pi.is_hydrogen, particles[i]);
+ }
+
+ FrameResiduePtr p = boost::make_shared<FrameResidue>(particles,
+ residue_idx);
+
+ return p;
+}
+
+
+FrameResiduePtr RotamerConstructor::ConstructSidechainFrameResidue(
+ const promod3::loop::AllAtomPositions& all_atom, uint aa_res_idx,
+ RotamerID id, uint residue_idx, Real phi, Real psi,
+ bool n_ter, bool c_ter) {
+
+ core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "RotamerConstructor::ConstructSidechainFrameResidue", 2);
+
+ if(id == XXX) {
+ throw promod3::Error("Cannot construct FrameResidue for unknown "
+ "rotamer id!");
+ }
+
+ id_ = id;
+ residue_idx_ = residue_idx;
+ phi_ = phi;
+ psi_ = psi;
+ n_ter_ = n_ter;
+ c_ter_ = c_ter;
+
+ const RotamerInfo& info = rotamer_lookup_.GetSidechainInfo(id);
+
+ for(uint i = 0; i < info.particles.size(); ++i){
+ if(!info.particles[i].is_hydrogen){
+ if(!all_atom.IsSet(aa_res_idx, info.particles[i].atom_idx)){
+ throw promod3::Error("Expected atom " + info.particles[i].name +
+ " to be set in all_atom");
+ }
+ pos_buffer_->SetPos(id, info.particles[i].atom_idx,
+ all_atom.GetPos(aa_res_idx, info.particles[i].atom_idx));
+ }
+ }
+
+ //set hydrogens
+ if(info.has_hydrogens){
+ // to construct hydrogens, we might also need backbone atoms in the buffer
+ const RotamerInfo& bb_info = rotamer_lookup_.GetBackboneInfo(id);
+
+ for(uint i = 0; i < bb_info.particles.size(); ++i){
+ if(!bb_info.particles[i].is_hydrogen){
+ if(!all_atom.IsSet(aa_res_idx, bb_info.particles[i].atom_idx)){
+ throw promod3::Error("Expected atom " + bb_info.particles[i].name +
+ " to be set in all_atom");
+ }
+ pos_buffer_->SetPos(id, bb_info.particles[i].atom_idx,
+ all_atom.GetPos(aa_res_idx, bb_info.particles[i].atom_idx));
+ }
+ }
+
+ promod3::loop::ConstructHydrogens(*pos_buffer_, id, *hydrogen_buffer_,
+ mode_ == POLAR_HYDROGEN_MODE,
+ promod3::loop::PROT_STATE_HISH);
+ }
+
+ int num_particles = info.particles.size();
+ std::vector<Particle> particles(num_particles);
+
+ for(int i = 0; i < num_particles; ++i) {
+ const ParticleInfo& pi = info.particles[i];
+ particles[i].SetName(pi.name);
+ this->ParametrizeParticle(pi.atom_idx, pi.is_hydrogen, particles[i]);
+ }
+
+ FrameResiduePtr p = boost::make_shared<FrameResidue>(particles,
+ residue_idx);
+
+ return p;
+}
+
+
+void RotamerConstructor::AssignInternalEnergies(RRMRotamerGroupPtr group,
+ RotamerID id,
+ uint residue_idx,
+ Real phi, Real psi,
+ bool n_ter, bool c_ter) {
for(uint i = 0; i < group->size(); ++i){
(*group)[i]->SetInternalEnergy(0.0);
}
}
-void RotamerConstructor::AssignInternalEnergies(FRMRotamerGroupPtr group) {
+
+void RotamerConstructor::AssignInternalEnergies(FRMRotamerGroupPtr group,
+ RotamerID id,
+ uint residue_idx,
+ Real phi, Real psi,
+ bool n_ter, bool c_ter) {
for(uint i = 0; i < group->size(); ++i){
(*group)[i]->SetInternalEnergy(0.0);
}
}
-void RotamerConstructor::SetPosBuffer(const ost::mol::ResidueHandle& res,
- RotamerID id) {
+
+RRMRotamerGroupPtr RotamerConstructor::ConstructRRMGroup(
+ std::pair<RotamerLibEntry*,uint> lib_entries,
+ Real probability_cutoff) {
+
+ core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "RotamerConstructor::ConstructRRMGroup", 2);
+
+ std::vector<RRMRotamerPtr> rotamers;
+ Real summed_prob = 0.0;
+
+ // in case of his, we have to move the backbone positions in the buffer
+ // to the locations defining his in the different protonation states
+ if(id_ == HIS && mode_ != HEAVY_ATOM_MODE){
+ MVBBPosBuffer(HIS, HSD);
+ MVBBPosBuffer(HIS, HSE);
+ }
+
+ // in case of alanine and glycine, the rotamer libraries won't have any
+ // entries. For consistency we nevertheless construct rotamers.
+ // We simply add a fake RotamerLibEntry in this case that has
+ // no sidechain dihedrals set. In case of Alanine we might still have
+ // some atoms in (depending on cb_in_sidechain flag)
+ std::vector<RotamerLibEntry> fake_rotamers(1);
+ if(lib_entries.second == 0 && (id_ == ALA || id_ == GLY)) {
+ // we have to make sure, that the according probability really is one!
+ fake_rotamers[0].probability = 1.0;
+ lib_entries = std::make_pair(&fake_rotamers[0], 1);
+ }
+ else if(lib_entries.second == 0) {
+ throw promod3::Error("Did not find any rotamers in Rotamer Library!");
+ }
+
+ for(uint i = 0; i < lib_entries.second; ++i){
+
+ probability_ = lib_entries.first[i].probability;
+ summed_prob += probability_;
+ chi_angles_[0] = lib_entries.first[i].chi1;
+ chi_angles_[1] = lib_entries.first[i].chi2;
+ chi_angles_[2] = lib_entries.first[i].chi3;
+ chi_angles_[3] = lib_entries.first[i].chi4;
+
+ if(mode_ == HEAVY_ATOM_MODE) {
+ rotamers.push_back(ConstructRRM());
+ } else {
+ // in POLAR_HYDROGEN_MODE or FULL_ATOMIC_MODE we're sampling
+ // polar hydrogens of SER/THR/TYR and construct different
+ // rotamers for HIS
+ switch(id_){
+ case HIS:{
+ id_ = HSE;
+ rotamers.push_back(ConstructRRM());
+ id_ = HSD;
+ rotamers.push_back(ConstructRRM());
+ id_ = HIS;
+ break;
+ }
+ case SER:{
+ chi_angles_[1] = Real(M_PI);
+ rotamers.push_back(ConstructRRM());
+ chi_angles_[1] = Real(M_PI) / 3.0;
+ rotamers.push_back(ConstructRRM());
+ chi_angles_[1] = -Real(M_PI) / 3.0;
+ rotamers.push_back(ConstructRRM());
+ break;
+ }
+ case THR:{
+ chi_angles_[1] = Real(M_PI);
+ rotamers.push_back(ConstructRRM());
+ chi_angles_[1] = Real(M_PI) / 3.0;
+ rotamers.push_back(ConstructRRM());
+ chi_angles_[1] = -Real(M_PI) / 3.0;
+ rotamers.push_back(ConstructRRM());
+ break;
+ }
+ case TYR:{
+ chi_angles_[2] = Real(M_PI);
+ rotamers.push_back(ConstructRRM());
+ chi_angles_[2] = Real(0.0);
+ rotamers.push_back(ConstructRRM());
+ break;
+ }
+ default:{
+ rotamers.push_back(ConstructRRM());
+ }
+ }
+ }
+
+ if(summed_prob >= probability_cutoff && !rotamers.empty()) break;
+ }
+
+ RRMRotamerGroupPtr group = boost::make_shared<RRMRotamerGroup>(rotamers,
+ residue_idx_);
+ this->AssignInternalEnergies(group, id_, residue_idx_, phi_, psi_, n_ter_, c_ter_);
+ return group;
+}
+
+
+FRMRotamerGroupPtr RotamerConstructor::ConstructFRMGroup(
+ std::pair<RotamerLibEntry*,uint> lib_entries,
+ Real probability_cutoff) {
+
+ core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "RotamerConstructor::ConstructFRMGroup", 2);
+
+ std::vector<FRMRotamerPtr> rotamers;
+ Real summed_prob = 0.0;
+
+ // in case of his, we have to move the backbone positions in the buffer
+ // to the locations defining his in the different protonation states
+ if(id_ == HIS && mode_ != HEAVY_ATOM_MODE){
+ MVBBPosBuffer(HIS, HSD);
+ MVBBPosBuffer(HIS, HSE);
+ }
+
+ // in case of alanine and glycine, the rotamer libraries won't have any
+ // entries. For consistency we nevertheless construct rotamers.
+ // We simply add a fake RotamerLibEntry in this case that has
+ // no sidechain dihedrals set. In case of Alanine we might still have
+ // some atoms in (depending on cb_in_sidechain flag)
+ std::vector<RotamerLibEntry> fake_rotamers(1);
+ if(lib_entries.second == 0 && (id_ == ALA || id_ == GLY)) {
+ // we have to make sure, that the according probability really is one!
+ fake_rotamers[0].probability = 1.0;
+ lib_entries = std::make_pair(&fake_rotamers[0], 1);
+ }
+ else if(lib_entries.second == 0) {
+ throw promod3::Error("Did not find any rotamers in Rotamer Library!");
+ }
+
+ for(uint i = 0; i < lib_entries.second; ++i){
+ probability_ = lib_entries.first[i].probability;
+ summed_prob += probability_;
+ chi_angles_[0] = lib_entries.first[i].chi1;
+ chi_angles_[1] = lib_entries.first[i].chi2;
+ chi_angles_[2] = lib_entries.first[i].chi3;
+ chi_angles_[3] = lib_entries.first[i].chi4;
+ chi_dev_[0] = lib_entries.first[i].sig1;
+ chi_dev_[1] = lib_entries.first[i].sig2;
+ chi_dev_[2] = lib_entries.first[i].sig3;
+ chi_dev_[3] = lib_entries.first[i].sig4;
+ if(mode_ == HEAVY_ATOM_MODE) {
+ rotamers.push_back(ConstructFRM());
+ } else {
+ switch(id_){
+ case HIS:{
+ id_ = HSE;
+ rotamers.push_back(ConstructFRM());
+ id_ = HSD;
+ rotamers.push_back(ConstructFRM());
+ id_ = HIS;
+ break;
+ }
+ case SER:{
+ chi_dev_[1] = Real(0.17453);
+ chi_angles_[1] = Real(M_PI);
+ rotamers.push_back(ConstructFRM());
+ chi_angles_[1] = Real(M_PI) / Real(3.0);
+ rotamers.push_back(ConstructFRM());
+ chi_angles_[1] = -Real(M_PI) / Real(3.0);
+ rotamers.push_back(ConstructFRM());
+ break;
+ }
+ case THR:{
+ chi_dev_[1] = Real(0.17453);
+ chi_angles_[1] = Real(M_PI);
+ rotamers.push_back(ConstructFRM());
+ chi_angles_[1] = Real(M_PI) / Real(3.0);
+ rotamers.push_back(ConstructFRM());
+ chi_angles_[1] = -Real(M_PI) / Real(3.0);
+ rotamers.push_back(ConstructFRM());
+ break;
+ }
+ case TYR:{
+ chi_dev_[2] = Real(0.17453);
+ chi_angles_[2] = Real(M_PI);
+ rotamers.push_back(ConstructFRM());
+ chi_angles_[2] = Real(0.0);
+ rotamers.push_back(ConstructFRM());
+ break;
+ }
+ default: rotamers.push_back(ConstructFRM());
+ }
+ }
+
+ if(summed_prob >= probability_cutoff && !rotamers.empty()) break;
+ }
+
+ FRMRotamerGroupPtr group = boost::make_shared<FRMRotamerGroup>(rotamers,
+ residue_idx_);
+ this->AssignInternalEnergies(group, id_, residue_idx_, phi_, psi_, n_ter_, c_ter_);
+
+ return group;
+}
+
+
+RRMRotamerPtr RotamerConstructor::ConstructRRM() {
+
+ core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "RotamerConstructor::ConstructRRM", 2);
+
+ const RotamerInfo& info = rotamer_lookup_.GetSidechainInfo(id_);
+
+ //set the positions
+ promod3::loop::ConstructSidechainAtoms(*pos_buffer_, id_, chi_angles_[0],
+ chi_angles_[1], chi_angles_[2],
+ chi_angles_[3]);
+
+ if(info.has_hydrogens){
+
+ promod3::loop::ConstructHydrogens(*pos_buffer_, id_, *hydrogen_buffer_,
+ mode_ == POLAR_HYDROGEN_MODE,
+ promod3::loop::PROT_STATE_HISH);
+
+ // If there are any custom rules, we apply them now and overrule the
+ // default hydrogen construction
+ if(!info.custom_hydrogens.empty()){
+ for(uint i = 0; i < info.custom_hydrogens.size(); ++i){
+ const CustomHydrogenInfo& h_info = info.custom_hydrogens[i];
+ geom::Vec3 anchor_one, anchor_two, anchor_three, new_h_pos;
+ anchor_one = pos_buffer_->GetPos(id_, h_info.anchor_idx_one);
+ anchor_two = pos_buffer_->GetPos(id_, h_info.anchor_idx_two);
+ anchor_three = pos_buffer_->GetPos(id_, h_info.anchor_idx_three);
+ promod3::core::ConstructAtomPos(anchor_one, anchor_two, anchor_three,
+ h_info.bond_length, h_info.angle,
+ chi_angles_[h_info.chi_idx], new_h_pos);
+ hydrogen_buffer_->SetPos(h_info.atom_idx, new_h_pos);
+ }
+ }
+ }
+
+ int num_particles = info.particles.size();
+ std::vector<Particle> particles(num_particles);
+ for(int i = 0; i < num_particles; ++i) {
+ const ParticleInfo& pi = info.particles[i];
+ particles[i].SetName(pi.name);
+ this->ParametrizeParticle(pi.atom_idx, pi.is_hydrogen, particles[i]);
+ }
+
+ RRMRotamerPtr rot = boost::make_shared<RRMRotamer>(particles,
+ probability_,
+ info.internal_e_prefactor);
+
+ return rot;
+}
+
+
+FRMRotamerPtr RotamerConstructor::ConstructFRM() {
+
+ core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "RotamerConstructor::ConstructFRM", 2);
+
+ const RotamerInfo& info = rotamer_lookup_.GetSidechainInfo(id_);
+
+ //set the positions
+ promod3::loop::ConstructSidechainAtoms(*pos_buffer_, id_, chi_angles_[0],
+ chi_angles_[1], chi_angles_[2],
+ chi_angles_[3]);
+ if(info.has_hydrogens){
+ promod3::loop::ConstructHydrogens(*pos_buffer_, id_, *hydrogen_buffer_,
+ mode_ == POLAR_HYDROGEN_MODE,
+ promod3::loop::PROT_STATE_HISH);
+ // If there are any custom rules, we apply them now an overrule the
+ // default hydrogen construction
+ if(!info.custom_hydrogens.empty()){
+ for(uint i = 0; i < info.custom_hydrogens.size(); ++i){
+ const CustomHydrogenInfo& h_info = info.custom_hydrogens[i];
+ geom::Vec3 anchor_one, anchor_two, anchor_three, new_h_pos;
+ anchor_one = pos_buffer_->GetPos(id_, h_info.anchor_idx_one);
+ anchor_two = pos_buffer_->GetPos(id_, h_info.anchor_idx_two);
+ anchor_three = pos_buffer_->GetPos(id_, h_info.anchor_idx_three);
+ promod3::core::ConstructAtomPos(anchor_one, anchor_two, anchor_three,
+ h_info.bond_length, h_info.angle,
+ chi_angles_[h_info.chi_idx], new_h_pos);
+ hydrogen_buffer_->SetPos(h_info.atom_idx, new_h_pos);
+ }
+ }
+ }
+
+ int num_rrm_particles = rotamer_lookup_.GetNumSidechainParticles(id_);
+ int num_particles = rotamer_lookup_.GetNumFRMSidechainParticles(id_);
+ std::vector<Particle> particles(num_particles);
+
+ for(int i = 0; i < num_rrm_particles; ++i) {
+ const ParticleInfo& pi = info.particles[i];
+ particles[i].SetName(pi.name);
+ this->ParametrizeParticle(pi.atom_idx, pi.is_hydrogen, particles[i]);
+ }
+
+ // Keep track of the subrotamers
+ std::vector<std::vector<int> > subrotamer_definitions;
+ std::vector<int> actual_definition;
+ actual_definition.resize(num_rrm_particles);
+ // Directly add the first particles as first subrotamer
+ for(int i = 0; i < num_rrm_particles; ++i) actual_definition[i] = i;
+ subrotamer_definitions.push_back(actual_definition);
+
+ const std::vector<FRMRule>& frm_rules = rotamer_lookup_.GetFRMRules(id_);
+ geom::Vec3 rot_axis, rot_anchor;
+ geom::Vec3 orig_pos, rot_pos;
+ geom::Mat4 transform;
+ int base_idx = num_rrm_particles;
+
+ for(uint frm_rule_idx = 0; frm_rule_idx < frm_rules.size(); ++frm_rule_idx){
+ const FRMRule& frm_rule = frm_rules[frm_rule_idx];
+ int num_fix_particles = frm_rule.fix_particles.size();
+ int num_rotating_particles = frm_rule.rotating_particles.size();
+
+ // Update the subrotamer definition... all particles that are fixed are
+ // taken from the first subrotamer.
+ for(int i = 0; i < num_fix_particles; ++i) {
+ actual_definition[i] = frm_rule.fix_particles[i];
+ }
+
+ // The data required for the rotation around the specified axis
+ rot_anchor = pos_buffer_->GetPos(id_, frm_rule.anchor_idx_two);
+ rot_axis = rot_anchor - pos_buffer_->GetPos(id_, frm_rule.anchor_idx_one);
+
+ // Every rotation results in a new subrotamer
+ for(uint prefac_idx = 0; prefac_idx < frm_rule.prefactors.size();
+ ++prefac_idx){
+
+ // Get the rotation matrix
+ Real rot_angle = frm_rule.prefactors[prefac_idx] * chi_dev_[frm_rule_idx];
+ transform = promod3::core::RotationAroundLine(rot_axis, rot_anchor,
+ rot_angle);
+
+ for(int i = 0; i < num_rotating_particles; ++i){
+ int orig_particle_idx = frm_rule.rotating_particles[i];
+ int new_particle_idx = base_idx + i;
+
+ // replace the old with the new index...
+ actual_definition[orig_particle_idx] = new_particle_idx;
+
+ // construct the rotated particle
+ particles[new_particle_idx] = particles[orig_particle_idx];
+ particles[new_particle_idx].ApplyTransform(transform);
+ }
+
+ subrotamer_definitions.push_back(actual_definition);
+
+ // start of next subrotamer
+ base_idx += num_rotating_particles;
+ }
+ }
+
+ FRMRotamerPtr r = boost::make_shared<FRMRotamer>(particles,
+ info.frm_t, probability_,
+ info.internal_e_prefactor);
+
+
+
+ for(uint i = 0; i < subrotamer_definitions.size(); ++i) {
+ r->AddSubrotamerDefinition(subrotamer_definitions[i]);
+ }
+
+ return r;
+}
+
+
+FrameResiduePtr RotamerConstructor::ConstructBackboneFrameResidue() {
+
+ const RotamerInfo& info = rotamer_lookup_.GetBackboneInfo(id_);
+
+ // set hydrogens (also enter if its an n_ter because proline would have no
+ // hydrogen)
+ if(info.has_hydrogens || n_ter_){
+ if(mode_ == FULL_ATOMIC_MODE) {
+ promod3::loop::ConstructHydrogens(*pos_buffer_, id_, *hydrogen_buffer_,
+ mode_ == POLAR_HYDROGEN_MODE,
+ promod3::loop::PROT_STATE_HISH);
+ }
+ if(n_ter_) {
+ promod3::loop::ConstructHydrogenNTerminal(*pos_buffer_, id_,
+ *hydrogen_buffer_);
+ } else {
+ promod3::loop::ConstructHydrogenN(*pos_buffer_, id_, phi_,
+ *hydrogen_buffer_);
+ }
+ }
+ if(c_ter_) {
+ promod3::core::ConstructCTerminalOxygens(
+ pos_buffer_->GetPos(id_, promod3::loop::BB_C_INDEX),
+ pos_buffer_->GetPos(id_, promod3::loop::BB_CA_INDEX),
+ pos_buffer_->GetPos(id_, promod3::loop::BB_N_INDEX),
+ terminal_o_pos_, terminal_oxt_pos_);
+ }
+ std::vector<Particle> particles;
+ if(n_ter_ || c_ter_) {
+ RotamerInfo terminal_info =
+ rotamer_lookup_.GetTerminalBackboneInfo(id_, n_ter_, c_ter_);
+ int num_particles = terminal_info.particles.size();
+ particles.resize(num_particles);
+ for(int i = 0; i < num_particles; ++i) {
+ ParticleInfo& pi = terminal_info.particles[i];
+ particles[i].SetName(pi.name);
+ this->ParametrizeParticle(pi.atom_idx, pi.is_hydrogen, particles[i]);
+ }
+ } else {
+ int num_particles = info.particles.size();
+ particles.resize(num_particles);
+ for(int i = 0; i < num_particles; ++i) {
+ const ParticleInfo& pi = info.particles[i];
+ particles[i].SetName(pi.name);
+ this->ParametrizeParticle(pi.atom_idx, pi.is_hydrogen, particles[i]);
+ }
+ }
+
+ FrameResiduePtr p = boost::make_shared<FrameResidue>(particles, residue_idx_);
+ return p;
+}
+
+
+void RotamerConstructor::SetPosBuffer(const ost::mol::ResidueHandle& res) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "SCWRL4RotamerConstructor::SetPosBuffer_residue", 2);
+ "RotamerConstructor::SetPosBuffer_residue", 2);
ost::mol::AtomHandle n = res.FindAtom("N");
ost::mol::AtomHandle ca = res.FindAtom("CA");
@@ -259,25 +977,26 @@ void RotamerConstructor::SetPosBuffer(const ost::mol::ResidueHandle& res,
"rotamer!");
}
- pos_buffer_->SetPos(id, promod3::loop::BB_N_INDEX, n.GetPos());
- pos_buffer_->SetPos(id, promod3::loop::BB_CA_INDEX, ca.GetPos());
- pos_buffer_->SetPos(id, promod3::loop::BB_C_INDEX, c.GetPos());
- pos_buffer_->SetPos(id, promod3::loop::BB_O_INDEX, o.GetPos());
+ pos_buffer_->SetPos(id_, promod3::loop::BB_N_INDEX, n.GetPos());
+ pos_buffer_->SetPos(id_, promod3::loop::BB_CA_INDEX, ca.GetPos());
+ pos_buffer_->SetPos(id_, promod3::loop::BB_C_INDEX, c.GetPos());
+ pos_buffer_->SetPos(id_, promod3::loop::BB_O_INDEX, o.GetPos());
- if(id != GLY) {
+ if(id_ != GLY) {
if(!cb.IsValid()) {
throw promod3::Error("All backbone atoms must be valid to construct "
"rotamer!");
}
- pos_buffer_->SetPos(id, promod3::loop::BB_CB_INDEX, cb.GetPos());
+ pos_buffer_->SetPos(id_, promod3::loop::BB_CB_INDEX, cb.GetPos());
}
}
+
void RotamerConstructor::SetPosBuffer(const promod3::loop::AllAtomPositions& all_atom_pos,
- uint all_atom_idx, RotamerID id) {
+ uint all_atom_idx) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "SCWRL4RotamerConstructor::SetPosBuffer_all_atom_pos", 2);
+ "RotamerConstructor::SetPosBuffer_all_atom_pos", 2);
if(!(all_atom_pos.IsSet(all_atom_idx, promod3::loop::BB_N_INDEX) &&
@@ -288,29 +1007,45 @@ void RotamerConstructor::SetPosBuffer(const promod3::loop::AllAtomPositions& all
"rotamer!");
}
- pos_buffer_->SetPos(id, promod3::loop::BB_N_INDEX,
+ pos_buffer_->SetPos(id_, promod3::loop::BB_N_INDEX,
all_atom_pos.GetPos(all_atom_idx,
promod3::loop::BB_N_INDEX));
- pos_buffer_->SetPos(id, promod3::loop::BB_CA_INDEX,
+ pos_buffer_->SetPos(id_, promod3::loop::BB_CA_INDEX,
all_atom_pos.GetPos(all_atom_idx,
promod3::loop::BB_CA_INDEX));
- pos_buffer_->SetPos(id, promod3::loop::BB_C_INDEX,
+ pos_buffer_->SetPos(id_, promod3::loop::BB_C_INDEX,
all_atom_pos.GetPos(all_atom_idx,
promod3::loop::BB_C_INDEX));
- pos_buffer_->SetPos(id, promod3::loop::BB_O_INDEX,
+ pos_buffer_->SetPos(id_, promod3::loop::BB_O_INDEX,
all_atom_pos.GetPos(all_atom_idx,
promod3::loop::BB_O_INDEX));
- if(id != GLY) {
+ if(id_ != GLY) {
if(!all_atom_pos.IsSet(all_atom_idx, promod3::loop::BB_CB_INDEX)) {
throw promod3::Error("All backbone atoms must be valid to construct "
"rotamer!");
}
- pos_buffer_->SetPos(id, promod3::loop::BB_CB_INDEX,
+ pos_buffer_->SetPos(id_, promod3::loop::BB_CB_INDEX,
all_atom_pos.GetPos(all_atom_idx,
promod3::loop::BB_CB_INDEX));
-
}
}
+
+void RotamerConstructor::MVBBPosBuffer(RotamerID from, RotamerID to) {
+ pos_buffer_->SetPos(to, promod3::loop::BB_N_INDEX,
+ pos_buffer_->GetPos(from, promod3::loop::BB_N_INDEX));
+ pos_buffer_->SetPos(to, promod3::loop::BB_CA_INDEX,
+ pos_buffer_->GetPos(from, promod3::loop::BB_CA_INDEX));
+ pos_buffer_->SetPos(to, promod3::loop::BB_C_INDEX,
+ pos_buffer_->GetPos(from, promod3::loop::BB_C_INDEX));
+ pos_buffer_->SetPos(to, promod3::loop::BB_O_INDEX,
+ pos_buffer_->GetPos(from, promod3::loop::BB_O_INDEX));
+ // Even though we officially count CB as a sidechain atom, we still move it
+ // since its completely independent of any sidechain dihedral angle and
+ // cannot be constructed anyway
+ pos_buffer_->SetPos(to, promod3::loop::BB_CB_INDEX,
+ pos_buffer_->GetPos(from, promod3::loop::BB_CB_INDEX));
+}
+
}} // ns
diff --git a/sidechain/src/rotamer_constructor.hh b/sidechain/src/rotamer_constructor.hh
index 4a496ef0e13e68be29730a3be01c04022e18c2ec..759d49d41cbd7cf04b424a2dba72fc02cc0af396 100644
--- a/sidechain/src/rotamer_constructor.hh
+++ b/sidechain/src/rotamer_constructor.hh
@@ -27,18 +27,22 @@
#include <promod3/sidechain/frame.hh>
#include <promod3/sidechain/rotamer_lib.hh>
#include <promod3/sidechain/bb_dep_rotamer_lib.hh>
+#include <promod3/sidechain/rotamer_lookup.hh>
namespace promod3 { namespace sidechain {
+
class RotamerConstructor;
typedef boost::shared_ptr<RotamerConstructor> RotamerConstructorPtr;
+
class RotamerConstructor {
public:
- RotamerConstructor();
+ RotamerConstructor(bool cb_in_sidechain, RotamerLookupMode mode,
+ const RotamerLookupParam& param = RotamerLookupParam());
virtual ~RotamerConstructor() { }
@@ -46,23 +50,39 @@ public:
RRMRotamerGroupPtr ConstructRRMRotamerGroup(
const ost::mol::ResidueHandle& res, RotamerID id,
uint residue_index, RotamerLibPtr rot_lib,
+ Real phi = -1.0472,
+ Real psi = -0.7854,
+ bool n_ter = false,
+ bool c_ter = false,
Real probability_cutoff = 0.98);
RRMRotamerGroupPtr ConstructRRMRotamerGroup(
const promod3::loop::AllAtomPositions& all_atom,
uint aa_res_idx, RotamerID id, uint residue_index,
RotamerLibPtr rot_lib,
+ Real phi = -1.0472,
+ Real psi = -0.7854,
+ bool n_ter = false,
+ bool c_ter = false,
Real probability_cutoff = 0.98);
FRMRotamerGroupPtr ConstructFRMRotamerGroup(
const ost::mol::ResidueHandle& res, RotamerID id,
- uint residue_index, RotamerLibPtr rot_lib,
+ uint residue_index, RotamerLibPtr rot_lib,
+ Real phi = -1.0472,
+ Real psi = -0.7854,
+ bool n_ter = false,
+ bool c_ter = false,
Real probability_cutoff = 0.98);
FRMRotamerGroupPtr ConstructFRMRotamerGroup(
const promod3::loop::AllAtomPositions& all_atom,
uint aa_res_idx, RotamerID id, uint residue_index,
- RotamerLibPtr rot_lib,
+ RotamerLibPtr rot_lib,
+ Real phi = -1.0472,
+ Real psi = -0.7854,
+ bool n_ter = false,
+ bool c_ter = false,
Real probability_cutoff = 0.98);
// Construct rotamer groups from backbone dependent library
@@ -71,6 +91,8 @@ public:
uint residue_index, BBDepRotamerLibPtr rot_lib,
Real phi = -1.0472,
Real psi = -0.7854,
+ bool n_ter = false,
+ bool c_ter = false,
Real probability_cutoff = 0.98);
RRMRotamerGroupPtr ConstructRRMRotamerGroup(
@@ -79,6 +101,8 @@ public:
BBDepRotamerLibPtr rot_lib,
Real phi = -1.0472,
Real psi = -0.7854,
+ bool n_ter = false,
+ bool c_ter = false,
Real probability_cutoff = 0.98);
FRMRotamerGroupPtr ConstructFRMRotamerGroup(
@@ -86,6 +110,8 @@ public:
uint residue_index, BBDepRotamerLibPtr rot_lib,
Real phi = -1.0472,
Real psi = -0.7854,
+ bool n_ter = false,
+ bool c_ter = false,
Real probability_cutoff = 0.98);
FRMRotamerGroupPtr ConstructFRMRotamerGroup(
@@ -94,6 +120,8 @@ public:
BBDepRotamerLibPtr rot_lib,
Real phi = -1.0472,
Real psi = -0.7854,
+ bool n_ter = false,
+ bool c_ter = false,
Real probability_cutoff = 0.98);
// Construct rotamer groups directly from rotamerlib entries
@@ -101,75 +129,148 @@ public:
const ost::mol::ResidueHandle& res, RotamerID id,
uint residue_index,
std::vector<RotamerLibEntry>& lib_entries,
+ Real phi = -1.0472,
+ Real psi = -0.7854,
+ bool n_ter = false,
+ bool c_ter = false,
Real probability_cutoff = 0.98);
RRMRotamerGroupPtr ConstructRRMRotamerGroup(
const promod3::loop::AllAtomPositions& all_atom,
uint aa_res_idx, RotamerID id, uint residue_index,
std::vector<RotamerLibEntry>& lib_entries,
+ Real phi = -1.0472,
+ Real psi = -0.7854,
+ bool n_ter = false,
+ bool c_ter = false,
Real probability_cutoff = 0.98);
FRMRotamerGroupPtr ConstructFRMRotamerGroup(
const ost::mol::ResidueHandle& res, RotamerID id,
uint residue_index,
std::vector<RotamerLibEntry>& lib_entries,
+ Real phi = -1.0472,
+ Real psi = -0.7854,
+ bool n_ter = false,
+ bool c_ter = false,
Real probability_cutoff = 0.98);
FRMRotamerGroupPtr ConstructFRMRotamerGroup(
const promod3::loop::AllAtomPositions& all_atom,
uint aa_res_idx, RotamerID id, uint residue_index,
std::vector<RotamerLibEntry>& lib_entries,
+ Real phi = -1.0472,
+ Real psi = -0.7854,
+ bool n_ter = false,
+ bool c_ter = false,
Real probability_cutoff = 0.98);
// Construct frame residues
- virtual FrameResiduePtr ConstructBackboneFrameResidue(
+ FrameResiduePtr ConstructBackboneFrameResidue(
const ost::mol::ResidueHandle& res, RotamerID id,
- uint residue_index, Real phi, bool n_ter = false,
- bool c_ter = false) = 0;
+ uint residue_index,
+ Real phi = -1.0472,
+ Real psi = -0.7854,
+ bool n_ter = false,
+ bool c_ter = false);
- virtual FrameResiduePtr ConstructBackboneFrameResidue(
+ FrameResiduePtr ConstructBackboneFrameResidue(
const promod3::loop::AllAtomPositions& all_atom,
uint aa_res_idx, RotamerID id, uint residue_index,
- Real phi = -1.0472, bool n_ter = false,
- bool c_ter = false) = 0;
+ Real phi = -1.0472,
+ Real psi = -0.7854,
+ bool n_ter = false,
+ bool c_ter = false);
- virtual FrameResiduePtr ConstructSidechainFrameResidue(
+ FrameResiduePtr ConstructSidechainFrameResidue(
const ost::mol::ResidueHandle& res, RotamerID id,
- uint residue_index) = 0;
+ uint residue_index,
+ Real phi = -1.0472,
+ Real psi = -0.7854,
+ bool n_ter = false,
+ bool c_ter = false);
- virtual FrameResiduePtr ConstructSidechainFrameResidue(
+ FrameResiduePtr ConstructSidechainFrameResidue(
const promod3::loop::AllAtomPositions& all_atom,
- uint aa_res_idx, RotamerID id, uint residue_index) = 0;
+ uint aa_res_idx, RotamerID id, uint residue_index,
+ Real phi = -1.0472,
+ Real psi = -0.7854,
+ bool n_ter = false,
+ bool c_ter = false);
// Assign internal energies to rotamer groups
- virtual void AssignInternalEnergies(RRMRotamerGroupPtr group);
+ // This implementation just sets the internal energy of every rotamer to 0.0
+ // Implement this function in the child class
+ virtual void AssignInternalEnergies(RRMRotamerGroupPtr group,
+ RotamerID id,
+ uint residue_index,
+ Real phi = -1.0472,
+ Real psi = -0.7854,
+ bool n_ter = false,
+ bool c_ter = false);
- virtual void AssignInternalEnergies(FRMRotamerGroupPtr group);
+ virtual void AssignInternalEnergies(FRMRotamerGroupPtr group,
+ RotamerID id,
+ uint residue_index,
+ Real phi = -1.0472,
+ Real psi = -0.7854,
+ bool n_ter = false,
+ bool c_ter = false);
protected:
- // Construct the rotamer groups after all backbone position information has
- // been set into the internal positin buffer objects
- virtual RRMRotamerGroupPtr ConstructRRMGroup(
- RotamerID id, uint residue_index,
- std::pair<RotamerLibEntry*,uint> lib_entries,
- Real probability_cutoff) = 0;
-
- virtual FRMRotamerGroupPtr ConstructFRMGroup(
- RotamerID id, uint residue_index,
- std::pair<RotamerLibEntry*,uint> lib_entries,
- Real probability_cutoff) = 0;
+ // Function that must be implemented by child class
+ // there are two special cases that have to be treatet separately:
+ // the terminal oxygens.
