diff --git a/modules/io/src/mol/omf.cc b/modules/io/src/mol/omf.cc
index 822c24ca9a190bc3188f781f6be96eafa97e5e23..afe2b9a71d366a0af01c1002dc1d2246a632d47d 100644
--- a/modules/io/src/mol/omf.cc
+++ b/modules/io/src/mol/omf.cc
@@ -930,7 +930,6 @@ ResidueDefinition::ResidueDefinition(const ost::mol::ResidueHandle& res) {
olc = res.GetOneLetterCode();
chem_type = char(res.GetChemType());
chem_class = char(res.GetChemClass());
- rotamer_setup = false;
ost::mol::AtomHandleList at_list = res.GetAtomList();
for(auto it = at_list.begin(); it != at_list.end(); ++it) {
anames.push_back(it->GetName());
@@ -1024,31 +1023,19 @@ int ResidueDefinition::GetIdx(const String& aname) const {
}
const std::set<int>& ResidueDefinition::GetRotamericAtoms() const {
- if(!rotamer_setup) {
- _InitRotamer();
- }
return rotameric_atoms;
}
const std::vector<ChiDefinition>& ResidueDefinition::GetChiDefinitions() const {
- if(!rotamer_setup) {
- _InitRotamer();
- }
return chi_definitions;
}
const std::vector<SidechainAtomRule>&
ResidueDefinition::GetSidechainAtomRules() const {
- if(!rotamer_setup) {
- _InitRotamer();
- }
return sidechain_atom_rules;
}
int ResidueDefinition::GetNChiAngles() const {
- if(!rotamer_setup) {
- _InitRotamer();
- }
return chi_definitions.size();
}
@@ -1059,384 +1046,21 @@ void ResidueDefinition::_InitIdxMapper() const {
}
}
-void ResidueDefinition::_InitRotamer() const {
- rotameric_atoms.clear();
- if(chem_type == 'A') {
- int n_idx = GetIdx("N");
- int ca_idx = GetIdx("CA");
- int cb_idx = GetIdx("CB");
- if(n_idx!=-1 && ca_idx!=-1 && cb_idx!=-1) {
- switch(olc) {
- case 'R': {
- int cg_idx = GetIdx("CG");
- int cd_idx = GetIdx("CD");
- int ne_idx = GetIdx("NE");
- int cz_idx = GetIdx("CZ");
- int nh1_idx = GetIdx("NH1");
- int nh2_idx = GetIdx("NH2");
- if(cg_idx!=-1 && cd_idx!=-1 && ne_idx!=-1 && cz_idx!=-1 &&
- nh1_idx!=-1 && nh2_idx!=-1) {
- _AddChiDefinition(n_idx, ca_idx, cb_idx, cg_idx);
- _AddChiDefinition(ca_idx, cb_idx, cg_idx, cd_idx);
- _AddChiDefinition(cb_idx, cg_idx, cd_idx, ne_idx);
- _AddChiDefinition(cg_idx, cd_idx, ne_idx, cz_idx);
- _AddAtomRule(cg_idx, n_idx, ca_idx, cb_idx,
- Real(1.5475), Real(2.02370926769), 0, Real(0.0));
- _AddAtomRule(cd_idx, ca_idx, cb_idx, cg_idx,
- Real(1.5384), Real(1.9898498802), 1, Real(0.0));
- _AddAtomRule(ne_idx, cb_idx, cg_idx, cd_idx,
- Real(1.5034), Real(1.86907309596), 2, Real(0.0));
- _AddAtomRule(cz_idx, cg_idx, cd_idx, ne_idx,
- Real(1.3401), Real(2.14762764458), 3, Real(0.0));
- _AddAtomRule(nh1_idx, cd_idx, ne_idx, cz_idx,
- Real(1.3311), Real(2.0605357149), 4, Real(0.0));
- _AddAtomRule(nh2_idx, cd_idx, ne_idx, cz_idx,
- Real(1.3292), Real(2.13174514839), 4, Real(M_PI));
- }
- break;
- }
- case 'N': {
- int cg_idx = GetIdx("CG");
- int od1_idx = GetIdx("OD1");
- int nd2_idx = GetIdx("ND2");
- if(cg_idx!=-1 && od1_idx!=-1 && nd2_idx!=-1) {
- _AddChiDefinition(n_idx, ca_idx, cb_idx, cg_idx);
- _AddChiDefinition(ca_idx, cb_idx, cg_idx, od1_idx);
- _AddAtomRule(cg_idx, n_idx, ca_idx, cb_idx,
- Real(1.5319), Real(1.99491133503), 0, Real(0.0));
- _AddAtomRule(od1_idx, ca_idx, cb_idx, cg_idx,
- Real(1.2323), Real(2.13907553124), 1, Real(0.0));
- _AddAtomRule(nd2_idx, ca_idx, cb_idx, cg_idx,
- Real(1.3521), Real(2.02719992619), 1, Real(M_PI));
- }
- break;
- }
- case 'D': {
- int cg_idx = GetIdx("CG");
- int od1_idx = GetIdx("OD1");
- int od2_idx = GetIdx("OD2");
- if(cg_idx!=-1 && od1_idx!=-1 && od2_idx!=-1) {
- _AddChiDefinition(n_idx, ca_idx, cb_idx, cg_idx);
- _AddChiDefinition(ca_idx, cb_idx, cg_idx, od1_idx);
- _AddAtomRule(cg_idx, n_idx, ca_idx, cb_idx,
- Real(1.5218), Real(1.96524073775), 0, Real(0.0));
- _AddAtomRule(od1_idx, ca_idx, cb_idx, cg_idx,
- Real(1.2565), Real(2.05931398443), 1, Real(0.0));
- _AddAtomRule(od2_idx, ca_idx, cb_idx, cg_idx,
- Real(1.2541), Real(2.0542525296), 1, Real(M_PI));
- }
- break;
- }
