"Fossies" - the Fresh Open Source Software Archive  

Source code changes of the file "layer2/ObjectMolecule2.cpp" between
pymol-v1.8.6.0.tar.bz2 and pymol-v2.1.0.tar.bz2

About: PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source version.

ObjectMolecule2.cpp  (pymol-v1.8.6.0.tar.bz2)	:	ObjectMolecule2.cpp  (pymol-v2.1.0.tar.bz2)
skipping to change at line 2801		skipping to change at line 2801
p = ncopy(cc, p, 2);		p = ncopy(cc, p, 2);
if(!sscanf(cc, "%s", ai->elem))		if(!sscanf(cc, "%s", ai->elem))
ai->elem[0] = 0;		ai->elem[0] = 0;
else if(!((((ai->elem[0] >= 'a') && (ai->elem[0] <= 'z')) || /* don't get confused by PDB misuse */		else if(!((((ai->elem[0] >= 'a') && (ai->elem[0] <= 'z')) || /* don't get confused by PDB misuse */
((ai->elem[0] >= 'A') && (ai->elem[0] <= 'Z'))) &&		((ai->elem[0] >= 'A') && (ai->elem[0] <= 'Z'))) &&
(((ai->elem[1] == 0) ||		(((ai->elem[1] == 0) ||
((ai->elem[1] >= 'a') && (ai->elem[1] <= 'z')) ||		((ai->elem[1] >= 'a') && (ai->elem[1] <= 'z')) ||
((ai->elem[1] >= 'A') && (ai->elem[1] <= 'Z'))))))		((ai->elem[1] >= 'A') && (ai->elem[1] <= 'Z'))))))
ai->elem[0] = 0;		ai->elem[0] = 0;
		else if (info->variant == PDB_VARIANT_PDBQT) {
		if (strcmp(ai->elem, "A") == 0) {
		// aromatic carbon
		ai->elem[0] = 'C';
		} else if (isupper(ai->elem[1])) {
		// h-bond donor or acceptor
		ai->elem[1] = 0;
		}
		}
if(!ai->elem[0]) {		if(!ai->elem[0]) {
if(((literal_name[0] == ' ') || ((literal_name[0] >= '0') && (literal_ name[0] <= '9'))) && (literal_name[1] >= 'A') && (literal_name[1] <= 'Z')) { /* infer element from name column */		if(((literal_name[0] == ' ') || ((literal_name[0] >= '0') && (literal_ name[0] <= '9'))) && (literal_name[1] >= 'A') && (literal_name[1] <= 'Z')) { /* infer element from name column */
ai->elem[0] = literal_name[1];		ai->elem[0] = literal_name[1];
ai->elem[1] = 0;		ai->elem[1] = 0;
} else if(((literal_name[0] >= 'A') && (literal_name[0] <= 'Z')) && (( (literal_name[1] >= 'A') && (literal_name[1] <= 'Z')) || ((literal_name[1] >= 'a ') && (literal_name[1] <= 'z')))) { /* infer element from name column */		} else if(((literal_name[0] >= 'A') && (literal_name[0] <= 'Z')) && (( (literal_name[1] >= 'A') && (literal_name[1] <= 'Z')) || ((literal_name[1] >= 'a ') && (literal_name[1] <= 'z')))) { /* infer element from name column */
ai->elem[0] = literal_name[0];		ai->elem[0] = literal_name[0];
ai->elem[2] = 0;		ai->elem[2] = 0;
if((literal_name[1] >= 'A') && (literal_name[1] <= 'Z')) { /* secon d letter is capitalized */		if((literal_name[1] >= 'A') && (literal_name[1] <= 'Z')) { /* secon d letter is capitalized */
if(bogus_name_alignment) {		if(bogus_name_alignment) {
skipping to change at line 3875		skipping to change at line 3884
PyList_SetItem(result, 8, PyInt_FromLong(I->DiscreteFlag));		PyList_SetItem(result, 8, PyInt_FromLong(I->DiscreteFlag));
PyList_SetItem(result, 9, PyInt_FromLong(I->DiscreteFlag ? I->NAtom : 0 /* NDi screte */));		PyList_SetItem(result, 9, PyInt_FromLong(I->DiscreteFlag ? I->NAtom : 0 /* NDi screte */));
