diff --git a/loop/src/CMakeLists.txt b/loop/src/CMakeLists.txt
index 5b28876070c4155e722397641332708a89510651..620e1495f58261ebfcdcab4cdbcd3721f5c0abb0 100644
--- a/loop/src/CMakeLists.txt
+++ b/loop/src/CMakeLists.txt
@@ -38,5 +38,5 @@ set(LOOP_SOURCES
)
module(NAME loop HEADERS ${LOOP_HEADERS} SOURCES ${LOOP_SOURCES}
- DEPENDS_ON promod3_core promod3_sidechain
+ DEPENDS_ON promod3_core
LINK ${OST_LIBRARIES} ${BOOST_LIBRARIES} ${LAPACK_LIBRARIES})
diff --git a/sidechain/pymod/_reconstruct_sidechains.py b/sidechain/pymod/_reconstruct_sidechains.py
index 589b00e758e165c7828c2f62e81c656404f942eb..6b9a900f8bd260cf71e5aa4b4db68e2d289ad2ce 100644
--- a/sidechain/pymod/_reconstruct_sidechains.py
+++ b/sidechain/pymod/_reconstruct_sidechains.py
@@ -75,7 +75,8 @@ def _AddBackboneFrameResidues(frame_residues, res_list, rotamer_ids,
try:
frame_residue = sidechain.ConstructBackboneFrameResidue(\
r.handle, rotamer_ids[i], i, rotamer_settings,
- phi_angles[i], r.HasProp("n_ter"), r.HasProp("c_ter"))
+ phi_angles[i], r.HasProp("n_ter"),
+ r.HasProp("c_ter"))
frame_residues.append(frame_residue)
except:
continue
diff --git a/sidechain/src/CMakeLists.txt b/sidechain/src/CMakeLists.txt
index acafe477a2b2bf8644445c2dcf3dc94c9798f1ed..38cde971e29dae838559e10aad4c5a5c420f146d 100644
--- a/sidechain/src/CMakeLists.txt
+++ b/sidechain/src/CMakeLists.txt
@@ -46,4 +46,4 @@ rotamer_cruncher.cc
)
module(NAME sidechain HEADERS ${SIDECHAIN_HEADERS} SOURCES ${SIDECHAIN_SOURCES}
- DEPENDS_ON promod3_core LINK ${OST_LIBRARIES} ${BOOST_LIBRARIES})
+ DEPENDS_ON promod3_core LINK ${OST_LIBRARIES} ${BOOST_LIBRARIES})
diff --git a/sidechain/src/frame_constructor.cc b/sidechain/src/frame_constructor.cc
index 415b26dbd4cafa90ef08584bd182284ea74624ad..95f8655b088e127694b747e2c3752473781bd070 100644
--- a/sidechain/src/frame_constructor.cc
+++ b/sidechain/src/frame_constructor.cc
@@ -132,11 +132,11 @@ FrameResiduePtr ConstructSidechainFrameARG(const ost::mol::ResidueHandle& res,
ost::mol::AtomHandle nh1 = res.FindAtom("NH1");
ost::mol::AtomHandle nh2 = res.FindAtom("NH2");
- if(!cg.IsValid() || !cd.IsValid() || !ne.IsValid() ||
- !cz.IsValid() || !nh1.IsValid() || !nh2.IsValid()){
+ if (!cg.IsValid() || !cd.IsValid() || !ne.IsValid() ||
+ !cz.IsValid() || !nh1.IsValid() || !nh2.IsValid()) {
std::stringstream ss;
- ss << "Cannot use sidechain of " << res.GetQualifiedName() << " as frameresidue,";
- ss << " not all atoms are present.";
+ ss << "Cannot use sidechain of " << res.GetQualifiedName()
+ << " as frameresidue, not all atoms are present.";
throw promod3::Error(ss.str());
}
@@ -224,8 +224,8 @@ FrameResiduePtr ConstructSidechainFrameASN(const ost::mol::ResidueHandle& res,
if(!cg.IsValid() || !od1.IsValid() || !nd2.IsValid()){
std::stringstream ss;
- ss << "Cannot use sidechain of " << res.GetQualifiedName() << " as frameresidue,";
- ss << " not all atoms are present.";
