diff --git a/doc/tests/scripts/sidechain_steps.py b/doc/tests/scripts/sidechain_steps.py
index bf1a3866356d84db21819df5fa63218a41575b58..aa903d2477f57fcdaee574060afddb3b6c4a013e 100644
--- a/doc/tests/scripts/sidechain_steps.py
+++ b/doc/tests/scripts/sidechain_steps.py
@@ -6,8 +6,8 @@ prot = io.LoadPDB('data/1CRN.pdb')
# load rotamer library
library = sidechain.LoadDunbrackLib()
# we need a rotamer constructor to create any rotamers or
-# frame residues
-rot_constructor = sidechain.SCWRLRotamerConstructor()
+# frame residues
+rot_constructor = sidechain.SCWRLRotamerConstructor(False)
# create new entity from protein only containing the amino acids
prot = mol.CreateEntityFromView(prot.Select("peptide=true"), True)
diff --git a/modelling/pymod/_reconstruct_sidechains.py b/modelling/pymod/_reconstruct_sidechains.py
index 26d31567bb76a95dd5703e3da840a77b937e70f5..cc465d832149d465348823cbfc67db6386235b93 100644
--- a/modelling/pymod/_reconstruct_sidechains.py
+++ b/modelling/pymod/_reconstruct_sidechains.py
@@ -1,5 +1,6 @@
from ost import geom, mol, conop
from promod3 import core, sidechain
+import traceback
###############################################################################
# helper functions
@@ -10,7 +11,6 @@ def _GetRotamerIDs(res_list):
rot_id = sidechain.TLCToRotID(r.GetName())
if rot_id == sidechain.XXX:
continue # no idea what it is, so we stick with ALA
- # => don't model sidechain
rotamer_ids[i] = rot_id
return rotamer_ids
@@ -105,12 +105,11 @@ def _AddLigandFrameResidues(frame_residues, ent_lig, rotamer_constructor, offset
fr1 = rotamer_constructor.ConstructBackboneFrameResidue(\
res.handle, rot_id, res_idx,
phi, n_ter, c_ter)
- if rot_id != sidechain.ALA and rot_id != sidechain.GLY:
- fr2 = rotamer_constructor.ConstructSidechainFrameResidue(\
- res.handle, rot_id, res_idx)
- frame_residues.extend([fr1,fr2])
- else:
- frame_residues.append(fr1)
+
+ fr2 = rotamer_constructor.ConstructSidechainFrameResidue(\
+ res.handle, rot_id, res_idx)
+
+ frame_residues.extend([fr1,fr2])
except:
pass # ignore peptide treatment and treat below
else:
@@ -148,9 +147,6 @@ def _AddSidechainFrameResidues(frame_residues, incomplete_sidechains,
cystein_indices.append(i)
continue
- if rotamer_ids[i] == sidechain.ALA or rotamer_ids[i] == sidechain.GLY:
- continue # no sidechain to model
-
try:
frame_residue = rotamer_constructor.ConstructSidechainFrameResidue(\
r.handle, rotamer_ids[i], i)
@@ -166,9 +162,6 @@ def _AddSidechainFrameResidues(frame_residues, incomplete_sidechains,
cystein_indices.append(i)
continue
- if rotamer_ids[i] == sidechain.ALA or rotamer_ids[i] == sidechain.GLY:
- continue # no sidechain to model
-
incomplete_sidechains.append(i)
def _AddCysteinFrameResidues(frame_residues, incomplete_sidechains,
@@ -231,7 +224,7 @@ def _GetRotamerGroups(res_list, rot_ids, indices, rot_lib, rot_constructor,
phi_angles, psi_angles, use_frm, bbdep, frame_residues):
'''Get list of rotamer groups from subset of res_list.
Residues are chosen as res_list[i] for i in indices and only if a rotamer
- group can be created (e.g. no ALA, GLY).
+ group can be created.
Rotamer groups are filtered to keep only best ones (given frame).
Returns list of rotamer groups and list of res. indices they belong to.
'''
@@ -249,9 +242,6 @@ def _GetRotamerGroups(res_list, rot_ids, indices, rot_lib, rot_constructor,
# get rotamer ID
r = res_list[i]
rot_id = rot_ids[i]
-
- if rot_id == sidechain.ALA or rot_id == sidechain.GLY:
- continue
if rot_id == sidechain.CYS:
rot_id = sidechain.CYH
@@ -442,7 +432,7 @@ def ReconstructSidechains(ent, keep_sidechains=False, build_disulfids=True,
if type(rotamer_library) is sidechain.BBDepRotamerLib:
bbdep = True
- rotamer_constructor = sidechain.SCWRLRotamerConstructor()
+ rotamer_constructor = sidechain.SCWRLRotamerConstructor(False)
# take out ligand chain and any non-peptides
prot = ent.Select("peptide=true and cname!='_'")
diff --git a/modelling/src/sidechain_env_listener.cc b/modelling/src/sidechain_env_listener.cc
index 18a1297eef220f6b2aa55227a17038b918216282..d72e09f30a9c918c87d1569aabe9be055c6de17f 100644
--- a/modelling/src/sidechain_env_listener.cc
+++ b/modelling/src/sidechain_env_listener.cc
@@ -150,10 +150,7 @@ void SidechainEnvListener::SetResidue_(loop::ConstAllAtomPositionsPtr all_pos,
// we only add data if BB is set
if (bb_set) {
// get positions
- const geom::Vec3& n_pos = all_pos->GetPos(idx_N);
const geom::Vec3& ca_pos = all_pos->GetPos(idx_CA);
- const geom::Vec3& c_pos = all_pos->GetPos(idx_C);
- const geom::Vec3& o_pos = all_pos->GetPos(idx_O);
geom::Vec3 cb_pos;
if (r_id != sidechain::GLY) cb_pos = all_pos->GetPos(idx_CB);
@@ -177,36 +174,33 @@ void SidechainEnvListener::SetResidue_(loop::ConstAllAtomPositionsPtr all_pos,
// set backbone frame res.
bb_frame_residue_[res_idx]
- = rot_constructor_.ConstructBackboneFrameResidue(n_pos, ca_pos, c_pos,
- o_pos, cb_pos,
+ = rot_constructor_.ConstructBackboneFrameResidue(*all_pos, res_idx,
r_id, res_idx,
phi_angle_[res_idx],
n_ter_[res_idx],
c_ter_[res_idx]);
- // do we have a sidechain?
- if (r_id != sidechain::ALA && r_id != sidechain::GLY) {
- // set sidechain frame res. if all set
- if (all_set) {
- sc_frame_residue_[res_idx]
- = rot_constructor_.ConstructSidechainFrameResidue(*all_pos, res_idx,
- r_id, res_idx);
- } else {
- sc_frame_residue_[res_idx].reset();
- }
- // set rotamer if needed
- if (all_rotamers_ || !all_set) {
- SetRotamer_(all_pos, n_pos, ca_pos, cb_pos, r_id, res_idx);
- } else {
- if (use_frm_) frm_rotamer_group_[res_idx].reset();
- else rrm_rotamer_group_[res_idx].reset();
- }
- // set extra cystein rotamer if needed
- if (add_cyd_rotamers_ && r_id == sidechain::CYS) {
- CreateRotamerGroup(cyd_frm_rotamer_group_[res_idx], n_pos, ca_pos,
- cb_pos, sidechain::CYD, res_idx);
- }
+ // set sidechain frame res. if all set
+ if (all_set) {
+ sc_frame_residue_[res_idx]
+ = rot_constructor_.ConstructSidechainFrameResidue(*all_pos, res_idx,
+ r_id, res_idx);
+ } else {
+ sc_frame_residue_[res_idx].reset();
+ }
+ // set rotamer if needed
+ if (all_rotamers_ || !all_set) {
+ SetRotamer_(all_pos, r_id, res_idx);
+ } else {
+ if (use_frm_) frm_rotamer_group_[res_idx].reset();
+ else rrm_rotamer_group_[res_idx].reset();
}
+ // set extra cystein rotamer if needed
+ if (add_cyd_rotamers_ && r_id == sidechain::CYS) {
+ CreateRotamerGroup(cyd_frm_rotamer_group_[res_idx], all_pos,
+ sidechain::CYD, res_idx);
+ }
+
} else {
// clear stuff
if (bb_frame_residue_[res_idx]) {
@@ -224,9 +218,6 @@ void SidechainEnvListener::SetResidue_(loop::ConstAllAtomPositionsPtr all_pos,
}
void SidechainEnvListener::SetRotamer_(loop::ConstAllAtomPositionsPtr all_pos,
- const geom::Vec3& n_pos,
- const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos,
const sidechain::RotamerID r_id,
const uint res_idx) {
// add rotamer anyways -> potentially need to change ID
@@ -245,10 +236,10 @@ void SidechainEnvListener::SetRotamer_(loop::ConstAllAtomPositionsPtr all_pos,
// -> same with RRM: 0.30s
// -> RRM w/o BBdep: 0.23s
if (use_frm_) {
- CreateRotamerGroup(frm_rotamer_group_[res_idx], n_pos, ca_pos, cb_pos,
+ CreateRotamerGroup(frm_rotamer_group_[res_idx], all_pos,
rg_r_id, res_idx);
} else {
- CreateRotamerGroup(rrm_rotamer_group_[res_idx], n_pos, ca_pos, cb_pos,
+ CreateRotamerGroup(rrm_rotamer_group_[res_idx], all_pos,
rg_r_id, res_idx);
}
}
diff --git a/modelling/src/sidechain_env_listener.hh b/modelling/src/sidechain_env_listener.hh
index a35a0b36b8f18f7a497ec8c27f70739fda4576bf..2f8c14a1349f80b6d36464debc298b7aa3161d01 100644
--- a/modelling/src/sidechain_env_listener.hh
+++ b/modelling/src/sidechain_env_listener.hh
@@ -119,40 +119,33 @@ public:
// create a rotamer group based on internal settings (no use_frm_ check!)