PyList_SetItem(result, 10, SymmetryAsPyList(I->Symmetry));		PyList_SetItem(result, 10, SymmetryAsPyList(I->Symmetry));
PyList_SetItem(result, 11, PyInt_FromLong(I->CurCSet));		PyList_SetItem(result, 11, PyInt_FromLong(I->CurCSet));
PyList_SetItem(result, 12, PyInt_FromLong(I->BondCounter));		PyList_SetItem(result, 12, PyInt_FromLong(I->BondCounter));
PyList_SetItem(result, 13, PyInt_FromLong(I->AtomCounter));		PyList_SetItem(result, 13, PyInt_FromLong(I->AtomCounter));
float pse_export_version = SettingGetGlobal_f(I->Obj.G, cSetting_pse_export_ve rsion);		float pse_export_version = SettingGetGlobal_f(I->Obj.G, cSetting_pse_export_ve rsion);
if(I->DiscreteFlag		if(I->DiscreteFlag
&& !SettingGetGlobal_b(I->Obj.G, cSetting_pse_binary_dump)		&& (pse_export_version || !SettingGetGlobal_b(I->Obj.G, cSetting_pse_binar y_dump))
&& pse_export_version < 1.7699) {		&& pse_export_version < 1.7699) {
int *dcs;		int *dcs;
int a;		int a;
CoordSet *cs;		CoordSet *cs;
/* get coordinate set indices */		/* get coordinate set indices */
for(a = 0; a < I->NCSet; a++) {		for(a = 0; a < I->NCSet; a++) {
cs = I->CSet[a];		cs = I->CSet[a];
if(cs) {		if(cs) {
skipping to change at line 3912		skipping to change at line 3921
FreeP(dcs);		FreeP(dcs);
} else {		} else {
PyList_SetItem(result, 14, PConvAutoNone(NULL));		PyList_SetItem(result, 14, PConvAutoNone(NULL));
PyList_SetItem(result, 15, PConvAutoNone(NULL));		PyList_SetItem(result, 15, PConvAutoNone(NULL));
}		}
return (PConvAutoNone(result));		return (PConvAutoNone(result));
}		}
/*========================================================================*/		/*========================================================================*/
		static
		float connect_cutoff_adjustment(
		const AtomInfoType * ai1,
		const AtomInfoType * ai2)
		{
		if (ai1->isHydrogen() || ai2->isHydrogen())
		return -0.2f;
		if (ai1->protons == cAN_S || ai2->protons == cAN_S)
		return 0.2f;
		return 0.f;
		}
		/*
		* True if two atoms should be bonded
		*/
		static
		bool is_distance_bonded(
		PyMOLGlobals * G,
		const CoordSet * cs,
		const AtomInfoType * ai1,
		const AtomInfoType * ai2,
		const float * v1,
		const float * v2,
		float cutoff,
		int connect_mode,
		int discrete_chains,
		bool connect_bonded,
		bool unbond_cations)
		{
		auto dst = (float) diff3f(v1, v2);
		dst -= (ai1->vdw + ai2->vdw) / 2;
		cutoff += connect_cutoff_adjustment(ai1, ai2);
		if (dst > cutoff)
		return false;
		if (ai1->isHydrogen() && ai2->isHydrogen())
		return false;
		if (discrete_chains > 0 && ai1->chain != ai2->chain)
		return false;
		if (!connect_bonded && ai1->bonded && ai2->bonded)
		return false;
		bool water_flag = (
		AtomInfoKnownWaterResName(G, LexStr(G, ai1->resn)) ||
		AtomInfoKnownWaterResName(G, LexStr(G, ai2->resn)));
		if (connect_mode != 3 &&
		cs->TmpBond && /* connectivity information present in file */
		ai1->hetatm &&
		ai2->hetatm &&
		!water_flag &&
		!(AtomInfoKnownPolymerResName(LexStr(G, ai1->resn)) &&
