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molfile_atom_t Struct Reference

#include <molfile_plugin.h>

List of all members.

Public Attributes

char name [16]
char type [16]
char resname [8]
int resid
char segid [8]
char chain [2]
char altloc [2]
char insertion [2]
float occupancy
float bfactor
float mass
float charge
float radius
int atomicnumber


Detailed Description

Per-atom attributes and information.

Definition at line 107 of file molfile_plugin.h.


Member Data Documentation

char molfile_atom_t::altloc[2]
 

optional PDB alternate location code

Definition at line 126 of file molfile_plugin.h.

Referenced by addAtoms, parseStructure, read_pdb_structure, vtf_parse_atom, vtf_parse_structure, write_structure, and write_timestep.

int molfile_atom_t::atomicnumber
 

optional element atomic number

Definition at line 133 of file molfile_plugin.h.

Referenced by addAtoms, DEN_POT_WFK_read_structure, GEO_read_structure, parse_parm7_atomicnumber, parseStructure, read_cpmdlog_structure, read_cube_structure, read_gamess_structure, read_gaussian_structure, read_hoomd_structure, read_js_structure, read_lammps_structure, read_molden_structure, read_orca_structure, read_pdb_structure, read_qcschema_structure, read_vasp5xdatcar_structure, read_vaspoutcar_structure, read_vaspposcar_structure, read_vaspxdatcar_structure, read_vaspxml_structure, read_xbgf_structure, read_xsf_structure, read_xyz_structure, vtf_parse_atom, write_js_structure, write_structure, write_timestep, write_xbgf_timestep, write_xyz_timestep, and xml_data_block.

float molfile_atom_t::bfactor
 

optional B-factor value

Definition at line 129 of file molfile_plugin.h.

Referenced by addAtoms, parseStructure, read_js_structure, read_lammps_structure, read_pdb_structure, read_xbgf_structure, vtf_parse_atom, vtf_parse_structure, write_js_structure, write_structure, write_timestep, and write_xbgf_timestep.

char molfile_atom_t::chain[2]
 

required chain name, or ""

Definition at line 123 of file molfile_plugin.h.

Referenced by DEN_POT_WFK_read_structure, GEO_read_structure, parseStructure, read_bgf_structure, read_car_structure, read_car_structure_line, read_cor_structure, read_cpmd_structure, read_cpmdlog_structure, read_cube_structure, read_dlpoly_config_structure, read_dlpoly_structure, read_g96_structure, read_gamess_structure, read_gaussian_structure, read_gro_structure, read_hoomd_structure, read_lammps_structure, read_mdf_structure, read_mdf_structure_line, read_mmtk_cdf_structure, read_mol2, read_molden_structure, read_orca_structure, read_parm7_structure, read_parm_structure, read_pdb_structure, read_pqr_structure, read_psf, read_qcschema_structure, read_tinker_structure, read_tng_structure, read_vasp5xdatcar_structure, read_vaspoutcar_structure, read_vaspposcar_structure, read_vaspxdatcar_structure, read_vaspxml_structure, read_xbgf_structure, read_xsf_structure, read_xyz_structure, set_atom_attributes, vtf_parse_atom, vtf_parse_structure, write_bgf_timestep, write_timestep, write_tng_structure, and write_xbgf_timestep.

float molfile_atom_t::charge
 

optional charge value

Definition at line 131 of file molfile_plugin.h.

Referenced by parse_parm7_charge, parseStructure, read_bgf_structure, read_car_structure_line, read_cpmdlog_structure, read_cube_structure, read_gaussian_structure, read_js_structure, read_lammps_structure, read_mdf_structure_line, read_mol2, read_parm_structure, read_pqr_structure, read_psf, read_xbgf_structure, vtf_parse_atom, vtf_parse_structure, write_bgf_timestep, write_js_structure, write_mol2_timestep, write_pqr_atom, write_pqr_structure, write_psf_structure, write_xbgf_timestep, and xml_data_block.

char molfile_atom_t::insertion[2]
 

optional PDB insertion code

Definition at line 127 of file molfile_plugin.h.

Referenced by addAtoms, parseStructure, read_pdb_structure, read_psf, read_xbgf_structure, vtf_parse_atom, vtf_parse_structure, write_structure, and write_timestep.

float molfile_atom_t::mass
 

optional mass value

Definition at line 130 of file molfile_plugin.h.