void CreateRotamerGroup(sidechain::FRMRotamerGroupPtr& rot_group,
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos,
+ loop::ConstAllAtomPositionsPtr all_pos,
const sidechain::RotamerID r_id, const uint res_idx) {
if (use_bbdep_lib_) {
- rot_group = rot_constructor_.ConstructFRMRotamerGroup(n_pos, ca_pos,
- cb_pos, r_id,
- res_idx,
+ rot_group = rot_constructor_.ConstructFRMRotamerGroup(*all_pos, res_idx,
+ r_id, res_idx,
bbdep_library_,
phi_angle_[res_idx],
psi_angle_[res_idx]);
} else {
- rot_group = rot_constructor_.ConstructFRMRotamerGroup(n_pos, ca_pos, cb_pos,
+ rot_group = rot_constructor_.ConstructFRMRotamerGroup(*all_pos, res_idx,
r_id, res_idx,
library_);
}
rot_constructor_.AssignInternalEnergies(rot_group);
}
void CreateRotamerGroup(sidechain::RRMRotamerGroupPtr& rot_group,
- const geom::Vec3& n_pos,
- const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos,
- const sidechain::RotamerID r_id,
- const uint res_idx) {
+ loop::ConstAllAtomPositionsPtr all_pos,
+ const sidechain::RotamerID r_id, const uint res_idx) {
if (use_bbdep_lib_) {
- rot_group = rot_constructor_.ConstructRRMRotamerGroup(n_pos, ca_pos,
- cb_pos, r_id,
- res_idx,
+ rot_group = rot_constructor_.ConstructRRMRotamerGroup(*all_pos, res_idx,
+ r_id, res_idx,
bbdep_library_,
phi_angle_[res_idx],
psi_angle_[res_idx]);
} else {
- rot_group = rot_constructor_.ConstructRRMRotamerGroup(n_pos, ca_pos,
- cb_pos, r_id,
- res_idx,
+ rot_group = rot_constructor_.ConstructRRMRotamerGroup(*all_pos, res_idx,
+ r_id, res_idx,
library_);
}
rot_constructor_.AssignInternalEnergies(rot_group);
@@ -163,9 +156,7 @@ private:
// set stuff for one residue
void SetResidue_(loop::ConstAllAtomPositionsPtr all_pos, const uint res_idx);
void SetRotamer_(loop::ConstAllAtomPositionsPtr all_pos,
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos, const sidechain::RotamerID r_id,
- const uint res_idx);
+ const sidechain::RotamerID r_id, const uint res_idx);
// global data
bool all_rotamers_; // construct rotamers for all res. with BB instead of
@@ -185,8 +176,8 @@ private:
// dynamic data per residue
// -> any data only set if BB set ("if (bb_frame_residue_[res_idx]) ...")
- // -> sc_frame_residue set if not ALA/GLY and all pos. available
- // -> xxx_rotamer_group set if not ALA/GLY and atoms missing or all_rotamers_
+ // -> sc_frame_residue set if not GLY and all pos. available
+ // -> xxx_rotamer_group set if no atoms are missing or all_rotamers_
// -> if use_frm_, only xxx = frm valid, else, only xxx = rrm
// -> CalculateInternalEnergies done for all rotamer groups
ScCBetaSpatialOrganizerItem* env_data_;
diff --git a/sidechain/doc/rotamer_constructor.rst b/sidechain/doc/rotamer_constructor.rst
index 316c0aba0559e2c0061d8a5ed23641967093a00f..2f9d7479e9cb43e9e6c052f2e8df1d524a19eeff 100644
--- a/sidechain/doc/rotamer_constructor.rst
+++ b/sidechain/doc/rotamer_constructor.rst
@@ -11,22 +11,33 @@ Constructing Rotamers and Frame Residues
--------------------------------------------------------------------------------
-.. class:: SCWRLRotamerConstructor()
+.. class:: SCWRLRotamerConstructor(cb_in_sidechain)
Constructing rotamers and frame residues that are parametrized according to
the SCWRL4 method. They contain all heavy atoms, but also the
- polar hydrogens. The rotamers start after the CB atom (typically CG).
+ polar hydrogens.
In case of the :class:`FrameResidue` construction, the
constructor distinguishes between backbone and sidechain frame residues.
+ :param cb_in_sidechain: If set to true, all constructed rotamers will contain
+ the cb atom. This flag also affects the construction
+ of frame residues and controls whether the cb atom
+ shows up in the backbone frame residues or sidechain
+ frame residues.
+ This is useful when you want to represent ALA or
+ GLY with actual rotamers, but be aware of increased
+ runtime. This flag can be set to False for most
+ modeling applications and you just don't generate
+ any rotamers for ALA and GLY.
+
+ :type cb_in_sidechain: :class:`bool`
+
+
.. 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(n_pos, ca_pos, cb_pos, id,\
- residue_index, rot_lib,\
- [probability_cutoff = 0.98])
.. method:: ConstructRRMRotamerGroup(res, id, residue_index, rot_lib,\
[phi = -1.0472, psi = -0.7854,\
probability_cutoff = 0.98])
@@ -34,18 +45,11 @@ Constructing Rotamers and Frame Residues
residue_index, rot_lib,\
[phi = -1.0472, psi = -0.7854,\
probability_cutoff = 0.98])
- .. method:: ConstructRRMRotamerGroup(n_pos, ca_pos, cb_pos, id,\
- residue_index, rot_lib,\
- [phi = -1.0472, psi = -0.7854,\
- probability_cutoff = 0.98])
.. method:: ConstructRRMRotamerGroup(res, id, residue_index, rot_lib_entries,\
[probability_cutoff = 0.98])
.. method:: ConstructRRMRotamerGroup(all_atom_pos, aa_res_idx, id,\
residue_index, rot_lib_entries,\
[probability_cutoff = 0.98])
- .. method:: ConstructRRMRotamerGroup(n_pos, ca_pos, cb_pos, id,\
- residue_index, rot_lib_entries,\
- [probability_cutoff = 0.98])
All functions are also avaible for their flexible rotamer model counterpart.
=>ConstructFRMRotamerGroup(...) with exactly the same parameters.
