Molconn-Z 4.00 Manual: Toolkit Programmers Guide

eduSoft LC Toolkit Programmers' Guide

Molecule Objects

Molecule Creation

eslc_create_molecule

Create a new molecule object and add it to the registered molecules list.

form

int eslc_create_molecule ( ehandle *molecule_handle )
input

none
output

molecule_handle
return

TRUE:success

FALSE:failure

eslc_delete_molecule

Delete an existing molecule object and remove it from the registered molecules list.

form

eslc_delete_molecule ( ehandle molecule_handle )
input

molecule_handle
output

none
return

TRUE:success

FALSE:failure

eslc_molecule_copy_molecule

Copy the data of a molecule object into a second molecule object that has previously been created.

form

int eslc_molecule_copy_molecule ( ehandle molecule_handle_old, ehandle molecule_handle_new, ehandle *atom_structure_handle_new )
input

molecule_handle_old

molecule_handle_new
output

atom_structure_handle_new
return

TRUE:success

FALSE:failure

eslc_molecule_copy_to_biomolecule

Copy the data of a molecule object into a new biomolecule object. Only biomolecules can support monomer structure, so this is one way to add substructure information to a molecule object.

form

int eslc_molecule_copy_to_biomolecule ( ehandle molecule_handle, ehandle *biomolecule_handle )
input

molecule_handle

biomolecule_handle
output

none
return

TRUE:success

FALSE:failure

eslc_molecule_copy_hydrogensuppressedmolecule

Copy the data of a molecule object into a second molecule object that has previously been created. The second molecule will be hydrogen-suppressed, that is, it will use united atom types.

form

int eslc_molecule_copy_hydrogensuppressedmolecule ( ehandle molecule_handle_old, ehandle molecule_handle_new, ehandle *atom_structure_handle_new )
input

molecule_handle_old

molecule_handle_new
output

atom_structure_handle_new
return

TRUE:success

FALSE:failure

eslc_molecule_copy_essentialatomsonlymolecule

Copy the data of a molecule object into a second molecule object that has previously been created. The second molecule will feature only heavy atoms and essential hydrogens, that is, it will use united atom types for apolar heavy atoms (carbon or silicon) and explicit hydrogens in all other cases.

form

int eslc_molecule_copy_essentialatomsonlymolecule ( ehandle molecule_handle_old, ehandle molecule_handle_new, ehandle *atom_structure_handle_new )
input

molecule_handle_old

molecule_handle_new
output

atom_structure_handle_new
return

TRUE:success

FALSE:failure

eslc_molecule_create_taff_water

Create a molecule object that contains one molecule of water. Use TAFF atom and bond type definitions for the molecule.

form

int eslc_molecule_create_taff_water ( ehandle *water_molecule_handle )
input

none
output

water_molecule_handle
return

TRUE:success

eslc_molecule_create_cvff_water

Create a molecule object that contains one molecule of water. Use CVFF atom and bond type definitions for the molecule.

form

int eslc_molecule_create_cvff_water ( ehandle *water_molecule_handle )
input

none
output

water_molecule_handle
return

TRUE:success

Molecule Attributes

eslc_set_molecule_name

Set the name of a molecule.

form

int eslc_set_molecule_name ( ehandle molecule_handle, char *molname )
input

molecule_handle

molecule name
output

none
return

TRUE:success

FALSE:failure

eslc_get_molecule_name

Get the name of a molecule.

form

int eslc_get_molecule_name ( ehandle molecule_handle, char *molname )
input

molecule_handle
output

molecule name
return

TRUE:success

FALSE:failure

eslc_bit_molecule_name

Verify the molecule name has been set.

form

int eslc_bit_molecule_name ( ehandle molecule_handle )
input

molecule_handle
output

none
return

TRUE:name has been set

FALSE:name has not been set

eslc_set_molecule_forcefield

Set the forcefield name associated with the molecule. See forcefields.html for a list of force field definitions supported by the toolkit.

form

int eslc_set_molecule_forcefield ( ehandle molecule_handle, int forcefield )
input

molecule_handle

forcefield
output

none
return

TRUE:success

FALSE:failure

eslc_get_molecule_forcefield

Get the forcefield name associated with the molecule. See forcefields.html for a list of force field definitions supported by the toolkit.

