Molconn-Z 4.00 Manual: Toolkit Programmers Guide

eduSoft LC Toolkit Programmers' Guide

Atom Objectss

Atom Attributes

eslc_set_atom_element

Set the element (atomic symbol) of an atom.

form

int eslc_set_atom_element ( ehandle molecule_handle, int atomnumber, ElementStr element )
input

molecule_handle

atomnumber

element
output

none
return

TRUE:success

FALSE:failure

eslc_get_atom_element

Get the element (atomic symbol) of an atom.

form

int eslc_get_atom_element ( ehandle molecule_handle, int atomnumber, ElementStr *element )
input

molecule_handle

atomnumber
output

element
return

TRUE:success

FALSE:failure

eslc_set_atom_all_elements

Set the elements (atomic symbols) for all atoms.

form

int eslc_set_atom_all_elements ( ehandle molecule_handle, ElementStr *elements )
input

molecule_handle

elements
output

none
return

TRUE:success

FALSE:failure

eslc_get_atom_all_elements

Get the elements (atomic symbols) for all atoms.

form

int eslc_get_atom_all_elements ( ehandle molecule_handle, ElementStr *elements )
input

molecule_handle
output

elements
return

TRUE:success

FALSE:failure

eslc_bit_atom_element

Verify that the element is set for an atom.

form

int eslc_bit_atom_element ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

TRUE:element is set

FALSE:element is not set

eslc_set_atom_atomicnumber

Set the atomic number of an atom.

form

int eslc_set_atom_atomicnumber ( ehandle molecule_handle, int atomnumber, int atomicnumber )
input

molecule_handle

atomnumber

atomicnumber
output

none
return

TRUE:success

FALSE:failure

eslc_get_atom_atomicnumber

Get the atomic number of an atom.

form

int eslc_get_atom_atomicnumber ( ehandle molecule_handle, int atomnumber, int *atomicnumber )
input

molecule_handle

atomnumber
output

atomicnumber
return

TRUE:success

FALSE:failure

eslc_set_atom_all_atomicnumbers

Set the atomic numbers for all atoms.

form

int eslc_set_atom_all_atomicnumbers ( ehandle molecule_handle, int *atomicnumbers )
input

molecule_handle

atomicnumbers
output

none
return

TRUE:success

FALSE:failure

eslc_get_atom_all_atomicnumbers

Get the atomic numbers for all atoms.

form

int eslc_get_atom_all_atomicnumbers ( ehandle molecule_handle, int *atomicnumbers )
input

molecule_handle
output

atomicnumbers
return

TRUE:success

FALSE:failure

eslc_bit_atom_atomicnumber

Verify that the atomic number is set for an atom.

form

int eslc_bit_atom_atomicnumber ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

TRUE:atomic number is set

FALSE:atomic number is not set

eslc_set_atom_name

Set the name of an atom.

form

int eslc_set_atom_name ( ehandle molecule_handle, int atomnumber, NameStr name )
input

molecule_handle

atomnumber

name
output

none
return

TRUE:success

FALSE:failure

eslc_get_atom_name

Get the name of an atom.

form

int eslc_get_atom_name ( ehandle molecule_handle, int atomnumber, NameStr *name )
input

molecule_handle

atomnumber
output

name
return

TRUE:success

FALSE:failure

eslc_set_atom_all_names

Set the names for all atoms.

form

int eslc_set_atom_all_names ( ehandle molecule_handle, NameStr *names )
input

molecule_handle

names
output

none
return

TRUE:success

FALSE:failure

eslc_get_atom_all_names

Get the names for all atoms.

form

int eslc_get_atom_all_names ( ehandle molecule_handle, NameStr *names )
input

molecule_handle
output

names
return

TRUE:success

FALSE:failure

eslc_bit_atom_name

Verify that the name is set for an atom.

form

int eslc_bit_atom_name ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

TRUE:name is set

FALSE:name is not set

eslc_set_atom_hydrogencount

Set the hydrogen count of an atom.

form

int eslc_set_atom_hydrogencount ( ehandle molecule_handle, int atomnumber, int hydrogencount )
input

molecule_handle

atomnumber

hydrogencount
output

none
return

TRUE:success

FALSE:failure

eslc_get_atom_hydrogencount

Get the hydrogen count of an atom.

form

int eslc_get_atom_hydrogencount ( ehandle molecule_handle, int atomnumber, int *hydrogencount )
input

molecule_handle

atomnumber
output

hydrogencount
return

TRUE:success

FALSE:failure

eslc_set_atom_all_hydrogencounts

Set the hydrogen counts for all atoms.

form

int eslc_set_atom_all_hydrogencounts ( ehandle molecule_handle, int *hydrogencounts )
input

molecule_handle

hydrogencounts
output

none
return

TRUE:success

FALSE:failure

eslc_get_atom_all_hydrogencounts

Get the hydrogen counts for all atoms.

form

int eslc_get_atom_all_hydrogencounts ( ehandle molecule_handle, int *hydrogencounts )
input

molecule_handle
output

hydrogencounts
return

TRUE:success

FALSE:failure

eslc_bit_atom_hydrogencount

Verify that the hydrogencount is set for an atom.