- case 'Q': {
- int cg_idx = GetIdx("CG");
- int cd_idx = GetIdx("CD");
- int oe1_idx = GetIdx("OE1");
- int ne2_idx = GetIdx("NE2");
- if(cg_idx!=-1 && cd_idx!=-1 && oe1_idx!=-1 && ne2_idx!=-1) {
- _AddChiDefinition(n_idx, ca_idx, cb_idx, cg_idx);
- _AddChiDefinition(ca_idx, cb_idx, cg_idx, cd_idx);
- _AddChiDefinition(cb_idx, cg_idx, cd_idx, oe1_idx);
- _AddAtomRule(cg_idx, n_idx, ca_idx, cb_idx,
- Real(1.5534), Real(2.0162043519), 0, Real(0.0));
- _AddAtomRule(cd_idx, ca_idx, cb_idx, cg_idx,
- Real(1.532), Real(1.96349540849), 1, Real(0.0));
- _AddAtomRule(oe1_idx, cb_idx, cg_idx, cd_idx,
- Real(1.2294), Real(2.12092410702), 2, Real(0.0));
- _AddAtomRule(ne2_idx, cb_idx, cg_idx, cd_idx,
- Real(1.353), Real(2.03924269803), 2, Real(M_PI));
- }
- break;
- }
- case 'E': {
- int cg_idx = GetIdx("CG");
- int cd_idx = GetIdx("CD");
- int oe1_idx = GetIdx("OE1");
- int oe2_idx = GetIdx("OE2");
- if(cg_idx!=-1 && cd_idx!=-1 && oe1_idx!=-1 && oe2_idx!=-1) {
- _AddChiDefinition(n_idx, ca_idx, cb_idx, cg_idx);
- _AddChiDefinition(ca_idx, cb_idx, cg_idx, cd_idx);
- _AddChiDefinition(cb_idx, cg_idx, cd_idx, oe1_idx);
- _AddAtomRule(cg_idx, n_idx, ca_idx, cb_idx,
- Real(1.5557), Real(2.01917141163), 0, Real(0.0));
- _AddAtomRule(cd_idx, ca_idx, cb_idx, cg_idx,
- Real(1.5307), Real(2.01986954333), 1, Real(0.0));
- _AddAtomRule(oe1_idx, cb_idx, cg_idx, cd_idx,
- Real(1.259), Real(2.00695410687), 2, Real(0.0));
- _AddAtomRule(oe2_idx, cb_idx, cg_idx, cd_idx,
- Real(1.2532), Real(2.09579136579), 2, Real(M_PI));
- }
- break;
- }
- case 'K': {
- int cg_idx = GetIdx("CG");
- int cd_idx = GetIdx("CD");
- int ce_idx = GetIdx("CE");
- int nz_idx = GetIdx("NZ");
- if(cg_idx!=-1 && cd_idx!=-1 && ce_idx!=-1 && nz_idx!=-1) {
- _AddChiDefinition(n_idx, ca_idx, cb_idx, cg_idx);
- _AddChiDefinition(ca_idx, cb_idx, cg_idx, cd_idx);
- _AddChiDefinition(cb_idx, cg_idx, cd_idx, ce_idx);
- _AddChiDefinition(cg_idx, cd_idx, ce_idx, nz_idx);
- _AddAtomRule(cg_idx, n_idx, ca_idx, cb_idx,
- Real(1.5435), Real(2.02039314211), 0, Real(0.0));
- _AddAtomRule(cd_idx, ca_idx, cb_idx, cg_idx,
- Real(1.5397), Real(1.97710897666), 1, Real(0.0));
- _AddAtomRule(ce_idx, cb_idx, cg_idx, cd_idx,
- Real(1.535), Real(1.96052834877), 2, Real(0.0));
- _AddAtomRule(nz_idx, cg_idx, cd_idx, ce_idx,
- Real(1.4604), Real(1.92789069175), 3, Real(0.0));
- }
- break;
- }
- case 'S': {
- int og_idx = GetIdx("OG");
- if(og_idx!=-1) {
- _AddChiDefinition(n_idx, ca_idx, cb_idx, og_idx);
- _AddAtomRule(og_idx, n_idx, ca_idx, cb_idx,
- Real(1.4341), Real(1.96262274387), 0, Real(0.0));
- }
- break;
- }
- case 'C': {
- int sg_idx = GetIdx("SG");
- if(sg_idx!=-1) {
- _AddChiDefinition(n_idx, ca_idx, cb_idx, sg_idx);
- _AddAtomRule(sg_idx, n_idx, ca_idx, cb_idx,
- Real(1.8359), Real(1.98740641925), 0, Real(0.0));
- }
- break;
- }
- case 'M': {
- int cg_idx = GetIdx("CG");
- int sd_idx = GetIdx("SD");
- int ce_idx = GetIdx("CE");
- if(cg_idx!=-1 && sd_idx!=-1 && ce_idx!=-1) {
- _AddChiDefinition(n_idx, ca_idx, cb_idx, cg_idx);
- _AddChiDefinition(ca_idx, cb_idx, cg_idx, sd_idx);
- _AddChiDefinition(cb_idx, cg_idx, sd_idx, ce_idx);
- _AddAtomRule(cg_idx, n_idx, ca_idx, cb_idx,
- Real(1.546), Real(2.02318566891), 0, Real(0.0));
- _AddAtomRule(sd_idx, ca_idx, cb_idx, cg_idx,
- Real(1.8219), Real(1.9247490991), 1, Real(0.0));
- _AddAtomRule(ce_idx, cb_idx, cg_idx, sd_idx,
- Real(1.8206), Real(1.72682876192), 2, Real(0.0));
- }
- break;
- }
- case 'W': {
- int cg_idx = GetIdx("CG");
- int cd1_idx = GetIdx("CD1");
- int cd2_idx = GetIdx("CD2");
- int ne1_idx = GetIdx("NE1");
- int ce2_idx = GetIdx("CE2");
- int ce3_idx = GetIdx("CE3");
- int cz2_idx = GetIdx("CZ2");
- int cz3_idx = GetIdx("CZ3");
- int ch2_idx = GetIdx("CH2");
- if(cg_idx!=-1 && cd1_idx!=-1 && cd2_idx!=-1 && ne1_idx!=-1 &&
- ce2_idx!=-1 && ce3_idx!=-1 && cz2_idx!=-1 && cz3_idx!=-1 &&
- ch2_idx!=-1) {