+ // atom_idx for terminal O is set to -1
+ // atom_idx for terminal OXT is set to -2
+ virtual void ParametrizeParticle(int atom_idx, bool is_hydrogen,
+ Particle& p) = 0;
+ // information that is available to the child class in order to parametrize
+ // the given particle
promod3::loop::AllAtomPositionsPtr pos_buffer_;
+ promod3::loop::HydrogenStoragePtr hydrogen_buffer_;
+ geom::Vec3 terminal_o_pos_;
+ geom::Vec3 terminal_oxt_pos_;
+ RotamerID id_;
+ uint residue_idx_;
+ Real phi_;
+ Real psi_;
+ bool n_ter_;
+ bool c_ter_;
private:
+ // Construct the rotamer groups after all backbone position information has
+ // been set into the internal position buffer objects
+ virtual RRMRotamerGroupPtr ConstructRRMGroup(
+ std::pair<RotamerLibEntry*,uint> lib_entries,
+ Real probability_cutoff);
+
+ virtual FRMRotamerGroupPtr ConstructFRMGroup(
+ std::pair<RotamerLibEntry*,uint> lib_entries,
+ Real probability_cutoff);
+
+ // assumes positions / probabilities, chi angles and chi deviations
+ // to be set in buffer
+ RRMRotamerPtr ConstructRRM();
+ FRMRotamerPtr ConstructFRM();
+ FrameResiduePtr ConstructBackboneFrameResidue();
+
// helpers
- void SetPosBuffer(const ost::mol::ResidueHandle& res,
- RotamerID id);
+ void SetPosBuffer(const ost::mol::ResidueHandle& res);
void SetPosBuffer(const promod3::loop::AllAtomPositions&,
- uint aa_res_index, RotamerID id);
+ uint aa_res_index);
+
+ void MVBBPosBuffer(RotamerID from, RotamerID to);
+
+ RotamerLookup rotamer_lookup_;
+ RotamerLookupMode mode_;
+ Real chi_angles_[4];
+ Real chi_dev_[4];
+ Real probability_;
};
}} // ns
diff --git a/sidechain/src/rotamer_lookup.cc b/sidechain/src/rotamer_lookup.cc
new file mode 100644
index 0000000000000000000000000000000000000000..6ca63be5dfd0a20ee08bfb680355243911f15140
--- /dev/null
+++ b/sidechain/src/rotamer_lookup.cc
@@ -0,0 +1,2140 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+#include <promod3/sidechain/rotamer_lookup.hh>
+#include <promod3/core/runtime_profiling.hh>
+
+namespace promod3 { namespace sidechain{
+
+RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
+ const RotamerLookupParam& param): mode_(mode) {
+
+ core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "RotamerLookup::RotamerLookup", 2);
+
+ // ARG
+ sidechain_infos_[ARG].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
+ mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[ARG].internal_e_prefactor =
+ param.internal_e_prefactor[ost::conop::ARG];
+ sidechain_infos_[ARG].frm_t = param.frm_t[ost::conop::ARG];
+
+ AddInfo(ARG, "CG", promod3::loop::ARG_CG_INDEX, false);
+ AddInfo(ARG, "CD", promod3::loop::ARG_CD_INDEX, false);
+ AddInfo(ARG, "NE", promod3::loop::ARG_NE_INDEX, false);
+ AddInfo(ARG, "CZ", promod3::loop::ARG_CZ_INDEX, false);
+ AddInfo(ARG, "NH1", promod3::loop::ARG_NH1_INDEX, false);
+ AddInfo(ARG, "NH2", promod3::loop::ARG_NH2_INDEX, false);
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddInfo(ARG, "HE", promod3::loop::ARG_HE_INDEX, true);
+ AddInfo(ARG, "HH11", promod3::loop::ARG_HH11_INDEX, true);
+ AddInfo(ARG, "HH12", promod3::loop::ARG_HH12_INDEX, true);
+ AddInfo(ARG, "HH21", promod3::loop::ARG_HH21_INDEX, true);
+ AddInfo(ARG, "HH22", promod3::loop::ARG_HH22_INDEX, true);
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddInfo(ARG, "HB2", promod3::loop::ARG_HB2_INDEX, true);
+ AddInfo(ARG, "HB3", promod3::loop::ARG_HB3_INDEX, true);
+ AddInfo(ARG, "HG2", promod3::loop::ARG_HG2_INDEX, true);
+ AddInfo(ARG, "HG3", promod3::loop::ARG_HG3_INDEX, true);
+ AddInfo(ARG, "HD2", promod3::loop::ARG_HD2_INDEX, true);
+ AddInfo(ARG, "HD3", promod3::loop::ARG_HB3_INDEX, true);
+ }
+
+ if(cb_in_sidechain) {
+ AddInfo(ARG, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddFRMRule(ARG, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX,
+ param.ARG_CA_CB_prefactors);
+ AddFRMRotatingParticle(ARG, 0, 0); // CG
+ AddFRMRotatingParticle(ARG, 0, 1); // CD
+ AddFRMRotatingParticle(ARG, 0, 2); // NE
+ AddFRMRotatingParticle(ARG, 0, 3); // CZ
+ AddFRMRotatingParticle(ARG, 0, 4); // NH1
+ AddFRMRotatingParticle(ARG, 0, 5); // NH2
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(ARG, 0, 6); // HE
+ AddFRMRotatingParticle(ARG, 0, 7); // HH11
+ AddFRMRotatingParticle(ARG, 0, 8); // HH12
+ AddFRMRotatingParticle(ARG, 0, 9); // HH21
+ AddFRMRotatingParticle(ARG, 0, 10); // HH22
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(ARG, 0, 11); // HB2
+ AddFRMRotatingParticle(ARG, 0, 12); // HB3
+ AddFRMRotatingParticle(ARG, 0, 13); // HG2
+ AddFRMRotatingParticle(ARG, 0, 14); // HG3
+ AddFRMRotatingParticle(ARG, 0, 15); // HD2
+ AddFRMRotatingParticle(ARG, 0, 16); // HD3
+ }
+
+ AddFRMRule(ARG, promod3::loop::BB_CB_INDEX, promod3::loop::ARG_CG_INDEX,
+ param.ARG_CB_CG_prefactors);
+ AddFRMFixParticle(ARG, 1, 0); // CG
+ AddFRMRotatingParticle(ARG, 1, 1); // CD
+ AddFRMRotatingParticle(ARG, 1, 2); // NE
+ AddFRMRotatingParticle(ARG, 1, 3); // CZ
+ AddFRMRotatingParticle(ARG, 1, 4); // NH1
+ AddFRMRotatingParticle(ARG, 1, 5); // NH2
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(ARG, 1, 6); // HE
+ AddFRMRotatingParticle(ARG, 1, 7); // HH11
+ AddFRMRotatingParticle(ARG, 1, 8); // HH12
+ AddFRMRotatingParticle(ARG, 1, 9); // HH21
+ AddFRMRotatingParticle(ARG, 1, 10); // HH22
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMFixParticle(ARG, 1, 11); // HB2
+ AddFRMFixParticle(ARG, 1, 12); // HB3
+ AddFRMRotatingParticle(ARG, 1, 13); // HG2
+ AddFRMRotatingParticle(ARG, 1, 14); // HG3
+ AddFRMRotatingParticle(ARG, 1, 15); // HD2
+ AddFRMRotatingParticle(ARG, 1, 16); // HD3
+ }
+
+ AddFRMRule(ARG, promod3::loop::ARG_CG_INDEX, promod3::loop::ARG_CD_INDEX,
+ param.ARG_CG_CD_prefactors);
+ AddFRMFixParticle(ARG, 2, 0); // CG
+ AddFRMFixParticle(ARG, 2, 1); // CD
+ AddFRMRotatingParticle(ARG, 2, 2); // NE
+ AddFRMRotatingParticle(ARG, 2, 3); // CZ
+ AddFRMRotatingParticle(ARG, 2, 4); // NH1
+ AddFRMRotatingParticle(ARG, 2, 5); // NH2
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(ARG, 2, 6); // HE
+ AddFRMRotatingParticle(ARG, 2, 7); // HH11
+ AddFRMRotatingParticle(ARG, 2, 8); // HH12
+ AddFRMRotatingParticle(ARG, 2, 9); // HH21
+ AddFRMRotatingParticle(ARG, 2, 10); // HH22
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMFixParticle(ARG, 2, 11); // HB2
+ AddFRMFixParticle(ARG, 2, 12); // HB3
+ AddFRMFixParticle(ARG, 2, 13); // HG2
+ AddFRMFixParticle(ARG, 2, 14); // HG3
+ AddFRMRotatingParticle(ARG, 2, 15); // HD2
+ AddFRMRotatingParticle(ARG, 2, 16); // HD3
+ }
+
+
+ AddFRMRule(ARG, promod3::loop::ARG_CD_INDEX, promod3::loop::ARG_NE_INDEX,
+ param.ARG_CD_NE_prefactors);
+ AddFRMFixParticle(ARG, 3, 0); // CG
+ AddFRMFixParticle(ARG, 3, 1); // CD
+ AddFRMFixParticle(ARG, 3, 2); // NE
+ AddFRMRotatingParticle(ARG, 3, 3); // CZ
+ AddFRMRotatingParticle(ARG, 3, 4); // NH1
+ AddFRMRotatingParticle(ARG, 3, 5); // NH2
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(ARG, 3, 6); // HE
+ AddFRMRotatingParticle(ARG, 3, 7); // HH11
+ AddFRMRotatingParticle(ARG, 3, 8); // HH12
+ AddFRMRotatingParticle(ARG, 3, 9); // HH21
+ AddFRMRotatingParticle(ARG, 3, 10); // HH22
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMFixParticle(ARG, 3, 11); // HB2
+ AddFRMFixParticle(ARG, 3, 12); // HB3
+ AddFRMFixParticle(ARG, 3, 13); // HG2
+ AddFRMFixParticle(ARG, 3, 14); // HG3
+ AddFRMFixParticle(ARG, 3, 15); // HD2
+ AddFRMFixParticle(ARG, 3, 16); // HD3
+ }
+
+
+ if(cb_in_sidechain) {
+ int cb_idx = 6;
+ if(mode == POLAR_HYDROGEN_MODE) {
+ cb_idx = 11;
+ }
+ if(mode == FULL_ATOMIC_MODE) {
+ cb_idx = 17;
+ }
+ AddFRMFixParticle(ARG, 0, cb_idx);
+ AddFRMFixParticle(ARG, 1, cb_idx);
+ AddFRMFixParticle(ARG, 2, cb_idx);
+ AddFRMFixParticle(ARG, 3, cb_idx);
+ }
+
+ backbone_infos_[ARG].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
+ mode == FULL_ATOMIC_MODE);
+ AddBBInfo(ARG, "N", promod3::loop::BB_N_INDEX, false);
+ AddBBInfo(ARG, "CA", promod3::loop::BB_CA_INDEX, false);
+ AddBBInfo(ARG, "C", promod3::loop::BB_C_INDEX, false);
+ AddBBInfo(ARG, "O", promod3::loop::BB_O_INDEX, false);
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(ARG, "H", promod3::loop::ARG_H_INDEX, true);
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(ARG, "HA", promod3::loop::ARG_HA_INDEX, true);
+ }
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(ARG, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+
+ // ASN
+ sidechain_infos_[ASN].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
+ mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[ASN].internal_e_prefactor =
+ param.internal_e_prefactor[ost::conop::ASN];
+ sidechain_infos_[ASN].frm_t = param.frm_t[ost::conop::ASN];
+
+ AddInfo(ASN, "CG", promod3::loop::ASN_CG_INDEX, false);
+ AddInfo(ASN, "OD1", promod3::loop::ASN_OD1_INDEX, false);
+ AddInfo(ASN, "ND2", promod3::loop::ASN_ND2_INDEX, false);
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddInfo(ASN, "HD21", promod3::loop::ASN_HD21_INDEX, true);
+ AddInfo(ASN, "HD22", promod3::loop::ASN_HD22_INDEX, true);
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddInfo(ASN, "HB2", promod3::loop::ASN_HB2_INDEX, true);
+ AddInfo(ASN, "HB3", promod3::loop::ASN_HB3_INDEX, true);
+ }
+
+ if(cb_in_sidechain) {
+ AddInfo(ASN, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddFRMRule(ASN, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX,
+ param.ASN_CA_CB_prefactors);
+ AddFRMRotatingParticle(ASN, 0, 0); // CG
+ AddFRMRotatingParticle(ASN, 0, 1); // OD1
+ AddFRMRotatingParticle(ASN, 0, 2); // ND2
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(ASN, 0, 3); // HD21
+ AddFRMRotatingParticle(ASN, 0, 4); // HD22
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(ASN, 0, 5); // HB2
+ AddFRMRotatingParticle(ASN, 0, 6); // HB3
+ }
+
+ AddFRMRule(ASN, promod3::loop::BB_CB_INDEX, promod3::loop::ASN_CG_INDEX,
+ param.ASN_CB_CG_prefactors);
+ AddFRMFixParticle(ASN, 1, 0); // CG
+ AddFRMRotatingParticle(ASN, 1, 1); // OD1
+ AddFRMRotatingParticle(ASN, 1, 2); // ND2
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(ASN, 1, 3); // HD21
+ AddFRMRotatingParticle(ASN, 1, 4); // HD22
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMFixParticle(ASN, 1, 5); // HB2
+ AddFRMFixParticle(ASN, 1, 6); // HB3
+ }
+
+ if(cb_in_sidechain) {
+ int cb_idx = 3;
+ if(mode == POLAR_HYDROGEN_MODE) {
+ cb_idx = 5;
+ }
+ if(mode == FULL_ATOMIC_MODE) {
+ cb_idx = 7;
+ }
+ AddFRMFixParticle(ASN, 0, cb_idx);
+ AddFRMFixParticle(ASN, 1, cb_idx);
+ }
+
+
+ backbone_infos_[ASN].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
+ mode == FULL_ATOMIC_MODE);
+ AddBBInfo(ASN, "N", promod3::loop::BB_N_INDEX, false);
+ AddBBInfo(ASN, "CA", promod3::loop::BB_CA_INDEX, false);
+ AddBBInfo(ASN, "C", promod3::loop::BB_C_INDEX, false);
+ AddBBInfo(ASN, "O", promod3::loop::BB_O_INDEX, false);
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(ASN, "H", promod3::loop::ASN_H_INDEX,true);
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(ASN, "HA", promod3::loop::ASN_HA_INDEX, true);
+ }
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(ASN, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+
+ // ASP
+ sidechain_infos_[ASP].has_hydrogens = (mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[ASP].internal_e_prefactor =
+ param.internal_e_prefactor[ost::conop::ASP];
+ sidechain_infos_[ASP].frm_t = param.frm_t[ost::conop::ASP];
+
+ AddInfo(ASP, "CG", promod3::loop::ASP_CG_INDEX, false);
+ AddInfo(ASP, "OD1", promod3::loop::ASP_OD1_INDEX, false);
+ AddInfo(ASP, "OD2", promod3::loop::ASP_OD2_INDEX, false);
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddInfo(ASP, "HB2", promod3::loop::ASP_HB2_INDEX, true);
+ AddInfo(ASP, "HB3", promod3::loop::ASP_HB3_INDEX, true);
+ }
+
+ if(cb_in_sidechain) {
+ AddInfo(ASP, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddFRMRule(ASP, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX,
+ param.ASP_CA_CB_prefactors);
+ AddFRMRotatingParticle(ASP, 0, 0); // CG
+ AddFRMRotatingParticle(ASP, 0, 1); // OD1
+ AddFRMRotatingParticle(ASP, 0, 2); // OD2
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(ASP, 0, 3); // HB2
+ AddFRMRotatingParticle(ASP, 0, 4); // HB3
+ }
+
+ AddFRMRule(ASP, promod3::loop::BB_CB_INDEX, promod3::loop::ASP_CG_INDEX,
+ param.ASP_CB_CG_prefactors);
+ AddFRMFixParticle(ASP, 1, 0); // CG
+ AddFRMRotatingParticle(ASP, 1, 1); // OD1
+ AddFRMRotatingParticle(ASP, 1, 2); // OD2
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMFixParticle(ASP, 1, 3); // HB2
+ AddFRMFixParticle(ASP, 1, 4); // HB3
+ }
+
+ if(cb_in_sidechain) {
+ int cb_idx = 3;
+ if(mode == FULL_ATOMIC_MODE) {
+ cb_idx = 5;
+ }
+ AddFRMFixParticle(ASP, 0, cb_idx);
+ AddFRMFixParticle(ASP, 1, cb_idx);
+ }
+
+ backbone_infos_[ASP].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
+ mode == FULL_ATOMIC_MODE);
+ AddBBInfo(ASP, "N", promod3::loop::BB_N_INDEX, false);
+ AddBBInfo(ASP, "CA", promod3::loop::BB_CA_INDEX, false);
+ AddBBInfo(ASP, "C", promod3::loop::BB_C_INDEX, false);
+ AddBBInfo(ASP, "O", promod3::loop::BB_O_INDEX, false);
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(ASP, "H", promod3::loop::ASP_H_INDEX,true);
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(ASP, "HA", promod3::loop::ASP_HA_INDEX, true);
+ }
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(ASP, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+
+ // GLN
+ sidechain_infos_[GLN].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
+ mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[GLN].internal_e_prefactor =
+ param.internal_e_prefactor[ost::conop::GLN];
+ sidechain_infos_[GLN].frm_t = param.frm_t[ost::conop::GLN];
+
+ AddInfo(GLN, "CG", promod3::loop::GLN_CG_INDEX, false);
+ AddInfo(GLN, "CD", promod3::loop::GLN_CD_INDEX, false);
+ AddInfo(GLN, "OE1", promod3::loop::GLN_OE1_INDEX, false);
+ AddInfo(GLN, "NE2", promod3::loop::GLN_NE2_INDEX, false);
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddInfo(GLN, "HE21", promod3::loop::GLN_HE21_INDEX, true);
+ AddInfo(GLN, "HE22", promod3::loop::GLN_HE22_INDEX, true);
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddInfo(GLN, "HB2", promod3::loop::GLN_HB2_INDEX, true);
+ AddInfo(GLN, "HB3", promod3::loop::GLN_HB3_INDEX, true);
+ AddInfo(GLN, "HG2", promod3::loop::GLN_HG2_INDEX, true);
+ AddInfo(GLN, "HG3", promod3::loop::GLN_HG3_INDEX, true);
+ }
+
+ if(cb_in_sidechain) {
+ AddInfo(GLN, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddFRMRule(GLN, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX,
+ param.GLN_CA_CB_prefactors);
+ AddFRMRotatingParticle(GLN, 0, 0); // CG
+ AddFRMRotatingParticle(GLN, 0, 1); // CD
+ AddFRMRotatingParticle(GLN, 0, 2); // OE1
+ AddFRMRotatingParticle(GLN, 0, 3); // NE2
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(GLN, 0, 4); // HE21
+ AddFRMRotatingParticle(GLN, 0, 5); // HE22
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(GLN, 0, 6); // HB2
+ AddFRMRotatingParticle(GLN, 0, 7); // HB3
+ AddFRMRotatingParticle(GLN, 0, 8); // HG2
+ AddFRMRotatingParticle(GLN, 0, 9); // HG3
+ }
+
+ AddFRMRule(GLN, promod3::loop::BB_CB_INDEX, promod3::loop::GLN_CG_INDEX,
+ param.GLN_CB_CG_prefactors);
+ AddFRMFixParticle(GLN, 1, 0); // CG
+ AddFRMRotatingParticle(GLN, 1, 1); // CD
+ AddFRMRotatingParticle(GLN, 1, 2); // OE1
+ AddFRMRotatingParticle(GLN, 1, 3); // NE2
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(GLN, 1, 4); // HE21
+ AddFRMRotatingParticle(GLN, 1, 5); // HE22
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMFixParticle(GLN, 1, 6); // HB2
+ AddFRMFixParticle(GLN, 1, 7); // HB3
+ AddFRMRotatingParticle(GLN, 1, 8); // HG2
+ AddFRMRotatingParticle(GLN, 1, 9); // HG3
+ }
+
+ AddFRMRule(GLN, promod3::loop::GLN_CG_INDEX, promod3::loop::GLN_CD_INDEX,
+ param.GLN_CG_CD_prefactors);
+ AddFRMFixParticle(GLN, 2, 0); // CG
+ AddFRMFixParticle(GLN, 2, 1); // CD
+ AddFRMRotatingParticle(GLN, 2, 2); // OE1
+ AddFRMRotatingParticle(GLN, 2, 3); // NE2
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(GLN, 2, 4); // HE21
+ AddFRMRotatingParticle(GLN, 2, 5); // HE22
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMFixParticle(GLN, 2, 6); // HB2
+ AddFRMFixParticle(GLN, 2, 7); // HB3
+ AddFRMFixParticle(GLN, 2, 8); // HG2
+ AddFRMFixParticle(GLN, 2, 9); // HG3
+ }
+
+ if(cb_in_sidechain) {
+ int cb_idx = 4;
+ if(mode == POLAR_HYDROGEN_MODE) {
+ cb_idx = 6;
+ }
+ if(mode == FULL_ATOMIC_MODE) {
+ cb_idx = 10;
+ }
+ AddFRMFixParticle(GLN, 0, cb_idx);
+ AddFRMFixParticle(GLN, 1, cb_idx);
+ AddFRMFixParticle(GLN, 2, cb_idx);
+ }
+
+
+ backbone_infos_[GLN].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
+ mode == FULL_ATOMIC_MODE);
+
+ AddBBInfo(GLN, "N", promod3::loop::BB_N_INDEX, false);
+ AddBBInfo(GLN, "CA", promod3::loop::BB_CA_INDEX, false);
+ AddBBInfo(GLN, "C", promod3::loop::BB_C_INDEX, false);
+ AddBBInfo(GLN, "O", promod3::loop::BB_O_INDEX, false);
+
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(GLN, "H", promod3::loop::GLN_H_INDEX,true);
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(GLN, "HA", promod3::loop::GLN_HA_INDEX, true);
+ }
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(GLN, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+
+ // GLU
+ sidechain_infos_[GLU].has_hydrogens = (mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[GLU].internal_e_prefactor =
+ param.internal_e_prefactor[ost::conop::GLU];
+ sidechain_infos_[GLU].frm_t = param.frm_t[ost::conop::GLU];
+
+ AddInfo(GLU, "CG", promod3::loop::GLU_CG_INDEX, false);
+ AddInfo(GLU, "CD", promod3::loop::GLU_CD_INDEX, false);
+ AddInfo(GLU, "OE1", promod3::loop::GLU_OE1_INDEX, false);
+ AddInfo(GLU, "OE2", promod3::loop::GLU_OE2_INDEX, false);
+
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddInfo(GLU, "HB2", promod3::loop::GLU_HB2_INDEX, true);
+ AddInfo(GLU, "HB3", promod3::loop::GLU_HB3_INDEX, true);
+ AddInfo(GLU, "HG2", promod3::loop::GLU_HG2_INDEX, true);
+ AddInfo(GLU, "HG3", promod3::loop::GLU_HG3_INDEX, true);
+ }
+
+ if(cb_in_sidechain) {
+ AddInfo(GLU, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddFRMRule(GLU, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX,
+ param.GLU_CA_CB_prefactors);
+ AddFRMRotatingParticle(GLU, 0, 0); // CG
+ AddFRMRotatingParticle(GLU, 0, 1); // CD
+ AddFRMRotatingParticle(GLU, 0, 2); // OE1
+ AddFRMRotatingParticle(GLU, 0, 3); // OE2
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(GLU, 0, 4); // HB2
+ AddFRMRotatingParticle(GLU, 0, 5); // HB3
+ AddFRMRotatingParticle(GLU, 0, 6); // HG2
+ AddFRMRotatingParticle(GLU, 0, 7); // HG3
+ }
+
+ AddFRMRule(GLU, promod3::loop::BB_CB_INDEX, promod3::loop::GLU_CG_INDEX,
+ param.GLU_CB_CG_prefactors);
+ AddFRMFixParticle(GLU, 1, 0); // CG
+ AddFRMRotatingParticle(GLU, 1, 1); // CD
+ AddFRMRotatingParticle(GLU, 1, 2); // OE1
+ AddFRMRotatingParticle(GLU, 1, 3); // OE2
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMFixParticle(GLU, 1, 4); // HB2
+ AddFRMFixParticle(GLU, 1, 5); // HB3
+ AddFRMRotatingParticle(GLU, 1, 6); // HG2
+ AddFRMRotatingParticle(GLU, 1, 7); // HG3
+ }
+
+ AddFRMRule(GLU, promod3::loop::GLU_CG_INDEX, promod3::loop::GLU_CD_INDEX,
+ param.GLU_CG_CD_prefactors);
+ AddFRMFixParticle(GLU, 2, 0); // CG
+ AddFRMFixParticle(GLU, 2, 1); // CD
+ AddFRMRotatingParticle(GLU, 2, 2); // OE1
+ AddFRMRotatingParticle(GLU, 2, 3); // OE2
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMFixParticle(GLU, 2, 4); // HB2
+ AddFRMFixParticle(GLU, 2, 5); // HB3
+ AddFRMFixParticle(GLU, 2, 6); // HG2
+ AddFRMFixParticle(GLU, 2, 7); // HG3
+ }
+
+ if(cb_in_sidechain) {
+ int cb_idx = 4;
+ if(mode == FULL_ATOMIC_MODE) {
+ cb_idx = 8;
+ }
+ AddFRMFixParticle(GLU, 0, cb_idx);
+ AddFRMFixParticle(GLU, 1, cb_idx);
+ AddFRMFixParticle(GLU, 2, cb_idx);
+ }
+
+
+ backbone_infos_[GLU].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
+ mode == FULL_ATOMIC_MODE);
+
+ AddBBInfo(GLU, "N", promod3::loop::BB_N_INDEX, false);
+ AddBBInfo(GLU, "CA", promod3::loop::BB_CA_INDEX, false);
+ AddBBInfo(GLU, "C", promod3::loop::BB_C_INDEX, false);
+ AddBBInfo(GLU, "O", promod3::loop::BB_O_INDEX, false);
+
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(GLU, "H", promod3::loop::GLU_H_INDEX,true);
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(GLU, "HA", promod3::loop::GLU_HA_INDEX, true);
+ }
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(GLU, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+
+ // LYS
+ sidechain_infos_[LYS].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
+ mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[LYS].internal_e_prefactor =
+ param.internal_e_prefactor[ost::conop::LYS];
+ sidechain_infos_[LYS].frm_t = param.frm_t[ost::conop::LYS];
+
+ AddInfo(LYS, "CG", promod3::loop::LYS_CG_INDEX,false);
+ AddInfo(LYS, "CD", promod3::loop::LYS_CD_INDEX,false);
+ AddInfo(LYS, "CE", promod3::loop::LYS_CE_INDEX,false);
+ AddInfo(LYS, "NZ", promod3::loop::LYS_NZ_INDEX,false);
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddInfo(LYS, "HZ1", promod3::loop::LYS_HZ1_INDEX,true);
+ AddInfo(LYS, "HZ2", promod3::loop::LYS_HZ2_INDEX,true);
+ AddInfo(LYS, "HZ3", promod3::loop::LYS_HZ3_INDEX,true);
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddInfo(LYS, "HB2", promod3::loop::LYS_HB2_INDEX, true);
+ AddInfo(LYS, "HB3", promod3::loop::LYS_HB3_INDEX, true);
+ AddInfo(LYS, "HG2", promod3::loop::LYS_HG2_INDEX, true);
+ AddInfo(LYS, "HG3", promod3::loop::LYS_HG3_INDEX, true);
+ AddInfo(LYS, "HD2", promod3::loop::LYS_HD2_INDEX, true);
+ AddInfo(LYS, "HD3", promod3::loop::LYS_HD3_INDEX, true);
+ AddInfo(LYS, "HE2", promod3::loop::LYS_HE2_INDEX, true);
+ AddInfo(LYS, "HE3", promod3::loop::LYS_HE3_INDEX, true);
+ }
+
+ if(cb_in_sidechain) {
+ AddInfo(LYS, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddFRMRule(LYS, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX,
+ param.LYS_CA_CB_prefactors);
+ AddFRMRotatingParticle(LYS, 0, 0); // CG
+ AddFRMRotatingParticle(LYS, 0, 1); // CD
+ AddFRMRotatingParticle(LYS, 0, 2); // CE
+ AddFRMRotatingParticle(LYS, 0, 3); // NZ
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(LYS, 0, 4); // HZ1
+ AddFRMRotatingParticle(LYS, 0, 5); // HZ2
+ AddFRMRotatingParticle(LYS, 0, 6); // HZ3
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(LYS, 0, 7); // HB2
+ AddFRMRotatingParticle(LYS, 0, 8); // HB3
+ AddFRMRotatingParticle(LYS, 0, 9); // HG2
+ AddFRMRotatingParticle(LYS, 0, 10); // HG3
+ AddFRMRotatingParticle(LYS, 0, 11); // HD2
+ AddFRMRotatingParticle(LYS, 0, 12); // HD3
+ AddFRMRotatingParticle(LYS, 0, 13); // HE2
+ AddFRMRotatingParticle(LYS, 0, 14); // HE3
+ }
+
+ AddFRMRule(LYS, promod3::loop::BB_CB_INDEX, promod3::loop::LYS_CG_INDEX,
+ param.LYS_CB_CG_prefactors);
+ AddFRMFixParticle(LYS, 1, 0); // CG
+ AddFRMRotatingParticle(LYS, 1, 1); // CD
+ AddFRMRotatingParticle(LYS, 1, 2); // CE
+ AddFRMRotatingParticle(LYS, 1, 3); // NZ
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(LYS, 1, 4); // HZ1
+ AddFRMRotatingParticle(LYS, 1, 5); // HZ2
+ AddFRMRotatingParticle(LYS, 1, 6); // HZ3
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMFixParticle(LYS, 1, 7); // HB2
+ AddFRMFixParticle(LYS, 1, 8); // HB3
+ AddFRMRotatingParticle(LYS, 1, 9); // HG2
+ AddFRMRotatingParticle(LYS, 1, 10); // HG3
+ AddFRMRotatingParticle(LYS, 1, 11); // HD2
+ AddFRMRotatingParticle(LYS, 1, 12); // HD3
+ AddFRMRotatingParticle(LYS, 1, 13); // HE2
+ AddFRMRotatingParticle(LYS, 1, 14); // HE3
+ }
+
+ AddFRMRule(LYS, promod3::loop::LYS_CG_INDEX, promod3::loop::LYS_CD_INDEX,
+ param.LYS_CG_CD_prefactors);
+ AddFRMFixParticle(LYS, 2, 0); // CG
+ AddFRMFixParticle(LYS, 2, 1); // CD
+ AddFRMRotatingParticle(LYS, 2, 2); // CE
+ AddFRMRotatingParticle(LYS, 2, 3); // NZ
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(LYS, 2, 4); // HZ1
+ AddFRMRotatingParticle(LYS, 2, 5); // HZ2
+ AddFRMRotatingParticle(LYS, 2, 6); // HZ3
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMFixParticle(LYS, 2, 7); // HB2
+ AddFRMFixParticle(LYS, 2, 8); // HB3
+ AddFRMFixParticle(LYS, 2, 9); // HG2
+ AddFRMFixParticle(LYS, 2, 10); // HG3
+ AddFRMRotatingParticle(LYS, 2, 11); // HD2
+ AddFRMRotatingParticle(LYS, 2, 12); // HD3
+ AddFRMRotatingParticle(LYS, 2, 13); // HE2
+ AddFRMRotatingParticle(LYS, 2, 14); // HE3
+ }
+
+ AddFRMRule(LYS, promod3::loop::LYS_CD_INDEX, promod3::loop::LYS_CE_INDEX,
+ param.LYS_CD_CE_prefactors);
+ AddFRMFixParticle(LYS, 3, 0); // CG
+ AddFRMFixParticle(LYS, 3, 1); // CD
+ AddFRMFixParticle(LYS, 3, 2); // CE
+ AddFRMRotatingParticle(LYS, 3, 3); // NZ
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(LYS, 3, 4); // HZ1
+ AddFRMRotatingParticle(LYS, 3, 5); // HZ2
+ AddFRMRotatingParticle(LYS, 3, 6); // HZ3
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMFixParticle(LYS, 3, 7); // HB2
+ AddFRMFixParticle(LYS, 3, 8); // HB3
+ AddFRMFixParticle(LYS, 3, 9); // HG2
+ AddFRMFixParticle(LYS, 3, 10); // HG3
+ AddFRMFixParticle(LYS, 3, 11); // HD2
+ AddFRMFixParticle(LYS, 3, 12); // HD3
+ AddFRMRotatingParticle(LYS, 3, 13); // HE2
+ AddFRMRotatingParticle(LYS, 3, 14); // HE3
+ }
+
+ if(cb_in_sidechain) {
+ int cb_idx = 4;
+ if(mode == POLAR_HYDROGEN_MODE) {
+ cb_idx = 7;
+ }
+ if(mode == FULL_ATOMIC_MODE) {
+ cb_idx = 15;
+ }
+ AddFRMFixParticle(LYS, 0, cb_idx);
+ AddFRMFixParticle(LYS, 1, cb_idx);
+ AddFRMFixParticle(LYS, 2, cb_idx);
+ AddFRMFixParticle(LYS, 3, cb_idx);
+ }
+
+ backbone_infos_[LYS].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
+ mode == FULL_ATOMIC_MODE);
+ AddBBInfo(LYS, "N", promod3::loop::BB_N_INDEX, false);
+ AddBBInfo(LYS, "CA", promod3::loop::BB_CA_INDEX, false);
+ AddBBInfo(LYS, "C", promod3::loop::BB_C_INDEX, false);
+ AddBBInfo(LYS, "O", promod3::loop::BB_O_INDEX, false);
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(LYS, "H", promod3::loop::LYS_H_INDEX, true);
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(LYS, "HA", promod3::loop::LYS_HA_INDEX, true);
+ }
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(LYS, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+
+ // SER
+ sidechain_infos_[SER].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
+ mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[SER].internal_e_prefactor =
+ param.internal_e_prefactor[ost::conop::SER];
+ sidechain_infos_[SER].frm_t = param.frm_t[ost::conop::SER];
+
+ AddInfo(SER, "OG", promod3::loop::SER_OG_INDEX, false);
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddInfo(SER, "HG", promod3::loop::SER_HG_INDEX, true);
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddInfo(SER, "HB2", promod3::loop::SER_HB2_INDEX, true);
+ AddInfo(SER, "HB3", promod3::loop::SER_HB3_INDEX, true);
+ }
+
+ if(cb_in_sidechain) {
+ AddInfo(SER, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddCustomHydrogenInfo(SER, promod3::loop::SER_HG_INDEX,
+ promod3::loop::BB_CA_INDEX,
+ promod3::loop::BB_CB_INDEX,
+ promod3::loop::SER_OG_INDEX,
+ 0.96, 1.85, 1);
+ }
+
+ AddFRMRule(SER, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX,
+ param.SER_CA_CB_prefactors);
+ AddFRMRotatingParticle(SER, 0, 0); // OG
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(SER, 0, 1); // HG
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(SER, 0, 2); // HB2
+ AddFRMRotatingParticle(SER, 0, 3); // HB3
+ }
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddFRMRule(SER, promod3::loop::BB_CB_INDEX, promod3::loop::SER_OG_INDEX,
+ param.SER_CB_OG_prefactors);
+ AddFRMFixParticle(SER, 1, 0); // OG
+ AddFRMRotatingParticle(SER, 1, 1); // HG
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMFixParticle(SER, 1, 2); // HB2
+ AddFRMFixParticle(SER, 1, 3); // HB3
+ }
+ }
+
+ if(cb_in_sidechain) {
+ int cb_idx = 1;
+ if(mode == POLAR_HYDROGEN_MODE) {
+ cb_idx = 2;
+ }
+ if(mode == FULL_ATOMIC_MODE) {
+ cb_idx = 4;
+ }
+ AddFRMFixParticle(SER, 0, cb_idx);
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddFRMFixParticle(SER, 1, cb_idx);
+ }
+ }
+
+ backbone_infos_[SER].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
+ mode == FULL_ATOMIC_MODE);
+ AddBBInfo(SER, "N", promod3::loop::BB_N_INDEX, false);
+ AddBBInfo(SER, "CA", promod3::loop::BB_CA_INDEX, false);
+ AddBBInfo(SER, "C", promod3::loop::BB_C_INDEX, false);
+ AddBBInfo(SER, "O", promod3::loop::BB_O_INDEX, false);
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(SER, "H", promod3::loop::SER_H_INDEX, true);