Referenced by DEN_POT_WFK_read_structure, GEO_read_structure, parse_parm7_mass, parseStructure, read_cpmdlog_structure, read_cube_structure, read_gaussian_structure, read_hoomd_structure, read_js_structure, read_lammps_structure, read_parm_structure, read_pdb_structure, read_psf, read_vasp5xdatcar_structure, read_vaspoutcar_structure, read_vaspposcar_structure, read_vaspxdatcar_structure, read_vaspxml_structure, read_xsf_structure, read_xyz_structure, vtf_parse_atom, vtf_parse_structure, write_js_structure, write_psf_structure, and xml_data_block.

char molfile_atom_t::name[16]
 

required atom name string

Definition at line 109 of file molfile_plugin.h.

Referenced by DEN_POT_WFK_read_structure, GEO_read_structure, get_atom_radius, parse_parm7_atoms, parseStructure, read_bgf_structure, read_car_structure_line, read_cor_structure, read_cpmd_structure, read_cpmdlog_structure, read_cube_structure, read_dlpoly_config_structure, read_dlpoly_structure, read_g96_structure, read_gamess_structure, read_gaussian_structure, read_gro_structure, read_lammps_structure, read_mdf_structure_line, read_mmtk_cdf_structure, read_mol2, read_molden_structure, read_orca_structure, read_parm_structure, read_pdb_structure, read_pqr_structure, read_psf, read_qcschema_structure, read_tinker_structure, read_tng_structure, read_vasp5xdatcar_structure, read_vaspoutcar_structure, read_vaspposcar_structure, read_vaspxdatcar_structure, read_vaspxml_structure, read_xbgf_structure, read_xsf_structure, read_xyz_structure, set_atom_attributes, vtf_parse_atom, vtf_parse_structure, write_bgf_timestep, write_gro_timestep, write_mol2_timestep, write_pqr_atom, write_psf_structure, write_timestep, write_tng_structure, write_xbgf_timestep, write_xyz_timestep, and xml_data_block.

float molfile_atom_t::occupancy
 

optional occupancy value

Definition at line 128 of file molfile_plugin.h.

Referenced by addAtoms, parseStructure, read_js_structure, read_lammps_structure, read_mdf_structure_line, read_pdb_structure, read_xbgf_structure, vtf_parse_atom, vtf_parse_structure, write_js_structure, write_structure, write_timestep, and write_xbgf_timestep.

float molfile_atom_t::radius
 

optional radius value

Definition at line 132 of file molfile_plugin.h.

Referenced by DEN_POT_WFK_read_structure, GEO_read_structure, parseStructure, read_cpmdlog_structure, read_cube_structure, read_gaussian_structure, read_hoomd_structure, read_js_structure, read_lammps_structure, read_pdb_structure, read_pqr_structure, read_vasp5xdatcar_structure, read_vaspoutcar_structure, read_vaspposcar_structure, read_vaspxdatcar_structure, read_vaspxml_structure, read_xsf_structure, read_xyz_structure, vtf_parse_atom, vtf_parse_structure, write_js_structure, write_pqr_atom, write_pqr_structure, and xml_data_block.

int molfile_atom_t::resid
 

required integer residue ID

Definition at line 112 of file molfile_plugin.h.

Referenced by DEN_POT_WFK_read_structure, GEO_read_structure, parse_parm7_respointers, parseStructure, read_bgf_structure, read_car_structure_line, read_cor_structure, read_cpmd_structure, read_cpmdlog_structure, read_cube_structure, read_dlpoly_config_structure, read_dlpoly_structure, read_g96_structure, read_gamess_structure, read_gaussian_structure, read_gro_structure, read_hoomd_structure, read_js_structure, read_lammps_structure, read_mdf_structure_line, read_mmtk_cdf_structure, read_mol2, read_molden_structure, read_orca_structure, read_parm_structure, read_pdb_structure, read_pqr_structure, read_psf, read_qcschema_structure, read_tinker_structure, read_tng_structure, read_vasp5xdatcar_structure, read_vaspoutcar_structure, read_vaspposcar_structure, read_vaspxdatcar_structure, read_vaspxml_structure, read_xbgf_structure, read_xsf_structure, read_xyz_structure, set_atom_attributes, vtf_parse_atom, vtf_parse_structure, write_bgf_timestep, write_gro_timestep, write_js_structure, write_mol2_timestep, write_pqr_atom, write_psf_structure, write_timestep, write_tng_structure, write_xbgf_timestep, and xml_data_block.

char molfile_atom_t::resname[8]
 

required residue name string

Definition at line 111 of file molfile_plugin.h.