+ ss << "Cannot use sidechain of " << res.GetQualifiedName()
+ << " as frameresidue, not all atoms are present.";
throw promod3::Error(ss.str());
}
@@ -280,8 +280,8 @@ FrameResiduePtr ConstructSidechainFrameASP(const ost::mol::ResidueHandle& res,
if(!cg.IsValid() || !od1.IsValid() || !od2.IsValid()){
std::stringstream ss;
- ss << "Cannot use sidechain of " << res.GetQualifiedName() << " as frameresidue,";
- ss << " not all atoms are present.";
+ ss << "Cannot use sidechain of " << res.GetQualifiedName()
+ << " as frameresidue, not all atoms are present.";
throw promod3::Error(ss.str());
}
@@ -317,8 +317,8 @@ FrameResiduePtr ConstructSidechainFrameGLN(const ost::mol::ResidueHandle& res,
if(!cg.IsValid() || !cd.IsValid() || !oe1.IsValid() || !ne2.IsValid()){
std::stringstream ss;
- ss << "Cannot use sidechain of " << res.GetQualifiedName() << " as frameresidue,";
- ss << " not all atoms are present.";
+ ss << "Cannot use sidechain of " << res.GetQualifiedName()
+ << " as frameresidue, not all atoms are present.";
throw promod3::Error(ss.str());
}
@@ -378,8 +378,8 @@ FrameResiduePtr ConstructSidechainFrameGLU(const ost::mol::ResidueHandle& res,
if(!cg.IsValid() || !cd.IsValid() || !oe1.IsValid() || !oe2.IsValid()){
std::stringstream ss;
- ss << "Cannot use sidechain of " << res.GetQualifiedName() << " as frameresidue,";
- ss << " not all atoms are present.";
+ ss << "Cannot use sidechain of " << res.GetQualifiedName()
+ << " as frameresidue, not all atoms are present.";
throw promod3::Error(ss.str());
}
@@ -417,8 +417,8 @@ FrameResiduePtr ConstructSidechainFrameLYS(const ost::mol::ResidueHandle& res,
if(!cg.IsValid() || !cd.IsValid() || !ce.IsValid() || !nz.IsValid()){
std::stringstream ss;
- ss << "Cannot use sidechain of " << res.GetQualifiedName() << " as frameresidue,";
- ss << " not all atoms are present.";
+ ss << "Cannot use sidechain of " << res.GetQualifiedName()
+ << " as frameresidue, not all atoms are present.";
throw promod3::Error(ss.str());
}
@@ -481,8 +481,8 @@ FrameResiduePtr ConstructSidechainFrameSER(const ost::mol::ResidueHandle& res,
if(!og.IsValid()){
std::stringstream ss;
- ss << "Cannot use sidechain of " << res.GetQualifiedName() << " as frameresidue,";
- ss << " not all atoms are present.";
+ ss << "Cannot use sidechain of " << res.GetQualifiedName()
+ << " as frameresidue, not all atoms are present.";
throw promod3::Error(ss.str());
}
@@ -540,8 +540,8 @@ FrameResiduePtr ConstructSidechainFrameCYS(const ost::mol::ResidueHandle& res,
if(!sg.IsValid()){
std::stringstream ss;
- ss << "Cannot use sidechain of " << res.GetQualifiedName() << " as frameresidue,";
- ss << " not all atoms are present.";
+ ss << "Cannot use sidechain of " << res.GetQualifiedName()
+ << " as frameresidue, not all atoms are present.";
throw promod3::Error(ss.str());
}
@@ -563,8 +563,8 @@ FrameResiduePtr ConstructSidechainFrameMET(const ost::mol::ResidueHandle& res,