form

int eslc_bit_atom_hydrogencount ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

TRUE:hydrogencount is set

FALSE:hydrogencount is not set

eslc_set_atom_pielectrons

Set the pi electron count of an atom.

form

int eslc_set_atom_pielectrons ( ehandle molecule_handle, int atomnumber, int pielectrons )
input

molecule_handle

atomnumber

pielectrons
output

none
return

TRUE:success

FALSE:failure

eslc_get_atom_pielectrons

Get the pi electrons count of an atom.

form

int eslc_get_atom_pielectrons ( ehandle molecule_handle, int atomnumber, int *pielectrons )
input

molecule_handle

atomnumber
output

pielectrons
return

TRUE:success

FALSE:failure

eslc_set_atom_all_pielectrons

Set the pi electron counts for all atoms.

form

int eslc_set_atom_all_pielectrons ( ehandle molecule_handle, int *pielectrons )
input

molecule_handle

pielectrons
output

none
return

TRUE:success

FALSE:failure

eslc_get_atom_all_pielectrons

Get the pi electron counts for all atoms.

form

int eslc_get_atom_all_pielectrons ( ehandle molecule_handle, int *pielectrons )
input

molecule_handle
output

pielectrons
return

TRUE:success

FALSE:failure

eslc_bit_atom_pielectrons

Verify that the pi electron count is set for an atom.

form

int eslc_bit_atom_pielectrons ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

TRUE:pi electron count is set

FALSE:pi electron count is not set

eslc_set_atom_coordinates

Set the three-dimensional cartesian coordinates of an atom.

form

int eslc_set_atom_coordinates ( ehandle molecule_handle, int atomnumber, float x, float y, float z )
input

molecule_handle

atomnumber

z
output

none
return

TRUE:success

FALSE:failure

eslc_get_atom_coordinates

Get the three-dimensional cartesian coordinates of an atom.

form

int eslc_get_atom_coordinates ( ehandle molecule_handle, int atomnumber, float *x, float *y, float *z )
input

molecule_handle

atomnumber
output

z
return

TRUE:success

FALSE:failure

eslc_set_atom_all_coordinates

Set the three-dimensional cartesian coordinates for all atoms.

form

int eslc_set_atom_all_coordinates ( ehandle molecule_handle, float *x, float *y, float *z )
input

molecule_handle

z
output

none
return

TRUE:success

FALSE:failure

eslc_get_atom_all_coordinates

Get the three-dimensional cartesian coordinates for all atoms.

form

int eslc_get_atom_all_coordinates ( ehandle molecule_handle, float *x, float *y, float *z )
input

molecule_handle
output

z
return

TRUE:success

FALSE:failure

eslc_bit_atom_coordinates

Verify that the three-dimensional cartesian coordinates are set for an atom.

form

int eslc_bit_atom_coordinates ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

TRUE:coordinates are set

FALSE:coordinates are not set

eslc_set_atom_formalcharge

Set the formal charge of an atom.

form

int eslc_set_atom_formalcharge ( ehandle molecule_handle, int atomnumber, float formalcharge )
input

molecule_handle

atomnumber

formalcharge
output

none
return

TRUE:success

FALSE:failure

eslc_get_atom_formalcharge

Get the formal charge of an atom.

form

int eslc_get_atom_formalcharge ( ehandle molecule_handle, int atomnumber, float *formalcharge )
input

molecule_handle

atomnumber
output

formalcharge
return

TRUE:success

FALSE:failure

eslc_set_atom_all_formalcharges

Set the formal charges for all atoms.

form

int eslc_set_atom_all_formalcharges ( ehandle molecule_handle, int *formalcharges )
input

molecule_handle

formalcharges
output

none
return

TRUE:success

FALSE:failure

eslc_get_atom_all_formalcharges

Get the formal charges for all atoms.

form

int eslc_get_atom_all_formalcharges ( ehandle molecule_handle, int *formalcharges )
input

molecule_handle
output

formalcharges
return

TRUE:success

FALSE:failure

eslc_bit_atom_formalcharge

Verify that the formal charge is set for an atom.

form

int eslc_bit_atom_formalcharge ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

TRUE:formal charge is set

FALSE:formal charge is not set

eslc_set_atom_partialcharge

Set the partial charge of an atom.

form

int eslc_set_atom_partialcharge ( ehandle molecule_handle, int atomnumber, float partialcharge )
input

molecule_handle

atomnumber

partialcharge
output

none
return

TRUE:success

FALSE:failure

eslc_get_atom_partialcharge

Get the partial charge of an atom.

form

int eslc_get_atom_partialcharge ( ehandle molecule_handle, int atomnumber, float *partialcharge )
input

molecule_handle

atomnumber
output

partialcharge
return

TRUE:success

FALSE:failure

eslc_set_atom_all_partialcharges

Set the partial charges for all atoms.

