#include <BaseMolecule.h>
Inheritance diagram for BaseMolecule:

Public Methods | |
| float * | radius () |
| float * | mass () |
| float * | charge () |
| float * | beta () |
| float * | occupancy () |
| float * | bondorders () |
| number of electron pairs, also fractional. More... | |
| void | setbondorder (int atom, int bond, float order) |
| float | getbondorder (int atom, int bond) |
| int | has_structure () const |
| has structure information already been loaded for this molecule? More... | |
| void | clear_bonds (void) |
| clear the entire bond list for all atoms. More... | |
| int | count_bonds (void) |
| return the number of unique bonds in the molecule. More... | |
| BaseMolecule (int) | |
| constructor takes molecule ID. More... | |
| virtual | ~BaseMolecule (void) |
| destructor. More... | |
| int | init_atoms (int n) |
| Try to set the number of atoms to n. n must be positive. May be called more than once with the same n. Return success. More... | |
| void | find_bonds_from_timestep () |
| compute molecule's bonds using distance bond search from 1st timestep. More... | |
| void | find_unique_bonds_from_timestep () |
| int | add_atom (char *name, char *type, int atomicnumber, char *resname, int resid, const char *chainid, const char *segname, char *insertion=(char *)"", const char *altloc="") |
| add a new atom; return it's index. More... | |
| int | add_bond (int, int, float, int=ATOMNORMAL) |
| add a new bond from a to b; return total number of bonds added so far. More... | |
| int | add_bond_dupcheck (int, int, float) |
| add a bond after checking for duplicates. More... | |
| void | analyze (void) |
| find higher level constructs given the atom/bond information. More... | |
| int | id (void) const |
| return id number of this molecule. More... | |
| const char * | molname () const |
| return molecule name. More... | |
| MolAtom * | atom (int n) |
| return Nth atom. More... | |
| Residue * | residue (int) |
| return Nth residue. More... | |
| Fragment * | fragment (int) |
| return Nth fragment. More... | |
| Residue * | atom_residue (int) |
| return residue atom is in. More... | |
| Fragment * | atom_fragment (int) |
| return fragment atom is in. More... | |
| void | add_volume_data (const char *name, const float *o, const float *xa, const float *ya, const float *za, int x, int y, int z, float *voldata) |
| add volumetric data to a molecule. More... | |
| int | num_volume_data () |
| return number of volume data sets in molecule. More... | |
| const VolumetricData * | get_volume_data (int) |
| return requested data set. More... | |
| void | compute_volume_gradient (VolumetricData *) |
| compute negated normalized volume gradient map. More... | |
| int | find_atom_in_residue (int atomnameindex, int residue) |
| find first occurance of an atom name in the residue, returns -3 not found. More... | |
| int | find_atom_in_residue (const char *atomname, int residue) |
| find first occurance of an atom name in the residue, returns -3 not found. More... | |
| float | default_charge (char *) |
| return 'default' charge, mass, occupancy value and beta value. More... | |
| float | default_mass (char *) |
| return 'default' charge, mass, occupancy value and beta value. More... | |
| float | default_radius (char *) |
| return 'default' charge, mass, occupancy value and beta value. More... | |
| float | default_occup (void) |
| return 'default' charge, mass, occupancy value and beta value. More... | |
| float | default_beta (void) |
| return 'default' charge, mass, occupancy value and beta value. More... | |
Public Attributes | |
| int | nAtoms |
| number of atoms. More... | |
| int | nResidues |
| number of residues. More... | |
| int | nWaters |
| number of waters. More... | |
| int | nSegments |
| number of segments. More... | |
| int | nFragments |
| total number of fragments. More... | |
| int | nProteinFragments |
| number of protein fragments. More... | |
| int | nNucleicFragments |
| number of nucleic fragments. More... | |
| NameList< int > | atomNames |
| list of unique atom names. More... | |
| NameList< int > | atomTypes |
| list of unique atom types. More... | |
| NameList< int > | resNames |
| list of unique residue names. More... | |
| NameList< int > | chainNames |
| list of unique chain names. More... | |
| NameList< int > | segNames |
| list of unique segment names. More... | |
| NameList< int > | altlocNames |
| list of alternate location names. More... | |
| ResizeArray< Residue * > | residueList |
| residue connectivity list. More... | |
| ResizeArray< Fragment * > | fragList |
| list of connected residues. More... | |
| ResizeArray< Fragment * > | pfragList |
| list of connected protein residues this is a single chain from N to C. More... | |
| ResizeArray< int > | pfragCyclic |
| flag indicating cyclic fragment. More... | |
| ResizeArray< Fragment * > | nfragList |
| ditto for nuc; from 5' to 3'. More... | |
| ResizeArray< int > | nfragCyclic |
| flag indicating cyclic fragment. More... | |
| NameList< float * > | extra |
Protected Attributes | |
| char * | moleculename |
| name of the molcule. More... | |
| int | need_find_bonds |
| whether to compute bonds from the first timestep. More... | |
| ResizeArray< VolumetricData * > | volumeList |
| array of volume data sets. More... | |
Definition at line 57 of file BaseMolecule.h.
