"Fossies" - the Fresh Open Source Software Archive  

Source code changes of the file "contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp" between
pymol-open-source-2.2.0.tar.gz and pymol-open-source-2.3.0.tar.gz

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.

maeffplugin.cpp  (pymol-open-source-2.2.0)	:	maeffplugin.cpp  (pymol-open-source-2.3.0)
skipping to change at line 802		skipping to change at line 802
ival=atoi(value.c_str());		ival=atoi(value.c_str());
}		}
static void get_float(const std::string &value, float &fval) {		static void get_float(const std::string &value, float &fval) {
fval=atof(value.c_str());		fval=atof(value.c_str());
}		}
};		};
#define GET_STR( val_, arr_) do { get_str(val_, arr_, sizeof(arr_)); } while(0)		#define GET_STR( val_, arr_) do { get_str(val_, arr_, sizeof(arr_)); } while(0)
class AtomArray : public Array {		class AtomArray : public Array {
int i_name, i_resname, i_resid, i_x, i_y, i_z, i_vx, i_vy, i_vz,		int i_name, i_resname, i_resid, i_x, i_y, i_z, i_vx, i_vy, i_vz,
		i_inscode,
i_anum, i_chain, i_segid, i_charge;		i_anum, i_chain, i_segid, i_charge;
std::vector<molfile_atom_t> &atoms;		std::vector<molfile_atom_t> &atoms;
std::vector<pos_t> &pos;		std::vector<pos_t> &pos;
std::vector<vel_t> &vel;		std::vector<vel_t> &vel;
int &natoms;		int &natoms;
public:		public:
AtomArray(Handle *h_, int ct)		AtomArray(Handle *h_, int ct)
: Array(h_, ct),		: Array(h_, ct),
i_name(-1), i_resname(-1), i_resid(-1),		i_name(-1), i_resname(-1), i_resid(-1),
i_x(-1), i_y(-1), i_z(-1),		i_x(-1), i_y(-1), i_z(-1),
i_vx(-1), i_vy(-1), i_vz(-1),		i_vx(-1), i_vy(-1), i_vz(-1),
		i_inscode(-1),
i_anum(-1), i_chain(-1), i_segid(-1),		i_anum(-1), i_chain(-1), i_segid(-1),
i_charge(0),		i_charge(0),
atoms( h->ctmap[m_ct].particles ),		atoms( h->ctmap[m_ct].particles ),
pos( h->ctmap[m_ct].position),		pos( h->ctmap[m_ct].position),
vel( h->ctmap[m_ct].velocity),		vel( h->ctmap[m_ct].velocity),
natoms( h->ctmap[m_ct].natoms )		natoms( h->ctmap[m_ct].natoms )
{		{
h->optflags = MOLFILE_NOOPTIONS; // ensure initialization		h->optflags = MOLFILE_NOOPTIONS; // ensure initialization
#if defined(DESRES_CTNUMBER)		#if defined(DESRES_CTNUMBER)
h->optflags = MOLFILE_CTNUMBER;		h->optflags = MOLFILE_CTNUMBER;
skipping to change at line 843		skipping to change at line 845
else if (attr=="m_x_coord") i_x=i;		else if (attr=="m_x_coord") i_x=i;
else if (attr=="m_y_coord") i_y=i;		else if (attr=="m_y_coord") i_y=i;
else if (attr=="m_z_coord") i_z=i;		else if (attr=="m_z_coord") i_z=i;
else if (attr=="ffio_x_vel") i_vx=i;		else if (attr=="ffio_x_vel") i_vx=i;
else if (attr=="ffio_y_vel") i_vy=i;		else if (attr=="ffio_y_vel") i_vy=i;
else if (attr=="ffio_z_vel") i_vz=i;		else if (attr=="ffio_z_vel") i_vz=i;
else if (attr=="m_atomic_number") { i_anum=i; h->optflags |= MOLFILE_AT OMICNUMBER; }		else if (attr=="m_atomic_number") { i_anum=i; h->optflags |= MOLFILE_AT OMICNUMBER; }
else if (attr=="m_chain_name") i_chain=i;		else if (attr=="m_chain_name") i_chain=i;
else if (attr=="m_pdb_segment_name") i_segid=i;		else if (attr=="m_pdb_segment_name") i_segid=i;
else if (attr=="m_formal_charge") { i_charge=i; h->optflags |= MOLFILE_ CHARGE; }		else if (attr=="m_formal_charge") { i_charge=i; h->optflags |= MOLFILE_ CHARGE; }
		else if (attr=="m_insertion_code") { i_inscode=i; }
}		}
}		}
virtual void insert_row(const Row &row) {		virtual void insert_row(const Row &row) {
molfile_atom_t a;		molfile_atom_t a;
memset(&a, 0, sizeof(molfile_atom_t));		memset(&a, 0, sizeof(molfile_atom_t));
if (i_name>=0) GET_STR(row[i_name], a.name);		if (i_name>=0) GET_STR(row[i_name], a.name);
if (i_name>=0) GET_STR(row[i_name], a.type);		if (i_name>=0) GET_STR(row[i_name], a.type);
if (i_resname>=0) GET_STR(row[i_resname], a.resname);		if (i_resname>=0) GET_STR(row[i_resname], a.resname);
if (i_resid>=0) get_int(row[i_resid], a.resid);		if (i_resid>=0) get_int(row[i_resid], a.resid);
if (i_segid>=0) GET_STR(row[i_segid], a.segid);		if (i_segid>=0) GET_STR(row[i_segid], a.segid);
if (i_chain>=0) GET_STR(row[i_chain], a.chain);		if (i_chain>=0) GET_STR(row[i_chain], a.chain);
		if (i_inscode>=0) GET_STR(row[i_inscode], a.insertion);
#if defined(DESRES_CTNUMBER)		#if defined(DESRES_CTNUMBER)
a.ctnumber = m_ct;		a.ctnumber = m_ct;
#endif		#endif
if (i_anum>=0) get_int(row[i_anum], a.atomicnumber);		if (i_anum>=0) get_int(row[i_anum], a.atomicnumber);
// if we didn't get an atom name, try to get one from the atomic number.		// if we didn't get an atom name, try to get one from the atomic number.
bool bad_name=true;		bool bad_name=true;
for (const char *p=a.name; *p; ++p) {		for (const char *p=a.name; *p; ++p) {
if (!isspace(*p)) {		if (!isspace(*p)) {
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