- _AddChiDefinition(n_idx, ca_idx, cb_idx, cg_idx);
- _AddChiDefinition(ca_idx, cb_idx, cg_idx, cd1_idx);
- _AddAtomRule(cg_idx, n_idx, ca_idx, cb_idx,
- Real(1.5233), Real(2.00957210075), 0, Real(0.0));
- _AddAtomRule(cd1_idx, ca_idx, cb_idx, cg_idx,
- Real(1.3679), Real(2.25461632773), 1, Real(0.0));
- _AddAtomRule(cd2_idx, ca_idx, cb_idx, cg_idx,
- Real(1.4407), Real(2.16333560785), 1, Real(M_PI));
- _AddAtomRule(ce2_idx, cd1_idx, cg_idx, cd2_idx,
- Real(1.4126), Real(1.86139364725), 4, Real(0.0));
- _AddAtomRule(ne1_idx, cg_idx, cd2_idx, ce2_idx,
- Real(1.3746), Real(1.88268666413), 4, Real(0.0));
- _AddAtomRule(ce3_idx, cd1_idx, cg_idx, cd2_idx,
- Real(1.4011), Real(2.31325939059), 4, Real(M_PI));
- _AddAtomRule(cz3_idx, ce2_idx, cd2_idx, ce3_idx,
- Real(1.4017), Real(2.06228104416), 4, Real(0.0));
- _AddAtomRule(ch2_idx, cd2_idx, ce3_idx, cz3_idx,
- Real(1.4019), Real(2.11132479614), 4, Real(0.0));
- _AddAtomRule(cz2_idx, ce3_idx, cz3_idx, ch2_idx,
- Real(1.403), Real(2.10957946689), 4, Real(0.0));
- }
- break;
- }
- case 'Y': {
- int cg_idx = GetIdx("CG");
- int cd1_idx = GetIdx("CD1");
- int cd2_idx = GetIdx("CD2");
- int ce1_idx = GetIdx("CE1");
- int ce2_idx = GetIdx("CE2");
- int cz_idx = GetIdx("CZ");
- int oh_idx = GetIdx("OH");
- if(cg_idx!=-1 && cd1_idx!=-1 && cd2_idx!=-1 && ce1_idx!=-1 &&
- ce2_idx!=-1 && cz_idx!=-1 && oh_idx!=-1) {
- _AddChiDefinition(n_idx, ca_idx, cb_idx, cg_idx);
- _AddChiDefinition(ca_idx, cb_idx, cg_idx, cd1_idx);
- _AddAtomRule(cg_idx, n_idx, ca_idx, cb_idx,
- Real(1.5113), Real(1.9711748572), 0, Real(0.0));
- _AddAtomRule(cd1_idx, ca_idx, cb_idx, cg_idx,
- Real(1.4064), Real(2.10294721573), 1, Real(0.0));
- _AddAtomRule(cd2_idx, ca_idx, cb_idx, cg_idx,
- Real(1.4068), Real(2.10242361695), 1, Real(M_PI));
- _AddAtomRule(ce1_idx, cd2_idx, cg_idx, cd1_idx,
- Real(1.4026), Real(2.1013764194), 4, Real(0.0));
- _AddAtomRule(ce2_idx, cd1_idx, cg_idx, cd2_idx,
- Real(1.4022), Real(2.1041689462), 4, Real(0.0));
- _AddAtomRule(cz_idx, cg_idx, cd1_idx, ce1_idx,
- Real(1.3978), Real(2.09596589872), 4, Real(0.0));
- _AddAtomRule(oh_idx, cd2_idx, ce2_idx, cz_idx,
- Real(1.4063), Real(2.09875842552), 4, Real(M_PI));
- }
- break;
- }
- case 'T': {
- int og1_idx = GetIdx("OG1");
- int cg2_idx = GetIdx("CG1");
- if(og1_idx!=-1 && cg2_idx!=-1) {
- _AddChiDefinition(n_idx, ca_idx, cb_idx, og1_idx);
- _AddAtomRule(og1_idx, n_idx, ca_idx, cb_idx,
- Real(1.4252), Real(1.95756128904), 0, Real(0.0));
- _AddAtomRule(cg2_idx, og1_idx, ca_idx, cb_idx,
- Real(1.5324), Real(2.02301113599), 4, Real(-2.1665));
- }
- break;
- }
-
- case 'V': {
- int cg1_idx = GetIdx("CG1");
- int cg2_idx = GetIdx("CG2");
- if(cg1_idx!=-1 && cg2_idx!=-1) {
- _AddChiDefinition(n_idx, ca_idx, cb_idx, cg1_idx);
- _AddAtomRule(cg1_idx, n_idx, ca_idx, cb_idx,
- Real(1.5441), Real(1.9891517485), 0, Real(0.0));
- _AddAtomRule(cg2_idx, cg1_idx, ca_idx, cb_idx,
- Real(1.5414), Real(1.95773582196), 4, Real(2.1640));
- }
- break;
- }
- case 'I': {
- int cg1_idx = GetIdx("CG1");
- int cg2_idx = GetIdx("CG2");
- int cd1_idx = GetIdx("CD1");
- if(cg1_idx!=-1 && cg2_idx!=-1 && cd1_idx!=-1) {
- _AddChiDefinition(n_idx, ca_idx, cb_idx, cg1_idx);
- _AddChiDefinition(ca_idx, cb_idx, cg1_idx, cd1_idx);
- _AddAtomRule(cg1_idx, n_idx, ca_idx, cb_idx,
- Real(1.5498), Real(1.98321762904), 0, Real(0.0));
- _AddAtomRule(cg2_idx, cg1_idx, ca_idx, cb_idx,
- Real(1.5452), Real(1.9884536168), 4, Real(-2.2696));
- _AddAtomRule(cd1_idx, ca_idx, cb_idx, cg1_idx,
- Real(1.5381), Real(1.9912461436), 1, Real(0.0));
- }
- break;
- }
- case 'L': {
- int cg_idx = GetIdx("CG");
- int cd1_idx = GetIdx("CD1");
- int cd2_idx = GetIdx("CD2");
- if(cg_idx!=-1 && cd1_idx!=-1 && cd2_idx!=-1) {
- _AddChiDefinition(n_idx, ca_idx, cb_idx, cg_idx);
- _AddChiDefinition(ca_idx, cb_idx, cg_idx, cd1_idx);
- _AddAtomRule(cg_idx, n_idx, ca_idx, cb_idx,