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(SER, "HA", promod3::loop::SER_HA_INDEX, true);
+ }
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(SER, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+
+ // CYS
+ sidechain_infos_[CYS].has_hydrogens = (mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[CYS].internal_e_prefactor =
+ param.internal_e_prefactor[ost::conop::CYS];
+ sidechain_infos_[CYS].frm_t = param.frm_t[ost::conop::CYS];
+
+ AddInfo(CYS, "SG", promod3::loop::CYS_SG_INDEX, false);
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddInfo(CYS, "HB2", promod3::loop::CYS_HB2_INDEX, true);
+ AddInfo(CYS, "HB3", promod3::loop::CYS_HB3_INDEX, true);
+ AddInfo(CYS, "HG", promod3::loop::CYS_HG_INDEX, true);
+ }
+
+ if(cb_in_sidechain) {
+ AddInfo(CYS, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddFRMRule(CYS, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX,
+ param.CYS_CA_CB_prefactors);
+ AddFRMRotatingParticle(CYS, 0, 0); // SG
+
+ if(FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(CYS, 0, 1); // HB2
+ AddFRMRotatingParticle(CYS, 0, 2); // HB3
+ AddFRMRotatingParticle(CYS, 0, 3); // HG
+ }
+
+ if(cb_in_sidechain) {
+ int cb_idx = 1;
+ if(FULL_ATOMIC_MODE) {
+ cb_idx = 4;
+ }
+ AddFRMFixParticle(CYS, 0, cb_idx);
+ }
+
+ backbone_infos_[CYS].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
+ mode == FULL_ATOMIC_MODE);
+ AddBBInfo(CYS, "N", promod3::loop::BB_N_INDEX, false);
+ AddBBInfo(CYS, "CA", promod3::loop::BB_CA_INDEX, false);
+ AddBBInfo(CYS, "C", promod3::loop::BB_C_INDEX, false);
+ AddBBInfo(CYS, "O", promod3::loop::BB_O_INDEX, false);
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(CYS, "H", promod3::loop::CYS_H_INDEX,true);
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(CYS, "HA", promod3::loop::CYS_HA_INDEX,true);
+ }
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(CYS, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+
+ // CYH
+ sidechain_infos_[CYH] = sidechain_infos_[CYS];
+ frm_rules_[CYH] = frm_rules_[CYS];
+ backbone_infos_[CYH] = backbone_infos_[CYS];
+
+
+ // CYD
+ sidechain_infos_[CYD].has_hydrogens = (mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[CYD].internal_e_prefactor =
+ param.internal_e_prefactor[ost::conop::CYS];
+ sidechain_infos_[CYD].frm_t = param.frm_t[ost::conop::CYS];
+
+ AddInfo(CYD, "SG", promod3::loop::CYS_SG_INDEX, false);
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddInfo(CYD, "HB2", promod3::loop::CYS_HB2_INDEX, true);
+ AddInfo(CYD, "HB3", promod3::loop::CYS_HB3_INDEX, true);
+ }
+
+ if(cb_in_sidechain) {
+ AddInfo(CYD, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddFRMRule(CYD, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX,
+ param.CYS_CA_CB_prefactors);
+ AddFRMRotatingParticle(CYD, 0, 0); // SG
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(CYD, 0, 1); // HB2
+ AddFRMRotatingParticle(CYD, 0, 2); // HB3
+ }
+
+ if(cb_in_sidechain) {
+ int cb_idx = 1;
+ if(FULL_ATOMIC_MODE) {
+ cb_idx = 3;
+ }
+ AddFRMFixParticle(CYD, 0, cb_idx);
+ }
+
+ backbone_infos_[CYD].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
+ mode == FULL_ATOMIC_MODE);
+ AddBBInfo(CYD, "N", promod3::loop::BB_N_INDEX, false);
+ AddBBInfo(CYD, "CA", promod3::loop::BB_CA_INDEX, false);
+ AddBBInfo(CYD, "C", promod3::loop::BB_C_INDEX, false);
+ AddBBInfo(CYD, "O", promod3::loop::BB_O_INDEX, false);
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(CYD, "H", promod3::loop::CYS_H_INDEX,true);
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(CYD, "HA", promod3::loop::CYS_HA_INDEX,true);
+ }
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(CYD, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+
+ // MET
+ sidechain_infos_[MET].has_hydrogens = (mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[MET].internal_e_prefactor =
+ param.internal_e_prefactor[ost::conop::MET];
+ sidechain_infos_[MET].frm_t = param.frm_t[ost::conop::MET];
+
+ AddInfo(MET, "CG", promod3::loop::MET_CG_INDEX,false);
+ AddInfo(MET, "SD", promod3::loop::MET_SD_INDEX,false);
+ AddInfo(MET, "CE", promod3::loop::MET_CE_INDEX,false);
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddInfo(MET, "HB2", promod3::loop::MET_HB2_INDEX, true);
+ AddInfo(MET, "HB3", promod3::loop::MET_HB3_INDEX, true);
+ AddInfo(MET, "HG2", promod3::loop::MET_HG2_INDEX, true);
+ AddInfo(MET, "HG3", promod3::loop::MET_HG3_INDEX, true);
+ AddInfo(MET, "HE1", promod3::loop::MET_HE1_INDEX, true);
+ AddInfo(MET, "HE2", promod3::loop::MET_HE2_INDEX, true);
+ AddInfo(MET, "HE3", promod3::loop::MET_HE3_INDEX, true);
+ }
+
+ if(cb_in_sidechain) {
+ AddInfo(MET, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddFRMRule(MET, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX,
+ param.MET_CA_CB_prefactors);
+ AddFRMRotatingParticle(MET, 0, 0); // CG
+ AddFRMRotatingParticle(MET, 0, 1); // SD
+ AddFRMRotatingParticle(MET, 0, 2); // CE
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(MET, 0, 3); // HB2
+ AddFRMRotatingParticle(MET, 0, 4); // HB3
+ AddFRMRotatingParticle(MET, 0, 5); // HG2
+ AddFRMRotatingParticle(MET, 0, 6); // HG3
+ AddFRMRotatingParticle(MET, 0, 7); // HE1
+ AddFRMRotatingParticle(MET, 0, 8); // HE2
+ AddFRMRotatingParticle(MET, 0, 9); // HE3
+ }
+
+ AddFRMRule(MET, promod3::loop::BB_CB_INDEX, promod3::loop::MET_CG_INDEX,
+ param.MET_CB_CG_prefactors);
+ AddFRMFixParticle(MET, 1, 0); // CG
+ AddFRMRotatingParticle(MET, 1, 1); // SD
+ AddFRMRotatingParticle(MET, 1, 2); // CE
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMFixParticle(MET, 1, 3); // HB2
+ AddFRMFixParticle(MET, 1, 4); // HB3
+ AddFRMRotatingParticle(MET, 1, 5); // HG2
+ AddFRMRotatingParticle(MET, 1, 6); // HG3
+ AddFRMRotatingParticle(MET, 1, 7); // HE1
+ AddFRMRotatingParticle(MET, 1, 8); // HE2
+ AddFRMRotatingParticle(MET, 1, 9); // HE3
+ }
+
+ AddFRMRule(MET, promod3::loop::MET_CG_INDEX, promod3::loop::MET_SD_INDEX,
+ param.MET_CG_SD_prefactors);
+ AddFRMFixParticle(MET, 2, 0);
+ AddFRMFixParticle(MET, 2, 1);
+ AddFRMRotatingParticle(MET, 2, 2);
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMFixParticle(MET, 2, 3); // HB2
+ AddFRMFixParticle(MET, 2, 4); // HB3
+ AddFRMFixParticle(MET, 2, 5); // HG2
+ AddFRMFixParticle(MET, 2, 6); // HG3
+ AddFRMRotatingParticle(MET, 2, 7); // HE1
+ AddFRMRotatingParticle(MET, 2, 8); // HE2
+ AddFRMRotatingParticle(MET, 2, 9); // HE3
+ }
+
+ if(cb_in_sidechain) {
+ int cb_idx = 3;
+ if(mode == FULL_ATOMIC_MODE) {
+ cb_idx = 10;
+ }
+ AddFRMFixParticle(MET, 0, cb_idx);
+ AddFRMFixParticle(MET, 1, cb_idx);
+ AddFRMFixParticle(MET, 2, cb_idx);
+ }
+
+ backbone_infos_[MET].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
+ mode == FULL_ATOMIC_MODE);
+ AddBBInfo(MET, "N", promod3::loop::BB_N_INDEX, false);
+ AddBBInfo(MET, "CA", promod3::loop::BB_CA_INDEX, false);
+ AddBBInfo(MET, "C", promod3::loop::BB_C_INDEX, false);
+ AddBBInfo(MET, "O", promod3::loop::BB_O_INDEX, false);
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(MET, "H", promod3::loop::MET_H_INDEX, true);
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(MET, "H", promod3::loop::MET_H_INDEX, true);
+ }
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(MET, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+
+ // TRP
+ sidechain_infos_[TRP].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
+ mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[TRP].internal_e_prefactor =
+ param.internal_e_prefactor[ost::conop::TRP];
+ sidechain_infos_[TRP].frm_t = param.frm_t[ost::conop::TRP];
+
+ AddInfo(TRP, "CG", promod3::loop::TRP_CG_INDEX,false);
+ AddInfo(TRP, "CD1", promod3::loop::TRP_CD1_INDEX,false);
+ AddInfo(TRP, "CD2", promod3::loop::TRP_CD2_INDEX,false);
+ AddInfo(TRP, "CE2", promod3::loop::TRP_CE2_INDEX,false);
+ AddInfo(TRP, "NE1", promod3::loop::TRP_NE1_INDEX,false);
+ AddInfo(TRP, "CE3", promod3::loop::TRP_CE3_INDEX,false);
+ AddInfo(TRP, "CZ3", promod3::loop::TRP_CZ3_INDEX,false);
+ AddInfo(TRP, "CH2", promod3::loop::TRP_CH2_INDEX,false);
+ AddInfo(TRP, "CZ2", promod3::loop::TRP_CZ2_INDEX,false);
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddInfo(TRP, "HE1", promod3::loop::TRP_HE1_INDEX,true);
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddInfo(TRP, "HB2", promod3::loop::TRP_HB2_INDEX, true);
+ AddInfo(TRP, "HB3", promod3::loop::TRP_HB3_INDEX, true);
+ AddInfo(TRP, "HD1", promod3::loop::TRP_HD1_INDEX, true);
+ AddInfo(TRP, "HE3", promod3::loop::TRP_HE3_INDEX, true);
+ AddInfo(TRP, "HZ2", promod3::loop::TRP_HZ2_INDEX, true);
+ AddInfo(TRP, "HZ3", promod3::loop::TRP_HZ3_INDEX, true);
+ AddInfo(TRP, "HH2", promod3::loop::TRP_HH2_INDEX, true);
+ }
+
+ if(cb_in_sidechain) {
+ AddInfo(TRP, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddFRMRule(TRP, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX,
+ param.TRP_CA_CB_prefactors);
+ AddFRMRotatingParticle(TRP, 0, 0); // CG
+ AddFRMRotatingParticle(TRP, 0, 1); // CD1
+ AddFRMRotatingParticle(TRP, 0, 2); // CD2
+ AddFRMRotatingParticle(TRP, 0, 3); // CE2
+ AddFRMRotatingParticle(TRP, 0, 4); // NE1
+ AddFRMRotatingParticle(TRP, 0, 5); // CE3
+ AddFRMRotatingParticle(TRP, 0, 6); // CZ3
+ AddFRMRotatingParticle(TRP, 0, 7); // CH2
+ AddFRMRotatingParticle(TRP, 0, 8); // CZ2
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(TRP, 0, 9); // HE1
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(TRP, 0, 10); // HB2
+ AddFRMRotatingParticle(TRP, 0, 11); // HB3
+ AddFRMRotatingParticle(TRP, 0, 12); // HD1
+ AddFRMRotatingParticle(TRP, 0, 13); // HE3
+ AddFRMRotatingParticle(TRP, 0, 14); // HZ2
+ AddFRMRotatingParticle(TRP, 0, 15); // HZ3
+ AddFRMRotatingParticle(TRP, 0, 16); // HH2
+ }
+
+ AddFRMRule(TRP, promod3::loop::BB_CB_INDEX, promod3::loop::TRP_CG_INDEX,
+ param.TRP_CB_CG_prefactors);
+ AddFRMFixParticle(TRP, 1, 0); // CG
+ AddFRMRotatingParticle(TRP, 1, 1); // CD1
+ AddFRMRotatingParticle(TRP, 1, 2); // CD2
+ AddFRMRotatingParticle(TRP, 1, 3); // CE2
+ AddFRMRotatingParticle(TRP, 1, 4); // NE1
+ AddFRMRotatingParticle(TRP, 1, 5); // CE3
+ AddFRMRotatingParticle(TRP, 1, 6); // CZ3
+ AddFRMRotatingParticle(TRP, 1, 7); // CH2
+ AddFRMRotatingParticle(TRP, 1, 8); // CZ2
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(TRP, 1, 9);
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMFixParticle(TRP, 1, 10); // HB2
+ AddFRMFixParticle(TRP, 1, 11); // HB3
+ AddFRMRotatingParticle(TRP, 1, 12); // HD1
+ AddFRMRotatingParticle(TRP, 1, 13); // HE3
+ AddFRMRotatingParticle(TRP, 1, 14); // HZ2
+ AddFRMRotatingParticle(TRP, 1, 15); // HZ3
+ AddFRMRotatingParticle(TRP, 1, 16); // HH2
+ }
+
+ if(cb_in_sidechain) {
+ int cb_idx = 9;
+ if(mode == POLAR_HYDROGEN_MODE) {
+ cb_idx = 10;
+ }
+ if(mode == FULL_ATOMIC_MODE) {
+ cb_idx = 17;
+ }
+ AddFRMFixParticle(TRP, 0, cb_idx);
+ AddFRMFixParticle(TRP, 1, cb_idx);
+ }
+
+ backbone_infos_[TRP].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
+ mode == FULL_ATOMIC_MODE);
+ AddBBInfo(TRP, "N", promod3::loop::BB_N_INDEX, false);
+ AddBBInfo(TRP, "CA", promod3::loop::BB_CA_INDEX, false);
+ AddBBInfo(TRP, "C", promod3::loop::BB_C_INDEX, false);
+ AddBBInfo(TRP, "O", promod3::loop::BB_O_INDEX, false);
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(TRP, "H", promod3::loop::TRP_H_INDEX, true);
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(TRP, "HA", promod3::loop::TRP_HA_INDEX, true);
+ }
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(TRP, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+
+ // TYR
+ sidechain_infos_[TYR].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
+ mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[TYR].internal_e_prefactor =
+ param.internal_e_prefactor[ost::conop::TYR];
+ sidechain_infos_[TYR].frm_t = param.frm_t[ost::conop::TYR];
+
+ AddInfo(TYR, "CG", promod3::loop::TYR_CG_INDEX, false);
+ AddInfo(TYR, "CD1", promod3::loop::TYR_CD1_INDEX, false);
+ AddInfo(TYR, "CD2", promod3::loop::TYR_CD2_INDEX, false);
+ AddInfo(TYR, "CE1", promod3::loop::TYR_CE1_INDEX, false);
+ AddInfo(TYR, "CE2", promod3::loop::TYR_CE2_INDEX, false);
+ AddInfo(TYR, "CZ", promod3::loop::TYR_CZ_INDEX, false);
+ AddInfo(TYR, "OH", promod3::loop::TYR_OH_INDEX, false);
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddInfo(TYR, "HH", promod3::loop::TYR_HH_INDEX, true);
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddInfo(TYR, "HB2", promod3::loop::TYR_HB2_INDEX, true);
+ AddInfo(TYR, "HB3", promod3::loop::TYR_HB3_INDEX, true);
+ AddInfo(TYR, "HD1", promod3::loop::TYR_HD1_INDEX, true);
+ AddInfo(TYR, "HD2", promod3::loop::TYR_HD2_INDEX, true);
+ AddInfo(TYR, "HE1", promod3::loop::TYR_HE1_INDEX, true);
+ AddInfo(TYR, "HE2", promod3::loop::TYR_HE2_INDEX, true);
+ }
+
+ if(cb_in_sidechain) {
+ AddInfo(TYR, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddCustomHydrogenInfo(TYR, promod3::loop::TYR_HH_INDEX,
+ promod3::loop::TYR_CE1_INDEX,
+ promod3::loop::TYR_CZ_INDEX,
+ promod3::loop::TYR_OH_INDEX,
+ 0.96, 1.885, 2);
+ }
+
+ AddFRMRule(TYR, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX,
+ param.TYR_CA_CB_prefactors);
+ AddFRMRotatingParticle(TYR, 0, 0); // CG
+ AddFRMRotatingParticle(TYR, 0, 1); // CD1
+ AddFRMRotatingParticle(TYR, 0, 2); // CD2
+ AddFRMRotatingParticle(TYR, 0, 3); // CE1
+ AddFRMRotatingParticle(TYR, 0, 4); // CE2
+ AddFRMRotatingParticle(TYR, 0, 5); // CZ
+ AddFRMRotatingParticle(TYR, 0, 6); // OH
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(TYR, 0, 7); // HH
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(TYR, 0, 8); // HB2
+ AddFRMRotatingParticle(TYR, 0, 9); // HB3
+ AddFRMRotatingParticle(TYR, 0, 10); // HD1
+ AddFRMRotatingParticle(TYR, 0, 11); // HD2
+ AddFRMRotatingParticle(TYR, 0, 12); // HE1
+ AddFRMRotatingParticle(TYR, 0, 13); // HE2
+ }
+
+ AddFRMRule(TYR, promod3::loop::BB_CB_INDEX, promod3::loop::TYR_CG_INDEX,
+ param.TYR_CB_CG_prefactors);
+ AddFRMFixParticle(TYR, 1, 0); // CG
+ AddFRMRotatingParticle(TYR, 1, 1); // CD1
+ AddFRMRotatingParticle(TYR, 1, 2); // CD2
+ AddFRMRotatingParticle(TYR, 1, 3); // CE1
+ AddFRMRotatingParticle(TYR, 1, 4); // CE2
+ AddFRMRotatingParticle(TYR, 1, 5); // CZ
+ AddFRMRotatingParticle(TYR, 1, 6); // OH
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(TYR, 1, 7); // HH
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMFixParticle(TYR, 1, 8); // HB2
+ AddFRMFixParticle(TYR, 1, 9); // HB3
+ AddFRMRotatingParticle(TYR, 1, 10); // HD1
+ AddFRMRotatingParticle(TYR, 1, 11); // HD2
+ AddFRMRotatingParticle(TYR, 1, 12); // HE1
+ AddFRMRotatingParticle(TYR, 1, 13); // HE2
+
+ }
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddFRMRule(TYR, promod3::loop::TYR_CZ_INDEX, promod3::loop::TYR_OH_INDEX,
+ param.TYR_CZ_OH_prefactors);
+ AddFRMFixParticle(TYR, 2, 0); // CG
+ AddFRMFixParticle(TYR, 2, 1); // CD1
+ AddFRMFixParticle(TYR, 2, 2); // CD2
+ AddFRMFixParticle(TYR, 2, 3); // CE1
+ AddFRMFixParticle(TYR, 2, 4); // CE2
+ AddFRMFixParticle(TYR, 2, 5); // CZ
+ AddFRMFixParticle(TYR, 2, 6); // OH
+
+ AddFRMRotatingParticle(TYR, 2, 7);
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMFixParticle(TYR, 2, 8); // HB2
+ AddFRMFixParticle(TYR, 2, 9); // HB3
+ AddFRMFixParticle(TYR, 2, 10); // HD1
+ AddFRMFixParticle(TYR, 2, 11); // HD2
+ AddFRMFixParticle(TYR, 2, 12); // HE1
+ AddFRMFixParticle(TYR, 2, 13); // HE2
+ }
+ }
+
+
+ if(cb_in_sidechain) {
+ int cb_idx = 7;
+ if(mode == POLAR_HYDROGEN_MODE) {
+ cb_idx = 8;
+ }
+ if(mode == FULL_ATOMIC_MODE) {
+ cb_idx = 14;
+ }
+ AddFRMFixParticle(TYR, 0, cb_idx);
+ AddFRMFixParticle(TYR, 1, cb_idx);
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddFRMFixParticle(TYR, 2, cb_idx);
+ }
+ }
+
+ backbone_infos_[TYR].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
+ mode == FULL_ATOMIC_MODE);
+ AddBBInfo(TYR, "N", promod3::loop::BB_N_INDEX, false);
+ AddBBInfo(TYR, "CA", promod3::loop::BB_CA_INDEX, false);
+ AddBBInfo(TYR, "C", promod3::loop::BB_C_INDEX, false);
+ AddBBInfo(TYR, "O", promod3::loop::BB_O_INDEX, false);
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(TYR, "H", promod3::loop::TYR_H_INDEX, true);
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(TYR, "HA", promod3::loop::TYR_HA_INDEX, true);
+ }
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(TYR, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+
+ // THR
+ sidechain_infos_[THR].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
+ mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[THR].internal_e_prefactor =
+ param.internal_e_prefactor[ost::conop::THR];
+ sidechain_infos_[THR].frm_t = param.frm_t[ost::conop::THR];
+
+ AddInfo(THR, "OG1", promod3::loop::THR_OG1_INDEX, false);
+ AddInfo(THR, "CG2", promod3::loop::THR_CG2_INDEX, false);
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddInfo(THR, "HG1", promod3::loop::THR_HG1_INDEX, true);
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddInfo(THR, "HB", promod3::loop::THR_HB_INDEX, true);
+ AddInfo(THR, "HG21", promod3::loop::THR_HG22_INDEX, true);
+ AddInfo(THR, "HG22", promod3::loop::THR_HG23_INDEX, true);
+ AddInfo(THR, "HG23", promod3::loop::THR_HG23_INDEX, true);
+ }
+
+ if(cb_in_sidechain) {
+ AddInfo(THR, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddCustomHydrogenInfo(THR, promod3::loop::THR_HG1_INDEX,
+ promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX,
+ promod3::loop::THR_OG1_INDEX,
+ 0.96, 1.85, 1);
+ }
+
+ AddFRMRule(THR, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX,
+ param.THR_CA_CB_prefactors);
+ AddFRMRotatingParticle(THR, 0, 0); // OG1
+ AddFRMRotatingParticle(THR, 0, 1); // CG2
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(THR, 0, 2); // HG1
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(THR, 0, 3); // HB
+ AddFRMRotatingParticle(THR, 0, 4); // HG21
+ AddFRMRotatingParticle(THR, 0, 5); // HG22
+ AddFRMRotatingParticle(THR, 0, 6); // HG23
+ }
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddFRMRule(THR, promod3::loop::BB_CB_INDEX, promod3::loop::THR_OG1_INDEX,
+ param.THR_CB_OG1_prefactors);
+ AddFRMFixParticle(THR, 1, 0); // OG1
+ AddFRMFixParticle(THR, 1, 1); //CG2
+ AddFRMRotatingParticle(THR, 1, 2); // HG1
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMFixParticle(THR, 1, 3); // HB
+ AddFRMFixParticle(THR, 1, 4); // HG21
+ AddFRMFixParticle(THR, 1, 5); // HG22
+ AddFRMFixParticle(THR, 1, 6); // HG23
+ }
+ }
+
+ if(cb_in_sidechain) {
+ int cb_idx = 2;
+ if(mode == POLAR_HYDROGEN_MODE) {
+ cb_idx = 3;
+ }
+ if(mode == FULL_ATOMIC_MODE) {
+ cb_idx = 7;
+ }
+ AddFRMFixParticle(THR, 0, cb_idx);
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddFRMFixParticle(THR, 1, cb_idx);
+ }
+ }
+
+ backbone_infos_[THR].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
+ mode == FULL_ATOMIC_MODE);
+ AddBBInfo(THR, "N", promod3::loop::BB_N_INDEX, false);
+ AddBBInfo(THR, "CA", promod3::loop::BB_CA_INDEX, false);
+ AddBBInfo(THR, "C", promod3::loop::BB_C_INDEX, false);
+ AddBBInfo(THR, "O", promod3::loop::BB_O_INDEX, false);
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(THR, "H", promod3::loop::THR_H_INDEX, true);
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(THR, "HA", promod3::loop::THR_HA_INDEX, true);
+ }
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(THR, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+
+ // VAL
+ sidechain_infos_[VAL].has_hydrogens = (mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[VAL].internal_e_prefactor =
+ param.internal_e_prefactor[ost::conop::VAL];
+ sidechain_infos_[VAL].frm_t = param.frm_t[ost::conop::VAL];
+
+ AddInfo(VAL, "CG1", promod3::loop::VAL_CG1_INDEX, false);
+ AddInfo(VAL, "CG2", promod3::loop::VAL_CG2_INDEX, false);
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddInfo(VAL, "HB", promod3::loop::VAL_HB_INDEX, true);
+ AddInfo(VAL, "HG11", promod3::loop::VAL_HG11_INDEX, true);
+ AddInfo(VAL, "HG12", promod3::loop::VAL_HG12_INDEX, true);
+ AddInfo(VAL, "HG13", promod3::loop::VAL_HG13_INDEX, true);
+ AddInfo(VAL, "HG21", promod3::loop::VAL_HG21_INDEX, true);
+ AddInfo(VAL, "HG22", promod3::loop::VAL_HG22_INDEX, true);
+ AddInfo(VAL, "HG23", promod3::loop::VAL_HG23_INDEX, true);
+ }
+
+ if(cb_in_sidechain) {
+ AddInfo(VAL, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddFRMRule(VAL, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX,
+ param.VAL_CA_CB_prefactors);
+ AddFRMRotatingParticle(VAL, 0, 0); // CG1
+ AddFRMRotatingParticle(VAL, 0, 1); // CG2
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(VAL, 0, 2); // HB
+ AddFRMRotatingParticle(VAL, 0, 3); // HG11
+ AddFRMRotatingParticle(VAL, 0, 4); // HG12
+ AddFRMRotatingParticle(VAL, 0, 5); // HG13
+ AddFRMRotatingParticle(VAL, 0, 6); // HG21
+ AddFRMRotatingParticle(VAL, 0, 7); // HG22
+ AddFRMRotatingParticle(VAL, 0, 8); // HG23
+ }
+
+ if(cb_in_sidechain) {
+ int cb_idx = 2;
+ if(mode == FULL_ATOMIC_MODE) {
+ cb_idx = 9;
+ }
+ AddFRMFixParticle(VAL, 0, cb_idx);
+ }
+
+ backbone_infos_[VAL].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
+ mode == FULL_ATOMIC_MODE);
+ AddBBInfo(VAL, "N", promod3::loop::BB_N_INDEX, false);
+ AddBBInfo(VAL, "CA", promod3::loop::BB_CA_INDEX, false);
+ AddBBInfo(VAL, "C", promod3::loop::BB_C_INDEX, false);
+ AddBBInfo(VAL, "O", promod3::loop::BB_O_INDEX, false);
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(VAL, "H", promod3::loop::VAL_H_INDEX, true);
+ }
+ if(mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(VAL, "HA", promod3::loop::VAL_HA_INDEX, true);
+ }
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(VAL, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+
+ // ILE
+ sidechain_infos_[ILE].has_hydrogens = (mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[ILE].internal_e_prefactor =
+ param.internal_e_prefactor[ost::conop::ILE];
+ sidechain_infos_[ILE].frm_t = param.frm_t[ost::conop::ILE];
+
+ AddInfo(ILE, "CG1", promod3::loop::ILE_CG1_INDEX, false);
+ AddInfo(ILE, "CG2", promod3::loop::ILE_CG2_INDEX, false);
+ AddInfo(ILE, "CD1", promod3::loop::ILE_CD1_INDEX, false);
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddInfo(ILE, "HB", promod3::loop::ILE_HB_INDEX, true);
+ AddInfo(ILE, "HG12", promod3::loop::ILE_HG12_INDEX, true);
+ AddInfo(ILE, "HG13", promod3::loop::ILE_HG13_INDEX, true);
+ AddInfo(ILE, "HG21", promod3::loop::ILE_HG21_INDEX, true);
+ AddInfo(ILE, "HG22", promod3::loop::ILE_HG22_INDEX, true);
+ AddInfo(ILE, "HG23", promod3::loop::ILE_HG23_INDEX, true);
+ AddInfo(ILE, "HD11", promod3::loop::ILE_HD11_INDEX, true);
+ AddInfo(ILE, "HD12", promod3::loop::ILE_HD12_INDEX, true);
+ AddInfo(ILE, "HD13", promod3::loop::ILE_HD13_INDEX, true);
+ }
+
+ if(cb_in_sidechain) {
+ AddInfo(ILE, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddFRMRule(ILE, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX,
+ param.ILE_CA_CB_prefactors);
+ AddFRMRotatingParticle(ILE, 0, 0); // CG1
+ AddFRMRotatingParticle(ILE, 0, 1); // CG2
+ AddFRMRotatingParticle(ILE, 0, 2); // CD1
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(ILE, 0, 3); // HB
+ AddFRMRotatingParticle(ILE, 0, 4); // HG12
+ AddFRMRotatingParticle(ILE, 0, 5); // HG13
+ AddFRMRotatingParticle(ILE, 0, 6); // HG21
+ AddFRMRotatingParticle(ILE, 0, 7); // HG22
+ AddFRMRotatingParticle(ILE, 0, 8); // HG23
+ AddFRMRotatingParticle(ILE, 0, 9); // HD11
+ AddFRMRotatingParticle(ILE, 0, 10); // HD12
+ AddFRMRotatingParticle(ILE, 0, 11); // HD13
+ }
+
+
+ AddFRMRule(ILE, promod3::loop::BB_CB_INDEX, promod3::loop::ILE_CG1_INDEX,
+ param.ILE_CB_CG1_prefactors);
+ AddFRMFixParticle(ILE, 1, 0); // CG1
+ AddFRMFixParticle(ILE, 1, 1); // CG2
+ AddFRMRotatingParticle(ILE, 1, 2); // CD1
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMFixParticle(ILE, 1, 3); // HB
+ AddFRMRotatingParticle(ILE, 1, 4); // HG12
+ AddFRMRotatingParticle(ILE, 1, 5); // HG13
+ AddFRMFixParticle(ILE, 1, 6); // HG21
+ AddFRMFixParticle(ILE, 1, 7); // HG22
+ AddFRMFixParticle(ILE, 1, 8); // HG23
+ AddFRMRotatingParticle(ILE, 1, 9); // HD11
+ AddFRMRotatingParticle(ILE, 1, 10); // HD12
+ AddFRMRotatingParticle(ILE, 1, 11); // HD13
+ }
+
+ if(cb_in_sidechain) {
+ int cb_idx = 3;
+ if(mode == FULL_ATOMIC_MODE) {
+ cb_idx = 12;
+ }
+ AddFRMFixParticle(ILE, 0, cb_idx);
+ AddFRMFixParticle(ILE, 1, cb_idx);
+ }
+
+ backbone_infos_[ILE].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
+ mode == FULL_ATOMIC_MODE);
+ AddBBInfo(ILE, "N", promod3::loop::BB_N_INDEX, false);
+ AddBBInfo(ILE, "CA", promod3::loop::BB_CA_INDEX, false);
+ AddBBInfo(ILE, "C", promod3::loop::BB_C_INDEX, false);
+ AddBBInfo(ILE, "O", promod3::loop::BB_O_INDEX, false);
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(ILE, "H", promod3::loop::ILE_H_INDEX, true);
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(ILE, "HA", promod3::loop::ILE_HA_INDEX, true);
+ }
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(ILE, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+
+ // LEU
+ sidechain_infos_[LEU].has_hydrogens = (mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[LEU].internal_e_prefactor =
+ param.internal_e_prefactor[ost::conop::LEU];
+ sidechain_infos_[LEU].frm_t = param.frm_t[ost::conop::LEU];
+
+ AddInfo(LEU, "CG", promod3::loop::LEU_CG_INDEX, false);
+ AddInfo(LEU, "CD1", promod3::loop::LEU_CD1_INDEX, false);
+ AddInfo(LEU, "CD2", promod3::loop::LEU_CD2_INDEX, false);
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddInfo(LEU, "HB2", promod3::loop::LEU_HB2_INDEX, true);
+ AddInfo(LEU, "HB3", promod3::loop::LEU_HB3_INDEX, true);
+ AddInfo(LEU, "HG", promod3::loop::LEU_HG_INDEX, true);
+ AddInfo(LEU, "HD11", promod3::loop::LEU_HD11_INDEX, true);
+ AddInfo(LEU, "HD12", promod3::loop::LEU_HD12_INDEX, true);
+ AddInfo(LEU, "HD13", promod3::loop::LEU_HD13_INDEX, true);
+ AddInfo(LEU, "HD21", promod3::loop::LEU_HD21_INDEX, true);
+ AddInfo(LEU, "HD22", promod3::loop::LEU_HD22_INDEX, true);
+ AddInfo(LEU, "HD23", promod3::loop::LEU_HD23_INDEX, true);
+ }
+
+ if(cb_in_sidechain) {
+ AddInfo(LEU, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+
+ AddFRMRule(LEU, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX,
+ param.LEU_CA_CB_prefactors);
+ AddFRMRotatingParticle(LEU, 0, 0); // CG
+ AddFRMRotatingParticle(LEU, 0, 1); // CD1
+ AddFRMRotatingParticle(LEU, 0, 2); // CD2
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(LEU, 0, 3); // HB2
+ AddFRMRotatingParticle(LEU, 0, 4); // HB3
+ AddFRMRotatingParticle(LEU, 0, 5); // HG
+ AddFRMRotatingParticle(LEU, 0, 6); // HD11
+ AddFRMRotatingParticle(LEU, 0, 7); // HD12
+ AddFRMRotatingParticle(LEU, 0, 8); // HD13
+ AddFRMRotatingParticle(LEU, 0, 9); // HD21
+ AddFRMRotatingParticle(LEU, 0, 10); // HD22
+ AddFRMRotatingParticle(LEU, 0, 11); // HD23
+ }
+
+ AddFRMRule(LEU, promod3::loop::BB_CB_INDEX, promod3::loop::LEU_CG_INDEX,
+ param.LEU_CB_CG_prefactors);
+ AddFRMFixParticle(LEU, 1, 0); // CG
+ AddFRMRotatingParticle(LEU, 1, 1); // CG1
+ AddFRMRotatingParticle(LEU, 1, 2); // CG2
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMFixParticle(LEU, 1, 3); // HB2
+ AddFRMFixParticle(LEU, 1, 4); // HB3
+ AddFRMRotatingParticle(LEU, 1, 5); // HG
+ AddFRMRotatingParticle(LEU, 1, 6); // HD11
+ AddFRMRotatingParticle(LEU, 1, 7); // HD12
+ AddFRMRotatingParticle(LEU, 1, 8); // HD13
+ AddFRMRotatingParticle(LEU, 1, 9); // HD21
+ AddFRMRotatingParticle(LEU, 1, 10); // HD22
+ AddFRMRotatingParticle(LEU, 1, 11); // HD23
+ }
+
+ if(cb_in_sidechain) {
+ int cb_idx = 3;
+ if(mode == FULL_ATOMIC_MODE) {
+ cb_idx = 12;
+ }
+ AddFRMFixParticle(LEU, 0, cb_idx);
+ AddFRMFixParticle(LEU, 1, cb_idx);
+ }
+
+ backbone_infos_[LEU].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
+ mode == FULL_ATOMIC_MODE);
+ AddBBInfo(LEU, "N", promod3::loop::BB_N_INDEX, false);
+ AddBBInfo(LEU, "CA", promod3::loop::BB_CA_INDEX, false);
+ AddBBInfo(LEU, "C", promod3::loop::BB_C_INDEX, false);
+ AddBBInfo(LEU, "O", promod3::loop::BB_O_INDEX, false);
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(LEU, "H", promod3::loop::LEU_H_INDEX, true);
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(LEU, "HA", promod3::loop::LEU_HA_INDEX, true);
+ }
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(LEU, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+
+ // PROLINES DO NOT HAVE FRM DEFINITIONS!
+ // large scale benchmarks showed, that varying around chi angles in case
+ // of prolines has a negative effect on performance => reduce to one single
+ // subrotamer...