if(!cg.IsValid() || !sd.IsValid() || !ce.IsValid()){
std::stringstream ss;
- ss << "Cannot use sidechain of " << res.GetQualifiedName() << " as frameresidue,";
- ss << " not all atoms are present.";
+ ss << "Cannot use sidechain of " << res.GetQualifiedName()
+ << " as frameresidue, not all atoms are present.";
throw promod3::Error(ss.str());
}
@@ -601,8 +601,8 @@ FrameResiduePtr ConstructSidechainFrameTRP(const ost::mol::ResidueHandle& res,
!ne1.IsValid() || !ce3.IsValid() || !cz3.IsValid() || !ch2.IsValid() ||
!cz2.IsValid()){
std::stringstream ss;
- ss << "Cannot use sidechain of " << res.GetQualifiedName() << " as frameresidue,";
- ss << " not all atoms are present.";
+ ss << "Cannot use sidechain of " << res.GetQualifiedName()
+ << " as frameresidue, not all atoms are present.";
throw promod3::Error(ss.str());
}
@@ -671,8 +671,8 @@ FrameResiduePtr ConstructSidechainFrameTYR(const ost::mol::ResidueHandle& res,
if(!cg.IsValid() || !cd1.IsValid() || !cd2.IsValid() || !ce1.IsValid() ||
!ce2.IsValid() || !cz.IsValid() || !oh.IsValid()){
std::stringstream ss;
- ss << "Cannot use sidechain of " << res.GetQualifiedName() << " as frameresidue,";
- ss << " not all atoms are present.";
+ ss << "Cannot use sidechain of " << res.GetQualifiedName()
+ << " as frameresidue, not all atoms are present.";
throw promod3::Error(ss.str());
}
@@ -748,8 +748,8 @@ FrameResiduePtr ConstructSidechainFrameTHR(const ost::mol::ResidueHandle& res,
//it is guaranteed from the calling function, that ca and cb exist...
if(!og1.IsValid() || !cg2.IsValid()){
std::stringstream ss;
- ss << "Cannot use sidechain of " << res.GetQualifiedName() << " as frameresidue,";
- ss << " not all atoms are present.";
+ ss << "Cannot use sidechain of " << res.GetQualifiedName()
+ << " as frameresidue, not all atoms are present.";
throw promod3::Error(ss.str());
}
@@ -807,8 +807,8 @@ FrameResiduePtr ConstructSidechainFrameVAL(const ost::mol::ResidueHandle& res,
if(!cg1.IsValid() || !cg2.IsValid()){
std::stringstream ss;
- ss << "Cannot use sidechain of " << res.GetQualifiedName() << " as frameresidue,";
- ss << " not all atoms are present.";
+ ss << "Cannot use sidechain of " << res.GetQualifiedName()
+ << " as frameresidue, not all atoms are present.";
throw promod3::Error(ss.str());
}
@@ -835,8 +835,8 @@ FrameResiduePtr ConstructSidechainFrameILE(const ost::mol::ResidueHandle& res,
if(!cg1.IsValid() || !cg2.IsValid() || !cd1.IsValid()){
std::stringstream ss;
- ss << "Cannot use sidechain of " << res.GetQualifiedName() << " as frameresidue,";
- ss << " not all atoms are present.";
+ ss << "Cannot use sidechain of " << res.GetQualifiedName()
+ << " as frameresidue, not all atoms are present.";
throw promod3::Error(ss.str());
}
@@ -863,8 +863,8 @@ FrameResiduePtr ConstructSidechainFrameLEU(const ost::mol::ResidueHandle& res,
if(!cg.IsValid() || !cd1.IsValid() || !cd2.IsValid()){
std::stringstream ss;