form

int eslc_set_atom_all_partialcharges ( ehandle molecule_handle, int *partialcharges )
input

molecule_handle

partialcharges
output

none
return

TRUE:success

FALSE:failure

eslc_get_atom_all_partialcharges

Get the partial charges for all atoms.

form

int eslc_get_atom_all_partialcharges ( ehandle molecule_handle, int *partialcharges )
input

molecule_handle
output

partialcharges
return

TRUE:success

FALSE:failure

eslc_bit_atom_partialcharge

Verify that the partial charge is set for an atom.

form

int eslc_bit_atom_partialcharge ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

TRUE:partial charge is set

FALSE:partial charge is not set

eslc_set_atom_typeid

Set type id of an atom. See atomtypeid.html or the molconnz.h file for a list of type id definitions. Type ids are also automatically set from other atomic parameters, i.e., element, bonds, formal charge, etc. by executing the molconnz toolkit.

form

int eslc_set_atom_typeid ( ehandle molecule_handle, int atomnumber, int type_id )
input

molecule_handle

atomnumber

type_id
output

none
return

TRUE:success

FALSE:failure

eslc_get_atom_typeid

Get the type id of an atom. See atomtypeid.html or the molconnz.h file for a list of type id definitions. The Atom Methods eslc_atom_number_find_typename and eslc_atom_typeid_find_typename will return a string descriptor of the atom type.

form

int eslc_get_atom_typeid ( ehandle molecule_handle, int atomnumber, int *type_id )
input

molecule_handle

atomnumber
output

type_id
return

TRUE:success

FALSE:failure

eslc_set_atom_all_typeids

Set the type ids for all atoms. See atomtypeid.html or the molconnz.h file for a list of type id definitions. Type ids are also automatically set from other atomic parameters, i.e., element, bonds, formal charge, etc. by executing the molconnz toolkit.

form

int eslc_set_atom_all_typeids ( ehandle molecule_handle, int *type_ids )
input

molecule_handle

type_ids
output

none
return

TRUE:success

FALSE:failure

eslc_get_atom_all_typeids

Get the type ids for all atoms. See atomtypeid.html or the molconnz.h file for a list of type id definitions. The Atom Methods eslc_atom_number_find_typename and eslc_atom_typeid_find_typename will return a string descriptor of the atom types.

form

int eslc_get_atom_all_typeids ( ehandle molecule_handle, int *type_ids )
input

molecule_handle
output

type_ids
return

TRUE:success

FALSE:failure

eslc_bit_atom_typeid

Verify that the type id is set for an atom.

form

int eslc_bit_atom_typeid ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

TRUE:type id is set

FALSE:type id is not set

eslc_get_atom_all_monomers

Get the monomer handles for all atoms. Note that this function returns an array of size "atomcount", such that each element of the array is a handle, and that monomers will likely have multiple atom members.

form

int eslc_get_atom_all_monomers ( ehandle molecule_handle, ehandle *monomers )
input

molecule_handle
output

monomers
return

TRUE:success

FALSE:failure

eslc_set_atom_all_monomers

Set the monomer handles for all atoms. Note that this function requires an array of size "atomcount", such that each element of the array is a handle, and that monomers will likely have multiple atom members.

form

int eslc_set_atom_all_monomers ( ehandle molecule_handle, ehandle *monomers )
input

molecule_handle

monomers
output

none
return

TRUE:success

FALSE:failure

eslc_get_atom_monomer

Get the monomer handle for an atom.

form

int eslc_get_atom_monomer ( ehandle molecule_handle, int atomnumber, ehandle *monomer )
input

molecule_handle

atomnumber
output

monomer
return

TRUE:success

FALSE:failure

eslc_set_atom_monomer

Set the monomer handle for an atom.

form

int eslc_set_atom_monomer ( ehandle molecule_handle, int atomnumber, ehandle monomer )
input

molecule_handle

atomnumber

monomer
output

none

TRUE:success

FALSE:failure

eslc_bit_atom_monomer

Verify that the monomer is set for an atom.

form

int eslc_bit_atom_monomer ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

TRUE:monomer is set

FALSE:monomer is not set

eslc_set_atom_isotope

Set the isotope of an atom. If the isotope is not set, then the atom is assumed to have the normal isotope or isotopic mixture for that element.

form

int eslc_set_atom_isotope ( ehandle molecule_handle, int atomnumber, int isotope )
input

molecule_handle

atomnumber

isotope
output

none
return

TRUE:success

FALSE:failure

eslc_get_atom_isotope

Get the isotope of an atom. If this is zero, then the atom should be assumed to have the normal isotope or isotopic mixture for that element.

form

int eslc_get_atom_isotope ( ehandle molecule_handle, int atomnumber, int *isotope )
input

molecule_handle

atomnumber
output

isotope
return

TRUE:success

FALSE:failure

eslc_bit_atom_isotope

Verify that the isotope is set for an atom.

form

int eslc_bit_atom_isotope ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

TRUE:isotope is set

FALSE:isotope is not set

eslc_set_atom_vdwradius

Set the van der Waals radius of an atom.