+
+ // PRO
+ sidechain_infos_[PRO].has_hydrogens = (mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[PRO].internal_e_prefactor =
+ param.internal_e_prefactor[ost::conop::PRO];
+ sidechain_infos_[PRO].frm_t = param.frm_t[ost::conop::PRO];
+
+ AddInfo(PRO, "CG", promod3::loop::PRO_CG_INDEX, false);
+ AddInfo(PRO, "CD", promod3::loop::PRO_CD_INDEX, false);
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddInfo(PRO, "HB2", promod3::loop::PRO_HB2_INDEX, true);
+ AddInfo(PRO, "HB3", promod3::loop::PRO_HB3_INDEX, true);
+ AddInfo(PRO, "HG2", promod3::loop::PRO_HG2_INDEX, true);
+ AddInfo(PRO, "HG3", promod3::loop::PRO_HG3_INDEX, true);
+ AddInfo(PRO, "HD2", promod3::loop::PRO_HD2_INDEX, true);
+ AddInfo(PRO, "HD3", promod3::loop::PRO_HD3_INDEX, true);
+ }
+
+ if(cb_in_sidechain) {
+ AddInfo(PRO, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ backbone_infos_[PRO].has_hydrogens = (mode == FULL_ATOMIC_MODE);
+ AddBBInfo(PRO, "N", promod3::loop::BB_N_INDEX, false);
+ AddBBInfo(PRO, "CA", promod3::loop::BB_CA_INDEX, false);
+ AddBBInfo(PRO, "C", promod3::loop::BB_C_INDEX, false);
+ AddBBInfo(PRO, "O", promod3::loop::BB_O_INDEX, false);
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(PRO, "HA", promod3::loop::PRO_HA_INDEX, true);
+ }
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(PRO, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+
+ // CPR
+ sidechain_infos_[CPR] = sidechain_infos_[PRO];
+ frm_rules_[CPR] = frm_rules_[PRO];
+ backbone_infos_[CPR] = backbone_infos_[PRO];
+
+
+ // TPR
+ sidechain_infos_[TPR] = sidechain_infos_[PRO];
+ frm_rules_[TPR] = frm_rules_[PRO];
+ backbone_infos_[TPR] = backbone_infos_[PRO];
+
+
+ // HSD
+ sidechain_infos_[HSD].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
+ mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[HSD].internal_e_prefactor =
+ param.internal_e_prefactor[ost::conop::HIS];
+ sidechain_infos_[HSD].frm_t = param.frm_t[ost::conop::HIS];
+
+ AddInfo(HSD, "CG", promod3::loop::HIS_CG_INDEX, false);
+ AddInfo(HSD, "ND1", promod3::loop::HIS_ND1_INDEX, false);
+ AddInfo(HSD, "CD2", promod3::loop::HIS_CD2_INDEX, false);
+ AddInfo(HSD, "CE1", promod3::loop::HIS_CE1_INDEX, false);
+ AddInfo(HSD, "NE2", promod3::loop::HIS_NE2_INDEX, false);
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddInfo(HSD, "HD1", promod3::loop::HIS_HD1_INDEX,true);
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddInfo(HSD, "HB2", promod3::loop::HIS_HB2_INDEX, true);
+ AddInfo(HSD, "HB3", promod3::loop::HIS_HB3_INDEX, true);
+ AddInfo(HSD, "HD2", promod3::loop::HIS_HD2_INDEX, true);
+ AddInfo(HSD, "HE1", promod3::loop::HIS_HE1_INDEX, true);
+ }
+
+ if(cb_in_sidechain) {
+ AddInfo(HSD, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddFRMRule(HSD, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX,
+ param.HIS_CA_CB_prefactors);
+ AddFRMRotatingParticle(HSD, 0, 0); // CG
+ AddFRMRotatingParticle(HSD, 0, 1); // ND1
+ AddFRMRotatingParticle(HSD, 0, 2); // CD2
+ AddFRMRotatingParticle(HSD, 0, 3); // CE1
+ AddFRMRotatingParticle(HSD, 0, 4); // NE2
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(HSD, 0, 5); // HD1
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(HSD, 0, 6); // HB2
+ AddFRMRotatingParticle(HSD, 0, 7); // HB3
+ AddFRMRotatingParticle(HSD, 0, 8); // HD2
+ AddFRMRotatingParticle(HSD, 0, 9); // HE1
+ }
+
+ AddFRMRule(HSD, promod3::loop::BB_CB_INDEX, promod3::loop::HIS_CG_INDEX,
+ param.HIS_CB_CG_prefactors);
+ AddFRMFixParticle(HSD, 1, 0); // CG
+ AddFRMRotatingParticle(HSD, 1, 1); // ND1
+ AddFRMRotatingParticle(HSD, 1, 2); // CD2
+ AddFRMRotatingParticle(HSD, 1, 3); // CE1
+ AddFRMRotatingParticle(HSD, 1, 4); // NE2
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(HSD, 1, 5); // HD1
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(HSD, 1, 6); // HB2
+ AddFRMRotatingParticle(HSD, 1, 7); // HB3
+ AddFRMRotatingParticle(HSD, 1, 8); // HD2
+ AddFRMRotatingParticle(HSD, 1, 9); // HE1
+ }
+
+ if(cb_in_sidechain) {
+ int cb_idx = 5;
+ if(mode == POLAR_HYDROGEN_MODE) {
+ cb_idx = 6;
+ }
+ if(mode == FULL_ATOMIC_MODE) {
+ cb_idx = 10;
+ }
+ AddFRMFixParticle(HSD, 0, cb_idx);
+ AddFRMFixParticle(HSD, 1, cb_idx);
+ }
+
+ backbone_infos_[HSD].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
+ mode == FULL_ATOMIC_MODE);
+ AddBBInfo(HSD, "N", promod3::loop::BB_N_INDEX, false);
+ AddBBInfo(HSD, "CA", promod3::loop::BB_CA_INDEX, false);
+ AddBBInfo(HSD, "C", promod3::loop::BB_C_INDEX, false);
+ AddBBInfo(HSD, "O", promod3::loop::BB_O_INDEX, false);
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(HSD, "H", promod3::loop::HIS_H_INDEX, true);
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(HSD, "HA", promod3::loop::HIS_HA_INDEX, true);
+ }
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(HSD, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+
+ // HSE
+ sidechain_infos_[HSE].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
+ mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[HSE].internal_e_prefactor =
+ param.internal_e_prefactor[ost::conop::HIS];
+ sidechain_infos_[HSE].frm_t = param.frm_t[ost::conop::HIS];
+
+ AddInfo(HSE, "CG", promod3::loop::HIS_CG_INDEX, false);
+ AddInfo(HSE, "ND1", promod3::loop::HIS_ND1_INDEX, false);
+ AddInfo(HSE, "CD2", promod3::loop::HIS_CD2_INDEX, false);
+ AddInfo(HSE, "CE1", promod3::loop::HIS_CE1_INDEX, false);
+ AddInfo(HSE, "NE2", promod3::loop::HIS_NE2_INDEX, false);
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddInfo(HSE, "HE2", promod3::loop::HIS_HE2_INDEX,true);
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddInfo(HSE, "HB2", promod3::loop::HIS_HB2_INDEX, true);
+ AddInfo(HSE, "HB3", promod3::loop::HIS_HB3_INDEX, true);
+ AddInfo(HSE, "HD2", promod3::loop::HIS_HD2_INDEX, true);
+ AddInfo(HSE, "HE1", promod3::loop::HIS_HE1_INDEX, true);
+ }
+
+ if(cb_in_sidechain) {
+ AddInfo(HSE, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddFRMRule(HSE, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX,
+ param.HIS_CA_CB_prefactors);
+ AddFRMRotatingParticle(HSE, 0, 0); // CG
+ AddFRMRotatingParticle(HSE, 0, 1); // ND1
+ AddFRMRotatingParticle(HSE, 0, 2); // CD2
+ AddFRMRotatingParticle(HSE, 0, 3); // CE1
+ AddFRMRotatingParticle(HSE, 0, 4); // NE2
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(HSE, 0, 5); // HE2
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(HSE, 0, 6); // HB2
+ AddFRMRotatingParticle(HSE, 0, 7); // HB3
+ AddFRMRotatingParticle(HSE, 0, 8); // HD2
+ AddFRMRotatingParticle(HSE, 0, 9); // HE1
+ }
+
+ AddFRMRule(HSE, promod3::loop::BB_CB_INDEX, promod3::loop::HIS_CG_INDEX,
+ param.HIS_CB_CG_prefactors);
+ AddFRMFixParticle(HSE, 1, 0); // CG
+ AddFRMRotatingParticle(HSE, 1, 1); // ND1
+ AddFRMRotatingParticle(HSE, 1, 2); // CD2
+ AddFRMRotatingParticle(HSE, 1, 3); // CE1
+ AddFRMRotatingParticle(HSE, 1, 4); // NE2
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(HSE, 1, 5); // HE2
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(HSE, 1, 6); // HB2
+ AddFRMRotatingParticle(HSE, 1, 7); // HB3
+ AddFRMRotatingParticle(HSE, 1, 8); // HD2
+ AddFRMRotatingParticle(HSE, 1, 9); // HE1
+ }
+
+ if(cb_in_sidechain) {
+ int cb_idx = 5;
+ if(mode == POLAR_HYDROGEN_MODE) {
+ cb_idx = 6;
+ }
+ if(mode == FULL_ATOMIC_MODE) {
+ cb_idx = 10;
+ }
+ AddFRMFixParticle(HSE, 0, cb_idx);
+ AddFRMFixParticle(HSE, 1, cb_idx);
+ }
+
+ backbone_infos_[HSE].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
+ mode == FULL_ATOMIC_MODE);
+ AddBBInfo(HSE, "N", promod3::loop::BB_N_INDEX, false);
+ AddBBInfo(HSE, "CA", promod3::loop::BB_CA_INDEX, false);
+ AddBBInfo(HSE, "C", promod3::loop::BB_C_INDEX, false);
+ AddBBInfo(HSE, "O", promod3::loop::BB_O_INDEX, false);
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(HSE, "H", promod3::loop::HIS_H_INDEX, true);
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(HSE, "HA", promod3::loop::HIS_HA_INDEX, true);
+ }
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(HSE, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ // HIS
+ // this is a bit hacky... we just assign HSD as determined by a fair
+ // random number generator.
+ sidechain_infos_[HIS] = sidechain_infos_[HSD];
+ frm_rules_[HIS] = frm_rules_[HSD];
+ backbone_infos_[HIS] = backbone_infos_[HSD];
+
+
+ // PHE
+ sidechain_infos_[PHE].has_hydrogens = (mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[PHE].internal_e_prefactor =
+ param.internal_e_prefactor[ost::conop::PHE];
+ sidechain_infos_[PHE].frm_t = param.frm_t[ost::conop::PHE];
+
+ AddInfo(PHE, "CG", promod3::loop::PHE_CG_INDEX, false);
+ AddInfo(PHE, "CD1", promod3::loop::PHE_CD1_INDEX, false);
+ AddInfo(PHE, "CD2", promod3::loop::PHE_CD2_INDEX, false);
+ AddInfo(PHE, "CE1", promod3::loop::PHE_CE1_INDEX, false);
+ AddInfo(PHE, "CE2", promod3::loop::PHE_CE2_INDEX, false);
+ AddInfo(PHE, "CZ", promod3::loop::PHE_CZ_INDEX, false);
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddInfo(PHE, "HB2", promod3::loop::PHE_HB2_INDEX, true);
+ AddInfo(PHE, "HB3", promod3::loop::PHE_HB3_INDEX, true);
+ AddInfo(PHE, "HD1", promod3::loop::PHE_HD1_INDEX, true);
+ AddInfo(PHE, "HD2", promod3::loop::PHE_HD2_INDEX, true);
+ AddInfo(PHE, "HE1", promod3::loop::PHE_HE1_INDEX, true);
+ AddInfo(PHE, "HE2", promod3::loop::PHE_HE2_INDEX, true);
+ AddInfo(PHE, "HZ", promod3::loop::PHE_HZ_INDEX, true);
+ }
+
+ if(cb_in_sidechain) {
+ AddInfo(PHE, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddFRMRule(PHE, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX,
+ param.PHE_CA_CB_prefactors);
+ AddFRMRotatingParticle(PHE, 0, 0); // CG
+ AddFRMRotatingParticle(PHE, 0, 1); // CD1
+ AddFRMRotatingParticle(PHE, 0, 2); // CD2
+ AddFRMRotatingParticle(PHE, 0, 3); // CE1
+ AddFRMRotatingParticle(PHE, 0, 4); // CE2
+ AddFRMRotatingParticle(PHE, 0, 5); // CZ
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMRotatingParticle(PHE, 0, 6); // HB2
+ AddFRMRotatingParticle(PHE, 0, 7); // HB3
+ AddFRMRotatingParticle(PHE, 0, 8); // HD1
+ AddFRMRotatingParticle(PHE, 0, 9); // HD2
+ AddFRMRotatingParticle(PHE, 0, 10); // HE1
+ AddFRMRotatingParticle(PHE, 0, 11); // HE2
+ AddFRMRotatingParticle(PHE, 0, 12); // HZ
+ }
+
+ AddFRMRule(PHE, promod3::loop::BB_CB_INDEX, promod3::loop::PHE_CG_INDEX,
+ param.PHE_CB_CG_prefactors);
+ AddFRMFixParticle(PHE, 1, 0); // CG
+ AddFRMRotatingParticle(PHE, 1, 1); // CD1
+ AddFRMRotatingParticle(PHE, 1, 2); // CD2
+ AddFRMRotatingParticle(PHE, 1, 3); // CE1
+ AddFRMRotatingParticle(PHE, 1, 4); // CE2
+ AddFRMRotatingParticle(PHE, 1, 5); // CZ
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddFRMFixParticle(PHE, 1, 6); // HB2
+ AddFRMFixParticle(PHE, 1, 7); // HB2
+ AddFRMRotatingParticle(PHE, 1, 8); // CD1
+ AddFRMRotatingParticle(PHE, 1, 9); // CD2
+ AddFRMRotatingParticle(PHE, 1, 10); // CE1
+ AddFRMRotatingParticle(PHE, 1, 11); // CE2
+ AddFRMRotatingParticle(PHE, 1, 12); // CZ
+ }
+
+ if(cb_in_sidechain) {
+ int cb_idx = 6;
+ if(mode == FULL_ATOMIC_MODE) {
+ cb_idx = 13;
+ }
+ AddFRMFixParticle(PHE, 0, cb_idx);
+ AddFRMFixParticle(PHE, 1, cb_idx);
+ }
+
+ backbone_infos_[PHE].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
+ mode == FULL_ATOMIC_MODE);
+ AddBBInfo(PHE, "N", promod3::loop::BB_N_INDEX, false);
+ AddBBInfo(PHE, "CA", promod3::loop::BB_CA_INDEX, false);
+ AddBBInfo(PHE, "C", promod3::loop::BB_C_INDEX, false);
+ AddBBInfo(PHE, "O", promod3::loop::BB_O_INDEX, false);
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(PHE, "H", promod3::loop::PHE_H_INDEX, true);
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(PHE, "HA", promod3::loop::PHE_HA_INDEX, true);
+ }
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(PHE, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+
+ // ALA
+
+ // The hydrogen situation is a bit special here...
+ // If its full atomic, we only put the hydrogens in the sidechains
+ // if the CBeta is also there. Otherwise, everything goes into the
+ // backbone.
+ sidechain_infos_[ALA].has_hydrogens = (mode == FULL_ATOMIC_MODE &&
+ cb_in_sidechain);
+ sidechain_infos_[ALA].internal_e_prefactor =
+ param.internal_e_prefactor[ost::conop::ALA];
+ sidechain_infos_[ALA].frm_t = param.frm_t[ost::conop::ALA];
+
+ if(cb_in_sidechain) {
+ AddInfo(ALA, "CB", promod3::loop::BB_CB_INDEX, false);
+ if(mode == FULL_ATOMIC_MODE) {
+ AddInfo(ALA, "HB1", promod3::loop::ALA_HB1_INDEX, true);
+ AddInfo(ALA, "HB2", promod3::loop::ALA_HB2_INDEX, true);
+ AddInfo(ALA, "HB3", promod3::loop::ALA_HB3_INDEX, true);
+ }
+ }
+
+ backbone_infos_[ALA].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
+ mode == FULL_ATOMIC_MODE);
+ AddBBInfo(ALA, "N", promod3::loop::BB_N_INDEX, false);
+ AddBBInfo(ALA, "CA", promod3::loop::BB_CA_INDEX, false);
+ AddBBInfo(ALA, "C", promod3::loop::BB_C_INDEX, false);
+ AddBBInfo(ALA, "O", promod3::loop::BB_O_INDEX, false);
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(ALA, "H", promod3::loop::ALA_H_INDEX, true);
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(ALA, "HA", promod3::loop::ALA_HA_INDEX, true);
+ }
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(ALA, "CB", promod3::loop::BB_CB_INDEX, false);
+ if(mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(ALA, "HB1", promod3::loop::ALA_HB1_INDEX, true);
+ AddBBInfo(ALA, "HB2", promod3::loop::ALA_HB2_INDEX, true);
+ AddBBInfo(ALA, "HB3", promod3::loop::ALA_HB3_INDEX, true);
+ }
+ }
+
+
+ // GLY
+ sidechain_infos_[GLY].has_hydrogens = false;
+ sidechain_infos_[GLY].internal_e_prefactor =
+ param.internal_e_prefactor[ost::conop::GLY];
+ sidechain_infos_[GLY].frm_t = param.frm_t[ost::conop::GLY];
+
+ backbone_infos_[GLY].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
+ mode == FULL_ATOMIC_MODE);
+ AddBBInfo(GLY, "N", promod3::loop::BB_N_INDEX, false);
+ AddBBInfo(GLY, "CA", promod3::loop::BB_CA_INDEX, false);
+ AddBBInfo(GLY, "C", promod3::loop::BB_C_INDEX, false);
+ AddBBInfo(GLY, "O", promod3::loop::BB_O_INDEX, false);
+
+ if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(GLY, "H", promod3::loop::GLY_H_INDEX, true);
+ }
+
+ if(mode == FULL_ATOMIC_MODE) {
+ AddBBInfo(GLY, "HA2", promod3::loop::GLY_HA2_INDEX, true);
+ AddBBInfo(GLY, "HA3", promod3::loop::GLY_HA3_INDEX, true);
+ }
+
+ for(uint i = 0; i <= XXX; ++i){
+ num_sidechain_particles_[i] = sidechain_infos_[i].particles.size();
+ num_frm_particles_[i] = num_sidechain_particles_[i];
+ for(uint j = 0; j < frm_rules_[i].size(); ++j){
+ num_frm_particles_[i] += (frm_rules_[i][j].prefactors.size() *
+ frm_rules_[i][j].rotating_particles.size());
+ }
+ }
+}
+
+
+RotamerInfo RotamerLookup::GetTerminalBackboneInfo(RotamerID id, bool n_ter,
+ bool c_ter) {
+ // get a copy to work on
+ RotamerInfo info = backbone_infos_[id];
+
+ if(n_ter && mode_ != HEAVY_ATOM_MODE) {
+ // find and delete particle with name "H", add particles of
+ // name "H1", "H2", "H3", only the first two in case of Proline
+ for(std::vector<ParticleInfo>::iterator it = info.particles.begin();
+ it != info.particles.end(); ++it) {
+ if(it->name == "H") {
+ info.particles.erase(it);
+ break;
+ }
+ }
+
+ ost::conop::AminoAcid aa = RotIDToAA(id);
+
+ ParticleInfo h1("H1", promod3::loop::AminoAcidLookup::GetInstance().GetH1Index(aa), true);
+ info.particles.push_back(h1);
+
+ ParticleInfo h2("H2", promod3::loop::AminoAcidLookup::GetInstance().GetH2Index(aa), true);
+ info.particles.push_back(h2);
+
+ if(aa != ost::conop::PRO) {
+ ParticleInfo h3("H3", promod3::loop::AminoAcidLookup::GetInstance().GetH3Index(aa), true);
+ info.particles.push_back(h3);
+ }
+ }
+
+ if(c_ter) {
+ // find particle with name "O" and mark it as terminal by setting its
+ // atom_index to -1
+ for(std::vector<ParticleInfo>::iterator it = info.particles.begin();
+ it != info.particles.end(); ++it) {
+ if(it->name == "O") {
+ it->atom_idx = -1;
+ break;
+ }
+ }
+ // atom_index of -2 marks terminal oxt
+ ParticleInfo oxt("OT", -2, false);
+ info.particles.push_back(oxt);
+ }
+
+ return info;
+}
+
+}} // ns
diff --git a/sidechain/src/rotamer_lookup.hh b/sidechain/src/rotamer_lookup.hh
new file mode 100644
index 0000000000000000000000000000000000000000..50215ce8954beb932f97085d228702e26ddec380
--- /dev/null
+++ b/sidechain/src/rotamer_lookup.hh
@@ -0,0 +1,307 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+#ifndef PROMOD3_ROTAMER_LOOKUP_HH
+#define PROMOD3_ROTAMER_LOOKUP_HH
+
+#include <vector>
+#include <ost/base.hh>
+#include <promod3/loop/amino_acid_atoms.hh>
+#include <promod3/sidechain/rotamer_id.hh>
+
+namespace promod3 { namespace sidechain {
+
+// Controls the particles that will be Constructed from the RotamerConstructor
+enum RotamerLookupMode{
+ HEAVY_ATOM_MODE,
+ POLAR_HYDROGEN_MODE,
+ FULL_ATOMIC_MODE
+};
+
+// Controls the parametrization of the rotamers
+// Must be filled by energy function specific RotamerConstructor and
+// passed to base class RotamerConstructor when calling constructor
+// of RotamerConstructor base class
+struct RotamerLookupParam {
+
+ RotamerLookupParam(bool default_parametrization = true) {
+
+ if(default_parametrization) {
+ for(int i = 0; i < ost::conop::XXX + 1; ++i) {
+ frm_t[i] = 1.0;
+ internal_e_prefactor[i] = 1.0;
+ }
+ std::vector<Real> default_prefactors;
+ default_prefactors.push_back(-1.0);
+ default_prefactors.push_back(1.0);
+ ARG_CA_CB_prefactors = default_prefactors;
+ ARG_CB_CG_prefactors = default_prefactors;
+ ARG_CG_CD_prefactors = default_prefactors;
+ ARG_CD_NE_prefactors = default_prefactors;
+ ASN_CA_CB_prefactors = default_prefactors;
+ ASN_CB_CG_prefactors = default_prefactors;
+ ASP_CA_CB_prefactors = default_prefactors;
+ ASP_CB_CG_prefactors = default_prefactors;
+ GLN_CA_CB_prefactors = default_prefactors;
+ GLN_CB_CG_prefactors = default_prefactors;
+ GLN_CG_CD_prefactors = default_prefactors;
+ GLU_CA_CB_prefactors = default_prefactors;
+ GLU_CB_CG_prefactors = default_prefactors;
+ GLU_CG_CD_prefactors = default_prefactors;
+ LYS_CA_CB_prefactors = default_prefactors;
+ LYS_CB_CG_prefactors = default_prefactors;
+ LYS_CG_CD_prefactors = default_prefactors;
+ LYS_CD_CE_prefactors = default_prefactors;
+ SER_CA_CB_prefactors = default_prefactors;
+ SER_CB_OG_prefactors = default_prefactors;
+ CYS_CA_CB_prefactors = default_prefactors;
+ MET_CA_CB_prefactors = default_prefactors;
+ MET_CB_CG_prefactors = default_prefactors;
+ MET_CG_SD_prefactors = default_prefactors;
+ TRP_CA_CB_prefactors = default_prefactors;
+ TRP_CB_CG_prefactors = default_prefactors;
+ TYR_CA_CB_prefactors = default_prefactors;
+ TYR_CB_CG_prefactors = default_prefactors;
+ TYR_CZ_OH_prefactors = default_prefactors;
+ THR_CA_CB_prefactors = default_prefactors;
+ THR_CB_OG1_prefactors = default_prefactors;
+ VAL_CA_CB_prefactors = default_prefactors;
+ ILE_CA_CB_prefactors = default_prefactors;
+ ILE_CB_CG1_prefactors = default_prefactors;
+ LEU_CA_CB_prefactors = default_prefactors;
+ LEU_CB_CG_prefactors = default_prefactors;
+ HIS_CA_CB_prefactors = default_prefactors;
+ HIS_CB_CG_prefactors = default_prefactors;
+ PHE_CA_CB_prefactors = default_prefactors;
+ PHE_CB_CG_prefactors = default_prefactors;
+ }
+ }
+
+ // the internal energy prefactor of the constructed rotamers
+ Real internal_e_prefactor[ost::conop::XXX + 1];
+
+ // frm temperature parameters
+ Real frm_t[ost::conop::XXX + 1];
+
+ // rotation bond specific frm prefactors
+ std::vector<Real> ARG_CA_CB_prefactors;
+ std::vector<Real> ARG_CB_CG_prefactors;
+ std::vector<Real> ARG_CG_CD_prefactors;
+ std::vector<Real> ARG_CD_NE_prefactors;
+
+ std::vector<Real> ASN_CA_CB_prefactors;
+ std::vector<Real> ASN_CB_CG_prefactors;
+
+ std::vector<Real> ASP_CA_CB_prefactors;
+ std::vector<Real> ASP_CB_CG_prefactors;
+
+ std::vector<Real> GLN_CA_CB_prefactors;
+ std::vector<Real> GLN_CB_CG_prefactors;
+ std::vector<Real> GLN_CG_CD_prefactors;
+
+ std::vector<Real> GLU_CA_CB_prefactors;
+ std::vector<Real> GLU_CB_CG_prefactors;
+ std::vector<Real> GLU_CG_CD_prefactors;
+
+ std::vector<Real> LYS_CA_CB_prefactors;
+ std::vector<Real> LYS_CB_CG_prefactors;
+ std::vector<Real> LYS_CG_CD_prefactors;
+ std::vector<Real> LYS_CD_CE_prefactors;
+
+ std::vector<Real> SER_CA_CB_prefactors;
+ std::vector<Real> SER_CB_OG_prefactors; // only relevant when hydrogen is
+ // constructed
+
+ std::vector<Real> CYS_CA_CB_prefactors;
+
+ std::vector<Real> MET_CA_CB_prefactors;
+ std::vector<Real> MET_CB_CG_prefactors;
+ std::vector<Real> MET_CG_SD_prefactors;
+
+ std::vector<Real> TRP_CA_CB_prefactors;
+ std::vector<Real> TRP_CB_CG_prefactors;
+
+ std::vector<Real> TYR_CA_CB_prefactors;
+ std::vector<Real> TYR_CB_CG_prefactors;
+ std::vector<Real> TYR_CZ_OH_prefactors; // only relevant when hydrogen is
+ // constructed
+
+ std::vector<Real> THR_CA_CB_prefactors;
+ std::vector<Real> THR_CB_OG1_prefactors; // only relevant when hydrogen is
+ // constructed
+
+ std::vector<Real> VAL_CA_CB_prefactors;
+
+ std::vector<Real> ILE_CA_CB_prefactors;
+ std::vector<Real> ILE_CB_CG1_prefactors;
+
+ std::vector<Real> LEU_CA_CB_prefactors;
+ std::vector<Real> LEU_CB_CG_prefactors;
+
+ std::vector<Real> HIS_CA_CB_prefactors;
+ std::vector<Real> HIS_CB_CG_prefactors;
+
+ std::vector<Real> PHE_CA_CB_prefactors;
+ std::vector<Real> PHE_CB_CG_prefactors;
+};
+
+
+struct ParticleInfo {
+
+ ParticleInfo() { }
+
+ ParticleInfo(const String& n, int idx, bool ih): name(n), atom_idx(idx),
+ is_hydrogen(ih) { }
+
+ String name;
+ int atom_idx; // for AllAtomPositions
+ // (idx in HydrogenStorage if is_hydrogen is true)
+ bool is_hydrogen;
+};
+
+
+struct CustomHydrogenInfo {
+
+ CustomHydrogenInfo() { }
+
+ CustomHydrogenInfo(int idx, int a_idx_one, int a_idx_two, int a_idx_three,
+ Real bl, Real a, int c_idx): atom_idx(idx),
+ anchor_idx_one(a_idx_one),
+ anchor_idx_two(a_idx_two),
+ anchor_idx_three(a_idx_three),
+ bond_length(bl), angle(a),
+ chi_idx(c_idx){ }
+ int atom_idx; //the idx in the hydrogen constructor
+ int anchor_idx_one; // idx in AllAtomPositions
+ int anchor_idx_two;
+ int anchor_idx_three;
+ Real bond_length;
+ Real angle;
+ int chi_idx;
+};
+
+
+struct FRMRule {
+
+ FRMRule() { }
+
+ int anchor_idx_one; // idx of heavy atom in RotamerConstructor::pos_buffer_
+ int anchor_idx_two; // idx of heavy atom in RotamerConstructor::pos_buffer_
+ std::vector<Real> prefactors;
+ // The following indices are NOT relative to any position buffer but rather
+ // to the ordering as the particles are defined in RotamerInfo
+ std::vector<int> fix_particles;
+ std::vector<int> rotating_particles;
+};
+
+
+struct RotamerInfo {
+
+ RotamerInfo() { }
+
+ std::vector<ParticleInfo> particles;
+ std::vector<CustomHydrogenInfo> custom_hydrogens;
+ Real internal_e_prefactor;
+ Real frm_t;
+ bool has_hydrogens;
+};
+
+
+class RotamerLookup{
+
+public:
+
+ RotamerLookup(bool cb_in_sidechain,
+ RotamerLookupMode mode,
+ const RotamerLookupParam& param = RotamerLookupParam());
+
+ // Data access
+ const RotamerInfo& GetSidechainInfo(RotamerID id) const {
+ return sidechain_infos_[id];
+ }
+
+ const RotamerInfo& GetBackboneInfo(RotamerID id) const {
+ return backbone_infos_[id];
+ }
+
+ RotamerInfo GetTerminalBackboneInfo(RotamerID id, bool n_ter,
+ bool c_ter);
+
+ const std::vector<FRMRule>& GetFRMRules(RotamerID id) const {
+ return frm_rules_[id];
+ }
+
+ int GetNumSidechainParticles(RotamerID id) const {
+ return num_sidechain_particles_[id];
+ }
+
+ int GetNumFRMSidechainParticles(RotamerID id) const {
+ return num_frm_particles_[id];
+ }
+
+private:
+
+ void AddInfo(RotamerID id, const String& name, int idx, bool is_h) {
+ ParticleInfo p(name, idx, is_h);
+ sidechain_infos_[id].particles.push_back(p);
+ }
+
+ void AddCustomHydrogenInfo(RotamerID id, int idx,
+ int a_idx_one, int a_idx_two, int a_idx_three,
+ Real bl, Real a, int c_idx) {
+ CustomHydrogenInfo i(idx, a_idx_one, a_idx_two, a_idx_three, bl, a, c_idx);
+ sidechain_infos_[id].custom_hydrogens.push_back(i);
+ }
+
+ void AddBBInfo(RotamerID id, const String& name, int idx, bool is_h) {
+ ParticleInfo p(name, idx, is_h);
+ backbone_infos_[id].particles.push_back(p);
+ }
+
+ void AddFRMRule(RotamerID id, int idx_one, int idx_two,
+ const std::vector<Real>& prefactors){
+ frm_rules_[id].push_back(FRMRule());
+ frm_rules_[id].back().anchor_idx_one = idx_one;
+ frm_rules_[id].back().anchor_idx_two = idx_two;
+ frm_rules_[id].back().prefactors = prefactors;
+ }
+
+ void AddFRMFixParticle(RotamerID id, int rule_idx, int p_idx){
+ frm_rules_[id][rule_idx].fix_particles.push_back(p_idx);
+ }
+
+ void AddFRMRotatingParticle(RotamerID id, int rule_idx, int p_idx){
+ frm_rules_[id][rule_idx].rotating_particles.push_back(p_idx);
+ }
+
+ // To construct classical rotamers or as lookup for sidechain frame residues
+ RotamerInfo sidechain_infos_[XXX + 1];
+
+ // To construct backbone frame residues
+ RotamerInfo backbone_infos_[XXX + 1];
+
+ // Additional info required for generating frm rotamers
+ std::vector<FRMRule> frm_rules_[XXX + 1];
+
+ int num_sidechain_particles_[XXX + 1];
+ int num_frm_particles_[XXX + 1];
+
+ RotamerLookupMode mode_;
+};
+
+
+}} // ns
+
+#endif
diff --git a/sidechain/src/scwrl4_rotamer_constructor.cc b/sidechain/src/scwrl4_rotamer_constructor.cc
index 7619d2ec8cef748701cf4ba50b046dd8cdc53ee4..687063f6cb9b59cdd9d9b3068f348b84a5f5a3af 100644
--- a/sidechain/src/scwrl4_rotamer_constructor.cc
+++ b/sidechain/src/scwrl4_rotamer_constructor.cc
@@ -22,7 +22,36 @@
#include <promod3/core/runtime_profiling.hh>
#include <ost/conop/conop.hh>
-namespace{
+namespace promod3 { namespace sidechain {
+
+/// \brief Types of lone pair construction
+enum SCWRL4LPRule {
+ LONE_PAIR_CARBONYL, LONE_PAIR_COH, LONE_PAIR_CNC
+};
+
+/// \brief Info for lone pair construction (always involves 3 particles)
+/// -> indices are in same order as particles. The lone pair gets finally added
+/// to particle with p_idx
+/// A, B and C are indices as they are stored in AllAtomPositions, p_idx is the
+/// index of the particle in the rotamer, where the lone pairs get added
+struct SCWRL4LPInfo {
+ SCWRL4LPInfo() { }
+ SCWRL4LPInfo(int idx_A, int idx_B, int idx_C,
+ bool a_ih, bool b_ih, bool c_ih,
+ SCWRL4LPRule r)
+ : index_A(idx_A), index_B(idx_B),
+ index_C(idx_C), A_is_hydrogen(a_ih),
+ B_is_hydrogen(b_ih), C_is_hydrogen(c_ih),
+ rule(r) { }
+ int index_A;
+ int index_B;
+ int index_C;
+ bool A_is_hydrogen;
+ bool B_is_hydrogen;
+ bool C_is_hydrogen;
+ SCWRL4LPRule rule;
+};
+
// add lone pairs for carbonyl (X-C-O) to O particle p
void _AddLonePairsCarbonyl(const geom::Vec3& x_pos, const geom::Vec3& c_pos,
@@ -37,6 +66,7 @@ void _AddLonePairsCarbonyl(const geom::Vec3& x_pos, const geom::Vec3& c_pos,
p->AddLonePair(lone_pair_center_two - o_pos);
}
+
// add lone pairs for C-O-H combos (SER / THR / TYR) to O particle p
void _AddLonePairsCOH(const geom::Vec3& c_pos, const geom::Vec3& o_pos,
const geom::Vec3& h_pos,
@@ -67,7 +97,7 @@ void _AddLonePairsCNC(const geom::Vec3& c1_pos, const geom::Vec3& n_pos,
}
void EvalLonePairRule(promod3::sidechain::SCWRL4Param* p,
- promod3::sidechain::SCWRLLPRule rule,
+ promod3::sidechain::SCWRL4LPRule rule,
const geom::Vec3& a,
const geom::Vec3& b,
const geom::Vec3& c) {
@@ -87,10 +117,12 @@ void EvalLonePairRule(promod3::sidechain::SCWRL4Param* p,
}
}
+
inline bool _IsHydrogen(const String& element) {
return element == "H" || element == "D";
}
+
// forward declaration
struct _AtomInfo;
@@ -183,1425 +215,617 @@ _AtomSpecCPList _GetCarboxylAtoms(const _AtomInfo& atom_info) {
return carbonyl_atoms;
}
-}
-
-namespace promod3 { namespace sidechain {
-
-SCWRLRotamerLookup::SCWRLRotamerLookup(bool cb_in_sidechain) {
-
- core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "SCWRLRotamerLookup::SCWRLRotamerLookup", 2);
-
- // ARG
- sidechain_infos_[ARG].has_hydrogens = true;
- sidechain_infos_[ARG].internal_e_prefactor = 2.27;
- sidechain_infos_[ARG].frm_t = 1.23;
-
- AddInfo(ARG, CH2Particle, 0.0, "CG", promod3::loop::ARG_CG_INDEX, false);
- AddInfo(ARG, CH2Particle, 0.1, "CD", promod3::loop::ARG_CD_INDEX, false);