		AtomInfoKnownPolymerResName(LexStr(G, ai2->resn))))
		return false;
		// don't connect water atoms in different residues
		if (water_flag && !AtomInfoSameResidue(G, ai1, ai2))
		return false;
		// don't connect atoms with different, non-NULL alternate conformations
		if (ai1->alt[0] != ai2->alt[0] && ai1->alt[0] && ai2->alt[0])
		return false;
		// if either is a cation, unbond is user wants
		if (unbond_cations &&
		(AtomInfoIsFreeCation(G, ai1) ||
		AtomInfoIsFreeCation(G, ai2)))
		return false;
		return true;
		}
		/*========================================================================*/
int ObjectMoleculeConnect(ObjectMolecule * I, int *nbond, BondType ** bond, Atom InfoType * ai,		int ObjectMoleculeConnect(ObjectMolecule * I, int *nbond, BondType ** bond, Atom InfoType * ai,
struct CoordSet *cs, int bondSearchMode,		struct CoordSet *cs, int bondSearchMode,
int connectModeOverride)		int connectModeOverride)
{		{
#define cMULT 1		#define cMULT 1
PyMOLGlobals *G = I->Obj.G;		PyMOLGlobals *G = I->Obj.G;
int a, b, c, d, e, f, i, j;		int a, b, c, d, e, f, i, j;
int a1, a2;		int a1, a2;
float *v1, *v2, dst;		float *v1, *v2, dst;
int maxBond;		int maxBond;
MapType *map;		MapType *map;
int nBond;		int nBond;
BondType *ii1, *ii2;		BondType *ii1, *ii2;
int flag;		int flag;
int order;		int order;
AtomInfoType *ai1, *ai2;		AtomInfoType *ai1, *ai2;
/* Sulfur cutoff */		/* Sulfur cutoff */
float cutoff_s;		float cutoff_s;
/* Hydrogen cutoff */
float cutoff_h;
float cutoff_v;		float cutoff_v;
float cutoff;
float max_cutoff;		float max_cutoff;
int water_flag;
int repeat = true;		int repeat = true;
int discrete_chains = SettingGetGlobal_i(G, cSetting_pdb_discrete_chains);		int discrete_chains = SettingGetGlobal_i(G, cSetting_pdb_discrete_chains);
int connect_bonded = SettingGetGlobal_b(G, cSetting_connect_bonded);		int connect_bonded = SettingGetGlobal_b(G, cSetting_connect_bonded);
int connect_mode = SettingGetGlobal_i(G, cSetting_connect_mode);		int connect_mode = SettingGetGlobal_i(G, cSetting_connect_mode);
int unbond_cations = SettingGetGlobal_i(G, cSetting_pdb_unbond_cations);		int unbond_cations = SettingGetGlobal_i(G, cSetting_pdb_unbond_cations);
int ok = true;		int ok = true;
cutoff_v = SettingGetGlobal_f(G, cSetting_connect_cutoff);		cutoff_v = SettingGetGlobal_f(G, cSetting_connect_cutoff);
cutoff_s = cutoff_v + 0.2F;		cutoff_s = cutoff_v + 0.2F;
cutoff_h = cutoff_v - 0.2F;
max_cutoff = cutoff_s;		max_cutoff = cutoff_s;
if(connectModeOverride >= 0)		if(connectModeOverride >= 0)
connect_mode = connectModeOverride;		connect_mode = connectModeOverride;
if(connect_mode == 2) { /* force use of distance-based connectivity,		if(connect_mode == 2) { /* force use of distance-based connectivity,
ignoring that provided with file */		ignoring that provided with file */
bondSearchMode = true;		bondSearchMode = true;
cs->NTmpBond = 0;		cs->NTmpBond = 0;
VLAFreeP(cs->TmpBond);		VLAFreeP(cs->TmpBond);
skipping to change at line 4035		skipping to change at line 4119