form

int eslc_set_atom_vdwradius ( ehandle molecule_handle, int atomnumber, float vdwradius )
input

molecule_handle

atomnumber

vdw radius
output

none
return

TRUE:success

FALSE:failure

eslc_get_atom_vdwradius

Get the van der Waals radius of an atom.

form

int eslc_get_atom_vdwradius ( ehandle molecule_handle, int atomnumber, float *vdwradius )
input

molecule_handle

atomnumber
output

vdw radius
return

TRUE:success

FALSE:failure

eslc_set_atom_all_vdwradii

Set the van der Waals radii of all atoms.

form

int eslc_set_atom_all_vdwradii ( ehandle molecule_handle, float *vdwradii )
input

molecule_handle

vdw radii
output

none
return

TRUE:success

FALSE:failure

eslc_get_atom_all_vdwradii

Get the van der Waals radii of all atoms.

form

int eslc_get_atom_all_vdwradii ( ehandle molecule_handle, float *vdwradii )
input

molecule_handle
output

vdw radii
return

TRUE:success

FALSE:failure

eslc_bit_atom_vdwradius

Verify that the van der Waals radius is set for an atom.

form

int eslc_bit_atom_vdwradius ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

TRUE:vdw radius is set

FALSE:vdw radius is not set

Bond Attributes

eslc_set_atom_connections

Set the connections (all atom numbers bonded to) an atom.

form

int eslc_set_atom_connections ( ehandle molecule_handle, int atomnumber, Connections connections )
input

molecule_handle

atomnumber

connections
output

none
return

TRUE:success

FALSE:failure

eslc_get_atom_connections

Get the connections (all atom numbers bonded to) an atom.

form

int eslc_get_atom_connections ( ehandle molecule_handle, int atomnumber, Connections connections )
input

molecule_handle

atomnumber
output

connections
return

TRUE:success

FALSE:failure

eslc_set_atom_all_connections

Set the connections (all atom numbers bonded to) all atoms.

form

int eslc_set_atom_all_connections ( ehandle molecule_handle, Connections *connections )
input

molecule_handle

connections
output

none
return

TRUE:success

FALSE:failure

eslc_get_atom_all_connections

Get the connections (all atom numbers bonded to) all atoms.

form

int eslc_get_atom_all_connections ( ehandle molecule_handle, Connections *connections )
input

molecule_handle
output

connections
return

TRUE:success

FALSE:failure

eslc_create_atom_atom_connection

Create a new connection between two atoms.

form

int eslc_create_atom_atom_connection ( ehandle molecule_handle, int atomnumber1, int atomnumber2 )
input

molecule_handle

atomnumber1

atomnumber2
output

none
return

TRUE:success

FALSE:failure

eslc_bit_atom_connections

Verify the connections are set for an atom.

form

int eslc_bit_atom_connections ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

TRUE:connections are set

FALSE:connections are not set

eslc_set_atom_bondorders

Set the bond orders for a set of connections. See bondorders.html or core.h for a list of definitions for bond orders.

form

int eslc_set_atom_bondorders ( ehandle molecule_handle, int atomnumber, BondOrders bondorders )
input

molecule_handle

atomnumber

bondorders
output

none
return

TRUE:success

FALSE:failure

eslc_get_atom_bondorders

Get the bond orders for a set of connections. See bondorders.html or core.h for a list of definitions for bond orders.

form

int eslc_get_atom_bondorders ( ehandle molecule_handle, int atomnumber, BondOrders bondorders )
input

molecule_handle

atomnumber
output

bondorders
return

TRUE:success

FALSE:failure

eslc_set_atom_all_bondorders

Set the bond orders for all connections in a molecule. See bondorders.html or core.h for a list of definitions for bond orders.

form

int eslc_set_atom_all_bondorders ( ehandle molecule_handle, BondOrders *bondorders )
input

molecule_handle

bondorders
output

none
return

TRUE:success

FALSE:failure

eslc_get_atom_all_bondorders

Get the bond orders for all connections in a molecule. See bondorders.html or core.h for a list of definitions for bond orders.

form

int eslc_get_atom_all_bondorders ( ehandle molecule_handle, BondOrders *bondorders )
input

molecule_handle
output

bondorders
return

TRUE:success

FALSE:failure

eslc_set_atom_atom_bondorder

Set the bond order for the connection between two atoms. See bondorders.html or core.h for a list of definitions for bond orders.

form

int eslc_set_atom_atom_bondorder ( ehandle molecule_handle, int atomnumber1, int atomnumber2, float bondorder )
input

molecule_handle

atomnumber1

atomnumber2

bondorder
output

none
return

TRUE:success

FALSE:failure

eslc_get_atom_atom_bondorder

Get the bond order for the connection between two atoms. See bondorders.html or core.h for a list of definitions for bond orders.

form

int eslc_get_atom_atom_bondorder ( ehandle molecule_handle, int atomnumber1, int atomnumber2, float *bondorder )
input

molecule_handle

atomnumber1

atomnumber2
output

bondorder
return

TRUE:success

FALSE:failure

eslc_bit_atom_bondorders

Verify the bond orders are set for the connections of an atom. See bondorders.html or core.h for a list of definitions for bond orders.