- AddInfo(ARG, NParticle, -0.4, "NE", promod3::loop::ARG_NE_INDEX, false);
- AddInfo(ARG, CParticle, 0.5, "CZ", promod3::loop::ARG_CZ_INDEX, false);
- AddInfo(ARG, NParticle, -0.45, "NH1", promod3::loop::ARG_NH1_INDEX, false);
- AddInfo(ARG, NParticle, -0.45, "NH2", promod3::loop::ARG_NH2_INDEX, false);
- AddInfo(ARG, HParticle, 0.3, "HE", promod3::loop::ARG_HE_INDEX, true);
- AddInfo(ARG, HParticle, 0.35, "HH11", promod3::loop::ARG_HH11_INDEX, true);
- AddInfo(ARG, HParticle, 0.35, "HH12", promod3::loop::ARG_HH12_INDEX, true);
- AddInfo(ARG, HParticle, 0.35, "HH21", promod3::loop::ARG_HH21_INDEX, true);
- AddInfo(ARG, HParticle, 0.35, "HH22", promod3::loop::ARG_HH22_INDEX, true);
-
- if(cb_in_sidechain) {
- AddInfo(ARG, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddPDir(ARG, promod3::loop::ARG_HE_INDEX, promod3::loop::ARG_NE_INDEX, 6);
- AddPDir(ARG, promod3::loop::ARG_HH11_INDEX, promod3::loop::ARG_NH1_INDEX, 7);
- AddPDir(ARG, promod3::loop::ARG_HH12_INDEX, promod3::loop::ARG_NH1_INDEX, 8);
- AddPDir(ARG, promod3::loop::ARG_HH21_INDEX, promod3::loop::ARG_NH2_INDEX, 9);
- AddPDir(ARG, promod3::loop::ARG_HH22_INDEX, promod3::loop::ARG_NH2_INDEX, 10);
-
- AddFRMRule(ARG, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
- AddFRMPrefactor(ARG, 0, -0.87);
- AddFRMPrefactor(ARG, 0, 0.87);
- AddFRMRotatingParticle(ARG, 0, 0);
- AddFRMRotatingParticle(ARG, 0, 1);
- AddFRMRotatingParticle(ARG, 0, 2);
- AddFRMRotatingParticle(ARG, 0, 3);
- AddFRMRotatingParticle(ARG, 0, 4);
- AddFRMRotatingParticle(ARG, 0, 5);
- AddFRMRotatingParticle(ARG, 0, 6);
- AddFRMRotatingParticle(ARG, 0, 7);
- AddFRMRotatingParticle(ARG, 0, 8);
- AddFRMRotatingParticle(ARG, 0, 9);
- AddFRMRotatingParticle(ARG, 0, 10);
-
- AddFRMRule(ARG, promod3::loop::BB_CB_INDEX, promod3::loop::ARG_CG_INDEX);
- AddFRMPrefactor(ARG, 1, -1.62);
- AddFRMPrefactor(ARG, 1, 1.62);
- AddFRMFixParticle(ARG, 1, 0);
- AddFRMRotatingParticle(ARG, 1, 1);
- AddFRMRotatingParticle(ARG, 1, 2);
- AddFRMRotatingParticle(ARG, 1, 3);
- AddFRMRotatingParticle(ARG, 1, 4);
- AddFRMRotatingParticle(ARG, 1, 5);
- AddFRMRotatingParticle(ARG, 1, 6);
- AddFRMRotatingParticle(ARG, 1, 7);
- AddFRMRotatingParticle(ARG, 1, 8);
- AddFRMRotatingParticle(ARG, 1, 9);
- AddFRMRotatingParticle(ARG, 1, 10);
-
- AddFRMRule(ARG, promod3::loop::ARG_CG_INDEX, promod3::loop::ARG_CD_INDEX);
- AddFRMPrefactor(ARG, 2, -1.67);
- AddFRMPrefactor(ARG, 2, 1.67);
- AddFRMFixParticle(ARG, 2, 0);
- AddFRMFixParticle(ARG, 2, 1);
- AddFRMRotatingParticle(ARG, 2, 2);
- AddFRMRotatingParticle(ARG, 2, 3);
- AddFRMRotatingParticle(ARG, 2, 4);
- AddFRMRotatingParticle(ARG, 2, 5);
- AddFRMRotatingParticle(ARG, 2, 6);
- AddFRMRotatingParticle(ARG, 2, 7);
- AddFRMRotatingParticle(ARG, 2, 8);
- AddFRMRotatingParticle(ARG, 2, 9);
- AddFRMRotatingParticle(ARG, 2, 10);
-
- AddFRMRule(ARG, promod3::loop::ARG_CD_INDEX, promod3::loop::ARG_NE_INDEX);
- AddFRMPrefactor(ARG, 3, -0.73);
- AddFRMPrefactor(ARG, 3, 0.73);
- AddFRMFixParticle(ARG, 3, 0);
- AddFRMFixParticle(ARG, 3, 1);
- AddFRMFixParticle(ARG, 3, 2);
- AddFRMRotatingParticle(ARG, 3, 3);
- AddFRMRotatingParticle(ARG, 3, 4);
- AddFRMRotatingParticle(ARG, 3, 5);
- AddFRMRotatingParticle(ARG, 3, 6);
- AddFRMRotatingParticle(ARG, 3, 7);
- AddFRMRotatingParticle(ARG, 3, 8);
- AddFRMRotatingParticle(ARG, 3, 9);
- AddFRMRotatingParticle(ARG, 3, 10);
-
- if(cb_in_sidechain) {
- AddFRMFixParticle(ARG, 0, 11);
- AddFRMFixParticle(ARG, 1, 11);
- AddFRMFixParticle(ARG, 2, 11);
- AddFRMFixParticle(ARG, 3, 11);
- }
-
- backbone_infos_[ARG].has_hydrogens = true;
- AddBBInfo(ARG, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
- AddBBInfo(ARG, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
- AddBBInfo(ARG, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
- AddBBInfo(ARG, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(ARG, HParticle, 0.25, "H", promod3::loop::ARG_H_INDEX,true);
-
- if(!cb_in_sidechain) {
- AddBBInfo(ARG, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddBBPDir(ARG, promod3::loop::ARG_H_INDEX, promod3::loop::BB_N_INDEX, 4);
- AddBBLP(ARG, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
- promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
-
- // ASN
- sidechain_infos_[ASN].has_hydrogens = true;
- sidechain_infos_[ASN].internal_e_prefactor = 1.80;
- sidechain_infos_[ASN].frm_t = 1.41;
-
- AddInfo(ASN, CParticle, 0.55, "CG", promod3::loop::ASN_CG_INDEX, false);
- AddInfo(ASN, OParticle, -0.55, "OD1", promod3::loop::ASN_OD1_INDEX, false);
- AddInfo(ASN, NParticle, -0.6, "ND2", promod3::loop::ASN_ND2_INDEX, false);
- AddInfo(ASN, HParticle, 0.3, "HD21", promod3::loop::ASN_HD21_INDEX, true);
- AddInfo(ASN, HParticle, 0.3, "HD22", promod3::loop::ASN_HD22_INDEX, true);
-
- if(cb_in_sidechain) {
- AddInfo(ASN, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddPDir(ASN, promod3::loop::ASN_HD21_INDEX, promod3::loop::ASN_ND2_INDEX, 3);
- AddPDir(ASN, promod3::loop::ASN_HD22_INDEX, promod3::loop::ASN_ND2_INDEX, 4);
- AddLP(ASN, promod3::loop::ASN_ND2_INDEX, promod3::loop::ASN_CG_INDEX,
- promod3::loop::ASN_OD1_INDEX, false, false, false, 1, LONE_PAIR_CARBONYL);
-
- AddFRMRule(ASN, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
- AddFRMPrefactor(ASN, 0, -0.62);
- AddFRMPrefactor(ASN, 0, 0.62);
- AddFRMRotatingParticle(ASN, 0, 0);
- AddFRMRotatingParticle(ASN, 0, 1);
- AddFRMRotatingParticle(ASN, 0, 2);
- AddFRMRotatingParticle(ASN, 0, 3);
- AddFRMRotatingParticle(ASN, 0, 4);
-
- AddFRMRule(ASN, promod3::loop::BB_CB_INDEX, promod3::loop::ASN_CG_INDEX);
- AddFRMPrefactor(ASN, 1, -1.93);
- AddFRMPrefactor(ASN, 1, 1.93);
- AddFRMFixParticle(ASN, 1, 0);
- AddFRMRotatingParticle(ASN, 1, 1);
- AddFRMRotatingParticle(ASN, 1, 2);
- AddFRMRotatingParticle(ASN, 1, 3);
- AddFRMRotatingParticle(ASN, 1, 4);
-
- if(cb_in_sidechain) {
- AddFRMFixParticle(ASN, 0, 5);
- AddFRMFixParticle(ASN, 1, 5);
- }
-
- backbone_infos_[ASN].has_hydrogens = true;
- AddBBInfo(ASN, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
- AddBBInfo(ASN, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
- AddBBInfo(ASN, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
- AddBBInfo(ASN, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(ASN, HParticle, 0.25, "H", promod3::loop::ASN_H_INDEX,true);
-
- if(!cb_in_sidechain) {
- AddBBInfo(ASN, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddBBPDir(ASN, promod3::loop::ASN_H_INDEX, promod3::loop::BB_N_INDEX, 4);
- AddBBLP(ASN, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
- promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
-
- // ASP
- sidechain_infos_[ASP].internal_e_prefactor = 2.44;
- sidechain_infos_[ASP].frm_t = 1.48;
- sidechain_infos_[ASP].has_hydrogens = false;
-
- AddInfo(ASP, CParticle, 0.36, "CG", promod3::loop::ASP_CG_INDEX, false);
- AddInfo(ASP, OParticle, -0.60, "OD1", promod3::loop::ASP_OD1_INDEX, false);
- AddInfo(ASP, OParticle, -0.60, "OD2", promod3::loop::ASP_OD2_INDEX, false);
-
- if(cb_in_sidechain) {
- AddInfo(ASP, CH2Particle, -0.16, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddLP(ASP, promod3::loop::ASP_OD2_INDEX, promod3::loop::ASP_CG_INDEX,
- promod3::loop::ASP_OD1_INDEX, false, false, false, 1, LONE_PAIR_CARBONYL);
- AddLP(ASP, promod3::loop::ASP_OD1_INDEX, promod3::loop::ASP_CG_INDEX,
- promod3::loop::ASP_OD2_INDEX, false, false, false, 2, LONE_PAIR_CARBONYL);
-
- AddFRMRule(ASP, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
- AddFRMPrefactor(ASP, 0, -1.59);
- AddFRMPrefactor(ASP, 0, 1.59);
- AddFRMRotatingParticle(ASP, 0, 0);
- AddFRMRotatingParticle(ASP, 0, 1);
- AddFRMRotatingParticle(ASP, 0, 2);
-
- AddFRMRule(ASP, promod3::loop::BB_CB_INDEX, promod3::loop::ASP_CG_INDEX);
- AddFRMPrefactor(ASP, 1, -0.63);
- AddFRMPrefactor(ASP, 1, 0.63);
- AddFRMFixParticle(ASP, 1, 0);
- AddFRMRotatingParticle(ASP, 1, 1);
- AddFRMRotatingParticle(ASP, 1, 2);
-
- if(cb_in_sidechain) {
- AddFRMFixParticle(ASP, 0, 3);
- AddFRMFixParticle(ASP, 1, 3);
- }
-
- backbone_infos_[ASP].has_hydrogens = true;
- AddBBInfo(ASP, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
- AddBBInfo(ASP, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
- AddBBInfo(ASP, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
- AddBBInfo(ASP, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(ASP, HParticle, 0.25, "H", promod3::loop::ASP_H_INDEX,true);
-
- if(!cb_in_sidechain) {
- AddBBInfo(ASP, CH2Particle, -0.16, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddBBPDir(ASP, promod3::loop::ASP_H_INDEX, promod3::loop::BB_N_INDEX, 4);
- AddBBLP(ASP, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
- promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
-
- // GLN
- sidechain_infos_[GLN].has_hydrogens = true;
- sidechain_infos_[GLN].internal_e_prefactor = 1.61;
- sidechain_infos_[GLN].frm_t = 1.32;
-
- AddInfo(GLN, CH2Particle, 0.0, "CG", promod3::loop::GLN_CG_INDEX, false);
- AddInfo(GLN, CParticle, 0.55, "CD", promod3::loop::GLN_CD_INDEX, false);
- AddInfo(GLN, OParticle, -0.55, "OE1", promod3::loop::GLN_OE1_INDEX, false);
- AddInfo(GLN, NParticle, -0.60, "NE2", promod3::loop::GLN_NE2_INDEX, false);
- AddInfo(GLN, HParticle, 0.3, "HE21", promod3::loop::GLN_HE21_INDEX, true);
- AddInfo(GLN, HParticle, 0.3, "HE22", promod3::loop::GLN_HE22_INDEX, true);
-
- if(cb_in_sidechain) {
- AddInfo(GLN, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddPDir(GLN, promod3::loop::GLN_HE21_INDEX, promod3::loop::GLN_NE2_INDEX, 4);
- AddPDir(GLN, promod3::loop::GLN_HE22_INDEX, promod3::loop::GLN_NE2_INDEX, 5);
- AddLP(GLN, promod3::loop::GLN_NE2_INDEX, promod3::loop::GLN_CD_INDEX,
- promod3::loop::GLN_OE1_INDEX, false, false, false, 2, LONE_PAIR_CARBONYL);
-
- AddFRMRule(GLN, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
- AddFRMPrefactor(GLN, 0, -1.55);
- AddFRMPrefactor(GLN, 0, 1.55);
- AddFRMRotatingParticle(GLN, 0, 0);
- AddFRMRotatingParticle(GLN, 0, 1);
- AddFRMRotatingParticle(GLN, 0, 2);
- AddFRMRotatingParticle(GLN, 0, 3);
- AddFRMRotatingParticle(GLN, 0, 4);
- AddFRMRotatingParticle(GLN, 0, 5);
-
- AddFRMRule(GLN, promod3::loop::BB_CB_INDEX, promod3::loop::GLN_CG_INDEX);
- AddFRMPrefactor(GLN, 1, -0.53);
- AddFRMPrefactor(GLN, 1, 0.53);
- AddFRMFixParticle(GLN, 1, 0);
- AddFRMRotatingParticle(GLN, 1, 1);
- AddFRMRotatingParticle(GLN, 1, 2);
- AddFRMRotatingParticle(GLN, 1, 3);
- AddFRMRotatingParticle(GLN, 1, 4);
- AddFRMRotatingParticle(GLN, 1, 5);
-
- AddFRMRule(GLN, promod3::loop::GLN_CG_INDEX, promod3::loop::GLN_CD_INDEX);
- AddFRMPrefactor(GLN, 2, -1.89);
- AddFRMPrefactor(GLN, 2, 1.89);
- AddFRMFixParticle(GLN, 2, 0);
- AddFRMFixParticle(GLN, 2, 1);
- AddFRMRotatingParticle(GLN, 2, 2);
- AddFRMRotatingParticle(GLN, 2, 3);
- AddFRMRotatingParticle(GLN, 2, 4);
- AddFRMRotatingParticle(GLN, 2, 5);
-
- if(cb_in_sidechain) {
- AddFRMFixParticle(GLN, 0, 6);
- AddFRMFixParticle(GLN, 1, 6);
- AddFRMFixParticle(GLN, 2, 6);
- }
-
- backbone_infos_[GLN].has_hydrogens = true;
- AddBBInfo(GLN, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
- AddBBInfo(GLN, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
- AddBBInfo(GLN, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
- AddBBInfo(GLN, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(GLN, HParticle, 0.25, "H", promod3::loop::GLN_H_INDEX,true);
-
- if(!cb_in_sidechain) {
- AddBBInfo(GLN, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddBBPDir(GLN, promod3::loop::GLN_H_INDEX, promod3::loop::BB_N_INDEX, 4);
- AddBBLP(GLN, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
- promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
-
- // GLU
- sidechain_infos_[GLU].has_hydrogens = false;
- sidechain_infos_[GLU].internal_e_prefactor = 1.85;
- sidechain_infos_[GLU].frm_t = 0.94;
-
- AddInfo(GLU, CH2Particle, -0.16, "CG", promod3::loop::GLU_CG_INDEX, false);
- AddInfo(GLU, CParticle, 0.36, "CD", promod3::loop::GLU_CD_INDEX, false);
- AddInfo(GLU, OParticle, -0.60, "OE1", promod3::loop::GLU_OE1_INDEX, false);
- AddInfo(GLU, OParticle, -0.60, "OE2", promod3::loop::GLU_OE2_INDEX, false);
-
- if(cb_in_sidechain) {
- AddInfo(GLU, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddLP(GLU, promod3::loop::GLU_OE2_INDEX, promod3::loop::GLU_CD_INDEX,
- promod3::loop::GLU_OE1_INDEX, false, false, false, 2, LONE_PAIR_CARBONYL);
- AddLP(GLU, promod3::loop::GLU_OE1_INDEX, promod3::loop::GLU_CD_INDEX,
- promod3::loop::GLU_OE2_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
-
- AddFRMRule(GLU, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
- AddFRMPrefactor(GLU, 0, -0.82);
- AddFRMPrefactor(GLU, 0, 0.82);
- AddFRMRotatingParticle(GLU, 0, 0);
- AddFRMRotatingParticle(GLU, 0, 1);
- AddFRMRotatingParticle(GLU, 0, 2);
- AddFRMRotatingParticle(GLU, 0, 3);
-
- AddFRMRule(GLU, promod3::loop::BB_CB_INDEX, promod3::loop::GLU_CG_INDEX);
- AddFRMPrefactor(GLU, 1, -1.57);
- AddFRMPrefactor(GLU, 1, 1.57);
- AddFRMFixParticle(GLU, 1, 0);
- AddFRMRotatingParticle(GLU, 1, 1);
- AddFRMRotatingParticle(GLU, 1, 2);
- AddFRMRotatingParticle(GLU, 1, 3);
-
- AddFRMRule(GLU, promod3::loop::GLU_CG_INDEX, promod3::loop::GLU_CD_INDEX);
- AddFRMPrefactor(GLU, 2, -0.76);
- AddFRMPrefactor(GLU, 2, 0.76);
- AddFRMFixParticle(GLU, 2, 0);
- AddFRMFixParticle(GLU, 2, 1);
- AddFRMRotatingParticle(GLU, 2, 2);
- AddFRMRotatingParticle(GLU, 2, 3);
-
- if(cb_in_sidechain) {
- AddFRMFixParticle(GLU, 0, 4);
- AddFRMFixParticle(GLU, 1, 4);
- AddFRMFixParticle(GLU, 2, 4);
- }
-
- backbone_infos_[GLU].has_hydrogens = true;
- AddBBInfo(GLU, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
- AddBBInfo(GLU, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
- AddBBInfo(GLU, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
- AddBBInfo(GLU, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(GLU, HParticle, 0.25, "H", promod3::loop::GLU_H_INDEX,true);
-
- if(!cb_in_sidechain) {
- AddBBInfo(GLU, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddBBPDir(GLU, promod3::loop::GLU_H_INDEX, promod3::loop::BB_N_INDEX, 4);
- AddBBLP(GLU, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
- promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
-
- // LYS
- sidechain_infos_[LYS].has_hydrogens = true;
- sidechain_infos_[LYS].internal_e_prefactor = 2.13;
- sidechain_infos_[LYS].frm_t = 1.27;
-
- AddInfo(LYS, CH2Particle, 0.0, "CG", promod3::loop::LYS_CG_INDEX,false);
- AddInfo(LYS, CH2Particle, 0.0, "CD", promod3::loop::LYS_CD_INDEX,false);
- AddInfo(LYS, CH2Particle, 0.25, "CE", promod3::loop::LYS_CE_INDEX,false);
- AddInfo(LYS, NParticle, -0.3, "NZ", promod3::loop::LYS_NZ_INDEX,false);
- AddInfo(LYS, HParticle, 0.35, "HZ1", promod3::loop::LYS_HZ1_INDEX,true);
- AddInfo(LYS, HParticle, 0.35, "HZ2", promod3::loop::LYS_HZ2_INDEX,true);
- AddInfo(LYS, HParticle, 0.35, "HZ3", promod3::loop::LYS_HZ3_INDEX,true);
-
- if(cb_in_sidechain) {
- AddInfo(LYS, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddPDir(LYS, promod3::loop::LYS_HZ1_INDEX, promod3::loop::LYS_NZ_INDEX, 4);
- AddPDir(LYS, promod3::loop::LYS_HZ2_INDEX, promod3::loop::LYS_NZ_INDEX, 5);
- AddPDir(LYS, promod3::loop::LYS_HZ3_INDEX, promod3::loop::LYS_NZ_INDEX, 6);
-
- AddFRMRule(LYS, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
- AddFRMPrefactor(LYS, 0, -1.62);
- AddFRMPrefactor(LYS, 0, 1.62);
- AddFRMRotatingParticle(LYS, 0, 0);
- AddFRMRotatingParticle(LYS, 0, 1);
- AddFRMRotatingParticle(LYS, 0, 2);
- AddFRMRotatingParticle(LYS, 0, 3);
- AddFRMRotatingParticle(LYS, 0, 4);
- AddFRMRotatingParticle(LYS, 0, 5);
- AddFRMRotatingParticle(LYS, 0, 6);
-
- AddFRMRule(LYS, promod3::loop::BB_CB_INDEX, promod3::loop::LYS_CG_INDEX);
- AddFRMPrefactor(LYS, 1, -0.99);
- AddFRMPrefactor(LYS, 1, 0.99);
- AddFRMFixParticle(LYS, 1, 0);
- AddFRMRotatingParticle(LYS, 1, 1);
- AddFRMRotatingParticle(LYS, 1, 2);
- AddFRMRotatingParticle(LYS, 1, 3);
- AddFRMRotatingParticle(LYS, 1, 4);
- AddFRMRotatingParticle(LYS, 1, 5);
- AddFRMRotatingParticle(LYS, 1, 6);
-
- AddFRMRule(LYS, promod3::loop::LYS_CG_INDEX, promod3::loop::LYS_CD_INDEX);
- AddFRMPrefactor(LYS, 2, -0.96);
- AddFRMPrefactor(LYS, 2, 0.96);
- AddFRMFixParticle(LYS, 2, 0);
- AddFRMFixParticle(LYS, 2, 1);
- AddFRMRotatingParticle(LYS, 2, 2);
- AddFRMRotatingParticle(LYS, 2, 3);
- AddFRMRotatingParticle(LYS, 2, 4);
- AddFRMRotatingParticle(LYS, 2, 5);
- AddFRMRotatingParticle(LYS, 2, 6);
-
- AddFRMRule(LYS, promod3::loop::LYS_CD_INDEX, promod3::loop::LYS_CE_INDEX);
- AddFRMPrefactor(LYS, 3, -1.49);
- AddFRMPrefactor(LYS, 3, 1.49);
- AddFRMFixParticle(LYS, 3, 0);
- AddFRMFixParticle(LYS, 3, 1);
- AddFRMFixParticle(LYS, 3, 2);
- AddFRMRotatingParticle(LYS, 3, 3);
- AddFRMRotatingParticle(LYS, 3, 4);
- AddFRMRotatingParticle(LYS, 3, 5);
- AddFRMRotatingParticle(LYS, 3, 6);
-
- if(cb_in_sidechain) {
- AddFRMFixParticle(LYS, 0, 7);
- AddFRMFixParticle(LYS, 1, 7);
- AddFRMFixParticle(LYS, 2, 7);
- AddFRMFixParticle(LYS, 3, 7);
- }
-
- backbone_infos_[LYS].has_hydrogens = true;
- AddBBInfo(LYS, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
- AddBBInfo(LYS, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
- AddBBInfo(LYS, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
- AddBBInfo(LYS, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(LYS, HParticle, 0.25, "H", promod3::loop::LYS_H_INDEX,true);
-
- if(!cb_in_sidechain) {
- AddBBInfo(LYS, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddBBPDir(LYS, promod3::loop::LYS_H_INDEX, promod3::loop::BB_N_INDEX, 4);
- AddBBLP(LYS, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
- promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
-
- // SER
- sidechain_infos_[SER].has_hydrogens = true;
- sidechain_infos_[SER].internal_e_prefactor = 2.78;
- sidechain_infos_[SER].frm_t = 3.53;
-
- AddInfo(SER, OParticle, -0.65, "OG", promod3::loop::SER_OG_INDEX, false);
- AddInfo(SER, HParticle, 0.40, "HG", promod3::loop::SER_HG_INDEX, true);
-
- if(cb_in_sidechain) {
- AddInfo(SER, CH2Particle, 0.25, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddPDir(SER, promod3::loop::SER_HG_INDEX, promod3::loop::SER_OG_INDEX, 1);
- AddLP(SER, promod3::loop::BB_CB_INDEX, promod3::loop::SER_OG_INDEX,
- promod3::loop::SER_HG_INDEX, false, false, true, 0, LONE_PAIR_COH);
- AddCustomHydrogenInfo(SER, promod3::loop::SER_HG_INDEX,
- promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX,
- promod3::loop::SER_OG_INDEX,
- 0.96, 1.85, 1);
-
- AddFRMRule(SER, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
- AddFRMPrefactor(SER, 0, -0.65);
- AddFRMPrefactor(SER, 0, 0.65);
- AddFRMRotatingParticle(SER, 0, 0);
- AddFRMRotatingParticle(SER, 0, 1);
-
- AddFRMRule(SER, promod3::loop::BB_CB_INDEX, promod3::loop::SER_OG_INDEX);
- AddFRMPrefactor(SER, 1, -2.98);
- AddFRMPrefactor(SER, 1, 2.98);
- AddFRMFixParticle(SER, 1, 0);
- AddFRMRotatingParticle(SER, 1, 1);
-
- if(cb_in_sidechain) {
- AddFRMFixParticle(SER, 0, 2);
- AddFRMFixParticle(SER, 1, 2);
- }
-
- backbone_infos_[SER].has_hydrogens = true;
- AddBBInfo(SER, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
- AddBBInfo(SER, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
- AddBBInfo(SER, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
- AddBBInfo(SER, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(SER, HParticle, 0.25, "H", promod3::loop::SER_H_INDEX,true);
-
- if(!cb_in_sidechain) {
- AddBBInfo(SER, CH2Particle, 0.25, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddBBPDir(SER, promod3::loop::SER_H_INDEX, promod3::loop::BB_N_INDEX, 4);
- AddBBLP(SER, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
- promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
-
- // CYS
- sidechain_infos_[CYS].has_hydrogens = false;
- sidechain_infos_[CYS].internal_e_prefactor = 4.07;
- sidechain_infos_[CYS].frm_t = 1.69;
-
- AddInfo(CYS, SParticle, -0.19, "SG", promod3::loop::CYS_SG_INDEX, false);
-
- if(cb_in_sidechain) {
- AddInfo(CYS, CH2Particle, 0.19, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddFRMRule(CYS, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
- AddFRMPrefactor(CYS, 0, -1.69);
- AddFRMPrefactor(CYS, 0, 1.69);
- AddFRMRotatingParticle(CYS, 0, 0);
-
- if(cb_in_sidechain) {
- AddFRMFixParticle(CYS, 0, 1);
- }
-
- backbone_infos_[CYS].has_hydrogens = true;
- AddBBInfo(CYS, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
- AddBBInfo(CYS, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
- AddBBInfo(CYS, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
- AddBBInfo(CYS, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(CYS, HParticle, 0.25, "H", promod3::loop::CYS_H_INDEX,true);
-
- if(!cb_in_sidechain) {
- AddBBInfo(CYS, CH2Particle, 0.19, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddBBPDir(CYS, promod3::loop::CYS_H_INDEX, promod3::loop::BB_N_INDEX, 4);
- AddBBLP(CYS, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
- promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
-
- // CYH
- sidechain_infos_[CYH] = sidechain_infos_[CYS];
- frm_rules_[CYH] = frm_rules_[CYS];
- backbone_infos_[CYH] = backbone_infos_[CYS];
-
- // CYD
- sidechain_infos_[CYD] = sidechain_infos_[CYS];
- frm_rules_[CYD] = frm_rules_[CYS];
- backbone_infos_[CYD] = backbone_infos_[CYS];
-
- // MET
- sidechain_infos_[MET].has_hydrogens = false;
- sidechain_infos_[MET].internal_e_prefactor = 1.95;
- sidechain_infos_[MET].frm_t = 1.77;
-
- AddInfo(MET, CH2Particle, 0.06, "CG", promod3::loop::MET_CG_INDEX,false);
- AddInfo(MET, SParticle, -0.12, "SD", promod3::loop::MET_SD_INDEX,false);
- AddInfo(MET, CH3Particle, 0.06, "CE", promod3::loop::MET_CE_INDEX,false);
-
- if(cb_in_sidechain) {
- AddInfo(MET, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddFRMRule(MET, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
- AddFRMPrefactor(MET, 0, -0.97);
- AddFRMPrefactor(MET, 0, 0.97);
- AddFRMRotatingParticle(MET, 0, 0);
- AddFRMRotatingParticle(MET, 0, 1);
- AddFRMRotatingParticle(MET, 0, 2);
-
- AddFRMRule(MET, promod3::loop::BB_CB_INDEX, promod3::loop::MET_CG_INDEX);
- AddFRMPrefactor(MET, 1, -1.54);
- AddFRMPrefactor(MET, 1, 1.54);
- AddFRMFixParticle(MET, 1, 0);
- AddFRMRotatingParticle(MET, 1, 1);
- AddFRMRotatingParticle(MET, 1, 2);
-
- AddFRMRule(MET, promod3::loop::MET_CG_INDEX, promod3::loop::MET_SD_INDEX);
- AddFRMPrefactor(MET, 2, -1.21);
- AddFRMPrefactor(MET, 2, 1.21);
- AddFRMFixParticle(MET, 2, 0);
- AddFRMFixParticle(MET, 2, 1);
- AddFRMRotatingParticle(MET, 2, 2);
-
- if(cb_in_sidechain) {
- AddFRMFixParticle(MET, 0, 3);
- AddFRMFixParticle(MET, 1, 3);
- AddFRMFixParticle(MET, 2, 3);
- }
-
- backbone_infos_[MET].has_hydrogens = true;
- AddBBInfo(MET, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
- AddBBInfo(MET, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
- AddBBInfo(MET, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
- AddBBInfo(MET, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(MET, HParticle, 0.25, "H", promod3::loop::MET_H_INDEX,true);
-
- if(!cb_in_sidechain) {
- AddBBInfo(MET, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddBBPDir(MET, promod3::loop::MET_H_INDEX, promod3::loop::BB_N_INDEX, 4);
- AddBBLP(MET, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
- promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
-
- // TRP
- sidechain_infos_[TRP].has_hydrogens = true;
- sidechain_infos_[TRP].internal_e_prefactor = 3.24;
- sidechain_infos_[TRP].frm_t = 0.99;
-
- AddInfo(TRP, CParticle,-0.03, "CG", promod3::loop::TRP_CG_INDEX,false);
- AddInfo(TRP, CParticle, 0.06, "CD1", promod3::loop::TRP_CD1_INDEX,false);
- AddInfo(TRP, CParticle, 0.10, "CD2", promod3::loop::TRP_CD2_INDEX,false);
- AddInfo(TRP, CParticle, -0.04, "CE2", promod3::loop::TRP_CE2_INDEX,false);
- AddInfo(TRP, NParticle, -0.36, "NE1", promod3::loop::TRP_NE1_INDEX,false);
- AddInfo(TRP, CParticle, -0.03, "CE3", promod3::loop::TRP_CE3_INDEX,false);
- AddInfo(TRP, CParticle, 0.00, "CZ3", promod3::loop::TRP_CZ3_INDEX,false);
- AddInfo(TRP, CParticle, 0.00, "CH2", promod3::loop::TRP_CH2_INDEX,false);
- AddInfo(TRP, CParticle, 0.00, "CZ2", promod3::loop::TRP_CZ2_INDEX,false);
- AddInfo(TRP, HParticle, 0.30, "HE1", promod3::loop::TRP_HE1_INDEX,true);
-
- if(cb_in_sidechain) {
- AddInfo(TRP, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddPDir(TRP, promod3::loop::TRP_HE1_INDEX, promod3::loop::TRP_NE1_INDEX, 9);
-
- AddFRMRule(TRP, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
- AddFRMPrefactor(TRP, 0, -1.28);
- AddFRMPrefactor(TRP, 0, 1.28);
- AddFRMRotatingParticle(TRP, 0, 0);
- AddFRMRotatingParticle(TRP, 0, 1);
- AddFRMRotatingParticle(TRP, 0, 2);
- AddFRMRotatingParticle(TRP, 0, 3);
- AddFRMRotatingParticle(TRP, 0, 4);
- AddFRMRotatingParticle(TRP, 0, 5);
- AddFRMRotatingParticle(TRP, 0, 6);
- AddFRMRotatingParticle(TRP, 0, 7);
- AddFRMRotatingParticle(TRP, 0, 8);
- AddFRMRotatingParticle(TRP, 0, 9);
-
- AddFRMRule(TRP, promod3::loop::BB_CB_INDEX, promod3::loop::TRP_CG_INDEX);
- AddFRMPrefactor(TRP, 1, -1.48);
- AddFRMPrefactor(TRP, 1, 1.48);
- AddFRMFixParticle(TRP, 1, 0);
- AddFRMRotatingParticle(TRP, 1, 1);
- AddFRMRotatingParticle(TRP, 1, 2);
- AddFRMRotatingParticle(TRP, 1, 3);
- AddFRMRotatingParticle(TRP, 1, 4);
- AddFRMRotatingParticle(TRP, 1, 5);
- AddFRMRotatingParticle(TRP, 1, 6);
- AddFRMRotatingParticle(TRP, 1, 7);
- AddFRMRotatingParticle(TRP, 1, 8);
- AddFRMRotatingParticle(TRP, 1, 9);
-
- if(cb_in_sidechain) {
- AddFRMFixParticle(TRP, 0, 10);
- AddFRMFixParticle(TRP, 1, 10);
- }
-
- backbone_infos_[TRP].has_hydrogens = true;
- AddBBInfo(TRP, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
- AddBBInfo(TRP, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
- AddBBInfo(TRP, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
- AddBBInfo(TRP, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(TRP, HParticle, 0.25, "H", promod3::loop::TRP_H_INDEX,true);
-
- if(!cb_in_sidechain) {
- AddBBInfo(TRP, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddBBPDir(TRP, promod3::loop::TRP_H_INDEX, promod3::loop::BB_N_INDEX, 4);
- AddBBLP(TRP, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
- promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
-
- // TYR
- sidechain_infos_[TYR].has_hydrogens = true;
- sidechain_infos_[TYR].internal_e_prefactor = 2.00;
- sidechain_infos_[TYR].frm_t = 1.96;
-
- AddInfo(TYR, CParticle, 0.0, "CG", promod3::loop::TYR_CG_INDEX,false);
- AddInfo(TYR, CParticle, 0.0, "CD1", promod3::loop::TYR_CD1_INDEX,false);
- AddInfo(TYR, CParticle, 0.0, "CD2", promod3::loop::TYR_CD2_INDEX,false);
- AddInfo(TYR, CParticle, 0.0, "CE1", promod3::loop::TYR_CE1_INDEX,false);
- AddInfo(TYR, CParticle, 0.0, "CE2", promod3::loop::TYR_CE2_INDEX,false);
- AddInfo(TYR, CParticle, 0.25, "CZ", promod3::loop::TYR_CZ_INDEX,false);
- AddInfo(TYR, OParticle, -0.65, "OH", promod3::loop::TYR_OH_INDEX,false);
- AddInfo(TYR, HParticle, 0.40, "HH", promod3::loop::TYR_HH_INDEX,true);
-
- if(cb_in_sidechain) {
- AddInfo(TYR, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddPDir(TYR, promod3::loop::TYR_HH_INDEX, promod3::loop::TYR_OH_INDEX, 7);
- AddLP(TYR, promod3::loop::TYR_CZ_INDEX, promod3::loop::TYR_OH_INDEX,
- promod3::loop::TYR_HH_INDEX, false, false, true, 6, LONE_PAIR_COH);
- AddCustomHydrogenInfo(TYR, promod3::loop::TYR_HH_INDEX,
- promod3::loop::TYR_CE1_INDEX,
- promod3::loop::TYR_CZ_INDEX,
- promod3::loop::TYR_OH_INDEX,
- 0.96, 1.885, 2);
-
- AddFRMRule(TYR, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
- AddFRMPrefactor(TYR, 0, -1.48);
- AddFRMPrefactor(TYR, 0, 1.48);
- AddFRMRotatingParticle(TYR, 0, 0);
- AddFRMRotatingParticle(TYR, 0, 1);
- AddFRMRotatingParticle(TYR, 0, 2);
- AddFRMRotatingParticle(TYR, 0, 3);
- AddFRMRotatingParticle(TYR, 0, 4);
- AddFRMRotatingParticle(TYR, 0, 5);
- AddFRMRotatingParticle(TYR, 0, 6);
- AddFRMRotatingParticle(TYR, 0, 7);
-
- AddFRMRule(TYR, promod3::loop::BB_CB_INDEX, promod3::loop::TYR_CG_INDEX);
- AddFRMPrefactor(TYR, 1, -0.73);
- AddFRMPrefactor(TYR, 1, 0.73);