form

int eslc_get_molecule_forcefield ( ehandle molecule_handle, int *forcefield )
input

molecule_handle
output

forcefield
return

TRUE:success

FALSE:failure

eslc_set_molecule_atomcount

Set the number of atoms in a molecule.

form

int eslc_set_molecule_atomcount ( ehandle molecule_handle, int atomcount )
input

molecule_handle

atomcount
output

none
return

TRUE:success

FALSE:failure

eslc_get_molecule_atomcount

Get the number of atoms in a molecule.

form

int eslc_get_molecule_atomcount ( ehandle molecule_handle, int *atomcount )
input

molecule_handle
output

atomcount
return

TRUE:success

FALSE:failure

eslc_bit_molecule_atomcount

Verify the molecule atomcount has been set.

form

int eslc_bit_molecule_atomcount ( ehandle molecule_handle )
input

molecule_handle
output

none
return

TRUE:atomcount has been set

FALSE:atomcount has not been set

eslc_molecule_create_atoms

Create an object containing the atoms for a molecule.

form

int eslc_molecule_create_atoms ( ehandle molecule_handle, ehandle *atom_structure_handle )
input

molecule_handle
output

atom_structure_handle
return

TRUE:success

FALSE:failure

eslc_get_molecule_atoms

Get the atom object handle for a molecule.

form

int eslc_get_molecule_atoms ( ehandle molecule_handle, ehandle *atom_structure_handle )
input

molecule_handle
output

atom_structure_handle
return

TRUE:success

FALSE:failure

eslc_bit_molecule_atoms

Verify the molecule atoms object has been created.

form

int eslc_bit_molecule_atoms ( ehandle molecule_handle )
input

molecule_handle
output

none
return

TRUE:atoms object has been created

FALSE:atoms object has not been created

eslc_set_molecule_bondcount

Set the number of bonds in a molecule.

form

int eslc_set_molecule_bondcount ( ehandle molecule_handle, int bondcount )
input

molecule_handle

bondcount
output

none
return

TRUE:success

FALSE:failure

eslc_get_molecule_bondcount

Get the number of bonds in a molecule.

form

int eslc_get_molecule_bondcount ( ehandle molecule_handle, int *bondcount )
input

molecule_handle
output

bondcount
return

TRUE:success

FALSE:failure

eslc_bit_molecule_bondcount

Verify the molecule bondcount has been set or otherwise determined.

form

int eslc_bit_molecule_bondcount ( ehandle molecule_handle )
input

molecule_handle
output

none
return

TRUE:bondcount has been set

FALSE:bondcount has not been set

Molecule Methods

eslc_molecule_create_atoms

Create an object containing the atoms for a molecule.

form

int eslc_molecule_create_atoms ( ehandle molecule_handle, ehandle *atom_structure_handle )
input

molecule_handle
output

atom_structure_handle
return

TRUE:success

FALSE:failure

eslc_molecule_delete_atoms

Delete the object containing the atoms for a molecule.

form

int eslc_molecule_delete_atoms ( ehandle molecule_handle )
input

molecule_handle
output

none
return

TRUE:success

FALSE:failure

eslc_molecule_delete_specifiedatoms

Delete specified atoms in the object containing the atoms for a molecule.

form

int eslc_molecule_delete_specifiedatoms ( ehandle molecule_handle, int deletedatomcount, int *deletelist )
input

molecule_handle

deletedatomcount
output

deletelist
return

TRUE:success

FALSE:failure

eslc_molecule_verify_connections

Check the symmetry and other aspects of the connection matrix.

form

int eslc_molecule_verify_connections ( ehandle molecule_handle )
input

molecule_handle
output

none
return

TRUE:connection matrix is OK

FALSE:connection matrix is flawed

eslc_molecule_calculate_molweight

Calculate the molecular weight of a molecule.

form

int eslc_molecule_calculate_molweight ( ehandle molecule_handle )
input

molecule_handle
output

none
return

TRUE:success

FALSE:failure

eslc_get_molecule_molweight

Get the molcular weight of a molecule.

form

int eslc_get_molecule_molweight ( ehandle molecule_handle, float *molecularweight )
input

molecule_handle
output

molecularweight
return

TRUE:success

FALSE:failure

eslc_bit_molecule_molweight

Verify that the emolecular weight has been calculated.

form

int eslc_bit_molecule_molweight ( ehandle molecule_handle )
input

molecule_handle
output

none
return

TRUE:molecular weight has been calculated

FALSE:molecular weight has not been calculated

eslc_calculate_molecule_formula

Calculate the molecular formula of a molecule.