@@ -105,10 +109,6 @@ Constructing Rotamers and Frame Residues
residue_index, Real phi,\
[n_ter = False, c_ter = False])
- .. method:: ConstructBackboneFrameResidue(n_pos, ca_pos, c_pos, o_pos, cb_pos,\
- id, residue_index, Real phi,\
- [n_ter = False, c_ter = False])
-
Constructs backbone frame residues for amino acid residues. It extracts
the n, ca, c, o and cb positions and constructs a frame residue based on
the parametrizations of SCWRL4. In case of **n_ter**, there are additional
diff --git a/sidechain/pymod/export_scwrl_rotamer_constructor.cc b/sidechain/pymod/export_scwrl_rotamer_constructor.cc
index 1d9cda258ed7f3fe39127025f2e2765aa3f8a0ae..539288e3e6363cee544e8815c484c83da32e6971 100644
--- a/sidechain/pymod/export_scwrl_rotamer_constructor.cc
+++ b/sidechain/pymod/export_scwrl_rotamer_constructor.cc
@@ -13,6 +13,10 @@ using namespace promod3;
namespace{
+SCWRLRotamerConstructorPtr WrapSCWRLRotamerConstructorInit(bool cb_in_sidechain) {
+ SCWRLRotamerConstructorPtr p(new SCWRLRotamerConstructor(cb_in_sidechain));
+ return p;
+}
RRMRotamerGroupPtr WrapRRMGroup_res(SCWRLRotamerConstructor& constructor,
const ost::mol::ResidueHandle& res,
@@ -36,18 +40,6 @@ RRMRotamerGroupPtr WrapRRMGroup_aa(SCWRLRotamerConstructor& constructor,
rot_lib, probability_cutoff);
}
-RRMRotamerGroupPtr WrapRRMGroup_pos(SCWRLRotamerConstructor& constructor,
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos,
- RotamerID rotamer_id,
- uint residue_idx,
- RotamerLibPtr rot_lib,
- Real probability_cutoff){
- return constructor.ConstructRRMRotamerGroup(n_pos, ca_pos, cb_pos,
- rotamer_id, residue_idx,
- rot_lib, probability_cutoff);
-}
-
FRMRotamerGroupPtr WrapFRMGroup_res(SCWRLRotamerConstructor& constructor,
const ost::mol::ResidueHandle& res,
RotamerID id,
@@ -70,18 +62,6 @@ FRMRotamerGroupPtr WrapFRMGroup_aa(SCWRLRotamerConstructor& constructor,
rot_lib, probability_cutoff);
}
-FRMRotamerGroupPtr WrapFRMGroup_pos(SCWRLRotamerConstructor& constructor,
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos,
- RotamerID rotamer_id,
- uint residue_idx,
- RotamerLibPtr rot_lib,
- Real probability_cutoff){
- return constructor.ConstructFRMRotamerGroup(n_pos, ca_pos, cb_pos,
- rotamer_id, residue_idx,
- rot_lib, probability_cutoff);
-}
-
RRMRotamerGroupPtr WrapRRMGroup_bbdep_res(SCWRLRotamerConstructor& constructor,
const ost::mol::ResidueHandle& res,
RotamerID id,
@@ -108,20 +88,6 @@ RRMRotamerGroupPtr WrapRRMGroup_bbdep_aa(SCWRLRotamerConstructor& constructor,
probability_cutoff);
}
-RRMRotamerGroupPtr WrapRRMGroup_bbdep_pos(SCWRLRotamerConstructor& constructor,
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos,
- RotamerID rotamer_id,
- uint residue_idx,
- BBDepRotamerLibPtr rot_lib,
- Real phi, Real psi,
- Real probability_cutoff){
- return constructor.ConstructRRMRotamerGroup(n_pos, ca_pos, cb_pos,
- rotamer_id, residue_idx,
- rot_lib, phi, psi,
- probability_cutoff);
-}
-
FRMRotamerGroupPtr WrapFRMGroup_bbdep_res(SCWRLRotamerConstructor& constructor,
const ost::mol::ResidueHandle& res,
RotamerID id,
@@ -148,20 +114,6 @@ FRMRotamerGroupPtr WrapFRMGroup_bbdep_aa(SCWRLRotamerConstructor& constructor,
probability_cutoff);
}
-FRMRotamerGroupPtr WrapFRMGroup_bbdep_pos(SCWRLRotamerConstructor& constructor,
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos,
- RotamerID rotamer_id,
- uint residue_idx,
- BBDepRotamerLibPtr rot_lib,
- Real phi, Real psi,
- Real probability_cutoff){
- return constructor.ConstructFRMRotamerGroup(n_pos, ca_pos, cb_pos,
- rotamer_id, residue_idx,
- rot_lib, phi, psi,
- probability_cutoff);
-}
-
RRMRotamerGroupPtr WrapRRMGroup_entries_res(SCWRLRotamerConstructor& constructor,
const ost::mol::ResidueHandle& res,
RotamerID id,
@@ -190,22 +142,6 @@ RRMRotamerGroupPtr WrapRRMGroup_entries_aa(SCWRLRotamerConstructor& constructor,
probability_cutoff);
}
-RRMRotamerGroupPtr WrapRRMGroup_entries_pos(SCWRLRotamerConstructor& constructor,
- const geom::Vec3& n_pos,
- const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos,
- RotamerID rotamer_id,
- uint residue_idx,
- const boost::python::list& entries,
- Real probability_cutoff){
- std::vector<RotamerLibEntry> v_entries;
- core::ConvertListToVector(entries, v_entries);
- return constructor.ConstructRRMRotamerGroup(n_pos, ca_pos, cb_pos,
- rotamer_id, residue_idx,
- v_entries,
- probability_cutoff);
-}
-
FRMRotamerGroupPtr WrapFRMGroup_entries_res(SCWRLRotamerConstructor& constructor,
const ost::mol::ResidueHandle& res,
RotamerID id,
@@ -234,23 +170,6 @@ FRMRotamerGroupPtr WrapFRMGroup_entries_aa(SCWRLRotamerConstructor& constructor,
probability_cutoff);
}
-FRMRotamerGroupPtr WrapFRMGroup_entries_pos(SCWRLRotamerConstructor& constructor,
- const geom::Vec3& n_pos,
- const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos,
- RotamerID rotamer_id,
- uint residue_idx,
- const boost::python::list& entries,
- Real probability_cutoff){
- std::vector<RotamerLibEntry> v_entries;
- core::ConvertListToVector(entries, v_entries);
- return constructor.ConstructFRMRotamerGroup(n_pos, ca_pos, cb_pos,
- rotamer_id, residue_idx,
- v_entries,
- probability_cutoff);
-}
-
-
FrameResiduePtr WrapBBFrame_res(SCWRLRotamerConstructor& constructor,
const ost::mol::ResidueHandle& residue,
RotamerID id, uint residue_index,
@@ -269,19 +188,6 @@ FrameResiduePtr WrapBBFrame_aa(SCWRLRotamerConstructor& constructor,
phi, n_ter, c_ter);
}
-FrameResiduePtr WrapBBFrame_pos(SCWRLRotamerConstructor& constructor,
- const geom::Vec3& n_pos,
- const geom::Vec3& ca_pos,
- const geom::Vec3& c_pos,
- const geom::Vec3& o_pos,
- const geom::Vec3& cb_pos,
- RotamerID id, uint residue_index,
- Real phi, bool n_ter, bool c_ter){
- return constructor.ConstructBackboneFrameResidue(n_pos, ca_pos, c_pos,
- o_pos, cb_pos, id,
- residue_index,
- phi, n_ter, c_ter);
-}
FrameResiduePtr WrapSCFrame_res(SCWRLRotamerConstructor& constructor,
const ost::mol::ResidueHandle& residue,
@@ -313,7 +219,8 @@ void AssignInternalEnergiesFRM(const SCWRLRotamerConstructor& constructor,
void export_SCWRLRotamerConstructor(){
- class_<SCWRLRotamerConstructor>("SCWRLRotamerConstructor", init<>())
+ class_<SCWRLRotamerConstructor, SCWRLRotamerConstructorPtr>("SCWRLRotamerConstructor", no_init)
+ .def("__init__", boost::python::make_constructor(&WrapSCWRLRotamerConstructorInit))
.def("ConstructRRMRotamerGroup", &WrapRRMGroup_res,(arg("residue"),
arg("rotamer_id"),
arg("residue_idx"),
@@ -325,13 +232,6 @@ void export_SCWRLRotamerConstructor(){
arg("residue_idx"),
arg("rot_lib"),
arg("probability_cutoff") = 0.98))
- .def("ConstructRRMRotamerGroup", &WrapRRMGroup_pos,(arg("n_pos"),
- arg("ca_pos"),
- arg("cb_pos"),
- arg("rotamer_id"),
- arg("residue_idx"),
- arg("rot_lib"),
- arg("probability_cutoff") = 0.98))
.def("ConstructFRMRotamerGroup", &WrapFRMGroup_res,(arg("residue"),
arg("rotamer_id"),
arg("residue_idx"),
@@ -343,13 +243,6 @@ void export_SCWRLRotamerConstructor(){
arg("residue_idx"),
arg("rot_lib"),
arg("probability_cutoff") = 0.98))
- .def("ConstructFRMRotamerGroup", &WrapFRMGroup_pos,(arg("n_pos"),
- arg("ca_pos"),
- arg("cb_pos"),
- arg("rotamer_id"),
- arg("residue_idx"),
- arg("rot_lib"),
- arg("probability_cutoff") = 0.98))
.def("ConstructRRMRotamerGroup", &WrapRRMGroup_bbdep_res,(arg("residue"),
arg("rotamer_id"),
arg("residue_idx"),
@@ -365,15 +258,6 @@ void export_SCWRLRotamerConstructor(){
arg("phi") = -1.0472,
arg("psi") = -0.7854,
arg("probability_cutoff") = 0.98))
- .def("ConstructRRMRotamerGroup", &WrapRRMGroup_bbdep_pos,(arg("n_pos"),
- arg("ca_pos"),
- arg("cb_pos"),
- arg("rotamer_id"),
- arg("residue_idx"),
- arg("rot_lib"),
- arg("phi") = -1.0472,
- arg("psi") = -0.7854,
- arg("probability_cutoff") = 0.98))
.def("ConstructFRMRotamerGroup", &WrapFRMGroup_bbdep_res,(arg("residue"),
arg("rotamer_id"),
arg("residue_idx"),
@@ -389,15 +273,6 @@ void export_SCWRLRotamerConstructor(){
arg("phi") = -1.0472,
arg("psi") = -0.7854,
arg("probability_cutoff") = 0.98))
- .def("ConstructFRMRotamerGroup", &WrapFRMGroup_bbdep_pos,(arg("n_pos"),
- arg("ca_pos"),
- arg("cb_pos"),
- arg("rotamer_id"),
- arg("residue_idx"),
- arg("rot_lib"),
- arg("phi") = -1.0472,
- arg("psi") = -0.7854,
- arg("probability_cutoff") = 0.98))
.def("ConstructRRMRotamerGroup", &WrapRRMGroup_entries_res,(arg("residue"),
arg("rotamer_id"),
arg("residue_idx"),
@@ -409,13 +284,6 @@ void export_SCWRLRotamerConstructor(){
arg("residue_idx"),
arg("entries"),
arg("probability_cutoff") = 0.98))
- .def("ConstructRRMRotamerGroup", &WrapRRMGroup_entries_pos,(arg("n_pos"),
- arg("ca_pos"),
- arg("cb_pos"),
- arg("rotamer_id"),
- arg("residue_idx"),
- arg("entries"),
- arg("probability_cutoff") = 0.98))
.def("ConstructFRMRotamerGroup", &WrapFRMGroup_entries_res,(arg("residue"),
arg("rotamer_id"),
arg("residue_idx"),
@@ -427,13 +295,6 @@ void export_SCWRLRotamerConstructor(){
arg("residue_idx"),
arg("entries"),
arg("probability_cutoff") = 0.98))
- .def("ConstructFRMRotamerGroup", &WrapFRMGroup_entries_pos,(arg("n_pos"),