- AddFRMFixParticle(TYR, 1, 0);
- AddFRMRotatingParticle(TYR, 1, 1);
- AddFRMRotatingParticle(TYR, 1, 2);
- AddFRMRotatingParticle(TYR, 1, 3);
- AddFRMRotatingParticle(TYR, 1, 4);
- AddFRMRotatingParticle(TYR, 1, 5);
- AddFRMRotatingParticle(TYR, 1, 6);
- AddFRMRotatingParticle(TYR, 1, 7);
-
- AddFRMRule(TYR, promod3::loop::TYR_CZ_INDEX, promod3::loop::TYR_OH_INDEX);
- AddFRMPrefactor(TYR, 2, -0.96);
- AddFRMPrefactor(TYR, 2, 0.96);
- AddFRMFixParticle(TYR, 2, 0);
- AddFRMFixParticle(TYR, 2, 1);
- AddFRMFixParticle(TYR, 2, 2);
- AddFRMFixParticle(TYR, 2, 3);
- AddFRMFixParticle(TYR, 2, 4);
- AddFRMFixParticle(TYR, 2, 5);
- AddFRMFixParticle(TYR, 2, 6);
- AddFRMRotatingParticle(TYR, 2, 7);
-
- if(cb_in_sidechain) {
- AddFRMFixParticle(TYR, 0, 8);
- AddFRMFixParticle(TYR, 1, 8);
- AddFRMFixParticle(TYR, 2, 8);
- }
-
- backbone_infos_[TYR].has_hydrogens = true;
- AddBBInfo(TYR, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
- AddBBInfo(TYR, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
- AddBBInfo(TYR, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
- AddBBInfo(TYR, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(TYR, HParticle, 0.25, "H", promod3::loop::TYR_H_INDEX,true);
-
- if(!cb_in_sidechain) {
- AddBBInfo(TYR, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddBBPDir(TYR, promod3::loop::TYR_H_INDEX, promod3::loop::BB_N_INDEX, 4);
- AddBBLP(TYR, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
- promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
-
- // THR
- sidechain_infos_[THR].has_hydrogens = true;
- sidechain_infos_[THR].internal_e_prefactor = 2.96;
- sidechain_infos_[THR].frm_t = 1.11;
-
- AddInfo(THR, OParticle, -0.65, "OG1", promod3::loop::THR_OG1_INDEX, false);
- AddInfo(THR, CH3Particle, 0.0, "CG2", promod3::loop::THR_CG2_INDEX, false);
- AddInfo(THR, HParticle, 0.40, "HG1", promod3::loop::THR_HG1_INDEX, true);
-
- if(cb_in_sidechain) {
- AddInfo(THR, CH2Particle, 0.25, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddPDir(THR, promod3::loop::THR_HG1_INDEX, promod3::loop::THR_OG1_INDEX, 2);
- AddLP(THR, promod3::loop::BB_CB_INDEX, promod3::loop::THR_OG1_INDEX,
- promod3::loop::THR_HG1_INDEX, false, false, true, 0, LONE_PAIR_COH);
- AddCustomHydrogenInfo(THR, promod3::loop::THR_HG1_INDEX,
- promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX,
- promod3::loop::THR_OG1_INDEX,
- 0.96, 1.85, 1);
-
- AddFRMRule(THR, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
- AddFRMPrefactor(THR, 0, -0.88);
- AddFRMPrefactor(THR, 0, 0.88);
- AddFRMRotatingParticle(THR, 0, 0);
- AddFRMRotatingParticle(THR, 0, 1);
- AddFRMRotatingParticle(THR, 0, 2);
-
- AddFRMRule(THR, promod3::loop::BB_CB_INDEX, promod3::loop::THR_OG1_INDEX);
- AddFRMPrefactor(THR, 1, -0.88);
- AddFRMPrefactor(THR, 1, 0.88);
- AddFRMFixParticle(THR, 1, 0);
- AddFRMFixParticle(THR, 1, 1);
- AddFRMRotatingParticle(THR, 1, 2);
-
- if(cb_in_sidechain) {
- AddFRMFixParticle(THR, 0, 3);
- AddFRMFixParticle(THR, 1, 3);
- }
-
- backbone_infos_[THR].has_hydrogens = true;
- AddBBInfo(THR, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
- AddBBInfo(THR, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
- AddBBInfo(THR, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
- AddBBInfo(THR, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(THR, HParticle, 0.25, "H", promod3::loop::THR_H_INDEX,true);
-
- if(!cb_in_sidechain) {
- AddBBInfo(THR, CH2Particle, 0.25, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddBBPDir(THR, promod3::loop::THR_H_INDEX, promod3::loop::BB_N_INDEX, 4);
- AddBBLP(THR, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
- promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
-
- // VAL
- sidechain_infos_[VAL].has_hydrogens = false;
- sidechain_infos_[VAL].internal_e_prefactor = 1.62;
- sidechain_infos_[VAL].frm_t = 2.20;
-
- AddInfo(VAL, CH3Particle, 0.0, "CG1", promod3::loop::VAL_CG1_INDEX, false);
- AddInfo(VAL, CH3Particle, 0.0, "CG2", promod3::loop::VAL_CG2_INDEX, false);
-
- if(cb_in_sidechain) {
- AddInfo(VAL, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddFRMRule(VAL, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
- AddFRMPrefactor(VAL, 0, -2.09);
- AddFRMPrefactor(VAL, 0, 2.09);
- AddFRMRotatingParticle(VAL, 0, 0);
- AddFRMRotatingParticle(VAL, 0, 1);
-
- if(cb_in_sidechain) {
- AddFRMFixParticle(VAL, 0, 2);
- }
-
- backbone_infos_[VAL].has_hydrogens = true;
- AddBBInfo(VAL, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
- AddBBInfo(VAL, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
- AddBBInfo(VAL, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
- AddBBInfo(VAL, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(VAL, HParticle, 0.25, "H", promod3::loop::VAL_H_INDEX,true);
-
- if(!cb_in_sidechain) {
- AddBBInfo(VAL, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddBBPDir(VAL, promod3::loop::VAL_H_INDEX, promod3::loop::BB_N_INDEX, 4);
- AddBBLP(VAL, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
- promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
-
- // ILE
- sidechain_infos_[ILE].has_hydrogens = false;
- sidechain_infos_[ILE].internal_e_prefactor = 2.18;
- sidechain_infos_[ILE].frm_t = 2.03;
-
- AddInfo(ILE, CH2Particle, 0.0, "CG1", promod3::loop::ILE_CG1_INDEX, false);
- AddInfo(ILE, CH3Particle, 0.0, "CG2", promod3::loop::ILE_CG2_INDEX, false);
- AddInfo(ILE, CH3Particle, 0.0, "CD1", promod3::loop::ILE_CD1_INDEX, false);
-
- if(cb_in_sidechain) {
- AddInfo(ILE, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddFRMRule(ILE, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
- AddFRMPrefactor(ILE, 0, -1.23);
- AddFRMPrefactor(ILE, 0, 1.23);
- AddFRMRotatingParticle(ILE, 0, 0);
- AddFRMRotatingParticle(ILE, 0, 1);
- AddFRMRotatingParticle(ILE, 0, 2);
-
- AddFRMRule(ILE, promod3::loop::BB_CB_INDEX, promod3::loop::ILE_CG1_INDEX);
- AddFRMPrefactor(ILE, 1, -0.98);
- AddFRMPrefactor(ILE, 1, 0.98);
- AddFRMFixParticle(ILE, 1, 0);
- AddFRMFixParticle(ILE, 1, 1);
- AddFRMRotatingParticle(ILE, 1, 2);
-
- if(cb_in_sidechain) {
- AddFRMFixParticle(ILE, 0, 3);
- AddFRMFixParticle(ILE, 1, 3);
- }
-
- backbone_infos_[ILE].has_hydrogens = true;
- AddBBInfo(ILE, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
- AddBBInfo(ILE, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
- AddBBInfo(ILE, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
- AddBBInfo(ILE, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(ILE, HParticle, 0.25, "H", promod3::loop::ILE_H_INDEX,true);
-
- if(!cb_in_sidechain) {
- AddBBInfo(ILE, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddBBPDir(ILE, promod3::loop::ILE_H_INDEX, promod3::loop::BB_N_INDEX, 4);
- AddBBLP(ILE, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
- promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
-
- // LEU
- sidechain_infos_[LEU].has_hydrogens = false;
- sidechain_infos_[LEU].internal_e_prefactor = 2.25;
- sidechain_infos_[LEU].frm_t = 2.55;
-
- AddInfo(LEU, CH1Particle, 0.0, "CG", promod3::loop::LEU_CG_INDEX, false);
- AddInfo(LEU, CH3Particle, 0.0, "CD1", promod3::loop::LEU_CD1_INDEX, false);
- AddInfo(LEU, CH3Particle, 0.0, "CD2", promod3::loop::LEU_CD2_INDEX, false);
-
- if(cb_in_sidechain) {
- AddInfo(LEU, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddFRMRule(LEU, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
- AddFRMPrefactor(LEU, 0, -1.15);
- AddFRMPrefactor(LEU, 0, 1.15);
- AddFRMRotatingParticle(LEU, 0, 0);
- AddFRMRotatingParticle(LEU, 0, 1);
- AddFRMRotatingParticle(LEU, 0, 2);
-
- AddFRMRule(LEU, promod3::loop::BB_CB_INDEX, promod3::loop::LEU_CG_INDEX);
- AddFRMPrefactor(LEU, 1, -1.48);
- AddFRMPrefactor(LEU, 1, 1.48);
- AddFRMFixParticle(LEU, 1, 0);
- AddFRMRotatingParticle(LEU, 1, 1);
- AddFRMRotatingParticle(LEU, 1, 2);
-
- if(cb_in_sidechain) {
- AddFRMFixParticle(LEU, 0, 3);
- AddFRMFixParticle(LEU, 1, 3);
- }
-
- backbone_infos_[LEU].has_hydrogens = true;
- AddBBInfo(LEU, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
- AddBBInfo(LEU, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
- AddBBInfo(LEU, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
- AddBBInfo(LEU, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(LEU, HParticle, 0.25, "H", promod3::loop::LEU_H_INDEX,true);
-
- if(!cb_in_sidechain) {
- AddBBInfo(LEU, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddBBPDir(LEU, promod3::loop::LEU_H_INDEX, promod3::loop::BB_N_INDEX, 4);
- AddBBLP(LEU, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
- promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
-
- // PROLINES DO NOT HAVE FRM DEFINITIONS!
- // large scale benchmarks showed, that varying around chi angles in case
- // of prolines has a negative effect on performance => reduce to one single
- // subrotamer...
-
- // PRO
- sidechain_infos_[PRO].has_hydrogens = false;
- sidechain_infos_[PRO].internal_e_prefactor = 0.76;
- sidechain_infos_[PRO].frm_t = 2.62;
-
- AddInfo(PRO, CH2Particle, 0.0, "CG", promod3::loop::PRO_CG_INDEX, false);
- AddInfo(PRO, CH2Particle, 0.0, "CD", promod3::loop::PRO_CD_INDEX, false);
-
- if(cb_in_sidechain) {
- AddInfo(PRO, CH2Particle, 0.25, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- backbone_infos_[PRO].has_hydrogens = false;
- AddBBInfo(PRO, NParticle, -0.20, "N", promod3::loop::BB_N_INDEX, false);
- AddBBInfo(PRO, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
- AddBBInfo(PRO, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
- AddBBInfo(PRO, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
-
- if(!cb_in_sidechain) {
- AddBBInfo(PRO, CH2Particle, 0.25, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddBBLP(PRO, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
- promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
-
- // CPR
- sidechain_infos_[CPR] = sidechain_infos_[PRO];
- frm_rules_[CPR] = frm_rules_[PRO];
- backbone_infos_[CPR] = backbone_infos_[PRO];
-
- // TPR
- sidechain_infos_[TPR] = sidechain_infos_[PRO];
- frm_rules_[TPR] = frm_rules_[PRO];
- backbone_infos_[TPR] = backbone_infos_[PRO];
-
- // HSD
- sidechain_infos_[HSD].has_hydrogens = true;
- sidechain_infos_[HSD].internal_e_prefactor = 2.01;
- sidechain_infos_[HSD].frm_t = 1.35;
-
- AddInfo(HSD, CParticle, 0.10, "CG", promod3::loop::HIS_CG_INDEX,false);
- AddInfo(HSD, NParticle, -0.40, "ND1", promod3::loop::HIS_ND1_INDEX,false);
- AddInfo(HSD, CParticle, 0.10, "CD2", promod3::loop::HIS_CD2_INDEX,false);
- AddInfo(HSD, CParticle, 0.30, "CE1", promod3::loop::HIS_CE1_INDEX,false);
- AddInfo(HSD, NParticle, -0.40, "NE2", promod3::loop::HIS_NE2_INDEX,false);
- AddInfo(HSD, HParticle, 0.30, "HD1", promod3::loop::HIS_HD1_INDEX,true);
-
- if(cb_in_sidechain) {
- AddInfo(HSD, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddPDir(HSD, promod3::loop::HIS_HD1_INDEX, promod3::loop::HIS_ND1_INDEX, 5);
- AddLP(HSD, promod3::loop::HIS_CD2_INDEX, promod3::loop::HIS_NE2_INDEX,
- promod3::loop::HIS_CE1_INDEX, false, false, false, 4, LONE_PAIR_CNC);
-
-
- AddFRMRule(HSD, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
- AddFRMPrefactor(HSD, 0, -1.84);
- AddFRMPrefactor(HSD, 0, 1.84);
- AddFRMRotatingParticle(HSD, 0, 0);
- AddFRMRotatingParticle(HSD, 0, 1);
- AddFRMRotatingParticle(HSD, 0, 2);
- AddFRMRotatingParticle(HSD, 0, 3);
- AddFRMRotatingParticle(HSD, 0, 4);
- AddFRMRotatingParticle(HSD, 0, 5);
-
- AddFRMRule(HSD, promod3::loop::BB_CB_INDEX, promod3::loop::HIS_CG_INDEX);
- AddFRMPrefactor(HSD, 1, -0.85);
- AddFRMPrefactor(HSD, 1, 0.85);
- AddFRMFixParticle(HSD, 1, 0);
- AddFRMRotatingParticle(HSD, 1, 1);
- AddFRMRotatingParticle(HSD, 1, 2);
- AddFRMRotatingParticle(HSD, 1, 3);
- AddFRMRotatingParticle(HSD, 1, 4);
- AddFRMRotatingParticle(HSD, 1, 5);
-
- if(cb_in_sidechain) {
- AddFRMFixParticle(HSD, 0, 6);
- AddFRMFixParticle(HSD, 1, 6);
- }
-
- backbone_infos_[HSD].has_hydrogens = true;
- AddBBInfo(HSD, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
- AddBBInfo(HSD, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
- AddBBInfo(HSD, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
- AddBBInfo(HSD, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(HSD, HParticle, 0.25, "H", promod3::loop::HIS_H_INDEX,true);
-
- if(!cb_in_sidechain) {
- AddInfo(HSD, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddBBPDir(HSD, promod3::loop::HIS_H_INDEX, promod3::loop::BB_N_INDEX, 4);
- AddBBLP(HSD, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
- promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
-
- // HSE
- sidechain_infos_[HSE].has_hydrogens = true;
- sidechain_infos_[HSE].internal_e_prefactor = 2.01;
- sidechain_infos_[HSE].frm_t = 1.35;
-
- AddInfo(HSE, CParticle, 0.10, "CG", promod3::loop::HIS_CG_INDEX,false);
- AddInfo(HSE, NParticle, -0.40, "ND1", promod3::loop::HIS_ND1_INDEX,false);
- AddInfo(HSE, CParticle, 0.10, "CD2", promod3::loop::HIS_CD2_INDEX,false);
- AddInfo(HSE, CParticle, 0.30, "CE1", promod3::loop::HIS_CE1_INDEX,false);
- AddInfo(HSE, NParticle, -0.40, "NE2", promod3::loop::HIS_NE2_INDEX,false);
- AddInfo(HSE, HParticle, 0.30, "HE2", promod3::loop::HIS_HE2_INDEX,true);
-
- if(cb_in_sidechain) {
- AddInfo(HSE, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddPDir(HSE, promod3::loop::HIS_HE2_INDEX, promod3::loop::HIS_NE2_INDEX, 5);
- AddLP(HSE, promod3::loop::HIS_CG_INDEX, promod3::loop::HIS_ND1_INDEX,
- promod3::loop::HIS_CE1_INDEX, false, false, false, 1, LONE_PAIR_CNC);
-
- AddFRMRule(HSE, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
- AddFRMPrefactor(HSE, 0, -1.84);
- AddFRMPrefactor(HSE, 0, 1.84);
- AddFRMRotatingParticle(HSE, 0, 0);
- AddFRMRotatingParticle(HSE, 0, 1);
- AddFRMRotatingParticle(HSE, 0, 2);
- AddFRMRotatingParticle(HSE, 0, 3);
- AddFRMRotatingParticle(HSE, 0, 4);
- AddFRMRotatingParticle(HSE, 0, 5);
-
- AddFRMRule(HSE, promod3::loop::BB_CB_INDEX, promod3::loop::HIS_CG_INDEX);
- AddFRMPrefactor(HSE, 1, -0.85);
- AddFRMPrefactor(HSE, 1, 0.85);
- AddFRMFixParticle(HSE, 1, 0);
- AddFRMRotatingParticle(HSE, 1, 1);
- AddFRMRotatingParticle(HSE, 1, 2);
- AddFRMRotatingParticle(HSE, 1, 3);
- AddFRMRotatingParticle(HSE, 1, 4);
- AddFRMRotatingParticle(HSE, 1, 5);
-
- if(cb_in_sidechain) {
- AddFRMFixParticle(HSE, 0, 6);
- AddFRMFixParticle(HSE, 1, 6);
- }
-
- backbone_infos_[HSE].has_hydrogens = true;
- AddBBInfo(HSE, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
- AddBBInfo(HSE, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
- AddBBInfo(HSE, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
- AddBBInfo(HSE, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(HSE, HParticle, 0.25, "H", promod3::loop::HIS_H_INDEX,true);
-
- if(!cb_in_sidechain) {
- AddBBInfo(HSE, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
- }
- AddBBPDir(HSE, promod3::loop::HIS_H_INDEX, promod3::loop::BB_N_INDEX, 4);
- AddBBLP(HSE, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
- promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
-
- // HIS
- // this is a bit hacky...
- sidechain_infos_[HIS] = sidechain_infos_[HSD];
- frm_rules_[HIS] = frm_rules_[HSD];
- backbone_infos_[HIS] = backbone_infos_[HSD];
-
- // PHE
- sidechain_infos_[PHE].has_hydrogens = false;
- sidechain_infos_[PHE].internal_e_prefactor = 1.71;
- sidechain_infos_[PHE].frm_t = 1.07;
-
- AddInfo(PHE, CParticle, 0.0, "CG", promod3::loop::PHE_CG_INDEX, false);
- AddInfo(PHE, CParticle, 0.0, "CD1", promod3::loop::PHE_CD1_INDEX, false);
- AddInfo(PHE, CParticle, 0.0, "CD2", promod3::loop::PHE_CD2_INDEX, false);
- AddInfo(PHE, CParticle, 0.0, "CE1", promod3::loop::PHE_CE1_INDEX, false);
- AddInfo(PHE, CParticle, 0.0, "CE2", promod3::loop::PHE_CE2_INDEX, false);
- AddInfo(PHE, CParticle, 0.0, "CZ", promod3::loop::PHE_CZ_INDEX, false);
-
- if(cb_in_sidechain) {
- AddInfo(PHE, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddFRMRule(PHE, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
- AddFRMPrefactor(PHE, 0, -1.45);
- AddFRMPrefactor(PHE, 0, 1.45);
- AddFRMRotatingParticle(PHE, 0, 0);
- AddFRMRotatingParticle(PHE, 0, 1);
- AddFRMRotatingParticle(PHE, 0, 2);
- AddFRMRotatingParticle(PHE, 0, 3);
- AddFRMRotatingParticle(PHE, 0, 4);
- AddFRMRotatingParticle(PHE, 0, 5);
-
- AddFRMRule(PHE, promod3::loop::BB_CB_INDEX, promod3::loop::PHE_CG_INDEX);
- AddFRMPrefactor(PHE, 1, -1.35);
- AddFRMPrefactor(PHE, 1, 1.35);
- AddFRMFixParticle(PHE, 1, 0);
- AddFRMRotatingParticle(PHE, 1, 1);
- AddFRMRotatingParticle(PHE, 1, 2);
- AddFRMRotatingParticle(PHE, 1, 3);
- AddFRMRotatingParticle(PHE, 1, 4);
- AddFRMRotatingParticle(PHE, 1, 5);
-
- if(cb_in_sidechain) {
- AddFRMFixParticle(PHE, 0, 6);
- AddFRMFixParticle(PHE, 1, 6);
- }
-
- backbone_infos_[PHE].has_hydrogens = true;
- AddBBInfo(PHE, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
- AddBBInfo(PHE, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
- AddBBInfo(PHE, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
- AddBBInfo(PHE, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(PHE, HParticle, 0.25, "H", promod3::loop::PHE_H_INDEX,true);
-
- if(!cb_in_sidechain) {
- AddBBInfo(PHE, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddBBPDir(PHE, promod3::loop::PHE_H_INDEX, promod3::loop::BB_N_INDEX, 4);
- AddBBLP(PHE, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
- promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
-
- // ALA
- sidechain_infos_[ALA].has_hydrogens = false;
- sidechain_infos_[ALA].internal_e_prefactor = 1.0;
- sidechain_infos_[ALA].frm_t = 1.0;
-
- if(cb_in_sidechain) {
- AddInfo(ALA, CH3Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- backbone_infos_[ALA].has_hydrogens = true;
- AddBBInfo(ALA, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
- AddBBInfo(ALA, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
- AddBBInfo(ALA, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
- AddBBInfo(ALA, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(ALA, HParticle, 0.25, "H", promod3::loop::ALA_H_INDEX,true);
-
- if(!cb_in_sidechain) {
- AddBBInfo(ALA, CH3Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
- }
-
- AddBBPDir(ALA, promod3::loop::ALA_H_INDEX, promod3::loop::BB_N_INDEX, 4);
- AddBBLP(ALA, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
- promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
-
- // GLY
- sidechain_infos_[GLY].has_hydrogens = false;
- sidechain_infos_[GLY].internal_e_prefactor = 1.0;
- sidechain_infos_[GLY].frm_t = 1.0;
-
- backbone_infos_[GLY].has_hydrogens = true;
- AddBBInfo(GLY, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
- AddBBInfo(GLY, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
- AddBBInfo(GLY, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
- AddBBInfo(GLY, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(GLY, HParticle, 0.25, "H", promod3::loop::GLY_H_INDEX,true);
- AddBBPDir(GLY, promod3::loop::GLY_H_INDEX, promod3::loop::BB_N_INDEX, 4);
- AddBBLP(GLY, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
- promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
-
- for(uint i = 0; i <= XXX; ++i){
- num_sidechain_particles_[i] = sidechain_infos_[i].particles.size();
- num_backbone_particles_[i] = backbone_infos_[i].particles.size();
- num_frm_particles_[i] = num_sidechain_particles_[i];
- for(uint j = 0; j < frm_rules_[i].size(); ++j){
- num_frm_particles_[i] += (frm_rules_[i][j].prefactors.size() *
- frm_rules_[i][j].rotating_particles.size());
+struct SCWRL4RotamerParam : public RotamerLookupParam {
+
+ SCWRL4RotamerParam() {
+
+ // overwrite default FRM prefactors from base class
+ ARG_CA_CB_prefactors[0] = -0.87;
+ ARG_CB_CG_prefactors[0] = -1.62;
+ ARG_CG_CD_prefactors[0] = -1.67;
+ ARG_CD_NE_prefactors[0] = -0.73;
+ ASN_CA_CB_prefactors[0] = -0.62;
+ ASN_CB_CG_prefactors[0] = -1.93;
+ ASP_CA_CB_prefactors[0] = -1.59;
+ ASP_CB_CG_prefactors[0] = -0.63;
+ GLN_CA_CB_prefactors[0] = -1.55;
+ GLN_CB_CG_prefactors[0] = -0.53;
+ GLN_CG_CD_prefactors[0] = -1.89;
+ GLU_CA_CB_prefactors[0] = -0.82;
+ GLU_CB_CG_prefactors[0] = -1.57;
+ GLU_CG_CD_prefactors[0] = -0.76;
+ LYS_CA_CB_prefactors[0] = -1.62;
+ LYS_CB_CG_prefactors[0] = -0.99;
+ LYS_CG_CD_prefactors[0] = -0.96;
+ LYS_CD_CE_prefactors[0] = -1.49;
+ SER_CA_CB_prefactors[0] = -0.65;
+ SER_CB_OG_prefactors[0] = -2.98;
+ CYS_CA_CB_prefactors[0] = -1.69;
+ MET_CA_CB_prefactors[0] = -0.97;
+ MET_CB_CG_prefactors[0] = -1.54;
+ MET_CG_SD_prefactors[0] = -1.21;
+ TRP_CA_CB_prefactors[0] = -1.28;
+ TRP_CB_CG_prefactors[0] = -1.48;
+ TYR_CA_CB_prefactors[0] = -1.48;
+ TYR_CB_CG_prefactors[0] = -0.73;
+ TYR_CZ_OH_prefactors[0] = -0.96;
+ THR_CA_CB_prefactors[0] = -0.88;
+ THR_CB_OG1_prefactors[0] = -0.88;
+ VAL_CA_CB_prefactors[0] = -2.09;
+ ILE_CA_CB_prefactors[0] = -1.23;
+ ILE_CB_CG1_prefactors[0] = -0.98;
+ LEU_CA_CB_prefactors[0] = -1.15;
+ LEU_CB_CG_prefactors[0] = -1.48;
+ HIS_CA_CB_prefactors[0] = -1.84;
+ HIS_CB_CG_prefactors[0] = -0.85;
+ PHE_CA_CB_prefactors[0] = -1.45;
+ PHE_CB_CG_prefactors[0] = -1.35;
+
+ ARG_CA_CB_prefactors[1] = 0.87;
+ ARG_CB_CG_prefactors[1] = 1.62;
+ ARG_CG_CD_prefactors[1] = 1.67;
+ ARG_CD_NE_prefactors[1] = 0.73;
+ ASN_CA_CB_prefactors[1] = 0.62;
+ ASN_CB_CG_prefactors[1] = 1.93;
+ ASP_CA_CB_prefactors[1] = 1.59;
+ ASP_CB_CG_prefactors[1] = 0.63;
+ GLN_CA_CB_prefactors[1] = 1.55;
+ GLN_CB_CG_prefactors[1] = 0.53;
+ GLN_CG_CD_prefactors[1] = 1.89;
+ GLU_CA_CB_prefactors[1] = 0.82;
+ GLU_CB_CG_prefactors[1] = 1.57;
+ GLU_CG_CD_prefactors[1] = 0.76;
+ LYS_CA_CB_prefactors[1] = 1.62;
+ LYS_CB_CG_prefactors[1] = 0.99;
+ LYS_CG_CD_prefactors[1] = 0.96;
+ LYS_CD_CE_prefactors[1] = 1.49;
+ SER_CA_CB_prefactors[1] = 0.65;
+ SER_CB_OG_prefactors[1] = 2.98;
+ CYS_CA_CB_prefactors[1] = 1.69;
+ MET_CA_CB_prefactors[1] = 0.97;
+ MET_CB_CG_prefactors[1] = 1.54;
+ MET_CG_SD_prefactors[1] = 1.21;
+ TRP_CA_CB_prefactors[1] = 1.28;
+ TRP_CB_CG_prefactors[1] = 1.48;
+ TYR_CA_CB_prefactors[1] = 1.48;
+ TYR_CB_CG_prefactors[1] = 0.73;
+ TYR_CZ_OH_prefactors[1] = 0.96;
+ THR_CA_CB_prefactors[1] = 0.88;
+ THR_CB_OG1_prefactors[1] = 0.88;
+ VAL_CA_CB_prefactors[1] = 2.09;
+ ILE_CA_CB_prefactors[1] = 1.23;
+ ILE_CB_CG1_prefactors[1] = 0.98;
+ LEU_CA_CB_prefactors[1] = 1.15;
+ LEU_CB_CG_prefactors[1] = 1.48;
+ HIS_CA_CB_prefactors[1] = 1.84;
+ HIS_CB_CG_prefactors[1] = 0.85;
+ PHE_CA_CB_prefactors[1] = 1.45;
+ PHE_CB_CG_prefactors[1] = 1.35;
+
+ // overwrite default frm_t from base class
+ frm_t[ost::conop::ARG] = 1.23;
+ frm_t[ost::conop::ASN] = 1.41;
+ frm_t[ost::conop::ASP] = 1.48;
+ frm_t[ost::conop::GLN] = 1.32;
+ frm_t[ost::conop::GLU] = 0.94;
+ frm_t[ost::conop::LYS] = 1.27;
+ frm_t[ost::conop::SER] = 3.53;
+ frm_t[ost::conop::CYS] = 1.69;
+ frm_t[ost::conop::MET] = 1.77;
+ frm_t[ost::conop::TRP] = 0.99;
+ frm_t[ost::conop::TYR] = 1.96;
+ frm_t[ost::conop::THR] = 1.11;
+ frm_t[ost::conop::VAL] = 2.20;
+ frm_t[ost::conop::ILE] = 2.03;
+ frm_t[ost::conop::LEU] = 2.55;
+ frm_t[ost::conop::PRO] = 2.62;
+ frm_t[ost::conop::HIS] = 1.35;
+ frm_t[ost::conop::PHE] = 1.07;
+
+ // overwrite default internal_e_prefactor from base class
+ internal_e_prefactor[ost::conop::ARG] = 2.27;
+ internal_e_prefactor[ost::conop::ASN] = 1.80;
+ internal_e_prefactor[ost::conop::ASP] = 2.44;
+ internal_e_prefactor[ost::conop::GLN] = 1.61;
+ internal_e_prefactor[ost::conop::GLU] = 1.85;
+ internal_e_prefactor[ost::conop::LYS] = 2.13;
+ internal_e_prefactor[ost::conop::SER] = 2.78;
+ internal_e_prefactor[ost::conop::CYS] = 4.07;
+ internal_e_prefactor[ost::conop::MET] = 1.95;
+ internal_e_prefactor[ost::conop::TRP] = 3.24;
+ internal_e_prefactor[ost::conop::TYR] = 2.00;
+ internal_e_prefactor[ost::conop::THR] = 2.96;
+ internal_e_prefactor[ost::conop::VAL] = 1.62;
+ internal_e_prefactor[ost::conop::ILE] = 2.18;
+ internal_e_prefactor[ost::conop::LEU] = 2.25;
+ internal_e_prefactor[ost::conop::PRO] = 0.76;
+ internal_e_prefactor[ost::conop::HIS] = 2.01;
+ internal_e_prefactor[ost::conop::PHE] = 1.71;
+
+ // set all parameters specific to SCWRL4RotamerParam to default values
+ for(uint i = 0 ; i < promod3::loop::XXX_NUM_HYDROGENS; ++i) {
+ hydrogen_charges_[i] = 0.0;
+ polar_anchor_[i] = -1;
}
- }
-}
-SCWRL4RotamerConstructor::SCWRL4RotamerConstructor(bool cb_in_sidechain):
- rotamer_lookup_(cb_in_sidechain) {
- hydrogen_buffer_ = boost::make_shared<promod3::loop::HydrogenStorage>();
-}
-
-
-FrameResiduePtr SCWRL4RotamerConstructor::ConstructBackboneFrameResidue(
- const ost::mol::ResidueHandle& res, RotamerID id, uint residue_index,
- Real phi, bool n_ter, bool c_ter) {
-
- core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "SCWRL4RotamerConstructor::ConstructBackboneFrameResidue", 2);
-
- if(id == XXX) {
- throw promod3::Error("Cannot construct FrameResidue for unknown "
- "rotamer id!");
- }
-
- const SCWRLRotamerInfo& info = rotamer_lookup_.GetBackboneInfo(id);
-
- for(uint i = 0; i < info.particles.size(); ++i){
- if(!info.particles[i].is_hydrogen){
- ost::mol::AtomHandle a = res.FindAtom(info.particles[i].name);
- if(!a.IsValid()){
- throw promod3::Error("Expected atom " + info.particles[i].name +
- " to be present in input residue!");
- }
- pos_buffer_->SetPos(id, info.particles[i].atom_idx, a.GetPos());
+ for(uint i = 0; i < promod3::loop::XXX_NUM_ATOMS; ++i) {
+ heavy_atom_charges_[i] = 0.0;
+ lone_pair_info_idx_[i] = -1;
}
- }
- //set bb hydrogen
- if(info.has_hydrogens){
- promod3::loop::ConstructHydrogenN(*pos_buffer_, id, phi, *hydrogen_buffer_);
- }
-
- int num_particles = info.particles.size();
- if(n_ter) num_particles += 2;
- if(c_ter) num_particles += 1;
- std::vector<Particle> particles(num_particles);
- this->ConstructBBFrameParticles(info, id, n_ter, c_ter, particles);
-
- FrameResiduePtr p = boost::make_shared<FrameResidue>(particles,
- residue_index);
-
- return p;
-}
-
-FrameResiduePtr SCWRL4RotamerConstructor::ConstructBackboneFrameResidue(
- const promod3::loop::AllAtomPositions& all_atom, uint aa_res_idx,
- RotamerID id, uint residue_index,
- Real phi, bool n_ter, bool c_ter) {
-
- core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "SCWRL4RotamerConstructor::ConstructBackboneFrameResidue", 2);
-
- if(id == XXX) {
- throw promod3::Error("Cannot construct FrameResidue for unknown "
- "rotamer id!");
- }
-
- const SCWRLRotamerInfo& info = rotamer_lookup_.GetBackboneInfo(id);
-
- for(uint i = 0; i < info.particles.size(); ++i){
- if(!info.particles[i].is_hydrogen){
-
- if(!all_atom.IsSet(aa_res_idx, info.particles[i].atom_idx)){
- throw promod3::Error("Expected atom " + info.particles[i].name +
- " to be set in all_atom");
+ // set anchor indices for all polar hydrogens