form

int eslc_calculate_molecule_formula ( ehandle molecule_handle )
input

molecule_handle
output

none
return

TRUE:success

FALSE:failure

eslc_molecule_find_formula_string

Find (and return as a string) the molecular formula of a molecule.

form

char *eslc_molecule_find_formula_string ( ehandle molecule_handle )
input

molecule_handle
output

none
return

a string in the format H(x)C(y)O(z)

eslc_bit_molecule_formula

Verify that the molecular formula has been calculated.

form

int eslc_bit_molecule_formula ( ehandle molecule_handle )
input

molecule_handle
output

none
return

TRUE:molecular formula has been calculated

FALSE:molecular formula has not been calculated

eslc_molecule_find_all_waters

Find (and return) the count of water "molecules" in the molecule object.

form

int eslc_molecule_find_all_waters ( ehandle molecule_handle, int *waterlist )
input

molecule_handle
output

waterlist
return

water count

eslc_molecule_find_atomcount_by_atomicnumber

Find (and return) the count of atoms in the molecule object for the input atomic number (i.e., element).

form

int eslc_molecule_find_atomcount_by_atomicnumber ( ehandle molecule_handle, int atomicnumber )
input

molecule_handle

atomicnumber
output

none
return

atom count

eslc_molecule_find_heavyatomcount

Find (and return) the number of heavy, i.e., non-hydrogen, atoms in a molecule.

form

int eslc_molecule_find_heavyatomcount ( ehandle molecule_handle )
input

molecule_handle
output

none
return

count of heavy atoms

eslc_molecule_find_essentialatomcount

Find (and return) the number of essential atoms in a molecule. Hydrogen atoms bonded to carbon or silicon are not counted.

form

int eslc_molecule_find_essentialatomcount ( ehandle molecule_handle )
input

molecule_handle
output

none
return

count of heavy atoms

eslc_molecule_find_organicatomcount

Find (and return) the number of orgainic, i.e., H, B, C, N, O, F, Si, P, S, Cl, Br and I, atoms in a molecule.

form

int eslc_molecule_find_organicatomcount ( ehandle molecule_handle )
input

molecule_handle
output

none
return

count of organic atoms

eslc_molecule_find_nonorganicatomcount

Find (and return) the number of non-organic, i.e., not H, B, C, N, O, F, Si, P, S, Cl, Br and I, atoms in a molecule.

form

int eslc_molecule_find_nonorganicatomcount ( ehandle molecule_handle )
input

molecule_handle
output

none
return

count of non-organic atoms

eslc_molecule_find_alkalimetalatomcount

Find (and return) the number of alkali metal atoms (i.e., Li, Be, Na, etc.) in a molecule.

form

int eslc_molecule_find_alkalimetalatomcount ( ehandle molecule_handle )
input

molecule_handle
output

none
return

count of alkali metal atoms

eslc_molecule_find_transitionmetalatomcount

Find (and return) the number of transition metal (d-block) atoms in a molecule.

form

int eslc_molecule_find_transitionmetalatomcount ( ehandle molecule_handle )
input

molecule_handle
output

none
return

count of transition metal atoms

eslc_molecule_find_lanthanidemetalatomcount

Find (and return) the number of lanthanide metal (4f block) atoms in a molecule.

form

int eslc_molecule_find_lanthanidemetalatomcount ( ehandle molecule_handle )
input

molecule_handle
output

none
return

count of lanthanide metal atoms

eslc_molecule_find_actinidemetalatomcount

Find (and return) the number of actinide metal (5f block) atoms in a molecule.

form

int eslc_molecule_find_actinidemetalatomcount ( ehandle molecule_handle )
input

molecule_handle
output

none
return

count of actinide metal atoms

eslc_molecule_find_all_rotatablepolarhydrogens

Create a list of "rotatable" polar atoms containing hydrogens within the molecule. Rotatable polar atoms include -OH, -SH, -NH₂ and -PH₂. Each rotatable atom is specified by a torsion with two parameters: the anchor atom that is the end of the torsion attached to the rest of the molecule and the swing atom that the hydrogens are bonded to. These can be potentially rotated within the molecule to improve hydrogen-bond overlap intermolecularly or intramolecularly.