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constructor takes molecule ID.
Definition at line 43 of file BaseMolecule.C. References moleculename, nAtoms, nfragList, NULL, and pfragList. |
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destructor.
Definition at line 62 of file BaseMolecule.C. References NameList< float * >::data, extra, fragList, nfragList, NameList< float * >::num, ResizeArray< VolumetricData * >::num, ResizeArray< Fragment * >::num, ResizeArray< Residue * >::num, pfragList, residueList, and volumeList. |
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add a new atom; return it's index.
Definition at line 145 of file BaseMolecule.C. References NameList< int >::add_name, MolAtom::altlocindex, altlocNames, atom, MolAtom::atomicnumber, atomNames, atomTypes, MolAtom::chainindex, chainNames, MolAtom::init, MolAtom::nameindex, nAtoms, NameList< int >::num, MolAtom::resnameindex, resNames, MolAtom::segnameindex, segNames, and MolAtom::typeindex. Referenced by MolFilePlugin::read_structure. |
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add a new bond from a to b; return total number of bonds added so far.
Definition at line 209 of file BaseMolecule.C. References MolAtom::add_bond, atom, MolAtom::bonds, MAXBONDERRORS, nAtoms, and setbondorder. Referenced by add_bond_dupcheck, PickModeAddBond::pick_molecule_end, MolFilePlugin::read_optional_structure, MolFilePlugin::read_structure, and vmd_bond_search. |
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add a bond after checking for duplicates.
Definition at line 263 of file BaseMolecule.C. References add_bond, atom, MolAtom::bonds, MolAtom::bondTo, and nAtoms. Referenced by MolFilePlugin::read_structure, and vmd_bond_search. |
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add volumetric data to a molecule.
Definition at line 1971 of file BaseMolecule.C. References ResizeArray< VolumetricData * >::append, VolumetricData::compute_volume_gradient, data, VolumetricData::datamax, VolumetricData::datamin, VolumetricData::name, and volumeList. Referenced by VMDApp::molecule_add_volumetric, and MolFilePlugin::read_volumetric. |
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find higher level constructs given the atom/bond information.
Definition at line 438 of file BaseMolecule.C. References atom, ATOMHYDROGEN, atomNames, ATOMNORMAL, MolAtom::atomType, ResizeArray< int >::clear, ResizeArray< Fragment * >::clear, ResizeArray< Residue * >::clear, count_bonds, fragList, IS_HYDROGEN, NameList< int >::name, MolAtom::nameindex, nAtoms, need_find_bonds, nfragCyclic, nfragList, nFragments, nNucleicFragments, nProteinFragments, nResidues, nSegments, ResizeArray< Fragment * >::num, nWaters, pfragCyclic, pfragList, residueList, MolAtom::residueType, RESNUCLEIC, and RESPROTEIN. Referenced by VMDApp::molecule_load, VMDApp::molecule_reanalyze, and MolFilePlugin::read_optional_structure. |
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return fragment atom is in.
Definition at line 343 of file BaseMolecule.C. References atom, fragment, Residue::fragment, NULL, residue, and MolAtom::uniq_resid. Referenced by PickModeForceFragment::pick_molecule_move, PickModeForceFragment::pick_molecule_start, PickModeMoveFragment::rotate, and PickModeMoveFragment::translate. |
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return residue atom is in.
Definition at line 332 of file BaseMolecule.C. References atom, NULL, residue, and MolAtom::uniq_resid. Referenced by PickModeForceResidue::pick_molecule_move, PickModeForceResidue::pick_molecule_start, PickModeMoveResidue::rotate, and PickModeMoveResidue::translate. |
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Definition at line 114 of file BaseMolecule.h. References NameList::data. Referenced by AtomColor::find, MolFilePlugin::read_optional_structure, MolFilePlugin::read_structure, and MolFilePlugin::write_structure. |
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number of electron pairs, also fractional.
Definition at line 118 of file BaseMolecule.h. References NameList::data. |
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Definition at line 113 of file BaseMolecule.h. References NameList::data. Referenced by GeometryMol::atom_formatted_name, compute_elect_energy, VolMapCreateSlowEnergy::compute_frame, AtomColor::find, measure_dipole, MolFilePlugin::read_optional_structure, MolFilePlugin::read_structure, and MolFilePlugin::write_structure. |
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clear the entire bond list for all atoms.