- Real(1.5472), Real(2.05006373939), 0, Real(0.0));
- _AddAtomRule(cd1_idx, ca_idx, cb_idx, cg_idx,
- Real(1.5361), Real(1.9282397576), 1, Real(0.0));
- _AddAtomRule(cd2_idx, cd1_idx, cb_idx, cg_idx,
- Real(1.536), Real(1.96471713897), 4, Real(2.0944));
-
- }
- break;
- }
- case 'P': {
- int cg_idx = GetIdx("CG");
- int cd_idx = GetIdx("CD");
- if(cg_idx!=-1 && cd_idx!=-1) {
- _AddChiDefinition(n_idx, ca_idx, cb_idx, cg_idx);
- _AddChiDefinition(ca_idx, cb_idx, cg_idx, cd_idx);
- _AddAtomRule(cg_idx, n_idx, ca_idx, cb_idx,
- Real(1.5322), Real(1.82194920616), 0, Real(0.0));
- _AddAtomRule(cd_idx, ca_idx, cb_idx, cg_idx,
- Real(1.5317), Real(1.80135432098), 1, Real(0.0));
- }
- break;
- }
- case 'H': {
- int cg_idx = GetIdx("CG");
- int nd1_idx = GetIdx("ND1");
- int cd2_idx = GetIdx("CD1");
- int ce1_idx = GetIdx("CE2");
- int ne2_idx = GetIdx("NE2");
-
- if(cg_idx!=-1 && nd1_idx!=-1 && cd2_idx!=-1 && ce1_idx!=-1 &&
- ne2_idx!=-1) {
- _AddChiDefinition(n_idx, ca_idx, cb_idx, cg_idx);
- _AddChiDefinition(ca_idx, cb_idx, cg_idx, nd1_idx);
- _AddAtomRule(cg_idx, n_idx, ca_idx, cb_idx,
- Real(1.5109), Real(2.04098802728), 0, Real(0.0));
- _AddAtomRule(nd1_idx, ca_idx, cb_idx, cg_idx,
- Real(1.3859), Real(2.09736216212), 1, Real(0.0));
- _AddAtomRule(cd2_idx, ca_idx, cb_idx, cg_idx,
- Real(1.3596), Real(2.26386657276), 1, Real(M_PI));
- _AddAtomRule(ce1_idx, cd2_idx, cg_idx, nd1_idx,
- Real(1.317), Real(1.8360863731), 4, Real(0.0));
- _AddAtomRule(ne2_idx, nd1_idx, cg_idx, cd2_idx,
- Real(1.3782), Real(1.84655834861), 4, Real(0.0));
- }
- break;
- }
- case 'F': {
- int cg_idx = GetIdx("CG");
- int cd1_idx = GetIdx("CD1");
- int cd2_idx = GetIdx("CD2");
- int ce1_idx = GetIdx("CE1");
- int ce2_idx = GetIdx("CE2");
- int cz_idx = GetIdx("CZ");
- if(cg_idx!=-1 && cd1_idx!=-1 && cd2_idx!=-1 && ce1_idx!=-1 &&
- ce2_idx!=-1 && cz_idx!=-1) {
- _AddChiDefinition(n_idx, ca_idx, cb_idx, cg_idx);
- _AddChiDefinition(ca_idx, cb_idx, cg_idx, cd1_idx);
- _AddAtomRule(cg_idx, n_idx, ca_idx, cb_idx,
- Real(1.5109), Real(1.96803326455), 0, Real(0.0));
- _AddAtomRule(cd1_idx, ca_idx, cb_idx, cg_idx,
- Real(1.4059), Real(2.099980156), 1, Real(0.0));
- _AddAtomRule(cd2_idx, ca_idx, cb_idx, cg_idx,
- Real(1.4062), Real(2.10765960471), 1, Real(M_PI));
- _AddAtomRule(ce1_idx, cd2_idx, cg_idx, cd1_idx,
- Real(1.4006), Real(2.10539067668), 4, Real(0.0));
- _AddAtomRule(ce2_idx, cd1_idx, cg_idx, cd2_idx,
- Real(1.4002), Real(2.10521614376), 4, Real(0.0));
- _AddAtomRule(cz_idx, cg_idx, cd1_idx, ce1_idx,
- Real(1.4004), Real(2.09317337192), 4, Real(0.0));
- }
- break;
- }
- }
- }
- }
-
- for(auto it = sidechain_atom_rules.begin();
- it != sidechain_atom_rules.end(); ++it) {
- rotameric_atoms.insert(it->sidechain_atom_idx);
- }
-
- rotamer_setup = true;
-}
-
void ResidueDefinition::_AddChiDefinition(int idx_one, int idx_two,
- int idx_three, int idx_four) const {
+ int idx_three, int idx_four) {
ChiDefinition chi_definition;
chi_definition.idx_one = idx_one;
chi_definition.idx_two = idx_two;
chi_definition.idx_three = idx_three;
chi_definition.idx_four = idx_four;
chi_definitions.push_back(chi_definition);
-
}
void ResidueDefinition::_AddAtomRule(int a_idx, int anch_one_idx,
int anch_two_idx, int anch_three_idx,
Real bond_length, Real angle,
int dihedral_idx,
- Real base_dihedral) const {
+ Real base_dihedral) {
SidechainAtomRule rule;
rule.sidechain_atom_idx = a_idx;
rule.anchor_idx[0] = anch_one_idx;
@@ -1605,7 +1229,7 @@ void ChainData::ToStream(std::ostream& stream,
std::set<int> skip_indices = def.GetRotamericAtoms();
int o_idx = -1;
if(def.chem_type == 'A') {
- // can reconstruct O if there is CA, C, no OXT, its not the last
+ // can reconstruct O if there is CA, C, no OXT, its not the last
// residue (res_idx < res_def_indices.size()-1) and the next residue is
// an amino acid too and has N.