form

int eslc_molecule_find_all_rotatablepolarhydrogens ( ehandle molecule_handle, int *anchorlist, int *swinglist )
input

molecule_handle
output

swinglist

anchorlist
return

count of rotatable polar hydrogens

eslc_molecule_find_all_XR2

Find (and return) the number of XR₂, where X=N and X=P atoms, in a molecule.

form

int eslc_molecule_find_all_XR2 ( ehandle molecule_handle, int *ionizationstates, int *anchorlist, int *swinglist )
input

molecule_handle
output

ionizationstates

anchorlist

swinglist
return

count of XR2 atoms:success

eslc_molecule_find_all_RXH

Find (and return) the number of RXH, where X=O and X=S, atoms in a molecule.

form

int eslc_molecule_find_all_RXH ( ehandle molecule_handle, int *ionizationstates, int *anchorlist, int *swinglist )
input

molecule_handle
output

ionizationstates

anchorlist

swinglist
return

count of RXH atoms:success

eslc_molecule_find_all_carboxylates

Find (and return) the number of carboxylate/carboxylic acid groups in a molecule. The two swing atoms are the two oxygen atoms of the group.

form

int eslc_molecule_find_all_carboxylates ( ehandle molecule_handle, int *ionizationstates, int *anchorlist, int *swinglist1, int *swinglist2 )
input

molecule_handle
output

ionizationstates

anchorlist

swinglist1

swinglist2
return

count of carboxylate atoms:success

eslc_molecule_calculate_taffatomtypes

Assign TAFF atom types to all atoms in the molecule based on the atomic and bond-order properties. See atomtypeid.html or atom.h for a description of the atom types.

form

int eslc_molecule_calculate_taffatomtypes ( ehandle molecule_handle )
input

molecule_handle
output

none
return

TRUE:success

FALSE:failure

eslc_molecule_calculate_cvffatomtypes

Assign CVFF atom types to all atoms in the molecule based on the atomic and bond-order properties. See atomtypeid.html or atom.h for a description of the atom types.

form

int eslc_molecule_calculate_cvffatomtypes ( ehandle molecule_handle )
input

molecule_handle
output

none
return

TRUE:success

FALSE:failure

eslc_molecule_translate

Translate all atoms in the molecule object by the input x, y and z values.

form

int eslc_molecule_translate ( ehandle molecule_handle, float x, float y, float z )
input

molecule_handle

z
output

none
return

TRUE:success

FALSE:failure

eslc_molecule_rotate

Rotate all atoms in the molecule object by the input alpha, beta and gamma angles. Important notes: 1) These angles are in radians, not degrees (2 pi = 360^o); b) alpha is defined as the angle of rotation around the x axis (positive alpha is rotation from the y axis towards the z axis), beta is defined as the angle of rotation around the y axis (positive beta is rotation from the z axis towards the x axis), gamma is defined as the angle of rotation around the z axis (positive gamma is rotation from the x axis towards the y axis).

form

int eslc_molecule_rotate ( ehandle molecule_handle, float alpha, float beta, float gamma )
input

molecule_handle

alpha

beta

gamma
output

none
return

TRUE:success

FALSE:failure

eslc_molecule_calculate_centerofgravity

Calculate and return the center of gravity for the molecule object. If weighting is on (TRUE), then this is a true center of gravity, i.e., including the atomic masses; if weighting is off (FALSE), then only the atomic positions are used in the calculation.

form

int eslc_molecule_calculate_centerofgravity ( ehandle molecule_handle, int weighting, float *xcen, float *ycen, float *zcen )
input

molecule_handle

weighting
output

xcen

ycen

zcen
return

TRUE:success

FALSE:failure

eslc_molecule_range_find_atomcount

Calculate and return the number of atoms in the target molecule that are within a specified maxrange (Angstroms) from the atoms of the source molecule.

form

int eslc_molecule_range_find_atomcount ( ehandle sourcemolecule_handle, ehandle targetmolecule_handle, float maxrange )
input

sourcemolecule_handle

targetmolecule_handle

maxrange
output

none
return

count of atoms

eslc_molecule_range_find_allatoms

Calculate and return a list of atoms (and the corresponding ranges) in the target molecule that are within a specified maxrange (Angstroms) from the atoms of the source molecule.

form

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

sourcemolecule_handle

targetmolecule_handle

maxrange
output

list

range return

count of atoms

eslc_molecule_range_find_monomercount

Find and return the number of monomers in the target biomolecule that are within "maxrange" of the atoms in the source molecule.