form

int eslc_bit_atom_bondorders ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

TRUE:bond orders are set

FALSE:bond orders are not set

Atom Methods

eslc_atom_calculate_all_hydrogencounts

From the other attributes of the atoms in a molecule, i.e., connections, bond orders, formal charge, etc., calculate the number of hydrogens to fill the valence of each atom.

form

int eslc_atom_calculate_all_hydrogencounts ( ehandle molecule_handle )br> input

molecule_handle
output

none
return

TRUE:success

FALSE:failure

eslc_atom_fix_hydrogencount

From the other attributes of an atom, i.e., connections, bond orders, formal charge, etc., including hydrogen atoms already accounted for, calculate the number of hydrogens to fill the valence of the atom.

form

int eslc_atom_fix_hydrogencount ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

TRUE:success

FALSE:failure

eslc_atom_fix_all_hydrogencounts

From the other attributes of the atoms in a molecule, i.e., connections, bond orders, formal charge, etc., including hydrogen atoms already accounted for, calculate the number of hydrogens to fill the valence of each atom.

form

int eslc_atom_fix_all_hydrogencounts ( ehandle molecule_handle )br> input

molecule_handle
output

none
return

TRUE:success

FALSE:failure

eslc_atom_calculate_hydrogencount

From the other attributes of an atom, i.e., connections, bond orders, formal charge, etc., calculate the number of hydrogens to fill the valence of the atom.

form

int eslc_atom_calculate_hydrogencount ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

TRUE:success

FALSE:failure

eslc_atom_calculate_all_pielectrons

From the other attributes of the atoms in a molecule, i.e., connections, bond orders, formal charge, etc., calculate the number of pi electrons on each atom.

form

int eslc_atom_calculate_all_pielectrons ( ehandle molecule_handle )
input

molecule_handle
output

none
return

TRUE:success

FALSE:failure

eslc_atom_calculate_pielectrons

From the other attributes of an atom, i.e., connections, bond orders, formal charge, etc., calculate the number of pi electrons on that atom.

form

int eslc_atom_calculate_pielectrons ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

TRUE:success

FALSE:failure

eslc_atom_find_explicithydrogencount

Find and return the count of hydriogens that are explicitly bonded to the atom. This does not include hydrogen atoms implicitly bonded.

form

int eslc_atom_find_explicithydrogencount ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

count of bonded hydrogen atoms

eslc_atom_find_alphafluorinecount

Find (and return) the number of fluorines alpha to an atom.

form

int eslc_atom_find_alphafluorinecount ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

number of alpha fluorines

eslc_atom_find_betafluorinecount

Find (and return) the count of fluorines beta to an atom.

form

int eslc_atom_find_betafluorinecount ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

number of beta fluorines

eslc_atom_find_alphachlorinecount

Find (and return) the count of chlorines alpha to an atom.

form

int eslc_atom_find_alphachlorinecount ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

number of alpha chlorines

eslc_atom_find_betachlorinecount

Find (and return) the count of chlorines beta to an atom.

form

int eslc_atom_find_betachlorinecount ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

number of beta chlorines

eslc_atom_find_alphabrominecount

Find (and return) the count of bromines alpha to an atom.

form

int eslc_atom_find_alphabrominecount ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

number of alpha bromines

eslc_atom_find_betabrominecount

Find (and return) the count of bromines beta to an atom.

form

int eslc_atom_find_betabrominecount ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

number of beta bromines

eslc_atom_find_alphaiodinecount

Find (and return) the count of iodines alpha to an atom.

form

int eslc_atom_find_alphaiodinecount ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

number of alpha iodines

eslc_atom_find_betaiodinecount

Find (and return) the count of iodines beta to an atom.

form

int eslc_atom_find_betaiodinecount ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

number of beta iodines

eslc_atom_find_alphaunsaturatedatomcount

Find (and return) the count of unsaturated atoms alpha to an atom.

form

int eslc_atom_find_alphaunsaturatedatomcount ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

number of alpha unsaturated atoms

eslc_atom_find_alphaunsaturatedcarboncount

Find (and return) the count of unsaturated carbons alpha to an atom.

form

int eslc_atom_find_alphaunsaturatedcarboncount ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

number of alpha unsaturated carbons

eslc_atom_find_all_alphaandbetaatoms

Find (and return) a list of atoms that are alpha or beta to the target atom.

form

int eslc_atom_find_all_alphaandbetaatoms ( ehandle molecule_handle, int atomnumber, int *list )
input

molecule_handle

atomnumber
output

list of atom numbers
return

number of alpha and beta atoms in list

eslc_atom_find_all_alphabetaandgammaatoms

Find (and return) a list of atoms that are alpha, beta or gamma to the target atom.

form

int eslc_atom_find_all_alphabetaandgammaatoms ( ehandle molecule_handle, int atomnumber, int *list )
input

molecule_handle

atomnumber
output

list of atom numbers
return

number of alpha, beta and gamma atoms in list

eslc_atom_number_find_typename

Find (and return) the type name (a string) for an atom. See forcefields.html for a list of force field definitions supported by the toolkit.