- arg("ca_pos"),
- arg("cb_pos"),
- arg("rotamer_id"),
- arg("residue_idx"),
- arg("entries"),
- arg("probability_cutoff") = 0.98))
.def("ConstructBackboneFrameResidue", &WrapBBFrame_res,(arg("residue"),
arg("rotamer_id"),
arg("residue_index"),
@@ -447,16 +308,6 @@ void export_SCWRLRotamerConstructor(){
arg("phi"),
arg("n_ter")=false,
arg("c_ter")=false))
- .def("ConstructBackboneFrameResidue", &WrapBBFrame_pos,(arg("n_pos"),
- arg("ca_pos"),
- arg("c_pos"),
- arg("o_pos"),
- arg("cb_pos"),
- arg("rotamer_id"),
- arg("residue_index"),
- arg("phi"),
- arg("n_ter")=false,
- arg("c_ter")=false))
.def("ConstructSidechainFrameResidue", &WrapSCFrame_res,(arg("residue"),
arg("rotamer_id"),
arg("residue_index")))
diff --git a/sidechain/src/scwrl_rotamer_constructor.cc b/sidechain/src/scwrl_rotamer_constructor.cc
index 1ef28876c408c19e689c00c0ca252d9c50cfce77..5ef45a293683b1976f54387fe82277e0b74e02bc 100644
--- a/sidechain/src/scwrl_rotamer_constructor.cc
+++ b/sidechain/src/scwrl_rotamer_constructor.cc
@@ -170,7 +170,7 @@ _AtomSpecCPList _GetCarboxylAtoms(const _AtomInfo& atom_info) {
namespace promod3 { namespace sidechain {
-SCWRLRotamerLookup::SCWRLRotamerLookup() {
+SCWRLRotamerLookup::SCWRLRotamerLookup(bool cb_in_sidechain) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"SCWRLRotamerLookup::SCWRLRotamerLookup", 2);
@@ -178,6 +178,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
@@ -189,11 +190,17 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
@@ -208,6 +215,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
@@ -222,6 +230,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
@@ -236,6 +245,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
@@ -250,14 +260,26 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(ARG, HParticle, 0.25, "H", promod3::loop::ARG_H_INDEX,true);
- AddBBPDir(ARG, promod3::loop::ARG_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ 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);
@@ -265,15 +287,22 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
@@ -282,6 +311,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
@@ -290,47 +320,76 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(ASN, HParticle, 0.25, "H", promod3::loop::ASN_H_INDEX,true);
- AddBBPDir(ASN, promod3::loop::ASN_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ 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
- AddInfo(ASP, CParticle, 0.36, "CG", promod3::loop::ASP_CG_INDEX, false);
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, CH2Particle, -0.16, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(ASP, HParticle, 0.25, "H", promod3::loop::ASP_H_INDEX,true);
- AddBBPDir(ASP, promod3::loop::ASP_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ 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);
@@ -338,16 +397,23 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
@@ -357,6 +423,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
@@ -366,6 +433,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
@@ -375,14 +443,25 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(GLN, HParticle, 0.25, "H", promod3::loop::GLN_H_INDEX,true);
- AddBBPDir(GLN, promod3::loop::GLN_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ 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);
@@ -390,14 +469,21 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
@@ -405,6 +491,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
@@ -412,6 +499,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
@@ -419,14 +507,25 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(GLU, HParticle, 0.25, "H", promod3::loop::GLU_H_INDEX,true);
- AddBBPDir(GLU, promod3::loop::GLU_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ 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);
@@ -434,6 +533,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
@@ -441,9 +541,15 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
@@ -454,6 +560,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
@@ -464,6 +571,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
@@ -474,6 +582,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
@@ -484,14 +593,26 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
+ }
+
sidechain_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, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(LYS, HParticle, 0.25, "H", promod3::loop::LYS_H_INDEX,true);
- AddBBPDir(LYS, promod3::loop::LYS_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ 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);
@@ -499,8 +620,14 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
@@ -508,24 +635,36 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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, CH2Particle, 0.25, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(SER, HParticle, 0.25, "H", promod3::loop::SER_H_INDEX,true);
- AddBBPDir(SER, promod3::loop::SER_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ 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);
@@ -533,19 +672,34 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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, CH2Particle, 0.19, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(CYS, HParticle, 0.25, "H", promod3::loop::CYS_H_INDEX,true);
- AddBBPDir(CYS, promod3::loop::CYS_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ 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);
@@ -563,35 +717,54 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(MET, HParticle, 0.25, "H", promod3::loop::MET_H_INDEX,true);
- AddBBPDir(MET, promod3::loop::MET_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ 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);
@@ -599,6 +772,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
@@ -609,7 +783,13 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
@@ -623,6 +803,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
@@ -636,14 +817,24 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(TRP, HParticle, 0.25, "H", promod3::loop::TRP_H_INDEX,true);
- AddBBPDir(TRP, promod3::loop::TRP_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ 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);
@@ -651,6 +842,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
@@ -659,6 +851,11 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
@@ -667,6 +864,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
@@ -678,6 +876,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
@@ -689,6 +888,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
@@ -700,14 +900,25 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(TYR, HParticle, 0.25, "H", promod3::loop::TYR_H_INDEX,true);
- AddBBPDir(TYR, promod3::loop::TYR_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ 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);
@@ -715,36 +926,54 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
- AddPDir(THR, promod3::loop::THR_HG1_INDEX, promod3::loop::THR_OG1_INDEX, 0);
+
+ 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, CH2Particle, 0.25, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(THR, HParticle, 0.25, "H", promod3::loop::THR_H_INDEX,true);
- AddBBPDir(THR, promod3::loop::THR_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ 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);
@@ -752,21 +981,36 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(VAL, HParticle, 0.25, "H", promod3::loop::VAL_H_INDEX,true);
- AddBBPDir(VAL, promod3::loop::VAL_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ 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);
@@ -774,29 +1018,46 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(ILE, HParticle, 0.25, "H", promod3::loop::ILE_H_INDEX,true);
- AddBBPDir(ILE, promod3::loop::ILE_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ 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);
@@ -804,49 +1065,76 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
+ 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, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(LEU, HParticle, 0.25, "H", promod3::loop::LEU_H_INDEX,true);
- AddBBPDir(LEU, promod3::loop::LEU_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ 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 onoe single
+ // 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);
- AddBBInfo(PRO, CH2Particle, 0.25, "CB", promod3::loop::BB_CB_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);
@@ -864,15 +1152,23 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
@@ -882,6 +1178,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
@@ -891,14 +1188,24 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(HSD, HParticle, 0.25, "H", promod3::loop::HIS_H_INDEX,true);
- AddBBPDir(HSD, promod3::loop::HIS_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ 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);
@@ -906,15 +1213,22 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