+ polar_anchor_[promod3::loop::ALA_H] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::ALA_H1] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::ALA_H2] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::ALA_H3] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::ARG_H] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::ARG_H1] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::ARG_H2] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::ARG_H3] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::ASN_H] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::ASN_H1] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::ASN_H2] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::ASN_H3] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::ASP_H] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::ASP_H1] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::ASP_H2] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::ASP_H3] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::GLN_H] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::GLN_H1] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::GLN_H2] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::GLN_H3] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::GLU_H] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::GLU_H1] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::GLU_H2] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::GLU_H3] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::LYS_H] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::LYS_H1] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::LYS_H2] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::LYS_H3] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::SER_H] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::SER_H1] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::SER_H2] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::SER_H3] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::CYS_H] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::CYS_H1] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::CYS_H2] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::CYS_H3] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::MET_H] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::MET_H1] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::MET_H2] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::MET_H3] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::TRP_H] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::TRP_H1] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::TRP_H2] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::TRP_H3] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::TYR_H] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::TYR_H1] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::TYR_H2] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::TYR_H3] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::THR_H] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::THR_H1] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::THR_H2] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::THR_H3] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::VAL_H] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::VAL_H1] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::VAL_H2] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::VAL_H3] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::ILE_H] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::ILE_H1] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::ILE_H2] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::ILE_H3] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::LEU_H] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::LEU_H1] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::LEU_H2] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::LEU_H3] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::GLY_H] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::GLY_H1] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::GLY_H2] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::GLY_H3] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::PRO_H1] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::PRO_H2] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::HIS_H] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::HIS_H1] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::HIS_H2] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::HIS_H3] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::PHE_H] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::PHE_H1] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::PHE_H2] = promod3::loop::BB_N_INDEX;
+ polar_anchor_[promod3::loop::PHE_H3] = promod3::loop::BB_N_INDEX;
+
+ polar_anchor_[promod3::loop::ARG_HE] = promod3::loop::ARG_NE_INDEX;
+ polar_anchor_[promod3::loop::ARG_HH11] = promod3::loop::ARG_NH1_INDEX;
+ polar_anchor_[promod3::loop::ARG_HH12] = promod3::loop::ARG_NH1_INDEX;
+ polar_anchor_[promod3::loop::ARG_HH21] = promod3::loop::ARG_NH2_INDEX;
+ polar_anchor_[promod3::loop::ARG_HH22] = promod3::loop::ARG_NH2_INDEX;
+ polar_anchor_[promod3::loop::ASN_HD21] = promod3::loop::ASN_ND2_INDEX;
+ polar_anchor_[promod3::loop::ASN_HD22] = promod3::loop::ASN_ND2_INDEX;
+ polar_anchor_[promod3::loop::GLN_HE21] = promod3::loop::GLN_NE2_INDEX;
+ polar_anchor_[promod3::loop::GLN_HE22] = promod3::loop::GLN_NE2_INDEX;
+ polar_anchor_[promod3::loop::LYS_HZ1] = promod3::loop::LYS_NZ_INDEX;
+ polar_anchor_[promod3::loop::LYS_HZ2] = promod3::loop::LYS_NZ_INDEX;
+ polar_anchor_[promod3::loop::LYS_HZ3] = promod3::loop::LYS_NZ_INDEX;
+ polar_anchor_[promod3::loop::SER_HG] = promod3::loop::SER_OG_INDEX;
+ polar_anchor_[promod3::loop::TRP_HE1] = promod3::loop::TRP_NE1_INDEX;
+ polar_anchor_[promod3::loop::TYR_HH] = promod3::loop::TYR_OH_INDEX;
+ polar_anchor_[promod3::loop::THR_HG1] = promod3::loop::THR_OG1_INDEX;
+ polar_anchor_[promod3::loop::HIS_HD1] = promod3::loop::HIS_ND1_INDEX;
+ polar_anchor_[promod3::loop::HIS_HE2] = promod3::loop::HIS_NE2_INDEX;
+
+ // set lone pair infos
+ // Special care has to be taken for the terminal oxygen and
+ // histidine
+ int o_lp_idx = AddLP(promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
+ promod3::loop::BB_O_INDEX, false, false, false,
+ LONE_PAIR_CARBONYL);
+ lone_pair_info_idx_[promod3::loop::ALA_O] = o_lp_idx;
+ lone_pair_info_idx_[promod3::loop::ARG_O] = o_lp_idx;
+ lone_pair_info_idx_[promod3::loop::ASN_O] = o_lp_idx;
+ lone_pair_info_idx_[promod3::loop::ASP_O] = o_lp_idx;
+ lone_pair_info_idx_[promod3::loop::GLN_O] = o_lp_idx;
+ lone_pair_info_idx_[promod3::loop::GLU_O] = o_lp_idx;
+ lone_pair_info_idx_[promod3::loop::LYS_O] = o_lp_idx;
+ lone_pair_info_idx_[promod3::loop::SER_O] = o_lp_idx;
+ lone_pair_info_idx_[promod3::loop::CYS_O] = o_lp_idx;
+ lone_pair_info_idx_[promod3::loop::MET_O] = o_lp_idx;
+ lone_pair_info_idx_[promod3::loop::TRP_O] = o_lp_idx;
+ lone_pair_info_idx_[promod3::loop::TYR_O] = o_lp_idx;
+ lone_pair_info_idx_[promod3::loop::THR_O] = o_lp_idx;
+ lone_pair_info_idx_[promod3::loop::VAL_O] = o_lp_idx;
+ lone_pair_info_idx_[promod3::loop::ILE_O] = o_lp_idx;
+ lone_pair_info_idx_[promod3::loop::LEU_O] = o_lp_idx;
+ lone_pair_info_idx_[promod3::loop::GLY_O] = o_lp_idx;
+ lone_pair_info_idx_[promod3::loop::PRO_O] = o_lp_idx;
+ lone_pair_info_idx_[promod3::loop::HIS_O] = o_lp_idx;
+ lone_pair_info_idx_[promod3::loop::PHE_O] = o_lp_idx;
+
+ AddLP(ASN, promod3::loop::ASN_OD1_INDEX,
+ promod3::loop::ASN_ND2_INDEX, promod3::loop::ASN_CG_INDEX,
+ promod3::loop::ASN_OD1_INDEX, false, false, false, LONE_PAIR_CARBONYL);
+
+ AddLP(ASP, promod3::loop::ASP_OD1_INDEX,
+ promod3::loop::ASP_OD2_INDEX, promod3::loop::ASP_CG_INDEX,
+ promod3::loop::ASP_OD1_INDEX, false, false, false, LONE_PAIR_CARBONYL);
+
+ AddLP(ASP, promod3::loop::ASP_OD2_INDEX,
+ promod3::loop::ASP_OD1_INDEX, promod3::loop::ASP_CG_INDEX,
+ promod3::loop::ASP_OD2_INDEX, false, false, false, LONE_PAIR_CARBONYL);
+
+ AddLP(GLN, promod3::loop::GLN_OE1_INDEX,
+ promod3::loop::GLN_NE2_INDEX, promod3::loop::GLN_CD_INDEX,
+ promod3::loop::GLN_OE1_INDEX, false, false, false, LONE_PAIR_CARBONYL);
+
+ AddLP(GLU, promod3::loop::GLU_OE1_INDEX,
+ promod3::loop::GLU_OE2_INDEX, promod3::loop::GLU_CD_INDEX,
+ promod3::loop::GLU_OE1_INDEX, false, false, false, LONE_PAIR_CARBONYL);
+
+ AddLP(GLU, promod3::loop::GLU_OE2_INDEX,
+ promod3::loop::GLU_OE1_INDEX, promod3::loop::GLU_CD_INDEX,
+ promod3::loop::GLU_OE2_INDEX, false, false, false, LONE_PAIR_CARBONYL);
+
+ AddLP(SER, promod3::loop::SER_OG_INDEX,
+ promod3::loop::BB_CB_INDEX, promod3::loop::SER_OG_INDEX,
+ promod3::loop::SER_HG_INDEX, false, false, true, LONE_PAIR_COH);
+
+ AddLP(TYR, promod3::loop::TYR_OH_INDEX,
+ promod3::loop::TYR_CZ_INDEX, promod3::loop::TYR_OH_INDEX,
+ promod3::loop::TYR_HH_INDEX, false, false, true, LONE_PAIR_COH);
+
+ AddLP(THR, promod3::loop::THR_OG1_INDEX,
+ promod3::loop::BB_CB_INDEX, promod3::loop::THR_OG1_INDEX,
+ promod3::loop::THR_HG1_INDEX, false, false, true, LONE_PAIR_COH);
+
+ AddLP(HIS, promod3::loop::HIS_NE2_INDEX,
+ promod3::loop::HIS_CD2_INDEX, promod3::loop::HIS_NE2_INDEX,
+ promod3::loop::HIS_CE1_INDEX, false, false, false, LONE_PAIR_CNC);
+
+ AddLP(HIS, promod3::loop::HIS_ND1_INDEX,
+ promod3::loop::HIS_CG_INDEX, promod3::loop::HIS_ND1_INDEX,
+ promod3::loop::HIS_CE1_INDEX, false, false, false, LONE_PAIR_CNC);
+
+ // set charges for polar hydrogen
+ hydrogen_charges_[promod3::loop::ALA_H] = 0.25;
+ hydrogen_charges_[promod3::loop::ALA_H1] = 0.35;
+ hydrogen_charges_[promod3::loop::ALA_H2] = 0.35;
+ hydrogen_charges_[promod3::loop::ALA_H3] = 0.35;
+ hydrogen_charges_[promod3::loop::ARG_H] = 0.25;
+ hydrogen_charges_[promod3::loop::ARG_H1] = 0.35;
+ hydrogen_charges_[promod3::loop::ARG_H2] = 0.35;
+ hydrogen_charges_[promod3::loop::ARG_H3] = 0.35;
+ hydrogen_charges_[promod3::loop::ASN_H] = 0.25;
+ hydrogen_charges_[promod3::loop::ASN_H1] = 0.35;
+ hydrogen_charges_[promod3::loop::ASN_H2] = 0.35;
+ hydrogen_charges_[promod3::loop::ASN_H3] = 0.35;
+ hydrogen_charges_[promod3::loop::ASP_H] = 0.25;
+ hydrogen_charges_[promod3::loop::ASP_H1] = 0.35;
+ hydrogen_charges_[promod3::loop::ASP_H2] = 0.35;
+ hydrogen_charges_[promod3::loop::ASP_H3] = 0.35;
+ hydrogen_charges_[promod3::loop::GLN_H] = 0.25;
+ hydrogen_charges_[promod3::loop::GLN_H1] = 0.35;
+ hydrogen_charges_[promod3::loop::GLN_H2] = 0.35;
+ hydrogen_charges_[promod3::loop::GLN_H3] = 0.35;
+ hydrogen_charges_[promod3::loop::GLU_H] = 0.25;
+ hydrogen_charges_[promod3::loop::GLU_H1] = 0.35;
+ hydrogen_charges_[promod3::loop::GLU_H2] = 0.35;
+ hydrogen_charges_[promod3::loop::GLU_H3] = 0.35;
+ hydrogen_charges_[promod3::loop::LYS_H] = 0.25;
+ hydrogen_charges_[promod3::loop::LYS_H1] = 0.35;
+ hydrogen_charges_[promod3::loop::LYS_H2] = 0.35;
+ hydrogen_charges_[promod3::loop::LYS_H3] = 0.35;
+ hydrogen_charges_[promod3::loop::SER_H] = 0.25;
+ hydrogen_charges_[promod3::loop::SER_H1] = 0.35;
+ hydrogen_charges_[promod3::loop::SER_H2] = 0.35;
+ hydrogen_charges_[promod3::loop::SER_H3] = 0.35;
+ hydrogen_charges_[promod3::loop::CYS_H] = 0.25;
+ hydrogen_charges_[promod3::loop::CYS_H1] = 0.35;
+ hydrogen_charges_[promod3::loop::CYS_H2] = 0.35;
+ hydrogen_charges_[promod3::loop::CYS_H3] = 0.35;
+ hydrogen_charges_[promod3::loop::MET_H] = 0.25;
+ hydrogen_charges_[promod3::loop::MET_H1] = 0.35;
+ hydrogen_charges_[promod3::loop::MET_H2] = 0.35;
+ hydrogen_charges_[promod3::loop::MET_H3] = 0.35;
+ hydrogen_charges_[promod3::loop::TRP_H] = 0.25;
+ hydrogen_charges_[promod3::loop::TRP_H1] = 0.35;
+ hydrogen_charges_[promod3::loop::TRP_H2] = 0.35;
+ hydrogen_charges_[promod3::loop::TRP_H3] = 0.35;
+ hydrogen_charges_[promod3::loop::TYR_H] = 0.25;
+ hydrogen_charges_[promod3::loop::TYR_H1] = 0.35;
+ hydrogen_charges_[promod3::loop::TYR_H2] = 0.35;
+ hydrogen_charges_[promod3::loop::TYR_H3] = 0.35;
+ hydrogen_charges_[promod3::loop::THR_H] = 0.25;
+ hydrogen_charges_[promod3::loop::THR_H1] = 0.35;
+ hydrogen_charges_[promod3::loop::THR_H2] = 0.35;
+ hydrogen_charges_[promod3::loop::THR_H3] = 0.35;
+ hydrogen_charges_[promod3::loop::VAL_H] = 0.25;
+ hydrogen_charges_[promod3::loop::VAL_H1] = 0.35;
+ hydrogen_charges_[promod3::loop::VAL_H2] = 0.35;
+ hydrogen_charges_[promod3::loop::VAL_H3] = 0.35;
+ hydrogen_charges_[promod3::loop::ILE_H] = 0.25;
+ hydrogen_charges_[promod3::loop::ILE_H1] = 0.35;
+ hydrogen_charges_[promod3::loop::ILE_H2] = 0.35;
+ hydrogen_charges_[promod3::loop::ILE_H3] = 0.35;
+ hydrogen_charges_[promod3::loop::LEU_H] = 0.25;
+ hydrogen_charges_[promod3::loop::LEU_H1] = 0.35;
+ hydrogen_charges_[promod3::loop::LEU_H2] = 0.35;
+ hydrogen_charges_[promod3::loop::LEU_H3] = 0.35;
+ hydrogen_charges_[promod3::loop::GLY_H] = 0.25;
+ hydrogen_charges_[promod3::loop::GLY_H1] = 0.35;
+ hydrogen_charges_[promod3::loop::GLY_H2] = 0.35;
+ hydrogen_charges_[promod3::loop::GLY_H3] = 0.35;
+ hydrogen_charges_[promod3::loop::PRO_H1] = 0.35;
+ hydrogen_charges_[promod3::loop::PRO_H2] = 0.35;
+ hydrogen_charges_[promod3::loop::HIS_H] = 0.25;
+ hydrogen_charges_[promod3::loop::HIS_H1] = 0.35;
+ hydrogen_charges_[promod3::loop::HIS_H2] = 0.35;
+ hydrogen_charges_[promod3::loop::HIS_H3] = 0.35;
+ hydrogen_charges_[promod3::loop::PHE_H] = 0.25;
+ hydrogen_charges_[promod3::loop::PHE_H1] = 0.35;
+ hydrogen_charges_[promod3::loop::PHE_H2] = 0.35;
+ hydrogen_charges_[promod3::loop::PHE_H3] = 0.35;
+ hydrogen_charges_[promod3::loop::ARG_HE] = 0.3;
+ hydrogen_charges_[promod3::loop::ARG_HH11] = 0.35;
+ hydrogen_charges_[promod3::loop::ARG_HH12] = 0.35;
+ hydrogen_charges_[promod3::loop::ARG_HH21] = 0.35;
+ hydrogen_charges_[promod3::loop::ARG_HH22] = 0.35;
+ hydrogen_charges_[promod3::loop::ASN_HD21] = 0.3;
+ hydrogen_charges_[promod3::loop::ASN_HD22] = 0.3;
+ hydrogen_charges_[promod3::loop::GLN_HE21] = 0.3;
+ hydrogen_charges_[promod3::loop::GLN_HE22] = 0.3;
+ hydrogen_charges_[promod3::loop::LYS_HZ1] = 0.35;
+ hydrogen_charges_[promod3::loop::LYS_HZ2] = 0.35;
+ hydrogen_charges_[promod3::loop::LYS_HZ3] = 0.35;
+ hydrogen_charges_[promod3::loop::SER_HG] = 0.40;
+ hydrogen_charges_[promod3::loop::TRP_HE1] = 0.30;
+ hydrogen_charges_[promod3::loop::TYR_HH] = 0.40;
+ hydrogen_charges_[promod3::loop::THR_HG1] = 0.40;
+ hydrogen_charges_[promod3::loop::HIS_HD1] = 0.30;
+ hydrogen_charges_[promod3::loop::HIS_HE2] = 0.30;
+
+ // set charges for hydrogen bond acceptors
+ heavy_atom_charges_[promod3::loop::ALA_O] = -0.55;
+ heavy_atom_charges_[promod3::loop::ARG_O] = -0.55;
+ heavy_atom_charges_[promod3::loop::ASN_O] = -0.55;
+ heavy_atom_charges_[promod3::loop::ASP_O] = -0.55;
+ heavy_atom_charges_[promod3::loop::GLN_O] = -0.55;
+ heavy_atom_charges_[promod3::loop::GLU_O] = -0.55;
+ heavy_atom_charges_[promod3::loop::LYS_O] = -0.55;
+ heavy_atom_charges_[promod3::loop::SER_O] = -0.55;
+ heavy_atom_charges_[promod3::loop::CYS_O] = -0.55;
+ heavy_atom_charges_[promod3::loop::MET_O] = -0.55;
+ heavy_atom_charges_[promod3::loop::TRP_O] = -0.55;
+ heavy_atom_charges_[promod3::loop::TYR_O] = -0.55;
+ heavy_atom_charges_[promod3::loop::THR_O] = -0.55;
+ heavy_atom_charges_[promod3::loop::VAL_O] = -0.55;
+ heavy_atom_charges_[promod3::loop::ILE_O] = -0.55;
+ heavy_atom_charges_[promod3::loop::LEU_O] = -0.55;
+ heavy_atom_charges_[promod3::loop::GLY_O] = -0.55;
+ heavy_atom_charges_[promod3::loop::PRO_O] = -0.55;
+ heavy_atom_charges_[promod3::loop::HIS_O] = -0.55;
+ heavy_atom_charges_[promod3::loop::PHE_O] = -0.55;
+ heavy_atom_charges_[promod3::loop::ASN_OD1] = -0.55;
+ heavy_atom_charges_[promod3::loop::ASP_OD1] = -0.60;
+ heavy_atom_charges_[promod3::loop::ASP_OD2] = -0.60;
+ heavy_atom_charges_[promod3::loop::GLN_OE1] = -0.55;
+ heavy_atom_charges_[promod3::loop::GLU_OE1] = -0.60;
+ heavy_atom_charges_[promod3::loop::GLU_OE2] = -0.60;
+ heavy_atom_charges_[promod3::loop::SER_OG] = -0.65;
+ heavy_atom_charges_[promod3::loop::TYR_OH] = -0.65;
+ heavy_atom_charges_[promod3::loop::THR_OG1] = -0.65;
+ heavy_atom_charges_[promod3::loop::HIS_NE2] = -0.40;
+ heavy_atom_charges_[promod3::loop::HIS_ND1] = -0.40;
+
+ // set most common atomtypes by element
+ for(int i = 0; i < promod3::loop::XXX_NUM_ATOMS; ++i) {
+ particle_types_[i] = CParticle;
+ promod3::loop::AminoAcidAtom aaa = promod3::loop::AminoAcidAtom(i);
+ const String& ele =
+ promod3::loop::AminoAcidLookup::GetInstance().GetElement(aaa);
+ if(ele == "N") {
+ particle_types_[i] = NParticle;
}
-
- pos_buffer_->SetPos(id, info.particles[i].atom_idx,
- all_atom.GetPos(aa_res_idx, info.particles[i].atom_idx));
- }
- }
-
- //set hydrogens
- if(info.has_hydrogens){
- promod3::loop::ConstructHydrogenN(*pos_buffer_, id, phi, *hydrogen_buffer_);
- }
-
- int num_particles = info.particles.size();
- if(n_ter) num_particles += 2;
- if(c_ter) num_particles += 1;
- std::vector<Particle> particles(num_particles);
- this->ConstructBBFrameParticles(info, id, n_ter, c_ter, particles);
-
- FrameResiduePtr p = boost::make_shared<FrameResidue>(particles,
- residue_index);
-
- return p;
-}
-
-FrameResiduePtr SCWRL4RotamerConstructor::ConstructSidechainFrameResidue(
- const ost::mol::ResidueHandle& res, RotamerID id, uint residue_index) {
-
- core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "SCWRL4RotamerConstructor::ConstructSidechainFrameResidue", 2);
-
- if(id == XXX) {
- throw promod3::Error("Cannot construct FrameResidue for unknown "
- "rotamer id!");
- }
-
- const SCWRLRotamerInfo& info = rotamer_lookup_.GetSidechainInfo(id);
-
- for(uint i = 0; i < info.particles.size(); ++i){
- if(!info.particles[i].is_hydrogen){
- ost::mol::AtomHandle a = res.FindAtom(info.particles[i].name);
- if(!a.IsValid()){
- throw promod3::Error("Expected atom " + info.particles[i].name +
- " to be present in input residue!");
+ if(ele == "O") {
+ particle_types_[i] = OParticle;
+ }
+ if(ele == "S") {
+ particle_types_[i] = SParticle;
}
- pos_buffer_->SetPos(id, info.particles[i].atom_idx, a.GetPos());
}
- }
- //set bb hydrogen
- if(info.has_hydrogens){
- // to construct hydrogens, we might also need backbone atoms in the buffer
- const SCWRLRotamerInfo& bb_info = rotamer_lookup_.GetBackboneInfo(id);
-
- for(uint i = 0; i < bb_info.particles.size(); ++i){
- if(!bb_info.particles[i].is_hydrogen){
- ost::mol::AtomHandle a = res.FindAtom(bb_info.particles[i].name);
- if(!a.IsValid()){
- throw promod3::Error("Expected atom " + bb_info.particles[i].name +
- " to be present in input residue!");
- }
- pos_buffer_->SetPos(id, bb_info.particles[i].atom_idx, a.GetPos());
- }
+ // atoms of following types must be set manually:
+ // CH1Particle, CH2Particle, CH3Particle, OCParticle
+ particle_types_[promod3::loop::ARG_CG] = CH2Particle;
+ particle_types_[promod3::loop::ARG_CD] = CH2Particle;
+ particle_types_[promod3::loop::ARG_CB] = CH2Particle;
+ particle_types_[promod3::loop::ARG_CA] = CH1Particle;
+ particle_types_[promod3::loop::ASN_CB] = CH2Particle;
+ particle_types_[promod3::loop::ASN_CA] = CH1Particle;
+ particle_types_[promod3::loop::ASP_CB] = CH2Particle;
+ particle_types_[promod3::loop::ASP_CA] = CH1Particle;
+ particle_types_[promod3::loop::GLN_CG] = CH2Particle;
+ particle_types_[promod3::loop::GLN_CB] = CH2Particle;
+ particle_types_[promod3::loop::GLN_CA] = CH1Particle;
+ particle_types_[promod3::loop::GLU_CG] = CH2Particle;
+ particle_types_[promod3::loop::GLU_CB] = CH2Particle;
+ particle_types_[promod3::loop::GLU_CA] = CH1Particle;
+ particle_types_[promod3::loop::LYS_CG] = CH2Particle;
+ particle_types_[promod3::loop::LYS_CD] = CH2Particle;
+ particle_types_[promod3::loop::LYS_CE] = CH2Particle;
+ particle_types_[promod3::loop::LYS_CB] = CH2Particle;
+ particle_types_[promod3::loop::LYS_CA] = CH1Particle;
+ particle_types_[promod3::loop::SER_CB] = CH2Particle;
+ particle_types_[promod3::loop::SER_CA] = CH1Particle;
+ particle_types_[promod3::loop::CYS_CB] = CH2Particle;
+ particle_types_[promod3::loop::CYS_CA] = CH1Particle;
+ particle_types_[promod3::loop::MET_CG] = CH2Particle;
+ particle_types_[promod3::loop::MET_CE] = CH3Particle;
+ particle_types_[promod3::loop::MET_CB] = CH2Particle;
+ particle_types_[promod3::loop::MET_CA] = CH1Particle;
+ particle_types_[promod3::loop::TRP_CB] = CH2Particle;
+ particle_types_[promod3::loop::TRP_CA] = CH1Particle;
+ particle_types_[promod3::loop::TYR_CB] = CH2Particle;
+ particle_types_[promod3::loop::TYR_CA] = CH1Particle;
+ particle_types_[promod3::loop::THR_CG2] = CH3Particle;
+ particle_types_[promod3::loop::THR_CB] = CH2Particle;
+ particle_types_[promod3::loop::THR_CA] = CH1Particle;
+ particle_types_[promod3::loop::VAL_CG1] = CH3Particle;
+ particle_types_[promod3::loop::VAL_CG2] = CH3Particle;
+ particle_types_[promod3::loop::VAL_CB] = CH2Particle;
+ particle_types_[promod3::loop::VAL_CA] = CH1Particle;
+ particle_types_[promod3::loop::ILE_CG1] = CH2Particle;
+ particle_types_[promod3::loop::ILE_CG2] = CH3Particle;
+ particle_types_[promod3::loop::ILE_CD1] = CH3Particle;
+ particle_types_[promod3::loop::ILE_CB] = CH2Particle;
+ particle_types_[promod3::loop::ILE_CA] = CH1Particle;
+ particle_types_[promod3::loop::LEU_CG] = CH1Particle;
+ particle_types_[promod3::loop::LEU_CD1] = CH3Particle;
+ particle_types_[promod3::loop::LEU_CD2] = CH3Particle;
+ particle_types_[promod3::loop::LEU_CB] = CH2Particle;
+ particle_types_[promod3::loop::LEU_CA] = CH1Particle;
+ particle_types_[promod3::loop::PRO_CG] = CH2Particle;
+ particle_types_[promod3::loop::PRO_CD] = CH2Particle;
+ particle_types_[promod3::loop::PRO_CB] = CH2Particle;
+ particle_types_[promod3::loop::PRO_CA] = CH1Particle;
+ particle_types_[promod3::loop::HIS_CB] = CH2Particle;
+ particle_types_[promod3::loop::HIS_CA] = CH1Particle;
+ particle_types_[promod3::loop::PHE_CB] = CH2Particle;
+ particle_types_[promod3::loop::PHE_CA] = CH1Particle;
+ particle_types_[promod3::loop::ALA_CB] = CH3Particle;
+ particle_types_[promod3::loop::ALA_CA] = CH1Particle;
+ particle_types_[promod3::loop::GLY_CA] = CH2Particle;
+ }
+
+
+ static const SCWRL4RotamerParam& Instance() {
+ static SCWRL4RotamerParam scwrl4_param;
+ return scwrl4_param;
+ }
+
+
+ Real GetHydrogenCharge(RotamerID rot_id, int hydrogen_idx) const{
+ ost::conop::AminoAcid aa = RotIDToAA(rot_id);
+ promod3::loop::AminoAcidHydrogen aah =
+ promod3::loop::AminoAcidLookup::GetInstance().GetAAH(aa, hydrogen_idx);
+ return hydrogen_charges_[aah];
+ }
+
+
+ Real GetHeavyAtomCharge(RotamerID rot_id, int atom_idx) const{
+ ost::conop::AminoAcid aa = RotIDToAA(rot_id);
+ promod3::loop::AminoAcidAtom aaa =
+ promod3::loop::AminoAcidLookup::GetInstance().GetAAA(aa, atom_idx);
+ return heavy_atom_charges_[aaa];
+ }
+
+
+ int GetPolarAnchor(RotamerID rot_id, int hydrogen_idx) const {
+ ost::conop::AminoAcid aa = RotIDToAA(rot_id);
+ promod3::loop::AminoAcidHydrogen aah =
+ promod3::loop::AminoAcidLookup::GetInstance().GetAAH(aa, hydrogen_idx);
+ return polar_anchor_[aah];
+ }
+
+
+ SCWRL4ParticleType GetParticleType(RotamerID rot_id, int atom_idx) const {
+ ost::conop::AminoAcid aa = RotIDToAA(rot_id);
+ promod3::loop::AminoAcidAtom aaa =
+ promod3::loop::AminoAcidLookup::GetInstance().GetAAA(aa, atom_idx);
+ return particle_types_[aaa];
+ }
+
+
+ int GetLPInfoIdx(RotamerID rot_id, int atom_idx) const {
+
+ // this is an ugly hack for histidine...
+ if((rot_id == HSD && atom_idx == promod3::loop::HIS_ND1_INDEX) ||
+ (rot_id == HSE && atom_idx == promod3::loop::HIS_NE2_INDEX)) {
+ return -1;
}
- promod3::loop::ConstructHydrogens(*pos_buffer_, id, *hydrogen_buffer_, true,
- promod3::loop::PROT_STATE_HISH);
+ ost::conop::AminoAcid aa = RotIDToAA(rot_id);
+ promod3::loop::AminoAcidAtom aaa =
+ promod3::loop::AminoAcidLookup::GetInstance().GetAAA(aa, atom_idx);
+ return lone_pair_info_idx_[aaa];
}
- int num_particles = info.particles.size();
- std::vector<Particle> particles(num_particles);
-
- this->ConstructBaseParticles(info, id, particles);
-
- FrameResiduePtr p = boost::make_shared<FrameResidue>(particles,
- residue_index);
- return p;
-}
-
-FrameResiduePtr SCWRL4RotamerConstructor::ConstructSidechainFrameResidue(
- const promod3::loop::AllAtomPositions& all_atom, uint aa_res_idx,
- RotamerID id, uint residue_index) {
-
- core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "SCWRL4RotamerConstructor::ConstructSidechainFrameResidue", 2);
-
- if(id == XXX) {
- throw promod3::Error("Cannot construct FrameResidue for unknown "
- "rotamer id!");
+ const SCWRL4LPInfo& GetLP(int idx) const {
+ return lone_pair_infos_[idx];
}
- const SCWRLRotamerInfo& info = rotamer_lookup_.GetSidechainInfo(id);
- for(uint i = 0; i < info.particles.size(); ++i){
- if(!info.particles[i].is_hydrogen){
- if(!all_atom.IsSet(aa_res_idx, info.particles[i].atom_idx)){
- throw promod3::Error("Expected atom " + info.particles[i].name +
- " to be set in all_atom");
- }
- pos_buffer_->SetPos(id, info.particles[i].atom_idx,
- all_atom.GetPos(aa_res_idx, info.particles[i].atom_idx));
- }
+ void AddLP(RotamerID id, int p_idx, int idx_a, int idx_b, int idx_c,
+ bool a_ih, bool b_ih, bool c_ih, SCWRL4LPRule r) {
+ ost::conop::AminoAcid aa = RotIDToAA(id);
+ promod3::loop::AminoAcidAtom aaa =
+ promod3::loop::AminoAcidLookup::GetInstance().GetAAA(aa, p_idx);
+ lone_pair_info_idx_[aaa] = lone_pair_infos_.size();
+ SCWRL4LPInfo lp(idx_a, idx_b, idx_c, a_ih, b_ih, c_ih, r);
+ lone_pair_infos_.push_back(lp);
}
- //set hydrogens
- if(info.has_hydrogens){
- // to construct hydrogens, we might also need backbone atoms in the buffer
- const SCWRLRotamerInfo& bb_info = rotamer_lookup_.GetBackboneInfo(id);
-
- for(uint i = 0; i < bb_info.particles.size(); ++i){
- if(!bb_info.particles[i].is_hydrogen){
- if(!all_atom.IsSet(aa_res_idx, bb_info.particles[i].atom_idx)){
- throw promod3::Error("Expected atom " + bb_info.particles[i].name +
- " to be set in all_atom");
- }
- pos_buffer_->SetPos(id, bb_info.particles[i].atom_idx,
- all_atom.GetPos(aa_res_idx, bb_info.particles[i].atom_idx));
- }
- }
- promod3::loop::ConstructHydrogens(*pos_buffer_, id, *hydrogen_buffer_, true,
- promod3::loop::PROT_STATE_HISH);
+ int AddLP(int idx_a, int idx_b, int idx_c,
+ bool a_ih, bool b_ih, bool c_ih, SCWRL4LPRule r) {
+ SCWRL4LPInfo lp(idx_a, idx_b, idx_c, a_ih, b_ih, c_ih, r);
+ lone_pair_infos_.push_back(lp);
+ return lone_pair_infos_.size() - 1;
}
+
- int num_particles = info.particles.size();
- std::vector<Particle> particles(num_particles);
+ Real hydrogen_charges_[promod3::loop::XXX_NUM_HYDROGENS];
+ Real heavy_atom_charges_[promod3::loop::XXX_NUM_ATOMS];
+ int polar_anchor_[promod3::loop::XXX_NUM_HYDROGENS];
+ int lone_pair_info_idx_[promod3::loop::XXX_NUM_ATOMS];
+ std::vector<SCWRL4LPInfo> lone_pair_infos_;
+ SCWRL4ParticleType particle_types_[promod3::loop::XXX_NUM_ATOMS];
+};
- this->ConstructBaseParticles(info, id, particles);
- FrameResiduePtr p = boost::make_shared<FrameResidue>(particles,
- residue_index);
+SCWRL4RotamerConstructor::SCWRL4RotamerConstructor(bool cb_in_sidechain):
+ RotamerConstructor(cb_in_sidechain, POLAR_HYDROGEN_MODE,
+ SCWRL4RotamerParam::Instance()) { }
- return p;
-}
FrameResiduePtr SCWRL4RotamerConstructor::ConstructFrameResidue(
const ost::mol::ResidueHandle& res, uint residue_index) {
@@ -1708,8 +932,11 @@ FrameResiduePtr SCWRL4RotamerConstructor::ConstructFrameResidueHeuristic(
}
-
-void SCWRL4RotamerConstructor::AssignInternalEnergies(RRMRotamerGroupPtr group) {
+void SCWRL4RotamerConstructor::AssignInternalEnergies(RRMRotamerGroupPtr group,
+ RotamerID id,
+ uint residue_index,
+ Real phi, Real psi,
+ bool n_ter, bool c_ter) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"SCWRL4RotamerConstructor::AssignInternalEnergies", 2);
@@ -1724,7 +951,12 @@ void SCWRL4RotamerConstructor::AssignInternalEnergies(RRMRotamerGroupPtr group)
}
}
-void SCWRL4RotamerConstructor::AssignInternalEnergies(FRMRotamerGroupPtr group) {
+
+void SCWRL4RotamerConstructor::AssignInternalEnergies(FRMRotamerGroupPtr group,
+ RotamerID id,
+ uint residue_index,
+ Real phi, Real psi,
+ bool n_ter, bool c_ter) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"SCWRL4RotamerConstructor::AssignInternalEnergies", 2);
@@ -1739,466 +971,70 @@ void SCWRL4RotamerConstructor::AssignInternalEnergies(FRMRotamerGroupPtr group)
}
}
-// INTERNAL FUNCTIONS
-
-RRMRotamerGroupPtr SCWRL4RotamerConstructor::ConstructRRMGroup(
- RotamerID id, uint residue_index,
- std::pair<RotamerLibEntry*,uint> lib_entries,
- Real probability_cutoff) {
-
- core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "SCWRL4RotamerConstructor::ConstructRRMGroup", 2);
-
- std::vector<RRMRotamerPtr> rotamers;
- Real summed_prob = 0.0;
-
- // in case of his, we have to move the backbone positions in the buffer
- // to the locations defining his in the different protonation states
- if(id == HIS){
- MVBBPosBuffer(HIS, HSD);
- MVBBPosBuffer(HIS, HSE);
- }
-
- // in case of alanine and glycine, the rotamer libraries won't have any
- // entries. For consistency we nevertheless construct rotamers.
- // We simply add a fake RotamerLibEntry in this case that has
- // no sidechain dihedrals set.
- std::vector<RotamerLibEntry> fake_rotamers(1);
- if(lib_entries.second == 0 && (id == ALA || id == GLY)) {
- // we have to make sure, that the according probability really is one!