if(def.GetIdx("CA") != -1 && def.GetIdx("C") != -1 &&
@@ -1726,7 +1350,6 @@ void ChainData::FromStream(std::istream& stream,
}
// infer
-
int start_idx = 0;
int chi_idx = 0;
for(int res_idx = 0; res_idx < n_res; ++res_idx) {
@@ -1778,67 +1401,6 @@ void ChainData::FromStream(std::istream& stream,
}
DefaultPepLib::DefaultPepLib() {
-
- /* hardcoded constructor created with:
-
- from ost import conop
- def ProcessCompound(comp_name, lib, skip_oxt=True, ca_only=False):
- c = lib.FindCompound(comp_name)
- anames = list()
- idx_mapper = dict()
- element_mapper = dict()
- for a_idx, a in enumerate(c.atom_specs):
- if a.element == "H":
- continue
- if skip_oxt and a.name == "OXT":
- continue
- if ca_only and a.name != "CA":
- continue
- idx_mapper[a_idx] = a.name
- anames.append(a.name)
- element_mapper[a.name] = a.element
- anames.sort()
- bond_data = list()
- for b in c.bond_specs:
- idx_one = b.atom_one
- idx_two = b.atom_two
- if idx_one in idx_mapper and idx_two in idx_mapper:
- aname_one = idx_mapper[idx_one]
- aname_two = idx_mapper[idx_two]
- idx_one = anames.index(aname_one)
- idx_two = anames.index(aname_two)
- if idx_one < idx_two:
- bond_data.append(((idx_one, idx_two), b.order))
- else:
- bond_data.append(((idx_two, idx_one), b.order))
- bond_data.sort()
- print(f" res_def = ResidueDefinition();")
- print(f" res_def.name = \"{comp_name}\";")
- print(f" res_def.olc = '{c.GetOneLetterCode()}';")
- print(f" res_def.chem_type = '{c.chem_type}';")
- print(f" res_def.chem_class = '{c.chem_class}';")
- for aname in anames:
- print(f" res_def.anames.push_back(\"{aname}\");")
- for aname in anames:
- print(f" res_def.elements.push_back(\"{element_mapper[aname]}\");")
- print(f" res_def.is_hetatm.assign({len(anames)}, false);")
- for b in bond_data:
- print(f" res_def.bonds.push_back({b[0][0]});")
- print(f" res_def.bonds.push_back({b[0][1]});")
- for b in bond_data:
- print(f" res_def.bond_orders.push_back({b[1]});")
- print(" residue_definitions.push_back(res_def);")
- print()
- lib = conop.GetDefaultLib()
- anames = ["ALA", "ARG", "ASN", "ASP", "GLN", "GLU", "LYS", "SER", "CYS",
- "MET", "TRP", "TYR", "THR", "VAL", "ILE", "LEU", "GLY", "PRO",
- "HIS", "PHE"]
- print(" ResidueDefinition res_def;")
- for aname in anames:
- ProcessCompound(aname, lib)
- ProcessCompound(aname, lib, skip_oxt = False)
- ProcessCompound(aname, lib, ca_only=True)
- */
ResidueDefinition res_def;
res_def = ResidueDefinition();
res_def.name = "ALA";
@@ -1973,6 +1535,17 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(2);
+ res_def._AddChiDefinition(6, 1, 2, 4);
+ res_def._AddChiDefinition(1, 2, 4, 3);
+ res_def._AddChiDefinition(2, 4, 3, 7);
+ res_def._AddChiDefinition(4, 3, 7, 5);
+ res_def._AddAtomRule(4, 6, 1, 2, 1.5475, 2.0237, 0, 0.0);
+ res_def._AddAtomRule(3, 1, 2, 4, 1.5384, 1.9898, 1, 0.0);
+ res_def._AddAtomRule(7, 2, 4, 3, 1.5034, 1.8691, 2, 0.0);
+ res_def._AddAtomRule(5, 4, 3, 7, 1.3401, 2.1476, 3, 0.0);
+ res_def._AddAtomRule(8, 3, 7, 5, 1.3311, 2.0605, 4, 0.0);
+ res_def._AddAtomRule(9, 3, 7, 5, 1.3292, 2.1317, 4, M_PI);
+ res_def.rotameric_atoms.insert({4, 3, 7, 5, 8, 9});
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -2038,6 +1611,10 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(2);
+ // same rotamer information as previous one
+ res_def.chi_definitions = residue_definitions.back().chi_definitions;
+ res_def.sidechain_atom_rules = residue_definitions.back().sidechain_atom_rules;
+ res_def.rotameric_atoms = residue_definitions.back().rotameric_atoms;
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -2093,6 +1670,12 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(2);
+ res_def._AddChiDefinition(4, 1, 2, 3);
+ res_def._AddChiDefinition(1, 2, 3, 7);
+ res_def._AddAtomRule(3, 4, 1, 2, 1.5319, 1.9949, 0, 0.0);
+ res_def._AddAtomRule(7, 1, 2, 3, 1.2323, 2.1391, 1, 0.0);
+ res_def._AddAtomRule(5, 1, 2, 3, 1.3521, 2.0272, 1, M_PI);
+ res_def.rotameric_atoms.insert({3, 7, 5});
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -2143,6 +1726,10 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(2);
+ // same rotamer information as previous one
+ res_def.chi_definitions = residue_definitions.back().chi_definitions;
+ res_def.sidechain_atom_rules = residue_definitions.back().sidechain_atom_rules;
+ res_def.rotameric_atoms = residue_definitions.back().rotameric_atoms;
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -2198,6 +1785,12 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(2);
res_def.bond_orders.push_back(1);
+ res_def._AddChiDefinition(4, 1, 2, 3);
+ res_def._AddChiDefinition(1, 2, 3, 6);
+ res_def._AddAtomRule(3, 4, 1, 2, 1.5218, 1.9652, 0, 0.0);
+ res_def._AddAtomRule(6, 1, 2, 3, 1.2565, 2.0593, 1, 0.0);
+ res_def._AddAtomRule(7, 1, 2, 3, 1.2541, 2.0543, 1, M_PI);
+ res_def.rotameric_atoms.insert({3, 6, 7});
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -2248,6 +1841,10 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(2);
res_def.bond_orders.push_back(1);
+ // same rotamer information as previous one
+ res_def.chi_definitions = residue_definitions.back().chi_definitions;
