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/*
* This file contains source code for the PyMOL computer program
* Copyright (c) Schrodinger, LLC.
*/
#include <algorithm>
#include "os_std.h"
#include "SideChainHelper.h"
#include "Lex.h"
/**
* Mark side_chain_helper atoms that are bonded to atoms without a visible
* cartoon or ribbon
*/
void SideChainHelperMarkNonCartoonBonded(bool * marked,
const ObjectMolecule * obj,
const CoordSet * cs,
bool cartoon_side_chain_helper,
bool ribbon_side_chain_helper)
{
auto G = obj->G;
auto b = obj->Bond.data();
auto b_end = b + obj->NBond;
for(; b < b_end; ++b) {
auto b1 = b->index[0];
auto b2 = b->index[1];
auto a1 = cs->atmToIdx(b1);
auto a2 = cs->atmToIdx(b2);
if (a1 < 0 || a2 < 0)
continue;
auto ati1 = obj->AtomInfo + b1;
auto ati2 = obj->AtomInfo + b2;
if (!(ati1->flags & ati2->flags & cAtomFlag_polymer))
continue;
if (!marked[b1]) {
marked[b1] =
((ati1->visRep & cRepCartoonBit) && !(ati2->visRep & cRepCartoonBit) &&
AtomSettingGetWD(G, ati1, cSetting_cartoon_side_chain_helper, cartoon_side_chain_helper)) ||
((ati1->visRep & cRepRibbonBit) && !(ati2->visRep & cRepRibbonBit) &&
AtomSettingGetWD(G, ati1, cSetting_ribbon_side_chain_helper, ribbon_side_chain_helper));
}
if (!marked[b2]) {
marked[b2] =
((ati2->visRep & cRepCartoonBit) && !(ati1->visRep & cRepCartoonBit) &&
AtomSettingGetWD(G, ati2, cSetting_cartoon_side_chain_helper, cartoon_side_chain_helper)) ||
((ati2->visRep & cRepRibbonBit) && !(ati1->visRep & cRepRibbonBit) &&
AtomSettingGetWD(G, ati2, cSetting_ribbon_side_chain_helper, ribbon_side_chain_helper));
}
}
}
// matches c0[35][*']
inline bool is_35prime(const char * p, char c0) {
return p[0] == c0 &&
(p[1] == '3' || p[1] == '5') &&
(p[2] == '*' || p[2] == '\'') && !p[3];
}
// matches C[45][*']
inline bool is_C45prime(const char * p) {
return p[0] == 'C' &&
(p[1] == '4' || p[1] == '5') &&
(p[2] == '*' || p[2] == '\'') && !p[3];
}
/**
* Return true if bond is hidden with side_chain_helper.
* c1/c2 are in-out variables for color transfer.
*/
bool SideChainHelperFilterBond(PyMOLGlobals * G,
const bool *marked,
const AtomInfoType *ati1,
const AtomInfoType *ati2,
int b1, int b2, int na_mode, int *c1, int *c2)
{
if (ati1->protons == cAN_H ||
ati2->protons == cAN_N ||
ati2->protons == cAN_O ||
(ati1->protons == cAN_C && ati2->protons == cAN_C && ati2->name == G->lex_const.CA)
) {
std::swap(ati1, ati2);
std::swap(b1, b2);
std::swap(c1, c2);
}
const char *name1 = LexStr(G, ati1->name);
int prot1 = ati1->protons;
const char *name2 = LexStr(G, ati2->name);
int prot2 = ati2->protons;
switch (prot1) {
case cAN_C:
if (ati1->name == G->lex_const.CA) { /* CA */
if(prot2 == cAN_C) {
if(ati2->name == G->lex_const.CB)
*c1 = *c2; /* CA-CB */
else if(ati2->name == G->lex_const.C && (!marked[b2]))
return true; /* suppress CA-C */
} else if(prot2 == cAN_H)
return true; /* suppress all CA-hydrogens */
} else if((na_mode == 1) && (prot2 == cAN_C)) {
if (is_C45prime(name2) && is_C45prime(name1))
/* supress C[45][*']-C[45][*'] */
return true;
}
break;
case cAN_N:
if (ati1->name == G->lex_const.N) { /* N */
if(prot2 == cAN_C) {
if (ati2->name == G->lex_const.CD)
*c1 = *c2; /* N->CD in PRO */
else if (ati2->name == G->lex_const.CA
&& (!marked[b1])) {
if(ati2->resn != G->lex_const.PRO)
return true; /* suppress N-CA, except in pro */
*c1 = *c2;
} else if (ati2->name == G->lex_const.C && (!marked[b1]))
return true; /* suppress N-C */
} else if(prot2 == cAN_H)
return true; /* suppress all N-hydrogens */
}
break;
case cAN_O:
if(prot2 == cAN_C) {
if ( ati2->name == G->lex_const.C &&
(ati1->name == G->lex_const.O ||
ati1->name == G->lex_const.OXT)
&& (!marked[b2]))
return true; /* suppress C-O,OXT */
else if(na_mode == 1) {
if (is_35prime(name2, 'C') && is_35prime(name1, 'O'))
/* supress O[35][*']-C[35][*'] */
return true;
}
} else if(prot2 == cAN_P) {
if (ati2->name == G->lex_const.P &&
strlen(name1) == 3 && name1[0] == 'O' && (
(name1[2] == 'P' && name1[1] >= '1' && name1[1] <= '3') ||
(name1[1] == 'P' && name1[2] >= '1' && name1[2] <= '3')))
/* suppress P-O([123]P|P[123]) */
return true;
else if(na_mode == 1) {
if (ati2->name == G->lex_const.P && is_35prime(name1, 'O'))
/* supress P-O[35][*'] */
return true;
}
}
break;
}
return false;
}
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