Referenced by DEN_POT_WFK_read_structure, GEO_read_structure, parse_parm7_respointers, parseStructure, read_bgf_structure, read_car_structure_line, read_cor_structure, read_cpmd_structure, read_cpmdlog_structure, read_cube_structure, read_dlpoly_config_structure, read_dlpoly_structure, read_g96_structure, read_gamess_structure, read_gaussian_structure, read_gro_structure, read_hoomd_structure, read_lammps_structure, read_mdf_structure_line, read_mmtk_cdf_structure, read_mol2, read_molden_structure, read_orca_structure, read_parm_structure, read_pdb_structure, read_pqr_structure, read_psf, read_qcschema_structure, read_tinker_structure, read_tng_structure, read_vasp5xdatcar_structure, read_vaspoutcar_structure, read_vaspposcar_structure, read_vaspxdatcar_structure, read_vaspxml_structure, read_xbgf_structure, read_xsf_structure, read_xyz_structure, set_atom_attributes, vtf_parse_atom, vtf_parse_structure, write_bgf_timestep, write_gro_timestep, write_mol2_timestep, write_pqr_atom, write_psf_structure, write_timestep, write_tng_structure, and write_xbgf_timestep.

char molfile_atom_t::segid[8]
 

required segment name string, or ""

Definition at line 113 of file molfile_plugin.h.

Referenced by DEN_POT_WFK_read_structure, GEO_read_structure, read_bgf_structure, read_car_structure_line, read_cor_structure, read_cpmd_structure, read_cpmdlog_structure, read_cube_structure, read_dlpoly_config_structure, read_dlpoly_structure, read_g96_structure, read_gamess_structure, read_gaussian_structure, read_gro_structure, read_hoomd_structure, read_lammps_structure, read_mdf_structure_line, read_mmtk_cdf_structure, read_mol2, read_molden_structure, read_orca_structure, read_parm7_structure, read_parm_structure, read_pdb_structure, read_pqr_structure, read_psf, read_qcschema_structure, read_tinker_structure, read_tng_structure, read_vasp5xdatcar_structure, read_vaspoutcar_structure, read_vaspposcar_structure, read_vaspxdatcar_structure, read_vaspxml_structure, read_xbgf_structure, read_xsf_structure, read_xyz_structure, vtf_parse_atom, vtf_parse_structure, write_psf_structure, write_timestep, and write_xbgf_timestep.

char molfile_atom_t::type[16]
 

required atom type string

Definition at line 110 of file molfile_plugin.h.

Referenced by DEN_POT_WFK_read_structure, GEO_read_structure, get_atom_radius, parse_parm7_atype, parseStructure, read_bgf_structure, read_car_structure_line, read_cor_structure, read_cpmd_structure, read_cpmdlog_structure, read_cube_structure, read_dlpoly_config_structure, read_dlpoly_structure, read_g96_structure, read_gamess_structure, read_gaussian_structure, read_gro_structure, read_lammps_structure, read_mdf_structure_line, read_mmtk_cdf_structure, read_mol2, read_molden_structure, read_orca_structure, read_parm_structure, read_pdb_structure, read_pqr_structure, read_psf, read_qcschema_structure, read_tinker_structure, read_tng_structure, read_vasp5xdatcar_structure, read_vaspoutcar_structure, read_vaspposcar_structure, read_vaspxdatcar_structure, read_vaspxml_structure, read_xbgf_structure, read_xsf_structure, read_xyz_structure, vtf_parse_atom, vtf_parse_structure, write_bgf_timestep, write_mol2_timestep, write_psf_structure, write_tng_structure, write_vaspposcar_timestep, write_xbgf_timestep, and xml_data_block.


The documentation for this struct was generated from the following file:
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