From 4a82e59d60134c0bb449152b0bb8c8275f17955b Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 1 Jun 2017 14:07:02 +0200
Subject: [PATCH] add vdw param for more residues
---
modules/mol/alg/src/accessibility.cc | 270 ++++++++++++++++++++++++++-
modules/mol/alg/src/accessibility.hh | 8 +-
2 files changed, 266 insertions(+), 12 deletions(-)
diff --git a/modules/mol/alg/src/accessibility.cc b/modules/mol/alg/src/accessibility.cc
index c4e2b2f6f..8867a2fad 100644
--- a/modules/mol/alg/src/accessibility.cc
+++ b/modules/mol/alg/src/accessibility.cc
@@ -574,8 +574,8 @@ void ASAParamFromAtomList(const ost::mol::AtomViewList& atom_list,
std::vector<Real>& z_pos,
std::vector<Real>& radii) {
- const ost::mol::alg::NACCESSParam& param =
- ost::mol::alg::NACCESSParam::GetInstance();
+ const ost::mol::alg::AccessibilityParam& param =
+ ost::mol::alg::AccessibilityParam::GetInstance();
String rname, aname, ele;
for(ost::mol::AtomViewList::const_iterator at_it = atom_list.begin();
@@ -634,7 +634,7 @@ Real SetAccessibilityProps(ost::mol::EntityView& ent,
for(uint idx = 0; idx < res_list.size(); ++idx) {
rname = res_list[idx].GetName();
Real tot_acc =
- ost::mol::alg::NACCESSParam::GetInstance().GetResidueAccessibility(rname);
+ ost::mol::alg::AccessibilityParam::GetInstance().GetResidueAccessibility(rname);
if(tot_acc == 0.0) {
// no accessibility found...
res_list[idx].SetFloatProp(asa_rel, 0.0);
@@ -656,7 +656,7 @@ Real SetAccessibilityProps(ost::mol::EntityView& ent,
namespace ost { namespace mol { namespace alg {
-NACCESSParam::NACCESSParam() {
+AccessibilityParam::AccessibilityParam() {
std::map<String, Real> ala_map;
std::map<String, Real> arg_map;
@@ -677,7 +677,19 @@ NACCESSParam::NACCESSParam() {
std::map<String, Real> thr_map;
std::map<String, Real> trp_map;
std::map<String, Real> tyr_map;
- std::map<String, Real> val_map;
+ std::map<String, Real> val_map;
+ std::map<String, Real> asx_map;
+ std::map<String, Real> glx_map;
+ std::map<String, Real> ace_map;
+ std::map<String, Real> __a_map;
+ std::map<String, Real> __c_map;
+ std::map<String, Real> __g_map;
+ std::map<String, Real> __t_map;
+ std::map<String, Real> __u_map;
+ std::map<String, Real> twomg_map;
+ std::map<String, Real> h2u_map;
+ std::map<String, Real> hem_map;
+ std::map<String, Real> hoh_map;
ala_map["N"] = 1.65;
ala_map["CA"] = 1.87;
@@ -865,6 +877,236 @@ NACCESSParam::NACCESSParam() {
val_map["CB"] = 1.87;
val_map["CG1"] = 1.87;
val_map["CG2"] = 1.87;
+
+ asx_map["N"] = 1.65;
+ asx_map["CA"] = 1.87;
+ asx_map["C"] = 1.76;
+ asx_map["O"] = 1.40;