Definition at line 426 of file BaseMolecule.C. References MolAtom::bonds, and nAtoms. Referenced by DrawMolecule::recalc_bonds. |
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compute negated normalized volume gradient map.
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return the number of unique bonds in the molecule.
Definition at line 409 of file BaseMolecule.C. References MolAtom::bonds, MolAtom::bondTo, and nAtoms. Referenced by analyze, and DrawMolecule::recalc_bonds. |
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return 'default' charge, mass, occupancy value and beta value.
Definition at line 333 of file BaseMolecule.h. Referenced by MolFilePlugin::read_structure. |
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return 'default' charge, mass, occupancy value and beta value.
Definition at line 400 of file BaseMolecule.C. Referenced by MolFilePlugin::read_structure. |
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return 'default' charge, mass, occupancy value and beta value.
Definition at line 376 of file BaseMolecule.C. Referenced by MolFilePlugin::read_structure. |
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return 'default' charge, mass, occupancy value and beta value.
Definition at line 332 of file BaseMolecule.h. Referenced by MolFilePlugin::read_structure. |
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return 'default' charge, mass, occupancy value and beta value.
Definition at line 353 of file BaseMolecule.C. Referenced by MolFilePlugin::read_structure. |
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find first occurance of an atom name in the residue, returns -3 not found.
Definition at line 967 of file BaseMolecule.C. References atomNames, find_atom_in_residue, residue, and NameList< int >::typecode. |
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find first occurance of an atom name in the residue, returns -3 not found.
Definition at line 315 of file BaseMolecule.h. References atom, Residue::atoms, MolAtom::nameindex, ResizeArray::num, and num. Referenced by find_atom_in_residue. |
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compute molecule's bonds using distance bond search from 1st timestep.
Definition at line 278 of file BaseMolecule.h. References need_find_bonds. Referenced by MolFilePlugin::read_structure. |
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Definition at line 279 of file BaseMolecule.h. References need_find_bonds. Referenced by MolFilePlugin::read_structure. |
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return Nth fragment.
Definition at line 325 of file BaseMolecule.C. References fragList. Referenced by atom_fragment. |
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return requested data set.
Definition at line 2004 of file BaseMolecule.C. References id, NULL, ResizeArray< VolumetricData * >::num, and volumeList. Referenced by atomsel_gridindex_array, atomsel_interp_volume_array, atomsel_volume_array, AtomColor::find, SaveTrajectoryFltkMenu::molchooser_activate_selection, GraphicsFltkMenu::update_molchooser, and GraphicsFltkMenu::volindex_update. |
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Definition at line 306 of file BaseMolecule.C. References atom, NameList< float * >::data, extra, MAXATOMBONDS, and NULL. Referenced by access_tcl_atomsel, assign_atoms, and MolFilePlugin::write_structure. |
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has structure information already been loaded for this molecule?
Definition at line 123 of file BaseMolecule.h. Referenced by VMDApp::molecule_load, and MolFilePlugin::write_structure. |
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Try to set the number of atoms to n. n must be positive. May be called more than once with the same n. Return success.
Definition at line 101 of file BaseMolecule.C. References NameList< float * >::add_name, NameList< float * >::data, data, extra, nAtoms, NULL, and NameList< float * >::num. Referenced by VMDApp::molecule_load, and MolFilePlugin::read_structure. |
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Definition at line 112 of file BaseMolecule.h. References NameList::data. Referenced by Tool::assign_rep, center_of_mass, AtomColor::find, measure_inertia, MolFilePlugin::read_optional_structure, MolFilePlugin::read_structure, Tool::target, Tool::tug, and MolFilePlugin::write_structure. |
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return molecule name.
Definition at line 301 of file BaseMolecule.h. References moleculename. Referenced by VMDApp::molecule_name, molinfo_get, and MolBrowser::update. |
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return number of volume data sets in molecule.
Definition at line 2000 of file BaseMolecule.C. References ResizeArray< VolumetricData * >::num, and volumeList. Referenced by AtomColor::find, SaveTrajectoryFltkMenu::molchooser_activate_selection, VMDApp::molecule_load, VMDApp::molecule_savetrajectory, MolBrowser::update, GraphicsFltkMenu::update_molchooser, and GraphicsFltkMenu::volindex_update. |
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Definition at line 115 of file BaseMolecule.h. References NameList::data. Referenced by VolMapCreateSlowEnergy::compute_frame, AtomColor::find, MolFilePlugin::read_optional_structure, MolFilePlugin::read_structure, and MolFilePlugin::write_structure. |
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Definition at line 111 of file BaseMolecule.h. References NameList::data. Referenced by VolMapCreateSlowEnergy::compute_frame, MolFilePlugin::read_optional_structure, MolFilePlugin::read_structure, vmd_bond_search, and MolFilePlugin::write_structure. |
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return Nth residue.