- ss << "Cannot use sidechain of " << res.GetQualifiedName() << " as frameresidue,";
- ss << " not all atoms are present.";
+ ss << "Cannot use sidechain of " << res.GetQualifiedName()
+ << " as frameresidue, not all atoms are present.";
throw promod3::Error(ss.str());
}
@@ -890,8 +890,8 @@ FrameResiduePtr ConstructSidechainFramePRO(const ost::mol::ResidueHandle& res,
if(!cg.IsValid() || !cd.IsValid()){
std::stringstream ss;
- ss << "Cannot use sidechain of " << res.GetQualifiedName() << " as frameresidue,";
- ss << " not all atoms are present.";
+ ss << "Cannot use sidechain of " << res.GetQualifiedName()
+ << " as frameresidue, not all atoms are present.";
throw promod3::Error(ss.str());
}
@@ -920,8 +920,8 @@ FrameResiduePtr ConstructSidechainFrameHIS(const ost::mol::ResidueHandle& res,
if(!cg.IsValid() || !nd1.IsValid() || !cd2.IsValid() ||
!ce1.IsValid() || !ne2.IsValid()){
std::stringstream ss;
- ss << "Cannot use sidechain of " << res.GetQualifiedName() << " as frameresidue,";
- ss << " not all atoms are present.";
+ ss << "Cannot use sidechain of " << res.GetQualifiedName()
+ << " as frameresidue, not all atoms are present.";
throw promod3::Error(ss.str());
}
@@ -991,8 +991,8 @@ FrameResiduePtr ConstructSidechainFrameHSD(const ost::mol::ResidueHandle& res,
if(!cg.IsValid() || !nd1.IsValid() || !cd2.IsValid() ||
!ce1.IsValid() || !ne2.IsValid()){
std::stringstream ss;
- ss << "Cannot use sidechain of " << res.GetQualifiedName() << " as frameresidue,";
- ss << " not all atoms are present.";
+ ss << "Cannot use sidechain of " << res.GetQualifiedName()
+ << " as frameresidue, not all atoms are present.";
throw promod3::Error(ss.str());
}
@@ -1048,8 +1048,8 @@ FrameResiduePtr ConstructSidechainFrameHSE(const ost::mol::ResidueHandle& res,
if(!cg.IsValid() || !nd1.IsValid() || !cd2.IsValid() ||
!ce1.IsValid() || !ne2.IsValid()){
std::stringstream ss;
- ss << "Cannot use sidechain of " << res.GetQualifiedName() << " as frameresidue,";
- ss << " not all atoms are present.";
+ ss << "Cannot use sidechain of " << res.GetQualifiedName()
+ << " as frameresidue, not all atoms are present.";
throw promod3::Error(ss.str());
}
@@ -1107,8 +1107,8 @@ FrameResiduePtr ConstructSidechainFramePHE(const ost::mol::ResidueHandle& res,
if(!cg.IsValid() || !cd1.IsValid() || !cd2.IsValid() ||
!ce1.IsValid() || !ce2.IsValid() || !cz.IsValid()){
std::stringstream ss;
- ss << "Cannot use sidechain of " << res.GetQualifiedName() << " as frameresidue,";
- ss << " not all atoms are present.";
+ ss << "Cannot use sidechain of " << res.GetQualifiedName()
+ << " as frameresidue, not all atoms are present.";
throw promod3::Error(ss.str());
}
diff --git a/sidechain/src/frame_constructor.hh b/sidechain/src/frame_constructor.hh
index 76b3b7a1c678c1b637cca30f8ff71297f5e48099..85dc3b428dc3da77c6a1feacef81dd016a0e00d8 100644
--- a/sidechain/src/frame_constructor.hh