form

int eslc_molecule_range_find_monomercount ( ehandle sourcemolecule_handle, ehandle targetbiomolecule_handle, float maxrange )
input

sourcemolecule_handle

targetbiomolecule_handle

maxrange
output

none
return

count of monomers

eslc_molecule_range_find_allmonomers

Find and return a list of monomer (handles) in the target biomolecule that are within "maxrange" of the atoms in the source molecule.

form

int eslc_molecule_range_find_allmonomers ( ehandle sourcemolecule_handle, ehandle targetbiomolecule_handle, float maxrange, ehandle *monomerlist )
input

sourcemolecule_handle

targetbiomolecule_handle

maxrange
output

monomerlist
return

count of all monomers

eslc_molecule_range_find_allmonomernumbers

Find and return a list of monomer (numbers) in the target biomolecule that are within "maxrange" of the atoms in the source molecule.

form

int eslc_molecule_range_find_allmonomernumbers ( ehandle sourcemolecule_handle, ehandle targetbiomolecule_handle, float maxrange, int *monomernumberlist )
input

sourcemolecule_handle

targetbiomolecule_handle

maxrange
output

monomernumberlist
return

count

BioMolecule Objects

BioMolecule Creation

eslc_create_biomolecule

Create a new biomolecule object and add it to the registered molecules list.

form

int eslc_create_biomolecule ( ehandle *biomolecule_handle )
input

none
output

biomolecule_handle
return

TRUE:success

FALSE:failure

eslc_delete_biomolecule

Delete the specified biomolecule object. The disposition of the inherent biomolecule monomers is controlled by the monomerdisposition parameter. See monomer.h or monomersrc.html for more information.

form

int eslc_delete_biomolecule ( ehandle biomolecule_handle, int monomerdisposition )
input

biomolecule_handle

monomerdisposition
output

none
return

TRUE:success

FALSE:failure

eslc_biomolecule_copy_biomolecule

Copy the specified (old) biomolecule into a new biomolecule object. The disposition of the inherent biomolecule monomers is controlled by the monomerdisposition parameter. See monomer.h or monomersrc.html for more information.

form

int eslc_biomolecule_copy_biomolecule ( ehandle biomolecule_handle_old, ehandle biomolecule_handle_new, int monomerdisposition, ehandle *atom_structure_handle_new )
input

biomolecule_handle_old

biomolecule_handle_new

monomerdisposition
output

atom_structure_handle_new
return

TRUE:success

FALSE:failure

eslc_biomolecule_copy_hydrogensuppressedbiomolecule

Copy the data of a biomolecule object into a second biomolecule object that has previously been created. The second biomolecule will be hydrogen-suppressed, that is, it will use united atom types.

form

int eslc_biomolecule_copy_hydrogensuppressedbiomolecule ( ehandle biomolecule_handle_old, ehandle biomolecule_handle_new, ehandle *atom_structure_handle_new )
input

biomolecule_handle_old

biomolecule_handle_new
output

atom_structure_handle_new
return

TRUE:success

FALSE:failure

eslc_biomolecule_copy_essentialatomsonlybiomolecule

Copy the data of a biomolecule object into a second biomolecule object that has previously been created. The second biomolecule will feature only heavy atoms and essential hydrogens, that is, it will use united atom types for apolar heavy atoms (carbon or silicon) and explicit hydrogens in all other cases.

form

int eslc_biomolecule_copy_essentialatomsonlybiomolecule ( ehandle biomolecule_handle_old, ehandle biomolecule_handle_new, ehandle *atom_structure_handle_new )
input

biomolecule_handle_old

biomolecule_handle_new
output

atom_structure_handle_new
return

TRUE:success

FALSE:failure

eslc_biomolecule_copy_specifiedmonomersbiomolecule

Copy the data of specified monomers in a biomolecule object into a second biomolecule object that has previously been created.

form

int eslc_biomolecule_copy_specifiedmonomersbiomolecule ( ehandle biomolecule_handle_old, ehandle biomolecule_handle_new, int monomercount, ehandle *monomerlist, ehandle *atom_structure_handle_new )
input

biomolecule_handle_old

biomolecule_handle_new

monomercount

monomerlist
output

atom_structure_handle_new
return

TRUE:success

FALSE:failure

BioMolecule Attributes

eslc_set_biomolecule_name

Set the name of a biomolecule.