+ res_def.sidechain_atom_rules = residue_definitions.back().sidechain_atom_rules;
+ res_def.rotameric_atoms = residue_definitions.back().rotameric_atoms;
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -2308,6 +1905,14 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(2);
+ res_def._AddChiDefinition(5, 1, 2, 4);
+ res_def._AddChiDefinition(1, 2, 4, 3);
+ res_def._AddChiDefinition(2, 4, 3, 8);
+ res_def._AddAtomRule(4, 5, 1, 2, 1.5534, 2.0162, 0, 0.0);
+ res_def._AddAtomRule(3, 1, 2, 4, 1.5320, 1.9635, 1, 0.0);
+ res_def._AddAtomRule(8, 2, 4, 3, 1.2294, 2.1209, 2, 0.0);
+ res_def._AddAtomRule(6, 2, 4, 3, 1.3530, 2.0392, 2, M_PI);
+ res_def.rotameric_atoms.insert({4, 3, 8, 6});
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -2363,6 +1968,10 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(2);
+ // same rotamer information as previous one
+ res_def.chi_definitions = residue_definitions.back().chi_definitions;
+ res_def.sidechain_atom_rules = residue_definitions.back().sidechain_atom_rules;
+ res_def.rotameric_atoms = residue_definitions.back().rotameric_atoms;
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -2423,6 +2032,14 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(2);
res_def.bond_orders.push_back(1);
+ res_def._AddChiDefinition(5, 1, 2, 4);
+ res_def._AddChiDefinition(1, 2, 4, 3);
+ res_def._AddChiDefinition(2, 4, 3, 7);
+ res_def._AddAtomRule(4, 5, 1, 2, 1.5557, 2.0192, 0, 0.0);
+ res_def._AddAtomRule(3, 1, 2, 4, 1.5307, 2.0199, 1, 0.0);
+ res_def._AddAtomRule(7, 2, 4, 3, 1.2590, 2.0070, 2, 0.0);
+ res_def._AddAtomRule(8, 2, 4, 3, 1.2532, 2.0958, 2, M_PI);
+ res_def.rotameric_atoms.insert({4, 3, 7, 8});
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -2478,6 +2095,10 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(2);
res_def.bond_orders.push_back(1);
+ // same rotamer information as previous one
+ res_def.chi_definitions = residue_definitions.back().chi_definitions;
+ res_def.sidechain_atom_rules = residue_definitions.back().sidechain_atom_rules;
+ res_def.rotameric_atoms = residue_definitions.back().rotameric_atoms;
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -2538,6 +2159,15 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
+ res_def._AddChiDefinition(6, 1, 2, 5);
+ res_def._AddChiDefinition(1, 2, 5, 3);
+ res_def._AddChiDefinition(2, 5, 3, 4);
+ res_def._AddChiDefinition(5, 3, 4, 7);
+ res_def._AddAtomRule(5, 6, 1, 2, 1.5435, 2.0204, 0, 0.0);
+ res_def._AddAtomRule(3, 1, 2, 5, 1.5397, 1.9771, 1, 0.0);
+ res_def._AddAtomRule(4, 2, 5, 3, 1.5350, 1.9605, 2, 0.0);
+ res_def._AddAtomRule(7, 5, 3, 4, 1.4604, 1.9279, 3, 0.0);
+ res_def.rotameric_atoms.insert({5, 3, 4, 7});
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -2593,6 +2223,10 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
+ // same rotamer information as previous one
+ res_def.chi_definitions = residue_definitions.back().chi_definitions;
+ res_def.sidechain_atom_rules = residue_definitions.back().sidechain_atom_rules;
+ res_def.rotameric_atoms = residue_definitions.back().rotameric_atoms;
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -2638,6 +2272,9 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
+ res_def._AddChiDefinition(3, 1, 2, 5);
+ res_def._AddAtomRule(5, 3, 1, 2, 1.4341, 1.9626, 0, 0.0);
+ res_def.rotameric_atoms.insert(5);
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -2678,6 +2315,10 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
+ // same rotamer information as previous one
+ res_def.chi_definitions = residue_definitions.back().chi_definitions;
+ res_def.sidechain_atom_rules = residue_definitions.back().sidechain_atom_rules;
+ res_def.rotameric_atoms = residue_definitions.back().rotameric_atoms;
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -2723,6 +2364,9 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
+ res_def._AddChiDefinition(3, 1, 2, 5);
+ res_def._AddAtomRule(5, 3, 1, 2, 1.8359, 1.9874, 0, 0.0);
+ res_def.rotameric_atoms.insert(5);
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -2763,6 +2407,9 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
+ res_def._AddChiDefinition(3, 1, 2, 6);
+ res_def._AddAtomRule(6, 3, 1, 2, 1.8359, 1.9874, 0, 0.0);
+ res_def.rotameric_atoms.insert(6);
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -2818,6 +2465,13 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
+ res_def._AddChiDefinition(5, 1, 2, 4);
+ res_def._AddChiDefinition(1, 2, 4, 7);
+ res_def._AddChiDefinition(2, 4, 7, 3);
+ res_def._AddAtomRule(4, 5, 1, 2, 1.5460, 2.0232, 0, 0.0);
+ res_def._AddAtomRule(7, 1, 2, 4, 1.8219, 1.9247, 1, 0.0);
+ res_def._AddAtomRule(3, 2, 4, 7, 1.8206, 1.7268, 2, 0.0);
+ res_def.rotameric_atoms.insert({4, 7, 3});
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -2868,6 +2522,13 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
+ res_def._AddChiDefinition(5, 1, 2, 4);
+ res_def._AddChiDefinition(1, 2, 4, 8);
+ res_def._AddChiDefinition(2, 4, 8, 3);
+ res_def._AddAtomRule(4, 5, 1, 2, 1.5460, 2.0232, 0, 0.0);
+ res_def._AddAtomRule(8, 1, 2, 4, 1.8219, 1.9247, 1, 0.0);