for(d = a - 1; ok && d <= a + 1; d++) {		for(d = a - 1; ok && d <= a + 1; d++) {
int *j_ptr1 = map->Head + d * dim12 + (b - 1) * dim2;		int *j_ptr1 = map->Head + d * dim12 + (b - 1) * dim2;
/* e = [b-1, b, b+1] */		/* e = [b-1, b, b+1] */
for(e = b - 1; ok && e <= b + 1; e++) {		for(e = b - 1; ok && e <= b + 1; e++) {
int *j_ptr2 = j_ptr1 + c - 1;		int *j_ptr2 = j_ptr1 + c - 1;
j_ptr1 += dim2;		j_ptr1 += dim2;
/* f = [c-1, c, c+1] */		/* f = [c-1, c, c+1] */
for(f = c - 1; ok && f <= c + 1; f++) {		for(f = c - 1; ok && f <= c + 1; f++) {
j = *(j_ptr2++); /* *MapFirst(map,d,e,f)); */		j = *(j_ptr2++); /* *MapFirst(map,d,e,f)); */
while(ok && j >= 0) {		while(ok && j >= 0) {
if(i < j) {		if(i < j) {
/* position in space for atom 2 */		/* position in space for atom 2 */
v2 = cs->Coord + (3 * j);		v2 = cs->Coord + (3 * j);
dst = (float) diff3f(v1, v2);
a2 = cs->IdxToAtm[j];		a2 = cs->IdxToAtm[j];
ai2 = ai + a2;		ai2 = ai + a2;
dst -= ((ai1->vdw + ai2->vdw) / 2);		flag = is_distance_bonded(G, cs, ai1, ai2, v1, v2,
		cutoff_v, connect_mode, discrete_chains,
/* quick hack for water detection.		connect_bonded, unbond_cations);
they don't usually don't have CONECT records
and may not be HETATMs though they are supposed to be
...
This checks whether either atom in the bond
is a known wter.
*/
water_flag = false;
if(AtomInfoKnownWaterResName(G, LexStr(G, ai1->resn)))
water_flag = true;
else if(AtomInfoKnownWaterResName(G, LexStr(G, ai2->resn
)))
water_flag = true;
/* workaround for hydrogens and sulfurs... */
if(ai1->isHydrogen() || ai2->isHydrogen())		{
cutoff = cutoff_h;
else if(((ai1->elem[0] == 'S') && (!ai1->elem[1])) ||
((ai2->elem[0] == 'S') && (!ai2->elem[1])))
cutoff = cutoff_s;
else
cutoff = cutoff_v;
/* here's our complex atomic connectivity allow / disallo
w */
if((dst <= cutoff) && /* too close to be non-covalent, A
ND*/
(!(ai1->isHydrogen() && ai2->isHydrogen())) && /* not
both hydrogen (what about H2?), AND */
(water_flag || /* known to be a water */
(!cs->TmpBond) || /* or no connectivity information
present in file */
((!(ai1->hetatm && ai2->hetatm) || /* or not both PD
B HETATMS */
(connect_mode == 3))) ||
((ai1->hetatm && ai2->hetatm) && /* both hetatms, an
d both recognized polymer residue? */
AtomInfoKnownPolymerResName(LexStr(G, ai1->resn)) &
& /* (new PDB rule allows these to be HETATMs */
AtomInfoKnownPolymerResName(LexStr(G, ai2->resn)))
) && /* or we're no excluding HETATM -> HETATM bonds
, AND*/
((discrete_chains < 1) || /* we allow intra-chain bon
ds */
(ai1->chain == ai2->chain)) && /* or atoms are in th
e same chain, AND */
(connect_bonded || /* we're allowing explicitly bonde
d atoms to be auto-connected */
(!(ai1->bonded && ai2->bonded))) /* or neither atom
was previously bonded */
) {
/* WE THINK WE HAVE A BOND */
flag = true;
/* unbond edge cases */
/* atoms in same water molecule or different? */
if(water_flag)
if(!AtomInfoSameResidue(G, ai1, ai2)) /* don't conne
ct water atoms in different residues */
flag = false;