+ asx_map["CB"] = 1.87;
+ asx_map["CG"] = 1.76;
+ asx_map["AD1"] = 1.50;
+ asx_map["AD2"] = 1.50;
+
+ glx_map["N"] = 1.65;
+ glx_map["CA"] = 1.87;
+ glx_map["C"] = 1.76;
+ glx_map["O"] = 1.40;
+ glx_map["CB"] = 1.87;
+ glx_map["CG"] = 1.76;
+ glx_map["CD"] = 1.87;
+ glx_map["AE1"] = 1.50;
+ glx_map["AE2"] = 1.50;
+
+ ace_map["C"] = 1.76;
+ ace_map["O"] = 1.40;
+ ace_map["CH3"] = 1.87;
+
+ __a_map["P"] = 1.90;
+ __a_map["O1P"] = 1.40;
+ __a_map["O2P"] = 1.40;
+ __a_map["O5*"] = 1.40;
+ __a_map["C5*"] = 1.80;
+ __a_map["C4*"] = 1.80;
+ __a_map["O4*"] = 1.40;
+ __a_map["C3*"] = 1.80;
+ __a_map["O3*"] = 1.40;
+ __a_map["C2*"] = 1.80;
+ __a_map["C1*"] = 1.80;
+ __a_map["N9"] = 1.60;
+ __a_map["C8"] = 1.80;
+ __a_map["N7"] = 1.60;
+ __a_map["C5"] = 1.80;
+ __a_map["C6"] = 1.80;
+ __a_map["N6"] = 1.60;
+ __a_map["N1"] = 1.60;
+ __a_map["C2"] = 1.80;
+ __a_map["N3"] = 1.60;
+ __a_map["C4"] = 1.80;
+
+ __c_map["P"] = 1.90;
+ __c_map["O1P"] = 1.40;
+ __c_map["O2P"] = 1.40;
+ __c_map["O5*"] = 1.40;
+ __c_map["C5*"] = 1.80;
+ __c_map["C4*"] = 1.80;
+ __c_map["O4*"] = 1.40;
+ __c_map["C3*"] = 1.80;
+ __c_map["O3*"] = 1.40;
+ __c_map["C2*"] = 1.80;
+ __c_map["C1*"] = 1.80;
+ __c_map["N1"] = 1.60;
+ __c_map["C2"] = 1.80;
+ __c_map["O2"] = 1.40;
+ __c_map["N3"] = 1.60;
+ __c_map["C4"] = 1.80;
+ __c_map["N4"] = 1.60;
+ __c_map["C5"] = 1.80;
+ __c_map["C6"] = 1.80;
+
+ __g_map["P"] = 1.90;
+ __g_map["O1P"] = 1.40;
+ __g_map["O2P"] = 1.40;
+ __g_map["O5*"] = 1.40;
+ __g_map["C5*"] = 1.80;
+ __g_map["C4*"] = 1.80;
+ __g_map["O4*"] = 1.40;
+ __g_map["C3*"] = 1.80;
+ __g_map["O3*"] = 1.40;
+ __g_map["C2*"] = 1.80;
+ __g_map["C1*"] = 1.80;
+ __g_map["N9"] = 1.60;
+ __g_map["C8"] = 1.80;
+ __g_map["N7"] = 1.60;
+ __g_map["C5"] = 1.80;
+ __g_map["C6"] = 1.80;
+ __g_map["O6"] = 1.40;
+ __g_map["N1"] = 1.60;
+ __g_map["C2"] = 1.80;
+ __g_map["N2"] = 1.60;
+ __g_map["N3"] = 1.60;
+ __g_map["C4"] = 1.80;
+
+ __t_map["P"] = 1.90;
+ __t_map["O1P"] = 1.40;
+ __t_map["O2P"] = 1.40;
+ __t_map["O5*"] = 1.40;
+ __t_map["C5*"] = 1.80;
+ __t_map["C4*"] = 1.80;
+ __t_map["O4*"] = 1.40;
+ __t_map["C3*"] = 1.80;
+ __t_map["O3*"] = 1.40;
+ __t_map["C2*"] = 1.80;
+ __t_map["C1*"] = 1.80;
+ __t_map["N1"] = 1.60;
+ __t_map["C2"] = 1.80;
+ __t_map["O2"] = 1.40;
+ __t_map["N3"] = 1.60;
+ __t_map["C4"] = 1.80;
+ __t_map["O4"] = 1.40;
+ __t_map["C5"] = 1.80;
+ __t_map["C5M"] = 1.80;
+ __t_map["C6"] = 1.80;
+
+ __u_map["P"] = 1.90;
+ __u_map["O1P"] = 1.40;
+ __u_map["O2P"] = 1.40;
+ __u_map["O5*"] = 1.40;
+ __u_map["C5*"] = 1.80;