Definition at line 319 of file BaseMolecule.C. References residueList. Referenced by atom_fragment, atom_residue, atomsel_fragment, AtomColor::find, find_atom_in_residue, PickModeForceFragment::pick_molecule_move, PickModeForceFragment::pick_molecule_start, PickModeMoveFragment::rotate, and PickModeMoveFragment::translate. |
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Definition at line 286 of file BaseMolecule.C. References NameList< float * >::add_name, atom, NameList< float * >::data, extra, MAXATOMBONDS, nAtoms, and NULL. Referenced by access_tcl_atomsel, and add_bond. |
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list of alternate location names.
Definition at line 75 of file BaseMolecule.h. Referenced by add_atom, MoleculeList::add_color_names, atomsel_altloc, atomsel_set_altloc, AtomColor::find, vmd_bond_search, and MolFilePlugin::write_structure. |
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list of unique atom names.
Definition at line 70 of file BaseMolecule.h. Referenced by add_atom, MoleculeList::add_color_names, analyze, GeometryMol::atom_formatted_name, GeometryMol::atom_short_name, atomsel_name, AtomColor::find, find_atom_in_residue, print_atom_info, vmd_bond_search, write_stride_record, and MolFilePlugin::write_structure. |
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list of unique atom types.
Definition at line 71 of file BaseMolecule.h. Referenced by add_atom, MoleculeList::add_color_names, atomsel_type, AtomColor::find, print_atom_info, and MolFilePlugin::write_structure. |
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list of unique chain names.
Definition at line 73 of file BaseMolecule.h. Referenced by add_atom, MoleculeList::add_color_names, AtomColor::find, print_atom_info, and MolFilePlugin::write_structure. |
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list of connected residues.
Definition at line 78 of file BaseMolecule.h. Referenced by analyze, fragment, and ~BaseMolecule. |
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name of the molcule.
Definition at line 255 of file BaseMolecule.h. Referenced by BaseMolecule, Molecule::Molecule, molname, Molecule::rename, and Molecule::~Molecule. |
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whether to compute bonds from the first timestep.
Definition at line 256 of file BaseMolecule.h. Referenced by analyze, DrawMolecule::append_frame, DrawMolecule::DrawMolecule, find_bonds_from_timestep, and find_unique_bonds_from_timestep. |
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flag indicating cyclic fragment.
Definition at line 90 of file BaseMolecule.h. Referenced by analyze. |
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ditto for nuc; from 5' to 3'.
Definition at line 89 of file BaseMolecule.h. Referenced by analyze, BaseMolecule, and ~BaseMolecule. |
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total number of fragments.
Definition at line 66 of file BaseMolecule.h. Referenced by analyze. |
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number of nucleic fragments.
Definition at line 68 of file BaseMolecule.h. Referenced by analyze. |
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number of protein fragments.
Definition at line 67 of file BaseMolecule.h. Referenced by analyze. |
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number of residues.
Definition at line 63 of file BaseMolecule.h. Referenced by analyze. |
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number of segments.
Definition at line 65 of file BaseMolecule.h. Referenced by analyze. |
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number of waters.
Definition at line 64 of file BaseMolecule.h. Referenced by analyze. |
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flag indicating cyclic fragment.
Definition at line 82 of file BaseMolecule.h. Referenced by analyze. |
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list of connected protein residues this is a single chain from N to C.
Definition at line 80 of file BaseMolecule.h. Referenced by analyze, BaseMolecule, and ~BaseMolecule. |
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residue connectivity list.
Definition at line 77 of file BaseMolecule.h. Referenced by analyze, read_stride_record, residue, and ~BaseMolecule. |
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list of unique residue names.
Definition at line 72 of file BaseMolecule.h. Referenced by add_atom, MoleculeList::add_color_names, GeometryMol::atom_formatted_name, GeometryMol::atom_short_name, atomsel_resname, AtomColor::find, print_atom_info, write_stride_record, and MolFilePlugin::write_structure. |
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list of unique segment names.
Definition at line 74 of file BaseMolecule.h. Referenced by add_atom, MoleculeList::add_color_names, AtomColor::find, print_atom_info, and MolFilePlugin::write_structure. |
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array of volume data sets.
Definition at line 346 of file BaseMolecule.h. Referenced by add_volume_data, DrawMolecule::cov, get_volume_data, num_volume_data, DrawMolecule::scale_factor, and ~BaseMolecule. |
1.2.14 written by Dimitri van Heesch,
© 1997-2002