- fake_rotamers[0].probability = 1.0;
- lib_entries = std::make_pair(&fake_rotamers[0], 1);
- }
- else if(lib_entries.second == 0) {
- throw promod3::Error("Did not find any rotamers in Rotamer Library!");
- }
-
- for(uint i = 0; i < lib_entries.second; ++i){
-
- probability_ = lib_entries.first[i].probability;
- summed_prob += probability_;
- chi_angles_[0] = lib_entries.first[i].chi1;
- chi_angles_[1] = lib_entries.first[i].chi2;
- chi_angles_[2] = lib_entries.first[i].chi3;
- chi_angles_[3] = lib_entries.first[i].chi4;
-
- switch(id){
- case HIS:{
- rotamers.push_back(ConstructRRM(HSE, residue_index));
- rotamers.push_back(ConstructRRM(HSD, residue_index));
- break;
- }
- case SER:{
- chi_angles_[1] = Real(M_PI);
- rotamers.push_back(ConstructRRM(id, residue_index));
- chi_angles_[1] = Real(M_PI) / 3.0;
- rotamers.push_back(ConstructRRM(id, residue_index));
- chi_angles_[1] = -Real(M_PI) / 3.0;
- rotamers.push_back(ConstructRRM(id, residue_index));
- break;
- }
- case THR:{
- chi_angles_[1] = Real(M_PI);
- rotamers.push_back(ConstructRRM(id, residue_index));
- chi_angles_[1] = Real(M_PI) / 3.0;
- rotamers.push_back(ConstructRRM(id, residue_index));
- chi_angles_[1] = -Real(M_PI) / 3.0;
- rotamers.push_back(ConstructRRM(id, residue_index));
- break;
- }
- case TYR:{
- chi_angles_[2] = Real(M_PI);
- rotamers.push_back(ConstructRRM(id, residue_index));
- chi_angles_[2] = Real(0.0);
- rotamers.push_back(ConstructRRM(id, residue_index));
- break;
- }
- default:{
- rotamers.push_back(ConstructRRM(id, residue_index));
- }
- }
-
- if(summed_prob >= probability_cutoff && !rotamers.empty()) break;
- }
-
- RRMRotamerGroupPtr group = boost::make_shared<RRMRotamerGroup>(rotamers,
- residue_index);
- this->AssignInternalEnergies(group);
- return group;
-}
-
-FRMRotamerGroupPtr SCWRL4RotamerConstructor::ConstructFRMGroup(
- RotamerID id, uint residue_index,
- std::pair<RotamerLibEntry*,uint> lib_entries,
- Real probability_cutoff) {
- core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "SCWRL4RotamerConstructor::ConstructFRMGroup", 2);
+void SCWRL4RotamerConstructor::ParametrizeParticle(int at_idx,
+ bool is_hydrogen,
+ Particle& particle) {
- std::vector<FRMRotamerPtr> rotamers;
- Real summed_prob = 0.0;
-
- // in case of his, we have to move the backbone positions in the buffer
- // to the locations defining his in the different protonation states
- if(id == HIS){
- MVBBPosBuffer(HIS, HSD);
- MVBBPosBuffer(HIS, HSE);
- }
-
- // in case of alanine and glycine, the rotamer libraries won't have any
- // entries. For consistency we nevertheless construct rotamers.
- // We simply add a fake RotamerLibEntry in this case that has
- // no sidechain dihedrals set.
- std::vector<RotamerLibEntry> fake_rotamers(1);
- if(lib_entries.second == 0 && (id == ALA || id == GLY)) {
- // we have to make sure, that the according probability really is one!
- fake_rotamers[0].probability = 1.0;
- lib_entries = std::make_pair(&fake_rotamers[0], 1);
- }
- else if(lib_entries.second == 0) {
- throw promod3::Error("Did not find any rotamers in Rotamer Library!");
- }
+ if(is_hydrogen) {
- for(uint i = 0; i < lib_entries.second; ++i){
- probability_ = lib_entries.first[i].probability;
- summed_prob += probability_;
- chi_angles_[0] = lib_entries.first[i].chi1;
- chi_angles_[1] = lib_entries.first[i].chi2;
- chi_angles_[2] = lib_entries.first[i].chi3;
- chi_angles_[3] = lib_entries.first[i].chi4;
- chi_dev_[0] = lib_entries.first[i].sig1;
- chi_dev_[1] = lib_entries.first[i].sig2;
- chi_dev_[2] = lib_entries.first[i].sig3;
- chi_dev_[3] = lib_entries.first[i].sig4;
-
- switch(id){
- case HIS:{
- rotamers.push_back(ConstructFRM(HSE, residue_index));
- rotamers.push_back(ConstructFRM(HSD, residue_index));
- break;
- }
- case SER:{
- chi_dev_[1] = Real(0.17453);
- chi_angles_[1] = Real(M_PI);
- rotamers.push_back(ConstructFRM(id, residue_index));
- chi_angles_[1] = Real(M_PI) / Real(3.0);
- rotamers.push_back(ConstructFRM(id, residue_index));
- chi_angles_[1] = -Real(M_PI) / Real(3.0);
- rotamers.push_back(ConstructFRM(id, residue_index));
- break;
- }
- case THR:{
- chi_dev_[1] = Real(0.17453);
- chi_angles_[1] = Real(M_PI);
- rotamers.push_back(ConstructFRM(id, residue_index));
- chi_angles_[1] = Real(M_PI) / Real(3.0);
- rotamers.push_back(ConstructFRM(id, residue_index));
- chi_angles_[1] = -Real(M_PI) / Real(3.0);
- rotamers.push_back(ConstructFRM(id, residue_index));
- break;
- }
- case TYR:{
- chi_dev_[2] = Real(0.17453);
- chi_angles_[2] = Real(M_PI);
- rotamers.push_back(ConstructFRM(id, residue_index));
- chi_angles_[2] = Real(0.0);
- rotamers.push_back(ConstructFRM(id, residue_index));
- break;
- }
- default: rotamers.push_back(ConstructFRM(id, residue_index));
- }
-
- if(summed_prob >= probability_cutoff && !rotamers.empty()) break;
- }
-
- FRMRotamerGroupPtr group = boost::make_shared<FRMRotamerGroup>(rotamers,
- residue_index);
- this->AssignInternalEnergies(group);
- return group;
-}
-
-RRMRotamerPtr SCWRL4RotamerConstructor::ConstructRRM(RotamerID id,
- uint residue_idx) {
-
- core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "SCWRL4RotamerConstructor::ConstructRRM", 2);
-
- const SCWRLRotamerInfo& info = rotamer_lookup_.GetSidechainInfo(id);
- int num_particles = rotamer_lookup_.GetNumSidechainParticles(id);
- std::vector<Particle> particles(num_particles);
-
- //set the positions
- promod3::loop::ConstructSidechainAtoms(*pos_buffer_, id, chi_angles_[0],
- chi_angles_[1], chi_angles_[2],
- chi_angles_[3]);
-
- if(info.has_hydrogens){
-
- promod3::loop::ConstructHydrogens(*pos_buffer_, id, *hydrogen_buffer_, true,
- promod3::loop::PROT_STATE_HISH);
-
- // If there are any custom rules, we apply them now and overrule the
- // default hydrogen construction
- if(!info.custom_hydrogens.empty()){
- for(uint i = 0; i < info.custom_hydrogens.size(); ++i){
- const SCWRLCustomHydrogenInfo& h_info = info.custom_hydrogens[i];
- geom::Vec3 anchor_one, anchor_two, anchor_three, new_h_pos;
- anchor_one = pos_buffer_->GetPos(id, h_info.anchor_idx_one);
- anchor_two = pos_buffer_->GetPos(id, h_info.anchor_idx_two);
- anchor_three = pos_buffer_->GetPos(id, h_info.anchor_idx_three);
- promod3::core::ConstructAtomPos(anchor_one, anchor_two, anchor_three,
- h_info.bond_length, h_info.angle,
- chi_angles_[h_info.chi_idx], new_h_pos);
- hydrogen_buffer_->SetPos(h_info.atom_idx, new_h_pos);
- }
- }
- }
-
- this->ConstructBaseParticles(info, id, particles);
-
- RRMRotamerPtr rot = boost::make_shared<RRMRotamer>(particles,
- probability_,
- info.internal_e_prefactor);
-
- return rot;
-}
-
-FRMRotamerPtr SCWRL4RotamerConstructor::ConstructFRM(RotamerID id,
- uint residue_idx) {
-
- core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "SCWRL4RotamerConstructor::ConstructFRM", 2);
-
- const SCWRLRotamerInfo& info = rotamer_lookup_.GetSidechainInfo(id);
- int num_rrm_particles = rotamer_lookup_.GetNumSidechainParticles(id);
- int num_particles = rotamer_lookup_.GetNumFRMSidechainParticles(id);
- std::vector<Particle> particles(num_particles);
-
- //set the positions
- promod3::loop::ConstructSidechainAtoms(*pos_buffer_, id, chi_angles_[0],
- chi_angles_[1], chi_angles_[2],
- chi_angles_[3]);
- if(info.has_hydrogens){
- promod3::loop::ConstructHydrogens(*pos_buffer_, id, *hydrogen_buffer_, true,
- promod3::loop::PROT_STATE_HISH);
- // If there are any custom rules, we apply them now an overrule the
- // default hydrogen construction
- if(!info.custom_hydrogens.empty()){
- for(uint i = 0; i < info.custom_hydrogens.size(); ++i){
- const SCWRLCustomHydrogenInfo& h_info = info.custom_hydrogens[i];
- geom::Vec3 anchor_one, anchor_two, anchor_three, new_h_pos;
- anchor_one = pos_buffer_->GetPos(id, h_info.anchor_idx_one);
- anchor_two = pos_buffer_->GetPos(id, h_info.anchor_idx_two);
- anchor_three = pos_buffer_->GetPos(id, h_info.anchor_idx_three);
- promod3::core::ConstructAtomPos(anchor_one, anchor_two, anchor_three,
- h_info.bond_length, h_info.angle,
- chi_angles_[h_info.chi_idx], new_h_pos);
- hydrogen_buffer_->SetPos(h_info.atom_idx, new_h_pos);
- }
+ Real charge = SCWRL4RotamerParam::Instance().GetHydrogenCharge(id_, at_idx);
+ SCWRL4Param* p = new SCWRL4Param(HParticle,
+ hydrogen_buffer_->GetPos(at_idx),
+ charge);
+ int polar_anchor = SCWRL4RotamerParam::Instance().GetPolarAnchor(id_, at_idx);
+ if(polar_anchor != -1) {
+ geom::Vec3 polar_direction = hydrogen_buffer_->GetPos(at_idx) -
+ pos_buffer_->GetPos(id_, polar_anchor);
+ p->SetPolarDirection(polar_direction);
}
- }
-
- this->ConstructBaseParticles(info, id, particles);
-
- // Keep track of the subrotamers
- std::vector<std::vector<int> > subrotamer_definitions;
- std::vector<int> actual_definition;
- actual_definition.resize(num_rrm_particles);
- // Directly add the first particles as first subrotamer
- for(int i = 0; i < num_rrm_particles; ++i) actual_definition[i] = i;
- subrotamer_definitions.push_back(actual_definition);
-
- const std::vector<SCWRLFRMRule>& frm_rules = rotamer_lookup_.GetFRMRules(id);
- geom::Vec3 rot_axis, rot_anchor;
- geom::Vec3 orig_pos, rot_pos;
- geom::Mat4 transform;
- int base_idx = num_rrm_particles;
-
- for(uint frm_rule_idx = 0; frm_rule_idx < frm_rules.size(); ++frm_rule_idx){
- const SCWRLFRMRule& frm_rule = frm_rules[frm_rule_idx];
- int num_fix_particles = frm_rule.fix_particles.size();
- int num_rotating_particles = frm_rule.rotating_particles.size();
-
- // Update the subrotamer definition... all particles that are fixed are
- // taken from the first subrotamer.
- for(int i = 0; i < num_fix_particles; ++i) {
- actual_definition[i] = frm_rule.fix_particles[i];
- }
-
- // The data required for the rotation around the specified axis
- rot_anchor = pos_buffer_->GetPos(id, frm_rule.anchor_idx_two);
- rot_axis = rot_anchor - pos_buffer_->GetPos(id, frm_rule.anchor_idx_one);
-
- // Every rotation results in a new subrotamer
- for(uint prefac_idx = 0; prefac_idx < frm_rule.prefactors.size();
- ++prefac_idx){
-
- // Get the rotation matrix
- Real rot_angle = frm_rule.prefactors[prefac_idx] * chi_dev_[frm_rule_idx];
- transform = promod3::core::RotationAroundLine(rot_axis, rot_anchor,
- rot_angle);
-
- for(int i = 0; i < num_rotating_particles; ++i){
- int orig_particle_idx = frm_rule.rotating_particles[i];
- int new_particle_idx = base_idx + i;
-
- // replace the old with the new index...
- actual_definition[orig_particle_idx] = new_particle_idx;
-
- // construct the rotated particle
- particles[new_particle_idx] = particles[orig_particle_idx];
- particles[new_particle_idx].ApplyTransform(transform);
- }
-
- subrotamer_definitions.push_back(actual_definition);
-
- // start of next subrotamer
- base_idx += num_rotating_particles;
- }
- }
-
- FRMRotamerPtr r = boost::make_shared<FRMRotamer>(particles,
- info.frm_t, probability_,
- info.internal_e_prefactor);
-
- for(uint i = 0; i < subrotamer_definitions.size(); ++i) {
- r->AddSubrotamerDefinition(subrotamer_definitions[i]);
- }
-
- return r;
-}
-
-void SCWRL4RotamerConstructor::MVBBPosBuffer(RotamerID from, RotamerID to) {
- pos_buffer_->SetPos(to, promod3::loop::BB_N_INDEX,
- pos_buffer_->GetPos(from, promod3::loop::BB_N_INDEX));
- pos_buffer_->SetPos(to, promod3::loop::BB_CA_INDEX,
- pos_buffer_->GetPos(from, promod3::loop::BB_CA_INDEX));
- pos_buffer_->SetPos(to, promod3::loop::BB_C_INDEX,
- pos_buffer_->GetPos(from, promod3::loop::BB_C_INDEX));
- pos_buffer_->SetPos(to, promod3::loop::BB_O_INDEX,
- pos_buffer_->GetPos(from, promod3::loop::BB_O_INDEX));
- // Even though we officially count CB as a sidechain atom, we still move it
- // since its completely independent of any sidechain dihedral angle and
- // cannot be constructed anyway
- pos_buffer_->SetPos(to, promod3::loop::BB_CB_INDEX,
- pos_buffer_->GetPos(from, promod3::loop::BB_CB_INDEX));
-}
-
-void SCWRL4RotamerConstructor::ConstructBaseParticles(const SCWRLRotamerInfo& info,
- RotamerID id,
- std::vector<Particle>& particles) {
-
- core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "SCWRL4RotamerConstructor::ConstructBaseParticles", 2);
-
- geom::Vec3 a, b, c;
-
- // generate the particles
- for(uint i = 0; i < info.particles.size(); ++i){
- const SCWRLPInfo& pinfo = info.particles[i];
- if(pinfo.is_hydrogen){
- a = hydrogen_buffer_->GetPos(pinfo.atom_idx);
- }
- else a = pos_buffer_->GetPos(id, pinfo.atom_idx);
- particles[i] = Particle(pinfo.name, new SCWRL4Param(pinfo.type, a,
- pinfo.charge));
- }
-
- // set the polar directions
- for(uint i = 0; i < info.polar_directions.size(); ++i){
- a = hydrogen_buffer_->GetPos(info.polar_directions[i].polar_idx);
- b = pos_buffer_->GetPos(id, info.polar_directions[i].anchor_idx);
- PScoringParam* p = particles[info.polar_directions[i].p_idx].GetSParam();
- reinterpret_cast<SCWRL4Param*>(p)->SetPolarDirection(a - b);
- }
-
- // set the lone pairs
- for(uint i = 0; i < info.lone_pairs.size(); ++i){
- const SCWRLLPInfo& lp = info.lone_pairs[i];
-
- if(lp.A_is_hydrogen) a = hydrogen_buffer_->GetPos(lp.index_A);
- else a = pos_buffer_->GetPos(id, lp.index_A);
+ particle.SetSParam(p);
+ } else {
+
+ // deal with terminal special cases
+ if(at_idx == -1) {
+ // manual setup
+ SCWRL4Param* p = new SCWRL4Param(OParticle, terminal_o_pos_, -0.55);
+ _AddLonePairsCarbonyl(pos_buffer_->GetPos(id_, promod3::loop::BB_CA_INDEX),
+ pos_buffer_->GetPos(id_, promod3::loop::BB_C_INDEX),
+ terminal_o_pos_, p);
+ particle.SetSParam(p);
+ } else if(at_idx == -2) {
+ // manual setup
+ SCWRL4Param* p = new SCWRL4Param(OParticle, terminal_oxt_pos_, -0.55);
+ _AddLonePairsCarbonyl(pos_buffer_->GetPos(id_, promod3::loop::BB_CA_INDEX),
+ pos_buffer_->GetPos(id_, promod3::loop::BB_C_INDEX),
+ terminal_oxt_pos_, p);
+ particle.SetSParam(p);
+ } else {
+ SCWRL4ParticleType particle_type =
+ SCWRL4RotamerParam::Instance().GetParticleType(id_, at_idx);
+ geom::Vec3 pos = pos_buffer_->GetPos(id_, at_idx);
+ Real charge =
+ SCWRL4RotamerParam::Instance().GetHeavyAtomCharge(id_, at_idx);
+ SCWRL4Param* p = new SCWRL4Param(particle_type, pos, charge);
+
+ int lpi_idx = SCWRL4RotamerParam::Instance().GetLPInfoIdx(id_, at_idx);
+
+ // check whether we have a valid lone pair idx, as well as whether we're
+ // with a n_terminal nitrogen. The latter also has no lone pair
+ //if(lpi_idx != -1 && !(n_ter_ && at_idx == promod3::loop::BB_N_INDEX)) {
+ if(lpi_idx != -1) {
+ const SCWRL4LPInfo& lp = SCWRL4RotamerParam::Instance().GetLP(lpi_idx);
+ geom::Vec3 a, b, c;
+
+ if(lp.A_is_hydrogen) a = hydrogen_buffer_->GetPos(lp.index_A);
+ else a = pos_buffer_->GetPos(id_, lp.index_A);
- if(lp.B_is_hydrogen) b = hydrogen_buffer_->GetPos(lp.index_B);
- else b = pos_buffer_->GetPos(id, lp.index_B);
+ if(lp.B_is_hydrogen) b = hydrogen_buffer_->GetPos(lp.index_B);
+ else b = pos_buffer_->GetPos(id_, lp.index_B);
- if(lp.C_is_hydrogen) c = hydrogen_buffer_->GetPos(lp.index_C);
- else c = pos_buffer_->GetPos(id, lp.index_C);
+ if(lp.C_is_hydrogen) c = hydrogen_buffer_->GetPos(lp.index_C);
+ else c = pos_buffer_->GetPos(id_, lp.index_C);
- EvalLonePairRule(reinterpret_cast<SCWRL4Param*>(particles[lp.p_idx].GetSParam()),
- lp.rule, a, b, c);
- }
-}
-
-void SCWRL4RotamerConstructor::ConstructBBFrameParticles(
- const SCWRLRotamerInfo& info, RotamerID id,
- bool n_ter, bool c_ter,
- std::vector<Particle>& particles) {
-
- core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "SCWRL4RotamerConstructor::ConstructBBFrameParticles", 2);
-
- ConstructBaseParticles(info, id, particles);
- if(!(n_ter || c_ter)) return; // we're already done
-
- int p_idx = info.particles.size();
-
- if(c_ter){
- geom::Vec3 oxt_pos;
- geom::Vec3 c_pos = pos_buffer_->GetPos(id, promod3::loop::BB_C_INDEX);
- geom::Vec3 ca_pos = pos_buffer_->GetPos(id, promod3::loop::BB_CA_INDEX);
- geom::Vec3 n_pos = pos_buffer_->GetPos(id, promod3::loop::BB_N_INDEX);
- geom::Vec3 o_pos = pos_buffer_->GetPos(id, promod3::loop::BB_O_INDEX);
- promod3::core::ConstructCTerminalOxygens(c_pos, ca_pos, n_pos,
- o_pos, oxt_pos);
- //manually add oxygen without a rule...
- particles[p_idx] = Particle("OT", new SCWRL4Param(OParticle,
- oxt_pos, -0.55));
- _AddLonePairsCarbonyl(ca_pos, c_pos, oxt_pos,
- reinterpret_cast<SCWRL4Param*>(particles[p_idx].GetSParam()));
- ++p_idx;
- }
-
- if(n_ter){
- geom::Vec3 ht1_pos, ht2_pos, ht3_pos;
- geom::Vec3 n_pos, ca_pos, c_pos;
- n_pos = pos_buffer_->GetPos(id, promod3::loop::BB_N_INDEX);
- ca_pos = pos_buffer_->GetPos(id, promod3::loop::BB_CA_INDEX);
- c_pos = pos_buffer_->GetPos(id, promod3::loop::BB_C_INDEX);
- promod3::core::ConstructAtomPos(c_pos, ca_pos, n_pos, 0.997, 2.042,
- 1.0472, ht1_pos);
- promod3::core::ConstructAtomPos(c_pos,ca_pos,n_pos,0.997, 2.042,
- -1.0472, ht2_pos);
- particles[p_idx] = Particle("HT1", new SCWRL4Param(HParticle,
- ht1_pos, 0.35));
- SCWRL4Param* p = reinterpret_cast<SCWRL4Param*>(particles[p_idx].GetSParam());
- p->SetPolarDirection(ht1_pos - n_pos);
-
- particles[p_idx + 1] = Particle("HT2", new SCWRL4Param(HParticle,
- ht2_pos, 0.35));
- p = reinterpret_cast<SCWRL4Param*>(particles[p_idx + 1].GetSParam());
- p->SetPolarDirection(ht2_pos - n_pos);
-
- if(id == PRO || id == TPR || id == CPR) {
- // there are only two hydrogens... please note, that they are not
- // optimally placed in case of proline.
- // we would have to consider CD for that. This costs a good bottle
- // of wine that I implement that correctly...
- return;
- }
-
- promod3::core::ConstructAtomPos(c_pos, ca_pos, n_pos, 0.997, 2.042,
- M_PI, ht3_pos);
- // we assume, that there is currently one hydrogen apart from ht1 and ht2
- // and replace it with ht3
- for(uint i = 0; i < info.particles.size(); ++i){
- if(info.particles[i].is_hydrogen){
- particles[i] = Particle("HT3", new SCWRL4Param(HParticle,
- ht3_pos, 0.35));
- SCWRL4Param* p = reinterpret_cast<SCWRL4Param*>(particles[i].GetSParam());
- p->SetPolarDirection(ht3_pos - n_pos);
- break;
- }
+ EvalLonePairRule(p, lp.rule, a, b, c);
+ }
+ particle.SetSParam(p);
}
}
}
diff --git a/sidechain/src/scwrl4_rotamer_constructor.hh b/sidechain/src/scwrl4_rotamer_constructor.hh
index 887ea3c39f71690123fd5c81f0e2def69455d225..ea2bdb33816c3731b470216bc45a6994d497ae2e 100644
--- a/sidechain/src/scwrl4_rotamer_constructor.hh
+++ b/sidechain/src/scwrl4_rotamer_constructor.hh
@@ -18,235 +18,12 @@
#define PROMOD3_SCWRL_ROTAMER_CONSTRUCTOR_HH
#include <promod3/sidechain/rotamer_constructor.hh>
-#include <promod3/sidechain/scwrl4_particle_scoring.hh>
namespace promod3 { namespace sidechain {
class SCWRL4RotamerConstructor;
typedef boost::shared_ptr<SCWRL4RotamerConstructor> SCWRL4RotamerConstructorPtr;
-/// \brief Types of lone pair construction
-enum SCWRLLPRule {
- LONE_PAIR_CARBONYL, LONE_PAIR_COH, LONE_PAIR_CNC
-};
-
-/// \brief Info for lone pair construction (always involves 3 particles)
-/// -> indices are in same order as particles. The lone pair gets finally added
-/// to particle with p_idx
-/// A, B and C are indices as they are stored in AllAtomPositions, p_idx is the
-/// index of the particle in the rotamer, where the lone pairs get added
-struct SCWRLLPInfo {
- SCWRLLPInfo() { }
- SCWRLLPInfo(int idx_A, int idx_B, int idx_C,
- bool a_ih, bool b_ih, bool c_ih,
- int p, SCWRLLPRule r)
- : index_A(idx_A), index_B(idx_B),
- index_C(idx_C), A_is_hydrogen(a_ih),
- B_is_hydrogen(b_ih), C_is_hydrogen(c_ih),
- p_idx(p), rule(r) { }
- int index_A;
- int index_B;
- int index_C;
- bool A_is_hydrogen;
- bool B_is_hydrogen;
- bool C_is_hydrogen;
- int p_idx;
- SCWRLLPRule rule;
-};
-
-/// \brief Info for polar direction construction. The polar direction is
-/// particle_pos[polar_idx] - particle_pos[anchor_idx]
-/// The direction gets finally added to the particle with p_idx
-/// polar_idx and anchor idx are indices as they are stored in
-/// AllAtomPositions, p_idx is the index of the particle in the
-/// rotamer
-struct SCWRLPDInfo {
- SCWRLPDInfo() { }
- SCWRLPDInfo(int pol_idx, int a_idx, int p_idx) : polar_idx(pol_idx),
- anchor_idx(a_idx),
- p_idx(p_idx) { }
- int polar_idx;
- int anchor_idx;
- int p_idx;
-};
-
-/// \brief Info for particle construction
-struct SCWRLPInfo {
- SCWRLPInfo() { }
- SCWRLPInfo(SCWRL4ParticleType t, Real c,
- const String& n, int idx, bool ih) : type(t), charge(c),
- name(n), atom_idx(idx),
- is_hydrogen(ih) { }
- SCWRL4ParticleType type;
- Real charge;
- String name; // PDB naming
- int atom_idx; // for AllAtomPositions
- // (idx in HydrogenStorage if is_hydrogen is true)
- bool is_hydrogen;
-};
-
-/// \brief Info for custom particle construction...
-/// In the example of SER / THR and TYR we construct several hydrogens
-/// looking in different directions, they do therefore not follow the
-/// default hydrogen positioning conventions.
-/// This rule defines how to construct them by using
-/// three indices of heavy atoms, a bond length and an angle.
-/// The dihedral is defined as an index and is set globally in
-/// SCWRL4RotamerConstructor. The default hydrogen construction
-/// gets overriden for cases defined with such a SCWRLCustomHydrogenInfo
-struct SCWRLCustomHydrogenInfo {
- SCWRLCustomHydrogenInfo() { }
- SCWRLCustomHydrogenInfo(int idx, int a_idx_one, int a_idx_two, int a_idx_three,
- Real bl, Real a, int c_idx): atom_idx(idx),
- anchor_idx_one(a_idx_one),
- anchor_idx_two(a_idx_two),
- anchor_idx_three(a_idx_three),
- bond_length(bl), angle(a),
- chi_idx(c_idx){ }
- int atom_idx; //the idx in the hydrogen constructor
- int anchor_idx_one; // idx in AllAtomPositions
- int anchor_idx_two;
- int anchor_idx_three;
- Real bond_length;
- Real angle;
- int chi_idx;
-};
-
-/// \brief Info to generate FRM rotamers
-/// The idea is to only rotate around one bond at a time.
-/// This bond gets defined by anchor_idx_one and anchor_idx_two.
-/// All particles defined in rotating_particles get then rotated by
-/// a user defined angle times the defined prefactors.
-/// (three prefactors result in three subrotamers)
-struct SCWRLFRMRule{
- SCWRLFRMRule() { }
- int anchor_idx_one;
- int anchor_idx_two;
- std::vector<Real> prefactors;
- std::vector<int> fix_particles;
- std::vector<int> rotating_particles;
-};
-
-/// \brief Info to construct a full rotamer.
-struct SCWRLRotamerInfo{
- SCWRLRotamerInfo() { }
- std::vector<SCWRLPInfo> particles;
- std::vector<SCWRLCustomHydrogenInfo> custom_hydrogens;
- std::vector<SCWRLLPInfo> lone_pairs;
- std::vector<SCWRLPDInfo> polar_directions;
- Real internal_e_prefactor;
- Real frm_t;
- bool has_hydrogens;
-};
-
-/// \brief Defines lookups to build rotamer stuff.
-class SCWRLRotamerLookup {
-public:
-
- SCWRLRotamerLookup(bool cb_in_sidechain);
-
- // Data access
- const SCWRLRotamerInfo& GetSidechainInfo(RotamerID id) const {
- return sidechain_infos_[id];
- }
-
- const SCWRLRotamerInfo& GetBackboneInfo(RotamerID id) const {
- return backbone_infos_[id];
- }
-
- const std::vector<SCWRLFRMRule>& GetFRMRules(RotamerID id) const {
- return frm_rules_[id];
- }
-
- int GetNumSidechainParticles(RotamerID id) const {
- return num_sidechain_particles_[id];
- }
-
- int GetNumBackboneParticles(RotamerID id) const {
- return num_sidechain_particles_[id];
- }
-
- int GetNumFRMSidechainParticles(RotamerID id) const {
- return num_frm_particles_[id];
- }
-
-private:
-
- void AddInfo(RotamerID id, SCWRL4ParticleType p_type, Real charge,
- const String& name, int idx, bool is_h){
- SCWRLPInfo p(p_type, charge, name, idx, is_h);
- sidechain_infos_[id].particles.push_back(p);
- }
-
- void AddCustomHydrogenInfo(RotamerID id, int idx,
- int a_idx_one, int a_idx_two, int a_idx_three,
- Real bl, Real a, int c_idx){
- SCWRLCustomHydrogenInfo i(idx, a_idx_one, a_idx_two, a_idx_three, bl,
- a, c_idx);
- sidechain_infos_[id].custom_hydrogens.push_back(i);
- }
-
- void AddBBInfo(RotamerID id, SCWRL4ParticleType p_type, Real charge,
- const String& name, int idx, bool is_h){
- SCWRLPInfo p(p_type, charge, name, idx, is_h);
- backbone_infos_[id].particles.push_back(p);
- }
-
- void AddPDir(RotamerID id, int polar_idx, int anchor_idx, int p_idx){
- SCWRLPDInfo p(polar_idx, anchor_idx, p_idx);
- sidechain_infos_[id].polar_directions.push_back(p);
- }
-
- void AddBBPDir(RotamerID id, int polar_idx, int anchor_idx, int p_idx){
- SCWRLPDInfo p(polar_idx, anchor_idx, p_idx);
- backbone_infos_[id].polar_directions.push_back(p);
- }
-
- void AddLP(RotamerID id, int idx_a, int idx_b, int idx_c,
- bool a_ih, bool b_ih, bool c_ih, int p_idx, SCWRLLPRule r){
- SCWRLLPInfo lp(idx_a, idx_b, idx_c, a_ih, b_ih, c_ih, p_idx, r);
- sidechain_infos_[id].lone_pairs.push_back(lp);
- }
-
- void AddBBLP(RotamerID id, int idx_a, int idx_b, int idx_c,
- bool a_ih, bool b_ih, bool c_ih, int p_idx, SCWRLLPRule r){
- SCWRLLPInfo lp(idx_a, idx_b, idx_c, a_ih, b_ih, c_ih, p_idx, r);
- backbone_infos_[id].lone_pairs.push_back(lp);
- }
-
- void AddFRMRule(RotamerID id, int idx_one, int idx_two){
- frm_rules_[id].push_back(SCWRLFRMRule());
- frm_rules_[id].back().anchor_idx_one = idx_one;
- frm_rules_[id].back().anchor_idx_two = idx_two;
- }
-
- void AddFRMPrefactor(RotamerID id, int rule_idx, Real prefactor){
- frm_rules_[id][rule_idx].prefactors.push_back(prefactor);
- }
-
- void AddFRMRotatingParticle(RotamerID id, int rule_idx, int p_idx){
- frm_rules_[id][rule_idx].rotating_particles.push_back(p_idx);
- }
-
- void AddFRMFixParticle(RotamerID id, int rule_idx, int p_idx){
- frm_rules_[id][rule_idx].fix_particles.push_back(p_idx);
- }
-
- // To construct classical rotamers or as lookup for sidechain frame residues
- SCWRLRotamerInfo sidechain_infos_[XXX + 1];
-
- // To construct backbone frame residues
- SCWRLRotamerInfo backbone_infos_[XXX + 1];
-
- // Additional info required for generating frm rotamers
- std::vector<SCWRLFRMRule> frm_rules_[XXX + 1];
-
- int num_sidechain_particles_[XXX + 1];
- int num_backbone_particles_[XXX + 1];
- int num_frm_particles_[XXX+1];
-};
-
-
class SCWRL4RotamerConstructor : public RotamerConstructor{
public:
@@ -255,26 +32,6 @@ public:
virtual ~SCWRL4RotamerConstructor() { }
- // Construct frame residues
- virtual FrameResiduePtr ConstructBackboneFrameResidue(
- const ost::mol::ResidueHandle& res, RotamerID id, uint residue_index,
- Real phi, bool n_ter = false,
- bool c_ter = false);
-
- virtual FrameResiduePtr ConstructBackboneFrameResidue(
- const promod3::loop::AllAtomPositions& all_atom, uint aa_res_idx,
- RotamerID id, uint residue_index,
- Real phi, bool n_ter = false,
- bool c_ter = false);
-
- virtual FrameResiduePtr ConstructSidechainFrameResidue(
- const ost::mol::ResidueHandle& res, RotamerID id,
- uint residue_index);
-
- virtual FrameResiduePtr ConstructSidechainFrameResidue(
- const promod3::loop::AllAtomPositions& all_atom, uint aa_res_idx,
- RotamerID id, uint residue_index);
-
FrameResiduePtr ConstructFrameResidue(const ost::mol::ResidueHandle& res,
uint residue_index);
@@ -283,44 +40,25 @@ public:
ost::conop::CompoundLibPtr comp_lib);
// Assign internal energies to rotamer groups
- virtual void AssignInternalEnergies(RRMRotamerGroupPtr group);
-
- virtual void AssignInternalEnergies(FRMRotamerGroupPtr group);
+ virtual void AssignInternalEnergies(RRMRotamerGroupPtr group,
+ RotamerID id,
+ uint residue_index,
+ Real phi = -1.0472,
+ Real psi = -0.7854,
+ bool n_ter = false,
+ bool c_ter = false);
+
+ virtual void AssignInternalEnergies(FRMRotamerGroupPtr group,
+ RotamerID id,
+ uint residue_index,
+ Real phi = -1.0472,
+ Real psi = -0.7854,
+ bool n_ter = false,
+ bool c_ter = false);
private:
- // Construct the rotamer groups after all backbone position information has
- // been set into the internal positin buffer objects
- virtual RRMRotamerGroupPtr ConstructRRMGroup(
- RotamerID id, uint residue_index,
- std::pair<RotamerLibEntry*,uint> lib_entries,
- Real probability_cutoff);
-
- virtual FRMRotamerGroupPtr ConstructFRMGroup(
- RotamerID id, uint residue_index,
- std::pair<RotamerLibEntry*,uint> lib_entries,
- Real probability_cutoff);
-
- // assumes positions / probabilities, chi angles and chi deviations
- // to be set in buffer
- RRMRotamerPtr ConstructRRM(RotamerID id, uint residue_idx);
- FRMRotamerPtr ConstructFRM(RotamerID id, uint residue_idx);
-
- // helpers
- void MVBBPosBuffer(RotamerID from, RotamerID to);
-
- void ConstructBaseParticles(const SCWRLRotamerInfo& info, RotamerID id,
- std::vector<Particle>& particles);
-
- void ConstructBBFrameParticles(const SCWRLRotamerInfo& info, RotamerID id,
- bool n_ter, bool c_ter,
- std::vector<Particle>& particles);
-
- Real chi_angles_[4];
- Real chi_dev_[4];
- Real probability_;
- SCWRLRotamerLookup rotamer_lookup_;
- promod3::loop::HydrogenStoragePtr hydrogen_buffer_;
+ void ParametrizeParticle(int atom_idx, bool is_hydrogen, Particle& p);
};
}} // ns