+++ b/sidechain/src/frame_constructor.hh
@@ -23,18 +23,22 @@ 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,
- RotamerSettingsPtr settings, Real phi, bool n_ter=false, bool c_ter=false);
+ RotamerSettingsPtr settings, Real phi, bool n_ter = false,
+ bool c_ter = false);
-FrameResiduePtr ConstructBackboneFrameResidue(const ost::mol::ResidueHandle& res, RotamerID id,
- uint residue_index, RotamerSettingsPtr settings,
- Real phi, bool n_ter = false, bool c_ter = false);
+FrameResiduePtr ConstructBackboneFrameResidue(
+ const ost::mol::ResidueHandle& res, RotamerID id, uint residue_index,
+ RotamerSettingsPtr settings, Real phi, bool n_ter = false,
+ bool c_ter = false);
-FrameResiduePtr ConstructSidechainFrameResidue(const ost::mol::ResidueHandle& res, RotamerID id,
- uint residue_index, RotamerSettingsPtr settings);
+FrameResiduePtr ConstructSidechainFrameResidue(
+ const ost::mol::ResidueHandle& res, RotamerID id, uint residue_index,
+ RotamerSettingsPtr settings);
-FrameResiduePtr ConstructFrameResidue(const ost::mol::ResidueHandle& res, uint residue_index);
+FrameResiduePtr ConstructFrameResidue(const ost::mol::ResidueHandle& res,
+ uint residue_index);
FrameResiduePtr ConstructFrameResidue(RRMRotamerPtr rot, uint index);
diff --git a/sidechain/src/rotamer_id.cc b/sidechain/src/rotamer_id.cc
index 8c9807f7e7ae2b2ced62d11321722a598a2450d9..efd547d98d4e0b79edf2762add660b38d214fa33 100644
--- a/sidechain/src/rotamer_id.cc
+++ b/sidechain/src/rotamer_id.cc
@@ -1,166 +1,112 @@
#include <promod3/sidechain/rotamer_id.hh>
#include <promod3/core/runtime_profiling.hh>
-namespace promod3{ namespace sidechain{
+namespace promod3 { namespace sidechain {
-RotamerID TLCToRotID(const String& tlc){
+RotamerID TLCToRotID(const String& tlc) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"sidechain::TLCToRotID", 2);
- switch(tlc[0]){
-
- case 'A':{
- if(tlc == "ARG"){
- return ARG;
- }
- if(tlc == "ASN"){
- return ASN;
- }
- if(tlc == "ASP"){
- return ASP;
- }
- if(tlc == "ALA"){
- return ALA;
- }
+ switch (tlc[0]) {
+
+ case 'A': {
+ if (tlc == "ARG") return ARG;
+ if (tlc == "ASN") return ASN;
+ if (tlc == "ASP") return ASP;
+ if (tlc == "ALA") return ALA;
break;
}
- case 'C':{
- if(tlc == "CYS"){
- return CYS;
- }
- if(tlc == "CYH"){
- return CYH;
- }
- if(tlc == "CYD"){
- return CYD;
- }
- if(tlc == "CPR"){
- return CPR;
- }
+ case 'C': {
+ if (tlc == "CYS") return CYS;
+ if (tlc == "CYH") return CYH;
+ if (tlc == "CYD") return CYD;
+ if (tlc == "CPR") return CPR;
break;
}
- case 'G':{
- if(tlc == "GLU"){
- return GLU;
- }
- if(tlc == "GLN"){
- return GLN;
- }
- if(tlc == "GLY"){
- return GLY;
- }
+ case 'G': {
+ if (tlc == "GLU") return GLU;
+ if (tlc == "GLN") return GLN;
+ if (tlc == "GLY") return GLY;
break;
}
- case 'H':{
- if(tlc == "HIS"){
- return HIS;
- }
- if(tlc == "HSE"){
- return HSE;
- }
- if(tlc == "HSD"){
- return HSD;
- }
+ case 'H': {