@@ -924,6 +1238,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
@@ -933,14 +1248,24 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(HSE, HParticle, 0.25, "H", promod3::loop::HIS_H_INDEX,true);
- AddBBPDir(HSE, promod3::loop::HIS_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ 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);
@@ -954,12 +1279,18 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
@@ -969,6 +1300,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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);
@@ -978,32 +1310,56 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
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, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(PHE, HParticle, 0.25, "H", promod3::loop::PHE_H_INDEX,true);
- AddBBPDir(PHE, promod3::loop::PHE_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ 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, CH3Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(ALA, HParticle, 0.25, "H", promod3::loop::ALA_H_INDEX,true);
- AddBBPDir(ALA, promod3::loop::ALA_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ 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);
@@ -1025,7 +1381,8 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
}
}
-SCWRLRotamerConstructor::SCWRLRotamerConstructor(){
+SCWRLRotamerConstructor::SCWRLRotamerConstructor(bool cb_in_sidechain):
+ rotamer_lookup_(cb_in_sidechain) {
String s(XXX,'X');
for(uint i = 0; i < XXX; ++i){
s[i] = RotIDToOLC(RotamerID(i));
@@ -1055,16 +1412,6 @@ RRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructRRMRotamerGroup(
probability_cutoff);
}
-RRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructRRMRotamerGroup(
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos, RotamerID id, uint residue_index,
- RotamerLibPtr rot_lib, Real probability_cutoff){
- std::pair<RotamerLibEntry*,uint> lib_entries = rot_lib->QueryLib(id);
- this->SetPosBuffer(n_pos, ca_pos, cb_pos, id);
- return this->ConstructRRMRotamerGroup(id, residue_index, lib_entries,
- probability_cutoff);
-}
-
FRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructFRMRotamerGroup(
const ost::mol::ResidueHandle& res, RotamerID id,
uint residue_index, RotamerLibPtr rot_lib,
@@ -1085,16 +1432,6 @@ FRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructFRMRotamerGroup(
probability_cutoff);
}
-FRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructFRMRotamerGroup(
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos, RotamerID id, uint residue_index,
- RotamerLibPtr rot_lib, Real probability_cutoff){
- std::pair<RotamerLibEntry*,uint> lib_entries = rot_lib->QueryLib(id);
- this->SetPosBuffer(n_pos, ca_pos, cb_pos, id);
- return this->ConstructFRMRotamerGroup(id, residue_index, lib_entries,
- probability_cutoff);
-}
-
RRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructRRMRotamerGroup(
const ost::mol::ResidueHandle& res, RotamerID id,
uint residue_index, BBDepRotamerLibPtr rot_lib,
@@ -1116,17 +1453,6 @@ RRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructRRMRotamerGroup(
probability_cutoff);
}
-RRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructRRMRotamerGroup(
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos, RotamerID id, uint residue_index,
- BBDepRotamerLibPtr rot_lib,
- Real phi, Real psi, Real probability_cutoff){
- std::pair<RotamerLibEntry*,uint> lib_entries = rot_lib->QueryLib(id, phi, psi);
- this->SetPosBuffer(n_pos, ca_pos, cb_pos, id);
- return this->ConstructRRMRotamerGroup(id, residue_index, lib_entries,
- probability_cutoff);
-}
-
FRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructFRMRotamerGroup(
const ost::mol::ResidueHandle& res, RotamerID id,
uint residue_index, BBDepRotamerLibPtr rot_lib,
@@ -1148,26 +1474,11 @@ FRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructFRMRotamerGroup(
probability_cutoff);
}
-FRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructFRMRotamerGroup(
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos, RotamerID id, uint residue_index,
- BBDepRotamerLibPtr rot_lib,
- Real phi, Real psi, Real probability_cutoff){
- std::pair<RotamerLibEntry*,uint> lib_entries = rot_lib->QueryLib(id, phi, psi);
- this->SetPosBuffer(n_pos, ca_pos, cb_pos, id);
- return this->ConstructFRMRotamerGroup(id, residue_index, lib_entries,
- probability_cutoff);
-}
-
RRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructRRMRotamerGroup(
const ost::mol::ResidueHandle& res, RotamerID id,
uint residue_index,
std::vector<RotamerLibEntry>& lib_entries,
Real probability_cutoff){
- if(lib_entries.empty()){
- throw promod3::Error("How do you want me to construct rotamers with an "
- "empty input?");
- }
std::pair<RotamerLibEntry*,uint> I_LIKE_CHEESE =
std::make_pair(&lib_entries[0], lib_entries.size());
this->SetPosBuffer(res, id);
@@ -1180,10 +1491,6 @@ RRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructRRMRotamerGroup(
uint aa_res_idx, RotamerID id, uint residue_index,
std::vector<RotamerLibEntry>& lib_entries,
Real probability_cutoff){
- if(lib_entries.empty()){
- throw promod3::Error("How do you want me to construct rotamers with an "
- "empty input?");
- }
std::pair<RotamerLibEntry*,uint> I_LIKE_CHEESE =
std::make_pair(&lib_entries[0], lib_entries.size());
this->SetPosBuffer(all_atom, aa_res_idx, id);
@@ -1191,30 +1498,10 @@ RRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructRRMRotamerGroup(
probability_cutoff);
}
-RRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructRRMRotamerGroup(
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos, RotamerID id, uint residue_index,
- std::vector<RotamerLibEntry>& lib_entries,
- Real probability_cutoff){
- if(lib_entries.empty()){
- throw promod3::Error("How do you want me to construct rotamers with an "
- "empty input?");
- }
- std::pair<RotamerLibEntry*,uint> I_LIKE_CHEESE =
- std::make_pair(&lib_entries[0], lib_entries.size());
- this->SetPosBuffer(n_pos, ca_pos, cb_pos, id);
- return this->ConstructRRMRotamerGroup(id, residue_index, I_LIKE_CHEESE,
- probability_cutoff);
-}
-
FRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructFRMRotamerGroup(
const ost::mol::ResidueHandle& res, RotamerID id,
uint residue_index, std::vector<RotamerLibEntry>& lib_entries,
Real probability_cutoff){
- if(lib_entries.empty()){
- throw promod3::Error("How do you want me to construct rotamers with an "
- "empty input?");
- }
std::pair<RotamerLibEntry*,uint> I_LIKE_CHEESE =
std::make_pair(&lib_entries[0], lib_entries.size());
this->SetPosBuffer(res, id);
@@ -1227,10 +1514,6 @@ FRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructFRMRotamerGroup(
uint aa_res_idx, RotamerID id, uint residue_index,
std::vector<RotamerLibEntry>& lib_entries,
Real probability_cutoff){
- if(lib_entries.empty()){
- throw promod3::Error("How do you want me to construct rotamers with an "
- "empty input?");
- }
std::pair<RotamerLibEntry*,uint> I_LIKE_CHEESE =
std::make_pair(&lib_entries[0], lib_entries.size());
this->SetPosBuffer(all_atom, aa_res_idx, id);
@@ -1238,22 +1521,6 @@ FRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructFRMRotamerGroup(
probability_cutoff);
}
-FRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructFRMRotamerGroup(
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos, RotamerID id, uint residue_index,
- std::vector<RotamerLibEntry>& lib_entries,
- Real probability_cutoff){
- if(lib_entries.empty()){
- throw promod3::Error("How do you want me to construct rotamers with an "
- "empty input?");
- }
- std::pair<RotamerLibEntry*,uint> I_LIKE_CHEESE =
- std::make_pair(&lib_entries[0], lib_entries.size());
- this->SetPosBuffer(n_pos, ca_pos, cb_pos, id);
- return this->ConstructFRMRotamerGroup(id, residue_index, I_LIKE_CHEESE,
- probability_cutoff);
-}
-
FrameResiduePtr SCWRLRotamerConstructor::ConstructBackboneFrameResidue(
const ost::mol::ResidueHandle& res, RotamerID id, uint residue_index,
@@ -1262,8 +1529,7 @@ FrameResiduePtr SCWRLRotamerConstructor::ConstructBackboneFrameResidue(
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"SCWRLRotamerConstructor::ConstructBackboneFrameResidue", 2);
- const SCWRLRotamerInfo& info =
- SCWRLRotamerLookup::GetInstance().GetBackboneInfo(id);
+ const SCWRLRotamerInfo& info = rotamer_lookup_.GetBackboneInfo(id);
for(uint i = 0; i < info.particles.size(); ++i){
if(!info.particles[i].is_hydrogen){
@@ -1301,8 +1567,7 @@ FrameResiduePtr SCWRLRotamerConstructor::ConstructBackboneFrameResidue(
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"SCWRLRotamerConstructor::ConstructBackboneFrameResidue", 2);
- const SCWRLRotamerInfo& info =
- SCWRLRotamerLookup::GetInstance().GetBackboneInfo(id);
+ const SCWRLRotamerInfo& info = rotamer_lookup_.GetBackboneInfo(id);
for(uint i = 0; i < info.particles.size(); ++i){
if(!info.particles[i].is_hydrogen){
@@ -1334,49 +1599,13 @@ FrameResiduePtr SCWRLRotamerConstructor::ConstructBackboneFrameResidue(