form

int eslc_set_biomolecule_name ( ehandle biomolecule_handle, char *molname )
input

biomolecule_handle

molname
output

none
return

TRUE:success

FALSE:failure

eslc_get_biomolecule_name

Get the name of a biomolecule.

form

int eslc_get_biomolecule_name ( ehandle biomolecule_handle, char *molname )
input

biomolecule_handle
output

molname
return

TRUE:success

FALSE:failure

eslc_bit_biomolecule_name

Verify the biomolecule name has been set.

form

int eslc_bit_biomolecule_name ( ehandle biomolecule_handle )
input

molecule_handle
output

none
return

TRUE:name has been set

FALSE:name has not been set

eslc_set_biomolecule_forcefield

Set the forcefield name associated with the biomolecule. See forcefields.html for a list of force field definitions supported by the toolkit.

form

int eslc_set_biomolecule_forcefield ( ehandle biomolecule_handle, int forcefield )
input

biomolecule_handle

forcefield
output

none
return

TRUE:success

FALSE:failure

eslc_get_biomolecule_forcefield

Get the forcefield name associated with the biomolecule. See forcefields.html for a list of force field definitions supported by the toolkit.

form

int eslc_get_biomolecule_forcefield ( ehandle biomolecule_handle, int *forcefield )
input

biomolecule_handle
output

forcefield
return

TRUE:success

FALSE:failure

eslc_set_biomolecule_atomcount

Set the number of atoms in a biomolecule.

form

int eslc_set_biomolecule_atomcount ( ehandle biomolecule_handle, int atomcount )
input

biomolecule_handle

atomcount
output

none
return

TRUE:success

FALSE:failure

eslc_get_biomolecule_atomcount

Get the number of atoms in a biomolecule.

form

int eslc_get_biomolecule_atomcount ( ehandle biomolecule_handle, int *atomcount )
input

biomolecule_handle
output

atomcount
return

TRUE:success

FALSE:failure

eslc_bit_biomolecule_atomcount

Verify the biomolecule atomcount has been set.

form

int eslc_bit_biomolecule_atomcount ( ehandle biomolecule_handle )
input

biomolecule_handle
output

none
return

TRUE:atomcount has been set

FALSE:atomcount has not been set

eslc_get_biomolecule_atoms

Get the atom object handle for a biomolecule.

form

int eslc_get_biomolecule_atoms ( ehandle biomolecule_handle, ehandle *atom_structure_handle )
input

biomolecule_handle
output

atom_structure_handle
return

TRUE:success

FALSE:failure

eslc_bit_biomolecule_atoms

Verify the biomolecule atoms object has been created.

form

int eslc_bit_biomolecule_atoms ( ehandle biomolecule_handle )
input

biomolecule_handle
output

none
return

TRUE:atoms object has been created

FALSE:atoms object has not been created

eslc_set_biomolecule_bondcount

Set the number of bonds in a biomolecule.

form

int eslc_set_biomolecule_bondcount ( ehandle biomolecule_handle, int bondcount )
input

biomolecule_handle

bondcount
output

none
return

TRUE:success

FALSE:failure

eslc_get_biomolecule_bondcount

Get the number of bonds in a biomolecule.

form

int eslc_get_biomolecule_bondcount ( ehandle biomolecule_handle, int *bondcount )
input

biomolecule_handle
output

bondcount
return

TRUE:success

FALSE:failure

eslc_bit_biomolecule_bondcount

Verify the biomolecule bondcount has been set or otherwise determined.

form

int eslc_bit_biomolecule_bondcount ( ehandle biomolecule_handle )
input

biomolecule_handle
output

none
return

TRUE:bondcount has been set

FALSE:bondcount has not been set

eslc_set_biomolecule_monomercount

Set the number of monomers in a biomolecule.

form

int eslc_set_biomolecule_monomercount ( ehandle biomolecule_handle, int monomercount )
input

biomolecule_handle

monomercount
output

none
return

TRUE:success

FALSE:failure

eslc_get_biomolecule_monomercount

Get the number of monomers in a biomolecule.

form

int eslc_get_biomolecule_monomercount ( ehandle biomolecule_handle, int *monomercount )
input

biomolecule_handle
output

monomercount
return

TRUE:success

FALSE:failure

eslc_bit_biomolecule_monomercount

Verify the biomolecule monomercount has been set or otherwise determined.