+ res_def._AddAtomRule(3, 2, 4, 8, 1.8206, 1.7268, 2, 0.0);
+ res_def.rotameric_atoms.insert({4, 8, 3});
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -2959,6 +2620,18 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(2);
res_def.bond_orders.push_back(2);
res_def.bond_orders.push_back(1);
+ res_def._AddChiDefinition(11, 1, 2, 7);
+ res_def._AddChiDefinition(1, 2, 7, 3);
+ res_def._AddAtomRule(7, 11, 1, 2, 1.5233, 2.0096, 0, 0.0);
+ res_def._AddAtomRule(3, 1, 2, 7, 1.3679, 2.2546, 1, 0.0);
+ res_def._AddAtomRule(4, 1, 2, 7, 1.4407, 2.1633, 1, M_PI);
+ res_def._AddAtomRule(5, 3, 7, 4, 1.4126, 1.8614, 4, 0.0);
+ res_def._AddAtomRule(12, 7, 4, 5, 1.3746, 1.8827, 4, 0.0);
+ res_def._AddAtomRule(6, 3, 7, 4, 1.4011, 2.3133, 4, M_PI);
+ res_def._AddAtomRule(10, 5, 4, 6, 1.4017, 2.0623, 4, 0.0);
+ res_def._AddAtomRule(8, 4, 6, 10, 1.4019, 2.1113, 4, 0.0);
+ res_def._AddAtomRule(9, 6, 10, 8, 1.4030, 2.1096, 4, 0.0);
+ res_def.rotameric_atoms.insert({7, 3, 4, 5, 12, 6, 10, 8, 9});
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -3045,6 +2718,10 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(2);
res_def.bond_orders.push_back(2);
res_def.bond_orders.push_back(1);
+ // same rotamer information as previous one
+ res_def.chi_definitions = residue_definitions.back().chi_definitions;
+ res_def.sidechain_atom_rules = residue_definitions.back().sidechain_atom_rules;
+ res_def.rotameric_atoms = residue_definitions.back().rotameric_atoms;
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -3123,6 +2800,16 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(2);
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
+ res_def._AddChiDefinition(9, 1, 2, 7);
+ res_def._AddChiDefinition(1, 2, 7, 3);
+ res_def._AddAtomRule(7, 9, 1, 2, 1.5113, 1.9712, 0, 0.0);
+ res_def._AddAtomRule(3, 1, 2, 7, 1.4064, 2.1029, 1, 0.0);
+ res_def._AddAtomRule(4, 1, 2, 7, 1.4068, 2.1024, 1, M_PI);
+ res_def._AddAtomRule(5, 4, 7, 3, 1.4026, 2.1014, 4, 0.0);
+ res_def._AddAtomRule(6, 3, 7, 4, 1.4022, 2.1042, 4, 0.0);
+ res_def._AddAtomRule(8, 7, 3, 5, 1.3978, 2.0960, 4, 0.0);
+ res_def._AddAtomRule(11, 4, 6, 8, 1.4063, 2.0988, 4, M_PI);
+ res_def.rotameric_atoms.insert({7, 3, 4, 5, 6, 8, 11});
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -3196,6 +2883,10 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(2);
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
+ // same rotamer information as previous one
+ res_def.chi_definitions = residue_definitions.back().chi_definitions;
+ res_def.sidechain_atom_rules = residue_definitions.back().sidechain_atom_rules;
+ res_def.rotameric_atoms = residue_definitions.back().rotameric_atoms;
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -3246,6 +2937,10 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
+ res_def._AddChiDefinition(4, 1, 2, 6);
+ res_def._AddAtomRule(6, 4, 1, 2, 1.4252, 1.9576, 0, 0.0);
+ res_def._AddAtomRule(3, 6, 1, 2, 1.5324, 2.0230, 4, -2.1665);
+ res_def.rotameric_atoms.insert({6, 3});
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -3291,6 +2986,10 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
+ // same rotamer information as previous one
+ res_def.chi_definitions = residue_definitions.back().chi_definitions;
+ res_def.sidechain_atom_rules = residue_definitions.back().sidechain_atom_rules;
+ res_def.rotameric_atoms = residue_definitions.back().rotameric_atoms;
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -3341,6 +3040,10 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
+ res_def._AddChiDefinition(5, 1, 2, 3);
+ res_def._AddAtomRule(3, 5, 1, 2, 1.5441, 1.9892, 0, 0.0);
+ res_def._AddAtomRule(4, 3, 1, 2, 1.5414, 1.9577, 4, 2.1640);
+ res_def.rotameric_atoms.insert({3, 4});
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -3386,6 +3089,10 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
+ // same rotamer information as previous one
+ res_def.chi_definitions = residue_definitions.back().chi_definitions;
+ res_def.sidechain_atom_rules = residue_definitions.back().sidechain_atom_rules;
+ res_def.rotameric_atoms = residue_definitions.back().rotameric_atoms;
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -3441,6 +3148,12 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
+ res_def._AddChiDefinition(6, 1, 2, 4);
+ res_def._AddChiDefinition(1, 2, 4, 3);
+ res_def._AddAtomRule(4, 6, 1, 2, 1.5498, 1.9832, 0, 0.0);
+ res_def._AddAtomRule(5, 4, 1, 2, 1.5452, 1.9885, 4, -2.2696);
+ res_def._AddAtomRule(3, 1, 2, 4, 1.5381, 1.9912, 1, 0.0);
+ res_def.rotameric_atoms.insert({4, 5, 3});
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -3491,6 +3204,10 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
+ // same rotamer information as previous one
+ res_def.chi_definitions = residue_definitions.back().chi_definitions;
+ res_def.sidechain_atom_rules = residue_definitions.back().sidechain_atom_rules;
+ res_def.rotameric_atoms = residue_definitions.back().rotameric_atoms;
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -3546,6 +3263,12 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