return p;
}
-FrameResiduePtr SCWRLRotamerConstructor::ConstructBackboneFrameResidue(
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& c_pos, const geom::Vec3& o_pos,
- const geom::Vec3& cb_pos,
- RotamerID id, uint residue_index,
- Real phi, bool n_ter, bool c_ter){
-
- core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "SCWRLRotamerConstructor::ConstructBackboneFrameResidue", 2);
-
- const SCWRLRotamerInfo& info =
- SCWRLRotamerLookup::GetInstance().GetBackboneInfo(id);
-
- pos_buffer_->SetPos(id, promod3::loop::BB_N_INDEX, n_pos);
- pos_buffer_->SetPos(id, promod3::loop::BB_CA_INDEX, ca_pos);
- pos_buffer_->SetPos(id, promod3::loop::BB_C_INDEX, c_pos);
- pos_buffer_->SetPos(id, promod3::loop::BB_O_INDEX, o_pos);
- if(id != GLY) pos_buffer_->SetPos(id, promod3::loop::BB_CB_INDEX, cb_pos);
-
- //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 SCWRLRotamerConstructor::ConstructSidechainFrameResidue(
const ost::mol::ResidueHandle& res, RotamerID id, uint residue_index){
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"SCWRLRotamerConstructor::ConstructSidechainFrameResidue", 2);
- const SCWRLRotamerInfo& info =
- SCWRLRotamerLookup::GetInstance().GetSidechainInfo(id);
+ const SCWRLRotamerInfo& info = rotamer_lookup_.GetSidechainInfo(id);
for(uint i = 0; i < info.particles.size(); ++i){
if(!info.particles[i].is_hydrogen){
@@ -1413,8 +1642,7 @@ FrameResiduePtr SCWRLRotamerConstructor::ConstructSidechainFrameResidue(
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"SCWRLRotamerConstructor::ConstructSidechainFrameResidue", 2);
- const SCWRLRotamerInfo& info =
- SCWRLRotamerLookup::GetInstance().GetSidechainInfo(id);
+ const SCWRLRotamerInfo& info = rotamer_lookup_.GetSidechainInfo(id);
for(uint i = 0; i < info.particles.size(); ++i){
if(!info.particles[i].is_hydrogen){
@@ -1597,6 +1825,20 @@ RRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructRRMRotamerGroup(
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;
@@ -1669,6 +1911,20 @@ FRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructFRMRotamerGroup(
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_;
@@ -1733,10 +1989,8 @@ RRMRotamerPtr SCWRLRotamerConstructor::ConstructRRMRotamer(RotamerID id,
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"SCWRLRotamerConstructor::ConstructRRMRotamer", 2);
- const SCWRLRotamerInfo& info =
- SCWRLRotamerLookup::GetInstance().GetSidechainInfo(id);
- int num_particles =
- SCWRLRotamerLookup::GetInstance().GetNumSidechainParticles(id);
+ const SCWRLRotamerInfo& info = rotamer_lookup_.GetSidechainInfo(id);
+ int num_particles = rotamer_lookup_.GetNumSidechainParticles(id);
std::vector<Particle> particles(num_particles);
//set the positions
@@ -1749,7 +2003,7 @@ RRMRotamerPtr SCWRLRotamerConstructor::ConstructRRMRotamer(RotamerID id,
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
+ // 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){
@@ -1781,12 +2035,9 @@ FRMRotamerPtr SCWRLRotamerConstructor::ConstructFRMRotamer(RotamerID id,
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"SCWRLRotamerConstructor::ConstructFRMRotamer", 2);
- const SCWRLRotamerInfo& info =
- SCWRLRotamerLookup::GetInstance().GetSidechainInfo(id);
- int num_rrm_particles =
- SCWRLRotamerLookup::GetInstance().GetNumSidechainParticles(id);
- int num_particles =
- SCWRLRotamerLookup::GetInstance().GetNumFRMSidechainParticles(id);
+ 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
@@ -1823,8 +2074,7 @@ FRMRotamerPtr SCWRLRotamerConstructor::ConstructFRMRotamer(RotamerID id,
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 =
- SCWRLRotamerLookup::GetInstance().GetFRMRules(id);
+ const std::vector<SCWRLFRMRule>& frm_rules = rotamer_lookup_.GetFRMRules(id);
geom::Vec3 rotation_axis, rotation_anchor;
geom::Vec3 orig_pos, rot_pos;
geom::Mat4 rot;
@@ -1836,8 +2086,10 @@ FRMRotamerPtr SCWRLRotamerConstructor::ConstructFRMRotamer(RotamerID id,
int num_rotating_particles = frm_rule.rotating_particles.size();
// Update the subrotamer definition... all particles that are fixed are taken
- // from the first subrotamer, the indices therefore start from 0
- for(int i = 0; i < num_fix_particles; ++i) actual_definition[i] = i;
+ // 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
rotation_anchor = pos_buffer_->GetPos(id, frm_rule.anchor_idx_two);
@@ -1853,9 +2105,10 @@ FRMRotamerPtr SCWRLRotamerConstructor::ConstructFRMRotamer(RotamerID id,
rotation_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;
- int orig_particle_idx = num_fix_particles + i;
+ // replace the old with the new index...
actual_definition[orig_particle_idx] = new_particle_idx;
// get the new position
@@ -1877,10 +2130,10 @@ FRMRotamerPtr SCWRLRotamerConstructor::ConstructFRMRotamer(RotamerID id,
// instead of building them from scratch, they get extracted from the
// initial particles and transformed
for(int i = 0; i < num_rotating_particles; ++i){
- int orig_particle_idx = num_fix_particles + i;
+ int orig_particle_idx = frm_rule.rotating_particles[i];
+ int new_particle_idx = base_idx + i;
if(particles[orig_particle_idx].IsHBondDonor()){
- int new_particle_idx = base_idx + i;
orig_pos = particles[orig_particle_idx].GetPos() +
particles[orig_particle_idx].GetPolarDirection();
rot_pos[0] = rot(0,0) * orig_pos[0] + rot(0,1) * orig_pos[1] +
@@ -1895,7 +2148,6 @@ FRMRotamerPtr SCWRLRotamerConstructor::ConstructFRMRotamer(RotamerID id,
}
if(particles[orig_particle_idx].IsHBondAcceptor()){
- int new_particle_idx = base_idx + i;
const std::vector<geom::Vec3>& lp =
particles[orig_particle_idx].GetLonePairs();
for(uint j = 0; j < lp.size(); ++j){
@@ -1939,14 +2191,26 @@ void SCWRLRotamerConstructor::SetPosBuffer(const ost::mol::ResidueHandle& res,
ost::mol::AtomHandle n = res.FindAtom("N");
ost::mol::AtomHandle ca = res.FindAtom("CA");
ost::mol::AtomHandle cb = res.FindAtom("CB");
+ ost::mol::AtomHandle c = res.FindAtom("C");
+ ost::mol::AtomHandle o = res.FindAtom("O");
- if(!(n.IsValid() && ca.IsValid() && cb.IsValid())){
- throw promod3::Error("N, CA and CB must be valid to construct rotamer!");
+ if(!(n.IsValid() && ca.IsValid() && c.IsValid() && o.IsValid())) {
+ throw promod3::Error("All backbone atoms must be valid to construct "
+ "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_CB_INDEX, cb.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(!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());
+ }
}
void SCWRLRotamerConstructor::SetPosBuffer(const promod3::loop::AllAtomPositions& all_atom_pos,
@@ -1955,31 +2219,38 @@ void SCWRLRotamerConstructor::SetPosBuffer(const promod3::loop::AllAtomPositions
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"SCWRLRotamerConstructor::SetPosBuffer_all_atom_pos", 2);
+
if(!(all_atom_pos.IsSet(all_atom_idx, promod3::loop::BB_N_INDEX) &&
all_atom_pos.IsSet(all_atom_idx, promod3::loop::BB_CA_INDEX) &&
- all_atom_pos.IsSet(all_atom_idx, promod3::loop::BB_CB_INDEX))){
- throw promod3::Error("N, CA and CB must be set to construct rotamer!");
+ all_atom_pos.IsSet(all_atom_idx, promod3::loop::BB_C_INDEX) &&
+ all_atom_pos.IsSet(all_atom_idx, promod3::loop::BB_O_INDEX))){
+ throw promod3::Error("All backbone atoms must be set to construct "
+ "rotamer!");
}
pos_buffer_->SetPos(id, promod3::loop::BB_N_INDEX,
- all_atom_pos.GetPos(all_atom_idx, 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,
- all_atom_pos.GetPos(all_atom_idx, promod3::loop::BB_CA_INDEX));
- pos_buffer_->SetPos(id, promod3::loop::BB_CB_INDEX,
- all_atom_pos.GetPos(all_atom_idx, promod3::loop::BB_CB_INDEX));
-}
-
-void SCWRLRotamerConstructor::SetPosBuffer(const geom::Vec3& n_pos,
- const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos,
- RotamerID id){
-
- core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "SCWRLRotamerConstructor::SetPosBuffer_vec3", 2);
+ all_atom_pos.GetPos(all_atom_idx,
+ promod3::loop::BB_CA_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,
+ all_atom_pos.GetPos(all_atom_idx,
+ promod3::loop::BB_O_INDEX));
+
+ 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,
+ all_atom_pos.GetPos(all_atom_idx,
+ promod3::loop::BB_CB_INDEX));
- pos_buffer_->SetPos(id, promod3::loop::BB_N_INDEX, n_pos);
- pos_buffer_->SetPos(id, promod3::loop::BB_CA_INDEX, ca_pos);
- pos_buffer_->SetPos(id, promod3::loop::BB_CB_INDEX, cb_pos);
+ }
}
void SCWRLRotamerConstructor::MVBBPosBuffer(RotamerID from, RotamerID to){
@@ -1987,6 +2258,13 @@ void SCWRLRotamerConstructor::MVBBPosBuffer(RotamerID from, RotamerID to){
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));
}
@@ -2062,54 +2340,38 @@ void SCWRLRotamerConstructor::ConstructBBFrameParticles(
}
if(n_ter){
- if(id == PRO || id == TPR || id == CPR){
- // there are two hydrogens
- geom::Vec3 ht1_pos, ht2_pos;
- geom::Vec3 cb_pos, ca_pos, n_pos;
- // Actually we would have to reconstruct the hydrogens using the prolines
- // CD atom... since we only have bb info, we use the CB atom.