form

char *eslc_atom_number_find_typename ( ehandle molecule_handle, int atomnumber, int forcefield )
input

atomnumber

forcefield
output

none
return

atom type name

eslc_atom_typeid_find_typename

Find (and return) the type name (a string) corresponding to an atom type id. See forcefields.html for a list of force field definitions supported by the toolkit.

form

char *eslc_atom_typeid_find_typename ( int type_id, int forcefield )
input

type_id

forcefield
output

none
return

atom type name

eslc_atom_typename_find_typeid

Find (and return) the type id corresponding to an atom type name (a string). See forcefields.html for a list of force field definitions supported by the toolkit.

form

int eslc_atom_typename_find_typeid ( char *typename, int forcefield )
input

typename

forcefield
output

none
return

atom type id

eslc_atom_number_find_officialtafftypename

Find the "official" TAFF atom type name, i.e., from the non-expanded set, for the input atom number.

form

char *eslc_atom_number_find_officialtafftypename ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

atom type name

eslc_atom_typeid_find_officialtafftypename

Find the "official" TAFF atom type name, i.e., from the non-expanded set, for the input atom type id.

form

char *eslc_atom_typeid_find_officialtafftypename ( int type_id )
input

type_id
output

none
return

atom type name

eslc_atomname_find_atomnumber

Find the atom number corresponding to the input atom name. If more than one or no atoms match that name in the molecule, FALSE is returned, else the atom number is returned.

form

int eslc_atomname_find_atomnumber ( ehandle molecule_handle, NameStr atomname )
input

molecule_handle

atomname
output

none
return

atomnumber

FALSE:failure

eslc_atomname_monomer_find_atomnumber

Find the atom number corresponding to the input atom name and monomer handle. If more than one or no atoms match that name in the monomer of the molecule, FALSE is returned, else the atom number is returned.

form

int eslc_atomname_monomer_find_atomnumber ( ehandle molecule_handle, ehandle monomer, NameStr atomname )
input

molecule_handle

monomer

atomname
output

none
return

atomnumber

FALSE:failure

eslc_atomname_monomername_find_atomnumber

Find the atom number corresponding to the input atom name and monomer name. If more than one or no atoms match that name in the monomer of the molecule, FALSE is returned, else the atom number is returned.

form

int eslc_atomname_monomername_find_atomnumber ( ehandle molecule_handle, NameStr monomername, NameStr atomname )
input

molecule_handle

monomername

atomname
output

none
return

atomnumber

FALSE:failure

eslc_atom_find_monomer_atoms

Find (and return) a list of all atoms in the monomer that the input atom is a mmember of.

form

int eslc_atom_find_monomer_atoms ( ehandle biomolecule_handle, int atomnumber, int *list )
input

biomolecule_handle

atomnumber
output

list
return

count of atoms in list

eslc_atom_range_find_allatoms

Find (and return) a list of atoms that are within maxrange distance of the source atom. An array of range distances, in one-to-one correspondance to the atom list, is also returned.

form

int eslc_atom_range_find_allatoms ( ehandle sourcemolecule_handle, int sourceatomnumber, ehandle targetmolecule_handle, float maxrange, int *list, float *range )
input

sourcemolecule_handle

sourceatomnumber

targetmolecule_handle

maxrange
output

list

range
return

count of atoms in list

eslc_atom_range_find_moleculesincontact

Find the count of (target) molecules that have atoms within a specified range of the source atom. Up to three molecules can be tested.

form

int eslc_atom_range_find_moleculesincontact ( ehandle sourcemolecule_handle, int sourceatomnumber, ehandle targetmolecule1_handle, ehandle targetmolecule2_handle, ehandle targetmolecule3_handle, int includehydrogens, float maxrange )
input

sourcemolecule_handle

sourceatomnumber

targetmolecule1_handle

targetmolecule2_handle

targetmolecule3_handle

includehydrogens TRUE/FALSE flag

range of test
output

none
return

number of molecules in contact

eslc_atom_find_ringsize

Find (and return) the ring size of the input atom. At present this algorithm will detect rings of up to eight atoms in the circuit. Note that the default value for any atom is to be in a ring of size 2.

form

int eslc_atom_find_ringsize ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

size of ring including atom

eslc_atom_find_aromaticity

Find (and return) the aromaticity status (TRUE, FALSE) of the atom. This algorithm defines aromaticity as an atom that is potentially aromatic (e.g., sp² hybridization) being the middle atom of a "chain" of at least five such atoms.

form

int eslc_atom_find_aromaticity ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

TRUE: atom is aromatic

FALSE: atom is not aromatic

eslc_atom_range_find_hydrogenbonddonoratoms

Find (and return) a list of atoms that are hydrogen bond donors and within maxrange distance of the source atom. An array of range distances, in one-to-one correspondance to the atom list, is also returned.