+ __u_map["C4*"] = 1.80;
+ __u_map["O4*"] = 1.40;
+ __u_map["C3*"] = 1.80;
+ __u_map["O3*"] = 1.40;
+ __u_map["C2*"] = 1.80;
+ __u_map["O2*"] = 1.40;
+ __u_map["C1*"] = 1.80;
+ __u_map["N1"] = 1.60;
+ __u_map["C2"] = 1.80;
+ __u_map["O2"] = 1.40;
+ __u_map["N3"] = 1.60;
+ __u_map["C4"] = 1.80;
+ __u_map["O4"] = 1.40;
+ __u_map["C5"] = 1.80;
+ __u_map["C6"] = 1.80;
+
+ twomg_map["P"] = 1.90;
+ twomg_map["O1P"] = 1.40;
+ twomg_map["O2P"] = 1.40;
+ twomg_map["O5*"] = 1.40;
+ twomg_map["C5*"] = 1.80;
+ twomg_map["C4*"] = 1.80;
+ twomg_map["O4*"] = 1.40;
+ twomg_map["C3*"] = 1.80;
+ twomg_map["O3*"] = 1.40;
+ twomg_map["C2*"] = 1.80;
+ twomg_map["O2*"] = 1.40;
+ twomg_map["C1*"] = 1.80;
+ twomg_map["N9"] = 1.60;
+ twomg_map["C8"] = 1.80;
+ twomg_map["N7"] = 1.60;
+ twomg_map["C5"] = 1.80;
+ twomg_map["C6"] = 1.80;
+ twomg_map["O6"] = 1.40;
+ twomg_map["N1"] = 1.60;
+ twomg_map["C2"] = 1.80;
+ twomg_map["N2"] = 1.60;
+ twomg_map["C2A"] = 1.80;
+ twomg_map["N3"] = 1.60;
+ twomg_map["C4"] = 1.80;
+
+ h2u_map["P"] = 1.90;
+ h2u_map["O1P"] = 1.40;
+ h2u_map["O2P"] = 1.40;
+ h2u_map["O5*"] = 1.40;
+ h2u_map["C5*"] = 1.80;
+ h2u_map["C4*"] = 1.80;
+ h2u_map["O4*"] = 1.40;
+ h2u_map["C3*"] = 1.80;
+ h2u_map["O3*"] = 1.40;
+ h2u_map["C2*"] = 1.80;
+ h2u_map["O2*"] = 1.40;
+ h2u_map["C1*"] = 1.80;
+ h2u_map["N1"] = 1.60;
+ h2u_map["C2"] = 1.80;
+ h2u_map["O2"] = 1.40;
+ h2u_map["N3"] = 1.60;
+ h2u_map["C4"] = 1.80;
+ h2u_map["O4"] = 1.40;
+ h2u_map["C5"] = 1.80;
+ h2u_map["C6"] = 1.80;
+
+ hem_map["FE"] = 1.47;
+ hem_map["CHA"] = 2.00;
+ hem_map["CHB"] = 2.00;
+ hem_map["CHC"] = 2.00;
+ hem_map["CHD"] = 2.00;
+ hem_map["N A"] = 1.55;
+ hem_map["C1A"] = 1.78;
+ hem_map["C2A"] = 1.78;
+ hem_map["C3A"] = 1.78;
+ hem_map["C4A"] = 1.78;
+ hem_map["CMA"] = 1.90;
+ hem_map["CAA"] = 1.90;
+ hem_map["CBA"] = 1.90;
+ hem_map["CGA"] = 1.90;
+ hem_map["N B"] = 1.55;
+ hem_map["C1B"] = 1.78;
+ hem_map["C2B"] = 1.78;
+ hem_map["C3B"] = 1.78;
+ hem_map["C4B"] = 1.78;
+ hem_map["CMB"] = 1.90;
+ hem_map["CAB"] = 1.90;
+ hem_map["CBB"] = 1.90;
+ hem_map["N C"] = 1.55;
+ hem_map["C1C"] = 1.78;
+ hem_map["C2C"] = 1.78;
+ hem_map["C3C"] = 1.78;
+ hem_map["C4C"] = 1.78;
+ hem_map["CMC"] = 1.90;
+ hem_map["CAC"] = 1.90;
+ hem_map["CBC"] = 1.90;
+ hem_map["N D"] = 1.55;
+ hem_map["C1D"] = 1.78;
+ hem_map["C2D"] = 1.78;
+ hem_map["C3D"] = 1.78;
+ hem_map["C4D"] = 1.78;
+ hem_map["CMD"] = 1.90;
+ hem_map["CAD"] = 1.90;
+ hem_map["CBD"] = 1.90;
+ hem_map["CGD"] = 1.90;
+ hem_map["O1A"] = 1.35;
+ hem_map["O2A"] = 1.35;
+ hem_map["O1D"] = 1.35;