form

int eslc_bit_biomolecule_monomercount ( ehandle biomolecule_handle )
input

biomolecule_handle
output

none
return

TRUE:monomercount has been set

FALSE:monomercount has not been set

eslc_get_biomolecule_all_monomers

Get the handles for all monomers in the biomolecule object.

form

int eslc_get_biomolecule_all_monomers ( ehandle biomolecule_handle, ehandle *monomers )
input

biomolecule_handle
output

monomers
return

TRUE:success

FALSE:failure

eslc_get_biomolecule_monomer

Get the handle for a monomer in the biomolecule object.

form

int eslc_get_biomolecule_monomer ( ehandle biomolecule_handle, int monomernumber, ehandle *monomer )
input

biomolecule_handle

monomernumber
output

monomer
return

TRUE:success

FALSE:failure

BioMolecule Methods

eslc_biomolecule_create_atoms

Create an object containing the atoms for a biomolecule.

form

int eslc_biomolecule_create_atoms ( ehandle biomolecule_handle, ehandle *atom_structure_handle )
input

biomolecule_handle
output

atom_structure_handle
return

TRUE:success

FALSE:failure

eslc_biomolecule_delete_atoms

Delete the object containing the atoms for a biomolecule.

form

int eslc_biomolecule_delete_atoms ( ehandle biomolecule_handle )
input

biomolecule_handle
output

none
return

TRUE:success

FALSE:failure

eslc_biomolecule_verify_connections

Check the symmetry and other aspects of the connection matrix.

form

int eslc_biomolecule_verify_connections ( ehandle biomolecule_handle )
input

biomolecule_handle
output

none
return

TRUE:connection matrix is OK

FALSE:connection matrix is flawed

eslc_biomolecule_find_molweight

Find (and return) the molcular weight of a biomolecule, i.e., the sum of the molecular weights of the monomers in the biomolecule.

form

float eslc_biomolecule_find_molweight ( ehandle biomolecule_handle )
input

biomolecule_handle
output

none
return

molecularweight

eslc_biomolecule_find_formula_string

Find (and return as a string) the molecular formula of a biomolecule.

form

char *eslc_biomolecule_find_formula_string ( ehandle biomolecule_handle )
input

biomolecule_handle
output

none
return

a string in the format H(x)C(y)O(z)

eslc_biomolecule_find_heavyatomcount

Find (and return) the number of heavy, i.e., non-hydrogen, atoms in a biomolecule.

form

int eslc_biomolecule_find_heavyatomcount ( ehandle biomolecule_handle )
input

biomolecule_handle
output

none
return

count of heavy atoms

eslc_biomolecule_find_essentialatomcount

Find (and return) the number of essential, i.e., non-hydrogen and polar hydrogen, atoms in a biomolecule. Hydrogen atoms bonded to carbon or silicon are not counted.

form

int eslc_biomolecule_find_essentialatomcount ( ehandle biomolecule_handle )
input

biomolecule_handle
output

none
return

count of heavy atoms

eslc_biomolecule_find_all_waters

Find (and return) a list of water molecule monomers in the biomolecule object.

form

int eslc_biomolecule_find_all_waters ( ehandle biomolecule_handle, int *waterlist )
input

biomolecule_handle
output

waterlist
return

count of water monomers

eslc_biomolecule_find_all_monomers_by_typeid

Find (and return) a list of monomer (handles) of the type specified by monomertype_id in the biomolecule object.

form

int eslc_biomolecule_find_all_monomers_by_typeid ( ehandle biomolecule_handle, int monomertype_id, ehandle *monomerlist )
input

biomolecule_handle

monomertype_id
output

monomerlist
return

count of monomers

eslc_biomolecule_find_all_monomernumbers_by_typeid

Find (and return) a list of monomer (numbers) of the type specified by monomertype_id in the biomolecule object.

form

int eslc_biomolecule_find_all_monomernumbers_by_typeid ( ehandle biomolecule_handle, int monomertype_id, int *monomernumberlist )
input

biomolecule_handle

monomertype_id
output

monomernumberlist
return

count of monomers

eslc_biomolecule_find_all_monomers_by_terminationtype

Find (and return) a list of monomer (handles) with the termination specified by terminationtype in the biomolecule object. See monomer.h or monomerprop.html for more information about monomer termination.