form

int eslc_atom_range_find_hydrogenbonddonoratoms ( ehandle sourcemolecule_handle, int sourceatomnumber, ehandle targetmolecule_handle, float maxrange, int *list, float *range )
input

sourcemolecule_handle

sourceatomnumber

targetmolecule_handle

maxrange
output

list

range
return

count of atoms in list

eslc_atom_range_find_hydrogenbondacceptoratoms

Find (and return) a list of atoms that are hydrogen bond acceptors and within maxrange distance of the source atom. An array of range distances, in one-to-one correspondance to the atom list, is also returned.

form

int eslc_atom_range_find_hydrogenbondacceptoratoms ( ehandle sourcemolecule_handle, int sourceatomnumber, ehandle targetmolecule_handle, float maxrange, int *list, float *range )
input

sourcemolecule_handle

sourceatomnumber

targetmolecule_handle

maxrange
output

list

range
return

count of atoms in list

eslc_atom_seed_find_bondedmolecule_atoms

Find (and return) a list of atoms that comprise a bonded molecule that contains the "seed" atom. For example, identifying one atom of a solvent, i.e., water, that is part of a "larger" molecule object, will return a list of all of the atoms of that solvent molecule. This list can later be used to create an independent molecule object for the solvent. Note: this routine will truncate atoms more than five bonds away from the "seed" atom and thus is most effective for "smaller" bonded molecules, in contrast to eslc_atom_path_find_bondedmolecule_atoms which will generally find molecules of any size.

form

int eslc_atom_seed_find_bondedmolecule_atoms ( ehandle molecule_handle, int atomnumber, int *list )
input

molecule_handle

atomnumber
output

list
return

count of atoms in list

eslc_atom_path_find_bondedmolecule_atoms

Find (and return) a list of atoms that comprise a bonded molecule having a "path" to the input atom. For example, identifying one atom of a solvent, i.e., water, that is part of a "larger" molecule object, will return a list of all of the atoms of that solvent molecule. This list can later be used to create an independent molecule object for the solvent. Note: this routine performs an exhaustive path search of all atoms in the molecule object to determine "bondedness". It is thus computationally inefficient to use this routine to identify, for example, a single water molecule within a protein molecule object. Use eslc_atom_seed_find_bondedmolecule_atoms instead.

form

int eslc_atom_path_find_bondedmolecule_atoms ( ehandle molecule_handle, int atomnumber, int *list )
input

molecule_handle

atomnumber
output

list
return

count of atoms in list

eslc_atom_find_fullspecificationstring

Return a string that is the formatted "full" specification for the atom. This includes chain, monomer, and atom name descriptors. The string will be justified according to the justify parameter.

form

char *eslc_atom_find_fullspecificationstring ( ehandle biomolecule_handle, int atomnumber, int justify )
input

biomolecule_handle

atomnumber

justify
output

none
return

atom specification string

eslc_atom_taffbondtype_find_bondorder

Return the (float) bond order for a TAFF bond type.

form

float eslc_atom_taffbondtype_find_bondorder ( char *taffbondtype )
input

taffbondtype
output

none
return

bond order

eslc_atom_cvffbondtype_find_bondorder

Return the (float) bond order for a CVFF bond type.

form

float eslc_atom_cvffbondtype_find_bondorder ( int cvffbondtype )
input

cvffbondtype
output

none
return

bond order

eslc_atom_bondorder_find_taffbondtype

Return the string naming the TAFF bond order from the internal (float) bond order.

form

char *eslc_atom_bondorder_find_taffbondtype ( float bondorder )
input

bondorder
output

none
return

bond order name

eslc_atom_bondorder_find_cvffbondtype

Return the integer code for the CVFF bond order from the internal (float) bond order.

form

int eslc_atom_bondorder_find_cvffbondtype ( float bondorder )
input

bondorder
output

none
return

bond order code

eslc_atom_bondorder_find_mconnbondtype

Return the string naming the Molconn-Z bond order from the internal (float) bond order.

form

char *eslc_atom_bondorder_find_mconnbondtype ( float bondorder )
input

bondorder
output

none
return

bond order name

eslc_atom_typeid_find_hydrogenadjustedtypeid

Return the atom type_id for atoms that have 1, 2 or 3 more (if positive) or less (if negative) hydrogens than the current atom type_id. See forcefields.html for a list of force field definitions supported by the toolkit.

form

int eslc_atom_typeid_find_hydrogenadjustedtypeid ( int type_id, int hydrogenadjustment, int forcefield )
input

type_id

hydrogenadjustment

forcefield
output

none
return

new type_id

eslc_atom_is_polarhydrogen

Determine if the atom is a polar hydrogen, i.e., attached to a polar heavy atom (N, O, P, S, etc.).

form

int eslc_atom_is_polarhydrogen ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

TRUE: atom is polar hydrogen

FALSE: atom is not polar hydrogen

eslc_atom_is_nonpolarhydrogenalphatohetero

Determine if the atom is a nonpolar hydrogen alpha to a hetero atom. These atoms may have some hydrogen-bonding ability and are treated as polar with the "semi-essential" hydrogen partitioning.

form

int eslc_atom_is_nonpolarhydrogenalphatohetero ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