+ if (tlc == "HIS") return HIS;
+ if (tlc == "HSE") return HSE;
+ if (tlc == "HSD") return HSD;
break;
}
- case 'I':{
- if(tlc == "ILE"){
- return ILE;
- }
+ case 'I': {
+ if (tlc == "ILE") return ILE;
break;
}
- case 'L':{
- if(tlc == "LEU"){
- return LEU;
- }
- if(tlc == "LYS"){
- return LYS;
- }
+ case 'L': {
+ if (tlc == "LEU") return LEU;
+ if (tlc == "LYS") return LYS;
break;
}
- case 'M':{
- if(tlc == "MET"){
- return MET;
- }
- if(tlc == "MSE"){
- return MET;
- }
+ case 'M': {
+ if (tlc == "MET") return MET;
+ if (tlc == "MSE") return MET;
break;
}
- case 'P':{
- if(tlc == "PRO"){
- return PRO;
- }
- if(tlc == "PHE"){
- return PHE;
- }
+ case 'P': {
+ if (tlc == "PRO") return PRO;
+ if (tlc == "PHE") return PHE;
break;
}
- case 'S':{
- if(tlc == "SER"){
- return SER;
- }
+ case 'S': {
+ if (tlc == "SER") return SER;
break;
}
- case 'T':{
- if(tlc == "THR"){
- return THR;
- }
- if(tlc == "TYR"){
- return TYR;
- }
- if(tlc == "TRP"){
- return TRP;
- }
- if(tlc == "TPR"){
- return TPR;
- }
+ case 'T': {
+ if (tlc == "THR") return THR;
+ if (tlc == "TYR") return TYR;
+ if (tlc == "TRP") return TRP;
+ if (tlc == "TPR") return TPR;
break;
}
- case 'V':{
- if(tlc == "VAL"){
- return VAL;
- }
+ case 'V': {
+ if (tlc == "VAL") return VAL;
break;
}
}
return XXX;
}
-RotamerID AAToRotID(ost::conop::AminoAcid aa){
- switch(aa){
- case ost::conop::ALA: return ALA;
- case ost::conop::ARG: return ARG;
- case ost::conop::ASN: return ASN;
- case ost::conop::ASP: return ASP;
- case ost::conop::GLN: return GLN;
- case ost::conop::GLU: return GLU;
- case ost::conop::LYS: return LYS;
- case ost::conop::SER: return SER;
- case ost::conop::CYS: return CYS;
- case ost::conop::MET: return MET;
- case ost::conop::TRP: return TRP;
- case ost::conop::TYR: return TYR;
- case ost::conop::THR: return THR;
- case ost::conop::VAL: return VAL;
- case ost::conop::ILE: return ILE;
- case ost::conop::LEU: return LEU;
- case ost::conop::GLY: return GLY;
- case ost::conop::PRO: return PRO;
- case ost::conop::HIS: return HIS;
- case ost::conop::PHE: return PHE;
- default: return XXX;
+RotamerID AAToRotID(ost::conop::AminoAcid aa) {
+ switch (aa) {
+ case ost::conop::ALA: return ALA;
+ case ost::conop::ARG: return ARG;
+ case ost::conop::ASN: return ASN;
+ case ost::conop::ASP: return ASP;
+ case ost::conop::GLN: return GLN;
+ case ost::conop::GLU: return GLU;
+ case ost::conop::LYS: return LYS;
+ case ost::conop::SER: return SER;
+ case ost::conop::CYS: return CYS;
+ case ost::conop::MET: return MET;
+ case ost::conop::TRP: return TRP;
+ case ost::conop::TYR: return TYR;
+ case ost::conop::THR: return THR;
+ case ost::conop::VAL: return VAL;
+ case ost::conop::ILE: return ILE;
+ case ost::conop::LEU: return LEU;
+ case ost::conop::GLY: return GLY;
+ case ost::conop::PRO: return PRO;
+ case ost::conop::HIS: return HIS;
+ case ost::conop::PHE: return PHE;
+ default: return XXX;
}
}