- // rather crude, I know...
- cb_pos = pos_buffer_->GetPos(id, promod3::loop::BB_CB_INDEX);
- ca_pos = pos_buffer_->GetPos(id, promod3::loop::BB_CA_INDEX);
- n_pos = pos_buffer_->GetPos(id, promod3::loop::BB_N_INDEX);
- promod3::core::ConstructAtomPos(cb_pos, ca_pos, n_pos, 0.997, 2.042,
- 2.0944, ht1_pos);
- promod3::core::ConstructAtomPos(cb_pos,ca_pos,n_pos,0.997, 2.042,
- -2.0944, ht2_pos);
- particles[p_idx] = Particle(HParticle, ht1_pos, 0.35, "HT1");
- particles[p_idx].SetPolarDirection(ht1_pos - n_pos);
- particles[p_idx + 1] = Particle(HParticle, ht2_pos, 0.35, "HT2");
- particles[p_idx + 1].SetPolarDirection(ht2_pos - n_pos);
+ 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(HParticle, ht1_pos, 0.35, "HT1");
+ particles[p_idx].SetPolarDirection(ht1_pos - n_pos);
+ particles[p_idx + 1] = Particle(HParticle, ht2_pos, 0.35, "HT2");
+ particles[p_idx + 1].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;
}
- else{
- // there are three hydrogens
- geom::Vec3 ht1_pos, ht2_pos, ht3_pos;
- geom::Vec3 cb_pos, ca_pos, n_pos;
- if(id == GLY) cb_pos = pos_buffer_->GetPos(id, promod3::loop::BB_C_INDEX);
- else cb_pos = pos_buffer_->GetPos(id, promod3::loop::BB_CB_INDEX);
- ca_pos = pos_buffer_->GetPos(id, promod3::loop::BB_CA_INDEX);
- n_pos = pos_buffer_->GetPos(id, promod3::loop::BB_N_INDEX);
- promod3::core::ConstructAtomPos(cb_pos, ca_pos, n_pos, 0.997, 2.042,
- M_PI, ht1_pos);
- promod3::core::ConstructAtomPos(cb_pos, ca_pos, n_pos, 0.997, 2.042,
- 1.0472, ht2_pos);
- promod3::core::ConstructAtomPos(cb_pos, ca_pos, n_pos, 0.997, 2.042,
- -1.0472, ht3_pos);
-
- // we assume, that there is currently one hydrogen and replace it with ht1
- for(uint i = 0; i < info.particles.size(); ++i){
- if(info.particles[i].is_hydrogen){
- particles[i] = Particle(HParticle, ht1_pos, 0.35, "HT1");
- particles[i].SetPolarDirection(ht1_pos - n_pos);
- break;
- }
- }
- // set ht2 and ht3
- particles[p_idx] = Particle(HParticle, ht2_pos, 0.35, "HT2");
- particles[p_idx].SetPolarDirection(ht2_pos - n_pos);
- particles[p_idx + 1] = Particle(HParticle, ht3_pos, 0.35, "HT3");
- particles[p_idx + 1].SetPolarDirection(ht3_pos - n_pos);
+ 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(HParticle, ht3_pos, 0.35, "HT3");
+ particles[i].SetPolarDirection(ht3_pos - n_pos);
+ break;
+ }
}
}
}
diff --git a/sidechain/src/scwrl_rotamer_constructor.hh b/sidechain/src/scwrl_rotamer_constructor.hh
index cc0b38b392d9a5231a9d94a335bd469f15920014..8beea0819bacefa5d12de50ce1500740b23c20ed 100644
--- a/sidechain/src/scwrl_rotamer_constructor.hh
+++ b/sidechain/src/scwrl_rotamer_constructor.hh
@@ -18,6 +18,9 @@
namespace promod3 { namespace sidechain {
+class SCWRLRotamerConstructor;
+typedef boost::shared_ptr<SCWRLRotamerConstructor> SCWRLRotamerConstructorPtr;
+
/// \brief Types of lone pair construction
enum SCWRLLPRule {
LONE_PAIR_CARBONYL, LONE_PAIR_COH, LONE_PAIR_CNC
@@ -135,11 +138,9 @@ struct SCWRLRotamerInfo{
/// \brief Defines lookups to build rotamer stuff.
class SCWRLRotamerLookup {
public:
- // Singleton access to one constant instance (see AminoAcidLookup for details)
- static const SCWRLRotamerLookup& GetInstance() {
- static SCWRLRotamerLookup instance;
- return instance;
- }
+
+ SCWRLRotamerLookup(bool cb_in_sidechain);
+
// Data access
const SCWRLRotamerInfo& GetSidechainInfo(RotamerID id) const {
return sidechain_infos_[id];
@@ -227,8 +228,6 @@ private:
frm_rules_[id][rule_idx].fix_particles.push_back(p_idx);
}
- SCWRLRotamerLookup();
-
// To construct classical rotamers or as lookup for sidechain frame residues
SCWRLRotamerInfo sidechain_infos_[XXX + 1];
@@ -248,7 +247,7 @@ class SCWRLRotamerConstructor{
public:
- SCWRLRotamerConstructor();
+ SCWRLRotamerConstructor(bool cb_in_sidechain = false);
// Construct rotamer groups from non backbone dependent library
RRMRotamerGroupPtr ConstructRRMRotamerGroup(
@@ -261,12 +260,6 @@ public:
uint aa_res_idx, RotamerID id, uint residue_index,
RotamerLibPtr rot_lib,
Real probability_cutoff = 0.98);
-
- RRMRotamerGroupPtr ConstructRRMRotamerGroup(
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos, RotamerID id, uint residue_index,
- RotamerLibPtr rot_lib,
- Real probability_cutoff = 0.98);
FRMRotamerGroupPtr ConstructFRMRotamerGroup(
const ost::mol::ResidueHandle& res, RotamerID id,
@@ -279,12 +272,6 @@ public:
RotamerLibPtr rot_lib,
Real probability_cutoff = 0.98);
- FRMRotamerGroupPtr ConstructFRMRotamerGroup(
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos, RotamerID id, uint residue_index,
- RotamerLibPtr rot_lib,
- Real probability_cutoff = 0.98);
-
// Construct rotamer groups from backbone dependent library
RRMRotamerGroupPtr ConstructRRMRotamerGroup(
const ost::mol::ResidueHandle& res, RotamerID id,
@@ -300,14 +287,6 @@ public:
Real phi = -1.0472,
Real psi = -0.7854,
Real probability_cutoff = 0.98);
-
- RRMRotamerGroupPtr ConstructRRMRotamerGroup(
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos, RotamerID id, uint residue_index,
- BBDepRotamerLibPtr rot_lib,
- Real phi = -1.0472,
- Real psi = -0.7854,
- Real probability_cutoff = 0.98);
FRMRotamerGroupPtr ConstructFRMRotamerGroup(
const ost::mol::ResidueHandle& res, RotamerID id,
@@ -324,14 +303,6 @@ public:
Real psi = -0.7854,
Real probability_cutoff = 0.98);
- FRMRotamerGroupPtr ConstructFRMRotamerGroup(
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos, RotamerID id, uint residue_index,
- BBDepRotamerLibPtr rot_lib,
- Real phi = -1.0472,
- Real psi = -0.7854,
- Real probability_cutoff = 0.98);
-
// Construct rotamer groups directly from rotamerlib entries
RRMRotamerGroupPtr ConstructRRMRotamerGroup(
const ost::mol::ResidueHandle& res, RotamerID id,
@@ -344,12 +315,6 @@ public:
uint aa_res_idx, RotamerID id, uint residue_index,
std::vector<RotamerLibEntry>& lib_entries,
Real probability_cutoff = 0.98);
-
- RRMRotamerGroupPtr ConstructRRMRotamerGroup(
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos, RotamerID id, uint residue_index,
- std::vector<RotamerLibEntry>& lib_entries,
- Real probability_cutoff = 0.98);
FRMRotamerGroupPtr ConstructFRMRotamerGroup(
const ost::mol::ResidueHandle& res, RotamerID id,
@@ -363,26 +328,12 @@ public:
std::vector<RotamerLibEntry>& lib_entries,
Real probability_cutoff = 0.98);
- FRMRotamerGroupPtr ConstructFRMRotamerGroup(
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos, RotamerID id, uint residue_index,
- std::vector<RotamerLibEntry>& lib_entries,