TRUE: atom is nonpolar hydrogen alpha to a hetero atom

FALSE: atom is not nonpolar hydrogen alpha to a hetero atom

eslc_atom_is_nonpolarhydrogenonunsaturatedcenter

Determine if the atom is a nonpolar hydrogen on an unsaturated center. These atoms may have some hydrogen-bonding ability and are treated as polar with the "semi-essential" hydrogen partitioning.

form

int eslc_atom_is_nonpolarhydrogenonunsaturatedcenter ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

TRUE: atom is nonpolar hydrogen on an unsaturated center

FALSE: atom is not nonpolar hydrogen on an unsaturated center

eslc_atom_typeid_update_atomproperties

Given an atom, where the typeid has been determined through indirect means, e.g., reading a file containing atom type codes, this routine will update other atomic properties to be consistent with the atom type. The atomic number, implicit hydrogens, pi electron count and formal charge are set. See forcefields.html for a list of force field definitions supported by the toolkit.

form

int eslc_atom_typeid_update_atomproperties ( ehandle molecule_handle, int atomnumber, int forcefield )
input

molecule_handle

atomnumber

forcefield
output

none
return

TRUE:success

FALSE:failure

eslc_find_atom_atom_distance

Calculate and return the distance (in Angstroms) between two atoms that are in the same or different molecule objects.

form

float eslc_find_atom_atom_distance ( ehandle molecule1_handle, int atomnumber1, ehandle molecule2_handle, int atomnumber2 )
input

molecule1_handle

atomnumber1

molecule2_handle

atomnumber2
output

none
return

atom-atom distance in Angstroms

eslc_find_minimum_atom_molecule_distance

Calculate and return the minimum distance between an atom in one molecule object and all atoms in a second molecule object. The atom number of that closest atom (in the second molecule object) is also returned.

form

float eslc_find_minimum_atom_molecule_distance ( ehandle molecule1_handle, int atomnumber1, ehandle molecule2_handle, int *closestatom )
input

molecule1_handle

atomnumber1

molecule2_handle
output

closest atom
return

atom-atom distance in Angstroms

eslc_find_maximum_atom_molecule_distance

Calculate and return the maximum distance between an atom in one molecule object and all atoms in a second molecule object. The atom number of that farthest atom (in the second molecule object) is also returned.

form

float eslc_find_maximum_atom_molecule_distance ( ehandle molecule1_handle, int atomnumber1, ehandle molecule2_handle, int *farthestatom )
input

molecule1_handle

atomnumber1

molecule2_handle
output

farthest atom
return

atom-atom distance in Angstroms

eslc_atom_torsion_find_rotatingatoms

Using as a torsion angle (defined by anchor and swing atoms) create a list of atoms that will be rotated when the torsion angle is varied.

form

int eslc_atom_torsion_find_rotatingatoms ( ehandle molecule_handle, int anchoratom, int swingatom, int *list )
input

molecule_handle

anchor atomnumber

swing atomnumber
output

list of atoms
return

number of atoms in list

eslc_atom_invent_name

Invent an atom name for the atom by combining the element type with the atom number.

form

int eslc_atom_invent_name ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

none

eslc_atom_invent_all_names

Invent atom names for all atoms in the molecule by combining the element types with the atom numbers.

form

int eslc_atom_invent_all_names ( ehandle molecule_handle )
input

molecule_handle
output

none
return

none

eslc_atom_add_explicit_hydrogens

Convert implicit hydrogens to explicit hydrogens for the named atom. Best estimate geometries will be applied, but structural optimization is recommended in many cases.

form

int eslc_atom_add_explicit_hydrogens ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

TRUE: requisite atoms were added to molecule

FALSE: requisite atoms were not added to molecule

eslc_atom_delete_explicit_hydrogens

Convert explicit hydrogens to implicit hydrogens for the named atom.

form

int eslc_atom_delete_explicit_hydrogens ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

TRUE: requisite atoms were deleted from molecule

FALSE: requisite atoms were not deleted from molecule

eslc_atom_find_explicithydrogens

Create a list of explicit hydrogens bonded to named atom.

form

int eslc_atom_find_explicithydrogens ( ehandle molecule_handle, int atomnumber, int *atomlist )
input

molecule_handle

atomnumber
output

list of bonded hydrogens
return

number of atoms in list

eslc_atom_set_null_properties

Set "null" properties for an atom, i.e., having no mass, charge, bonds, etc.

form

int eslc_atom_set_null_properties ( ehandle molecule_handle, int atomnumber )
input

molecule_handle

atomnumber
output

none
return

TRUE: atom was nulled

FALSE: atoms was not nulled

eslc_atom_swingatom_find_anchoratom

Identify the unique anchor atom for a torsion (if one exists).

form

int eslc_atom_swingatom_find_anchoratom ( ehandle molecule_handle, int swingatomnumber )
input

molecule_handle

swing atomnumber
output

none
return

TRUE: atom number of anchor

FALSE: no unique anchor

eduSoft LC Toolkit Programmers' Guide

Atom Objectss

Header File

Atom Attributes

Bond Attributes

Atom Methods