Skip to content

improve bond detection between hydrogens, sulfurs, atoms with alt codes and prevent bonds between different models #2

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
speleo3 wants to merge 2 commits into
base: master
Choose a base branch
from
Open

improve bond detection between hydrogens, sulfurs, atoms with alt codes and prevent bonds between different models #2

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
ed54754
new "test_bonded" function for bonddistance=0.0
speleo3 Oct 17, 2015
72997d9
Merge remote-tracking branch 'upstream/master'
speleo3 Nov 4, 2017
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
52 changes: 44 additions & 8 deletions code/graphics.c
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -307,6 +307,46 @@ depthcue (double depth, state *st)
}


/*------------------------------------------------------------*/
static boolean
test_bonded (const at3d * at1, const at3d * at2, double bonddistance)
{
double dist = v3_distance (&(at1->xyz), &(at2->xyz));

// identical position
if (dist < 0.001)
return FALSE;

// use bonddistance parameter if not zero
if (bonddistance > 0.001)
return dist < bonddistance;

// no bonds between different alt locations
if (at1->altloc > ' ' &&
at2->altloc > ' ' &&
at1->altloc != at2->altloc)
return FALSE;

// no bonds between different models
if (at1->res->mol->model != at2->res->mol->model)
return FALSE;

// take radii into account
dist -= (at1->radius + at2->radius) / 2.0;

// hydrogen cutoff
if (at1->element == 1 || at2->element == 1)
return dist < 0.15;

// sulfur cutoff
if (at1->element == 16 || at2->element == 16)
return dist < 0.55;

// generic cutoff
return dist < 0.35;
}


/*------------------------------------------------------------*/
void
ball_and_stick (int single_selection)
Expand Down Expand Up @@ -378,8 +418,7 @@ ball_and_stick (int single_selection)

v2 = &(atoms2[slot2]->xyz);

dist = v3_distance (v1, v2);
if ((dist > current_state->bonddistance) || (dist < 0.001)) continue;
if (!test_bonded (atoms1[slot1], atoms2[slot2], current_state->bonddistance)) continue;

if (colour_unequal (&(atoms1[slot1]->colour),
&(atoms2[slot2]->colour))) {
Expand Down Expand Up @@ -415,8 +454,7 @@ ball_and_stick (int single_selection)

v2 = &(atoms2[slot2]->xyz);

dist = v3_distance (v1, v2);
if ((dist > current_state->bonddistance) || (dist < 0.001)) continue;
if (!test_bonded (atoms1[slot1], atoms2[slot2], current_state->bonddistance)) continue;

output_stick (v1, v2,
0.25 * atoms1[slot1]->radius,
Expand Down Expand Up @@ -507,8 +545,7 @@ bonds (int single_selection)
v2 = &(atoms2[slot2]->xyz);
if (v2 == v1) continue;

dist = v3_distance (v1, v2);
if ((dist > current_state->bonddistance) || (dist < 0.001)) continue;
if (!test_bonded (atoms1[slot1], atoms2[slot2], current_state->bonddistance)) continue;

if (colour_unequal (col1, &(atoms2[slot2]->colour))) {
v3_middle (&middle, v1, v2);
Expand Down Expand Up @@ -556,8 +593,7 @@ bonds (int single_selection)
v2 = &(atoms2[slot2]->xyz);
if (v2 == v1) continue;

dist = v3_distance (v1, v2);
if ((dist > current_state->bonddistance) || (dist < 0.001)) continue;
if (!test_bonded (atoms1[slot1], atoms2[slot2], current_state->bonddistance)) continue;

ls = line_segment_next();
ls->p = *v1;
Expand Down
6 changes: 1 addition & 5 deletions code/state.c
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -300,11 +300,7 @@ set_bonddistance (void)
{
assert (dstack_size == 1);

if (dstack[0] <= 0.0) {
yyerror ("invalid bonddistance value");
} else {
current_state->bonddistance = dstack[0];
}
current_state->bonddistance = dstack[0];
clear_dstack();
}

Expand Down
6 changes: 6 additions & 0 deletions docs/state.html
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -244,6 +244,12 @@ <h3>
<a href="atom_commands.html#ball-and-stick">sticks</a>
drawn between them, otherwise not, when selected in the respective
command. The unit is &Aring;ngstr&ouml;m.

<br>
<br><b>New (Oct 2015):</b> A value of 0.0 will detect bonds based
on atom radii overlap. It will also prevent bonding between different
alt locations and different models.

<p>
<b>Default:</b> 1.9
<br>
Expand Down