HINT 3.00 Manual: Toolkit Programmers Guide

Crystallographer's PDB Toolkit Programmer's Guide

PDB Molecule Objects

PDB Molecule Creation

eslc_create_biomolecule_from_pdb_file

Create an eslc_biomolecule structure for the molecule(s) in the pdb file pdb_file_name using the settings stored in the eslc_pdb_control_panel structure control_panel (See eslc_init_pdb) to control various attributes of the biomolecule. Note that an eslc_pdb_control_panel structure must be created and modified using the various eslc_pdb_set routines described herein before creating a biomolecule.

form

eslc_create_biomolecule_from_pdb_file(char *molecule_name, char *pdb_file_name, ehandle control_panel, ehandle *a_biomolecule)
input

molecule_name

pdb_file_name

control_panel
output

a_biomolecule
return

TRUE: success

FALSE: failure

PDB Control Panel Creation

eslc_init_pdb

Create an eslc_pdb_control_panel structure which controls various attributes of a subsequently created pdb biomolecule.

form

eslc_init_pdb(ehandle *control_panel)
input

output

control_panel
return

TRUE: success

FALSE: failure

eslc_destroy_pdb

Destroy an eslc_pdb_control structure.

form

eslc_destroy_pdb(ehandle control_panel)
input

control_panel
output

return

TRUE: success

FALSE: failure

PDB Molecule Atrributes

eslc_pdb_get_forcefield

Get the value of forcefield associated with a pdb control panel which controls the mapping of pdb atom names to HINT atom names/types.

form

eslc_pdb_getforcefield(ehandle control_panel, int *forcefield)
input

a_pdb_control_panel
output

forcefield
return

TRUE: success

FALSE: failure

eslc_pdb_set_forcefield

Set the forcefield type associated with a pdb control panel. The forcefield type will be used in subsequent creations of biomolecules using the pdb control panel to control the translation of pdb atom names to HINT atom names/types. See forcefields.html for a list of forcefield definitions supported by the toolkit.

form

eslc_pdb_set_forcefield(ehandle control_panel, int forcefield)
input

control_panel

forcefield
output

return

TRUE: success

FALSE: failure

eslc_pdb_getresidueacidbasebehaviour

Get the value of residueacidbasebehaviour associated with a pdb control panel which controls if protonation states of residues in an input pdb file are used to set the value of of the acidbase flag associated with individual residues.

form

eslc_pdb_getresidueacidbasehaviour(ehandle control_panel, int *residueacidbasebehaviour)
input

control_panel
output

residueacidbaebehaviour
return

TRUE: success

FALSE: failure

eslc_pdb_setresidueacidbasebehaviour

Set the value of residueacidbasebehaviour which controls if protonation states for residues in an input pdb file are used to set values the acidbase flag associated with individual residues. See pdb_props.html for a list of possible values of residueacidbasebehaviour.

form

eslc_pdb_setresidueacidbasebehaviour(ehandle control_panel, int residueacidbasebehaviour)
input

control_panel

residueacidbasebehaviour
output

return

TRUE: success

FALSE: failure

eslc_pdb_getdefaultacidbasetype

Get the value of acidbasetype which controls the deault value assigned to the residue acidbase flag, provided that the residueacidbasebehaviour flag is set to use the value set in eslc_pdb_setdefaultacidbasetype.

form

eslc_pdb_getdefaultacidbasetype(ehandle control_panel, int *acidbasebetype)
input

control_panel

acidbasetype
output

acidbasetype
return

TRUE: success

FALSE: failure

eslc_pdb_setdefaultacidbasetype

Set the value of acidbasetype which controls the default value assigned to the residue acidbase flag, provided that the residueacidbasebehaviour flag is set to use the value set in this routine. determination of acidbase status. See monoprops.html for a list of acidbase values recognized by the toolkit.

form

eslc_pdb_setdefaultacidbasetype(ehandle control_panel, int acidbasebetype)
input

control_panel

acidbasetype
output

return

TRUE: success

FALSE: failure

eslc_pdb_gettranslateiupachydrogens

Get the value of translate_iupac_names which controls the translation of IUPAC hydrogen names in pdb files into TAFF hydrogen names.

form

eslc_pdb_gettranslateiupachydrogens(ehandle control_panel, int *translate_iupac_hydrogens)
input

control_panel
output

translate_iupac_hydrogens
return

TRUE: success

FALSE: failure

eslc_pdb_settranslateiupachydrogens

Set the value of translate_iupac_names which controls the translation of IUPAC hydrogen names in pdb files into TAFF hydrogen names. See pdb_props.html for a list of possible values of translate_iupac_names.

form

eslc_pdb_settranslateiupachydrogens(ehandle control_panel, int translate_iupac_hydrogens)
input

control_panel

translate_iupac_hydrogens
output

return

TRUE: success

FALSE: failure

eslc_pdb_getmissingatomsbehaviour

Get the value of missing_atoms_behaviour which controls the behaviour of eslc_create_biomolecule_from_pdb_file when heavy atoms expected for an amino acid residue are missing from the input pdb file

form

eslc_pdb_getmissingatomsbehaviour(ehandle control_panel, int *missingatomsbehaviour)
input

control_panel
output

missingatomsbehaviour
return

TRUE: success

FALSE: failure

eslc_pdb_setmissingatomsbehaviour

Set the value of missing_atoms_behaviour which controls the behaviour of eslc_create_biomolecule_from_pdb_file when heavy atoms expected for a particular amino acid residue are missing from the input pdb file. Possible values are See pdb_props.html for a list of possible values of missing_atom_behaviour.