- Real probability_cutoff = 0.98);
-
// Construct frame residues
FrameResiduePtr ConstructBackboneFrameResidue(
const ost::mol::ResidueHandle& res, RotamerID id, uint residue_index,
Real phi, bool n_ter = false,
bool c_ter = false);
- FrameResiduePtr ConstructBackboneFrameResidue(
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& c_pos, const geom::Vec3& o_pos,
- const geom::Vec3& cb_pos,
- RotamerID id, uint residue_index,
- Real phi, bool n_ter = false,
- bool c_ter = false);
-
FrameResiduePtr ConstructBackboneFrameResidue(
const promod3::loop::AllAtomPositions& all_atom, uint aa_res_idx,
RotamerID id, uint residue_index,
@@ -434,9 +385,6 @@ private:
void SetPosBuffer(const promod3::loop::AllAtomPositions&,
uint aa_res_index, RotamerID id);
- void SetPosBuffer(const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos, RotamerID id);
-
void MVBBPosBuffer(RotamerID from, RotamerID to);
void ConstructBaseParticles(const SCWRLRotamerInfo& info, RotamerID id,
@@ -449,6 +397,7 @@ private:
Real chi_angles_[4];
Real chi_dev_[4];
Real probability_;
+ SCWRLRotamerLookup rotamer_lookup_;
promod3::loop::AllAtomPositionsPtr pos_buffer_;
promod3::loop::HydrogenStoragePtr hydrogen_buffer_;
};
diff --git a/sidechain/tests/test_frame_construction.cc b/sidechain/tests/test_frame_construction.cc
index edae739c5d13546fd4d3f3f550de1726e6fafc46..5c6801168270bd96ee3ae08bde1c0486fa8ce8b0 100644
--- a/sidechain/tests/test_frame_construction.cc
+++ b/sidechain/tests/test_frame_construction.cc
@@ -59,13 +59,7 @@ void CheckBackboneFrameConstruction(ost::mol::ResidueHandleList& res_list,
// frame residues
fr1 = rc.ConstructBackboneFrameResidue(res_list[i], r_id, i,
phi, n_ter, c_ter);
- const geom::Vec3 n_pos = all_atoms.GetPos(i, loop::BB_N_INDEX);
- const geom::Vec3 ca_pos = all_atoms.GetPos(i, loop::BB_CA_INDEX);
- const geom::Vec3 c_pos = all_atoms.GetPos(i, loop::BB_C_INDEX);
- const geom::Vec3 o_pos = all_atoms.GetPos(i, loop::BB_O_INDEX);
- if (r_id != GLY) cb_pos = all_atoms.GetPos(i, loop::BB_CB_INDEX);
- fr2 = rc.ConstructBackboneFrameResidue(n_pos, ca_pos, c_pos, o_pos, cb_pos,
- r_id, i, phi, n_ter, c_ter);
+ fr2 = rc.ConstructBackboneFrameResidue(all_atoms, i, r_id, i, phi, n_ter, c_ter);
CompareFrameResidues(*fr1, *fr2);
}
}
diff --git a/sidechain/tests/test_rotamers.cc b/sidechain/tests/test_rotamers.cc
index 702bfd1d5c246bc7dca25132ea18b29b5ff8a90c..0b49ec0bd4a76442941fdc4555df4ec18aa99c8d 100644
--- a/sidechain/tests/test_rotamers.cc
+++ b/sidechain/tests/test_rotamers.cc
@@ -96,7 +96,6 @@ void CheckRotamerGroupConstruction(ost::mol::ResidueHandleList& res_list,
RotamerLibPtr rot_lib) {
// check all frames
BOOST_CHECK_EQUAL(res_list.size(), all_atoms.GetNumResidues());
- geom::Vec3 cb_pos;
RRMRotamerGroupPtr rrm1, rrm2;
FRMRotamerGroupPtr frm1, frm2;
SCWRLRotamerConstructor rot_constructor;
@@ -108,81 +107,33 @@ void CheckRotamerGroupConstruction(ost::mol::ResidueHandleList& res_list,
// angles
const Real phi = (n_ter) ? -1.0472 : all_atoms.GetPhiTorsion(i);
const Real psi = (c_ter) ? -0.7854 : all_atoms.GetPsiTorsion(i);
- // pos
- const geom::Vec3 n_pos = all_atoms.GetPos(i, loop::BB_N_INDEX);
- const geom::Vec3 ca_pos = all_atoms.GetPos(i, loop::BB_CA_INDEX);
- if (r_id != GLY) cb_pos = all_atoms.GetPos(i, loop::BB_CB_INDEX);
// do it
- if (r_id == ALA || r_id == GLY) {
- // should all throw exceptions
- BOOST_CHECK_THROW(
- rot_constructor.ConstructRRMRotamerGroup(res_list[i], r_id, i,
- bbd_rot_lib,
- phi, psi),
- promod3::Error);
- BOOST_CHECK_THROW(
- rot_constructor.ConstructRRMRotamerGroup(n_pos, ca_pos, cb_pos,
- r_id, i, bbd_rot_lib,
- phi, psi),
- promod3::Error);
- BOOST_CHECK_THROW(
- rot_constructor.ConstructRRMRotamerGroup(res_list[i], r_id, i,
- rot_lib),
- promod3::Error);
- BOOST_CHECK_THROW(
- rot_constructor.ConstructRRMRotamerGroup(n_pos, ca_pos, cb_pos,
- r_id, i, rot_lib),
- promod3::Error);
- BOOST_CHECK_THROW(
- rot_constructor.ConstructFRMRotamerGroup(res_list[i], r_id, i,
- bbd_rot_lib,
- phi, psi),
- promod3::Error);
- BOOST_CHECK_THROW(
- rot_constructor.ConstructFRMRotamerGroup(n_pos, ca_pos, cb_pos,
- r_id, i,
- bbd_rot_lib,
- phi, psi),
- promod3::Error);
- BOOST_CHECK_THROW(
- rot_constructor.ConstructFRMRotamerGroup(res_list[i], r_id, i,
- rot_lib),
- promod3::Error);
- BOOST_CHECK_THROW(
- rot_constructor.ConstructFRMRotamerGroup(n_pos, ca_pos, cb_pos,
- r_id, i, rot_lib),
- promod3::Error);
- } else {
- // RRM ROTAMER (bbdep)
- rrm1 = rot_constructor.ConstructRRMRotamerGroup(res_list[i], r_id, i,
- bbd_rot_lib,
- phi, psi);
-
- rrm2 = rot_constructor.ConstructRRMRotamerGroup(n_pos, ca_pos, cb_pos,
- r_id, i, bbd_rot_lib,
- phi, psi);
- CompareRotamerGroups(*rrm1, *rrm2);
- // RRM ROTAMER (non-bbdep)
- rrm1 = rot_constructor.ConstructRRMRotamerGroup(res_list[i], r_id, i,
- rot_lib);
- rrm2 = rot_constructor.ConstructRRMRotamerGroup(n_pos, ca_pos, cb_pos,
- r_id, i, rot_lib);
- CompareRotamerGroups(*rrm1, *rrm2);
- // FRM ROTAMER (bbdep)
- frm1 = rot_constructor.ConstructFRMRotamerGroup(res_list[i], r_id, i,
- bbd_rot_lib,
- phi, psi);
- frm2 = rot_constructor.ConstructFRMRotamerGroup(n_pos, ca_pos, cb_pos,
- r_id, i, bbd_rot_lib,
- phi, psi);
- CompareRotamerGroups(*frm1, *frm2);
- // RRM ROTAMER (non-bbdep)
- frm1 = rot_constructor.ConstructFRMRotamerGroup(res_list[i], r_id, i,
- rot_lib);
- frm2 = rot_constructor.ConstructFRMRotamerGroup(n_pos, ca_pos, cb_pos,
- r_id, i, rot_lib);
- CompareRotamerGroups(*frm1, *frm2);
- }
+ // RRM ROTAMER (bbdep)
+ rrm1 = rot_constructor.ConstructRRMRotamerGroup(res_list[i], r_id, i,
+ bbd_rot_lib,
+ phi, psi);
+
+ rrm2 = rot_constructor.ConstructRRMRotamerGroup(all_atoms, i, r_id, i,
+ bbd_rot_lib, phi, psi);
+ CompareRotamerGroups(*rrm1, *rrm2);
+ // RRM ROTAMER (non-bbdep)
+ rrm1 = rot_constructor.ConstructRRMRotamerGroup(res_list[i], r_id, i,
+ rot_lib);
+ rrm2 = rot_constructor.ConstructRRMRotamerGroup(all_atoms, i, r_id, i,
+ rot_lib);
+ CompareRotamerGroups(*rrm1, *rrm2);
+ // FRM ROTAMER (bbdep)
+ frm1 = rot_constructor.ConstructFRMRotamerGroup(res_list[i], r_id, i,
+ bbd_rot_lib, phi, psi);
+ frm2 = rot_constructor.ConstructFRMRotamerGroup(all_atoms, i, r_id, i,
+ bbd_rot_lib, phi, psi);
+ CompareRotamerGroups(*frm1, *frm2);
+ // RRM ROTAMER (non-bbdep)
+ frm1 = rot_constructor.ConstructFRMRotamerGroup(res_list[i], r_id, i,
+ rot_lib);
+ frm2 = rot_constructor.ConstructFRMRotamerGroup(all_atoms, i, r_id, i,
+ rot_lib);
+ CompareRotamerGroups(*frm1, *frm2);
}
}