/* atoms have same alt. conformations? from same molecu
le? */
if(flag) {
if(ai1->alt[0] != ai2->alt[0]) { /* handle altern
ate conformers */
if(ai1->alt[0] && ai2->alt[0])
flag = false; /* don't connect atoms with diff
erent, non-NULL
alternate conformations */
} else if(ai1->alt[0] && ai2->alt[0])
if(!AtomInfoSameResidue(G, ai1, ai2))
if(ai1->alt[0] != ai2->alt[0])
flag = false; /* don't connect different, non-
NULL
alt conformations in
different residues */
}
/* do not bond different water molecules, even if their
alt. confs. match */
if(flag) {
if(ai1->alt[0] || ai2->alt[0])
if(water_flag) /* hack to clean up water bonds
*/
if(!AtomInfoSameResidue(G, ai1, ai2))
flag = false;
}
/* if either is a cation, unbond is user wants */
if(flag && unbond_cations) {
if(AtomInfoIsFreeCation(G, ai1))
flag = false;
else if(AtomInfoIsFreeCation(G, ai2))
flag = false;
}
/* we have a bond, now process it */		/* we have a bond, now process it */
if(flag) {		if(flag) {
VLACheck((*bond), BondType, nBond);		VLACheck((*bond), BondType, nBond);
CHECKOK(ok, (*bond));		CHECKOK(ok, (*bond));
if (ok){		if (ok){
(*bond)[nBond].index[0] = a1;		(*bond)[nBond].index[0] = a1;
(*bond)[nBond].index[1] = a2;		(*bond)[nBond].index[1] = a2;
(*bond)[nBond].stereo = 0;		(*bond)[nBond].stereo = 0;
order = 1;		order = 1;
skipping to change at line 4166		skipping to change at line 4162
if(violations > (cs->NIndex >> 3)) {		if(violations > (cs->NIndex >> 3)) {
/* if more than 12% of the structure has excessi ve #'s of bonds... */		/* if more than 12% of the structure has excessi ve #'s of bonds... */
PRINTFB(G, FB_ObjectMolecule, FB_Blather)		PRINTFB(G, FB_ObjectMolecule, FB_Blather)
" ObjectMoleculeConnect: Assuming chains are d iscrete...\n"		" ObjectMoleculeConnect: Assuming chains are d iscrete...\n"
ENDFB(G);		ENDFB(G);
discrete_chains = 1;		discrete_chains = 1;
repeat = true;		repeat = true;
goto do_it_again;		goto do_it_again;
}		}
}		}
/* selenomethionine; double-bond the carbonyl if pres
ent */		if(!ai1->hetatm || ai1->resn == G->lex_const.MSE) {
if(ai1->hetatm) { /* common HETATMs we should
know about... */
if (ai1->resn == G->lex_const.MSE) {
if ((ai1->name == G->lex_const.C && ai2->name ==
G->lex_const.O) ||
(ai1->name == G->lex_const.O && ai2->name ==
G->lex_const.C)) {
/* if carbonyl in same residue, double bond it
*/
if(AtomInfoSameResidue(G, ai1, ai2)) {
order = 2;
}
}
}
} else {
if(AtomInfoSameResidue(I->Obj.G, ai1, ai2)) {		if(AtomInfoSameResidue(I->Obj.G, ai1, ai2)) {
/* hookup standard disconnected PDB residue */		/* hookup standard disconnected PDB residue */
assign_pdb_known_residue(G, ai1, ai2, &order);		assign_pdb_known_residue(G, ai1, ai2, &order);
}		}
}		}
(*bond)[nBond].order = -order; /* store tentati ve valence as negative */		(*bond)[nBond].order = -order; /* store tentati ve valence as negative */
nBond++;		nBond++;
}		}
}		}
}		}
End of changes. 12 change blocks.
136 lines changed or deleted		96 lines changed or added

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