form

eslc_pdb_setmissingatomsbehaviour(ehandle control_panel, int missingatomsbehaviour)
input

control_panel

missingatomsbehaviour
output

return

TRUE: success

FALSE: failure

eslc_pdb_getmissimgmutatedotherhydrogensbehaviour

Get the value of missing_other_hydrogens_on_mutate_behaviour which controls the behaviour of eslc_create_biomolecule_from_pdb_file when one or more beta methyl hydrogens are missing in an alanine residue created as a result of mutating a non-alanine residue to alanine due to missing sidechain atoms in the input pdb file.

form

eslc_pdb_getmissingmutatedotherhydrogensbehaviour(ehandle control_panel, int *missinghydrogensbehaviour)
input

control_panel
output

missingotherhydrogensbehaviour
return

TRUE: success

FALSE: failure

eslc_pdb_setmissimgmutatedotherhydrogensbehaviour

Set the value of missing_other_hydrogens_on_mutate_behaviour which controls the behaviour of eslc_create_biomolecule_from_pdb_file when one or more beta methyl hydrogens are missing in an alanine residue created as a result of mutating a non-alanine residue to alanine due to missing sidechain atoms in the input pdb file. See pdb_props.html for a list of possible values of missing_other_hydrogens_on_mutate_behaviour.

form

eslc_pdb_setmissingmutatedotherhydrogensbehaviour(ehandle control_panel, int missinghydrogensbehaviour)
input

control_panel

missingotherhydrogensbehaviour
output

return

TRUE: success

FALSE: failure

eslc_pdb_getproteinterminibehaviour

Get the value of default_termination_type which controls whether charged or neutral termini are assigned by default when a biomolecule is created by eslc_create_biomolecule_from_pdb_file .

form

eslc_pdb_getproteinterminbehaviourbehaviour(ehandle control_panel, int *protein_termini_behaviour)
input

control_panel
output

*protein_termini_behaviour
return

TRUE: success

FALSE: failure

eslc_pdb_setproteinterminibehaviour

Set the value of default_termination_type which controls whether charged or neutral termini are assigned by default when a biomolecule is created by eslc_create_biomolecule_from_pdb_file . See pdb_props.html for a list of possible values of default_termination_type.

form
of possible values of translate_iupac_names.

eslc_pdb_getproteinterminbehaviourbehaviour(ehandle control_panel, int protein_termini_behaviour)
input

control_panel

protein_termin_behaviour
output

return

TRUE: success

FALSE: failure

eslc_pdb_getunknownelementdisposition

Get the value of unknown_element_disposition which controls the behaviour eslc_create_biomolecule_from_pdb_file when an element unknown to the toolkit is encountered in the input file.

form

eslc_pdb_getunknownelementdisposition(ehandle control_panel, int *unknown_element_disposition)
input

control_panel
output

*unknown_element_disposition
return

TRUE: success

FALSE: failure

eslc_pdb_setunknownelementdisposition

Set the value of unknown_element_disposition which controls the behaviour of eslc_create_biomolecule_from_pdb_file . See pdb_props.html for a list of possible values of unknown_element_disposition.

form

eslc_pdb_setunknownelementbehaviour(ehandle control_panel, int unknown_element_behaviour)
input

control_panel

unknown_element_behaviour
output

return

TRUE: success

FALSE: failure

eslc_pdb_gettopologypath

Get the value of default_topology_dir which is the directory where residue topology files are assumed to reside.

form

eslc_pdb_gettopologypath(ehandle control_panel, char *topology_dir)
input

control_panel
output

*topology_dir
return

TRUE: success

FALSE: failure

eslc_pdb_settopologypath

Set the value of default_topology_dir which is the directory where residue topology files are assumed to reside.

form

eslc_pdb_settopologypath(ehandle control_panel, char *topology_dir)
input

control_panel

topology_dir
output

return

TRUE: success

FALSE: failure

eslc_pdb_addtopologyfile

Adds the contents of the file *topology_path to the internal residue topology database database used by eslc_create_biomolecule_from_pdb_file to construct atomic connectivities and to assign HINT atom types to atoms in the input pdb file. If not specified, topology files are assumed to reside in the directory specified in the last call to eslc_pdb_settopologypath . The parameter topology_type is used to specify the class(es) of residues whose topologies are defined in the file *topology_path . See pdb_props.html for a list of topology types recognized by the toolkit.

form

eslc_pdb_addtopologyfile(int topology_type, ehandle control_panel, char *topology_path)
input

topology_type

control_panel

topology_path
output

return

TRUE: success

FALSE: failure

Crystallographer's PDB Toolkit Programmer's Guide

PDB Molecule Objects

Header Files

PDB Molecule Creation

PDB Control Panel Creation

PDB Molecule Atrributes