+ res_def._AddChiDefinition(6, 1, 2, 5);
+ res_def._AddChiDefinition(1, 2, 5, 3);
+ res_def._AddAtomRule(5, 6, 1, 2, 1.5472, 2.0501, 0, 0.0);
+ res_def._AddAtomRule(3, 1, 2, 5, 1.5361, 1.9282, 1, 0.0);
+ res_def._AddAtomRule(4, 3, 2, 5, 1.5360, 1.9647, 4, 2.0944);
+ res_def.rotameric_atoms.insert({5, 3, 4});
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -3596,6 +3319,10 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
+ // same rotamer information as previous one
+ res_def.chi_definitions = residue_definitions.back().chi_definitions;
+ res_def.sidechain_atom_rules = residue_definitions.back().sidechain_atom_rules;
+ res_def.rotameric_atoms = residue_definitions.back().rotameric_atoms;
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -3714,6 +3441,11 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
+ res_def._AddChiDefinition(5, 1, 2, 4);
+ res_def._AddChiDefinition(1, 2, 4, 3);
+ res_def._AddAtomRule(4, 5, 1, 2, 1.5322, 1.8219, 0, 0.0);
+ res_def._AddAtomRule(3, 1, 2, 4, 1.5317, 1.8014, 1, 0.0);
+ res_def.rotameric_atoms.insert({4, 3});
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -3762,6 +3494,10 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
+ // same rotamer information as previous one
+ res_def.chi_definitions = residue_definitions.back().chi_definitions;
+ res_def.sidechain_atom_rules = residue_definitions.back().sidechain_atom_rules;
+ res_def.rotameric_atoms = residue_definitions.back().rotameric_atoms;
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -3830,6 +3566,14 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(2);
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
+ res_def._AddChiDefinition(6, 1, 2, 5);
+ res_def._AddChiDefinition(1, 2, 5, 7);
+ res_def._AddAtomRule(5, 6, 1, 2, 1.5109, 2.0410, 0, 0.0);
+ res_def._AddAtomRule(7, 1, 2, 5, 1.3859, 2.0974, 1, 0.0);
+ res_def._AddAtomRule(3, 1, 2, 5, 1.3596, 2.2639, 1, M_PI);
+ res_def._AddAtomRule(4, 3, 5, 7, 1.3170, 1.8361, 4, 0.0);
+ res_def._AddAtomRule(8, 7, 5, 3, 1.3782, 1.8466, 4, 0.0);
+ res_def.rotameric_atoms.insert({5, 7, 3, 4, 8});
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -3893,6 +3637,10 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(2);
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(1);
+ // same rotamer information as previous one
+ res_def.chi_definitions = residue_definitions.back().chi_definitions;
+ res_def.sidechain_atom_rules = residue_definitions.back().sidechain_atom_rules;
+ res_def.rotameric_atoms = residue_definitions.back().rotameric_atoms;
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -3966,6 +3714,15 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(2);
res_def.bond_orders.push_back(1);
+ res_def._AddChiDefinition(9, 1, 2, 7);
+ res_def._AddChiDefinition(1, 2, 7, 3);
+ res_def._AddAtomRule(7, 9, 1, 2, 1.5109, 1.9680, 0, 0.0);
+ res_def._AddAtomRule(3, 1, 2, 7, 1.4059, 2.0100, 1, 0.0);
+ res_def._AddAtomRule(4, 1, 2, 7, 1.4062, 2.1077, 1, M_PI);
+ res_def._AddAtomRule(5, 4, 7, 3, 1.4006, 2.1054, 4, 0.0);
+ res_def._AddAtomRule(6, 3, 7, 4, 1.4002, 2.1052, 4, 0.0);
+ res_def._AddAtomRule(8, 7, 3, 5, 1.4004, 2.0932, 4, 0.0);
+ res_def.rotameric_atoms.insert({7, 3, 4, 5, 6, 8});
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
@@ -4034,6 +3791,10 @@ DefaultPepLib::DefaultPepLib() {
res_def.bond_orders.push_back(1);
res_def.bond_orders.push_back(2);
res_def.bond_orders.push_back(1);
+ // same rotamer information as previous one
+ res_def.chi_definitions = residue_definitions.back().chi_definitions;
+ res_def.sidechain_atom_rules = residue_definitions.back().sidechain_atom_rules;
+ res_def.rotameric_atoms = residue_definitions.back().rotameric_atoms;
residue_definitions.push_back(res_def);
res_def = ResidueDefinition();
diff --git a/modules/io/src/mol/omf.hh b/modules/io/src/mol/omf.hh
index e832b829c5b867c3ff07c1aafe835f1919d55250..7cd4e81dd9611ee5dea091a96d5cd2e51d73c5be 100644
--- a/modules/io/src/mol/omf.hh
+++ b/modules/io/src/mol/omf.hh
@@ -61,7 +61,7 @@ struct ChiDefinition{
struct ResidueDefinition {
- ResidueDefinition(): rotamer_setup(false) { };
+ ResidueDefinition() { };
ResidueDefinition(const ost::mol::ResidueHandle& res);
@@ -97,15 +97,13 @@ struct ResidueDefinition {
void _InitIdxMapper() const;
- void _InitRotamer() const;
-
void _AddChiDefinition(int idx_one, int idx_two, int idx_three,
- int idx_four) const;
+ int idx_four);
void _AddAtomRule(int a_idx, int anch_one_idx,
int anch_two_idx, int anch_three_idx,
Real bond_length, Real angle, int dihedral_idx,
- Real base_dihedral) const;
+ Real base_dihedral);
String name;
char olc;
@@ -116,11 +114,10 @@ struct ResidueDefinition {
std::vector<bool> is_hetatm;
std::vector<int> bonds;
std::vector<int> bond_orders;
- mutable bool rotamer_setup;
mutable std::map<String, int> idx_mapper;
- mutable std::set<int> rotameric_atoms;
- mutable std::vector<ChiDefinition> chi_definitions;
- mutable std::vector<SidechainAtomRule> sidechain_atom_rules;
+ std::set<int> rotameric_atoms;
+ std::vector<ChiDefinition> chi_definitions;
+ std::vector<SidechainAtomRule> sidechain_atom_rules;
};