+ hem_map["O2D"] = 1.35;
+
+ hoh_map["O"] = 1.40;
+
+
+
+
+
+
+
+
vdw_radii_["ALA"] = ala_map;
vdw_radii_["ARG"] = arg_map;
@@ -886,6 +1128,18 @@ NACCESSParam::NACCESSParam() {
vdw_radii_["TRP"] = trp_map;
vdw_radii_["TYR"] = tyr_map;
vdw_radii_["VAL"] = val_map;
+ vdw_radii_["ASX"] = asx_map;
+ vdw_radii_["GLX"] = glx_map;
+ vdw_radii_["ACE"] = ace_map;
+ vdw_radii_["__A"] = __a_map;
+ vdw_radii_["__C"] = __c_map;
+ vdw_radii_["__G"] = __g_map;
+ vdw_radii_["__T"] = __t_map;
+ vdw_radii_["__U"] = __u_map;
+ vdw_radii_["2MG"] = twomg_map;
+ vdw_radii_["H2U"] = h2u_map;
+ vdw_radii_["HEM"] = hem_map;
+ vdw_radii_["HOH"] = hoh_map;
accessibilities_["ALA"] = 107.95;
accessibilities_["CYS"] = 134.28;
@@ -910,7 +1164,7 @@ NACCESSParam::NACCESSParam() {
}
-Real NACCESSParam::GuessRadius(const String& ele) const{
+Real AccessibilityParam::GuessRadius(const String& ele) const{
if(ele == "C") return 1.80;
if(ele == "N") return 1.60;
if(ele == "S") return 1.85;
@@ -927,7 +1181,7 @@ Real NACCESSParam::GuessRadius(const String& ele) const{
}
-Real NACCESSParam::GetVdWRadius(const String& rname, const String& aname,
+Real AccessibilityParam::GetVdWRadius(const String& rname, const String& aname,
const String& ele) const{
std::map<String, std::map<String, Real> >::const_iterator res_map_it =
vdw_radii_.find(rname);
@@ -940,7 +1194,7 @@ Real NACCESSParam::GetVdWRadius(const String& rname, const String& aname,
}
-Real NACCESSParam::GetResidueAccessibility(const String& rname) const{
+Real AccessibilityParam::GetResidueAccessibility(const String& rname) const{
std::map<String, Real>::const_iterator it = accessibilities_.find(rname);
if(it != accessibilities_.end()) return it->second;
else return 0.0;
diff --git a/modules/mol/alg/src/accessibility.hh b/modules/mol/alg/src/accessibility.hh
index e880ab522..cd0a57638 100644
--- a/modules/mol/alg/src/accessibility.hh
+++ b/modules/mol/alg/src/accessibility.hh
@@ -26,12 +26,12 @@
namespace ost { namespace mol { namespace alg {
-class NACCESSParam {
+class AccessibilityParam {
public:
// Singleton access to one constant instance
- static const NACCESSParam& GetInstance() {
- static NACCESSParam instance;
+ static const AccessibilityParam& GetInstance() {
+ static AccessibilityParam instance;
return instance;
}
// Data access
@@ -46,7 +46,7 @@ public:
private:
// construction only inside here
- NACCESSParam();
+ AccessibilityParam();
std::map<String, std::map<String, Real> > vdw_radii_;
std::map<String, Real> accessibilities_;
--
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