form

int eslc_biomolecule_find_all_monomers_by_terminationtype ( ehandle biomolecule_handle, int terminationtype, ehandle *monomerlist )
input

biomolecule_handle

terminationtype
output

monomerlist
return

count of monomers

eslc_biomolecule_find_all_monomernumbers_by_terminationtype

Find (and return) a list of monomer (numbers) with the termination specified by terminationtype in the biomolecule object. See monomer.h or monomerprop.html for more information about monomer termination.

form

int eslc_biomolecule_find_all_monomernumbers_by_terminationtype ( ehandle biomolecule_handle, int terminationtype, int *monomernumberlist )
input

biomolecule_handle

terminationtype
output

monomernumberlist
return

count of monomers

eslc_biomolecule_create_monomer

Create a new monomer object associated with the biomolecule object. The new monomer has a default of zero atoms.

form

int eslc_biomolecule_create_monomer ( ehandle biomolecule_handle, ehandle *monomer_handle )
input

biomolecule_handle
output

monomer_handle
return

TRUE:success

FALSE:failure

eslc_biomolecule_delete_monomer

Delete a monomer object associated with the biomolecule object. Note that this will not remove references to the monomer that may exist in the atom records.

form

int eslc_biomolecule_delete_monomer ( ehandle biomolecule_handle, ehandle monomer_handle )
input

biomolecule_handle

monomer_handle
output

none
return

TRUE:success

FALSE:failure

eslc_biomolecule_add_molecule_as_monomer

Add the specified (small) molecule to an existing biomolecule as a monomer. This is useful, for example, when one wants to create a solvent array of water or othe rmolecules.

form

int eslc_biomolecule_add_molecule_as_monomer ( ehandle biomolecule_handle, ehandle addedmolecule_handle, ehandle *monomer_handle )
input

biomolecule_handle

addedmolecule_handle
output

monomer_handle
return

TRUE:success

FALSE:failure

eslc_biomolecule_find_all_rotatablepolarhydrogens

Create a list of "rotatable" polar atoms containing hydrogens within the biomolecule. Rotatable polar atoms include -OH, -SH, -NH₂ and -PH₂. Each rotatable atom is specified by a torson with two parameters: the anchor atom where the torsion is attached to the rest of the molecule and the swing atom that the hydrogens are bonded to. These can be potentially rotated within the biomolecule to improve hydrogen-bond overlap intermolecularly or intramolecularly.

form

int eslc_biomolecule_find_all_rotatablepolarhydrogens ( ehandle biomolecule_handle, int *anchorlist, int *swinglist )
input

biomolecule_handle
output

anchorlist

swinglist
return

count of rotatable polar hydrogens

eslc_biomolecule_translate

Translate all atoms in the biomolecule object by the input x, y and z values.

form

int eslc_biomolecule_translate ( ehandle biomolecule_handle, float x, float y, float z )
input

biomolecule_handle

z
output

none
return

TRUE:success

FALSE:failure

eslc_biomolecule_rotate

Rotate all atoms in the biomolecule object by the input alpha, beta and gamma angles. Important notes: 1) These angles are in radians, not degrees (2 pi = 360^o); b) alpha is defined as the angle of rotation around the x axis (positive alpha is rotation from the y axis towards the z axis), beta is defined as the angle of rotation around the y axis (positive beta is rotation from the z axis towards the x axis), gamma is defined as the angle of rotation around the z axis (positive gamma is rotation from the x axis towards the y axis).

form

int eslc_biomolecule_rotate ( ehandle biomolecule_handle, float alpha, float beta, float gamma )
input

biomolecule_handle

alpha

beta

gamma
output

none
return

TRUE:success

FALSE:failure

eslc_biomolecule_calculate_centerofgravity

Calculate and return the center of gravity for the biomolecule object. If weighting is on (TRUE), then this is a true center of gravity, i.e., including the atomic masses; if weighting is off (FALSE), then only the atomic positions are used in the calculation.

form

int eslc_biomolecule_calculate_centerofgravity ( ehandle biomolecule_handle, int weighting, float *xcen, float *ycen, float *zcen )
input

biomolecule_handle

weighting
output

xcen

ycen

zcen
return

TRUE:success

FALSE:failure

eslc_biomolecule_range_find_allmonomers

Find and return a list of monomer (handles) in the target biomolecule that are within "maxrange" of the atoms in the source biomolecule.

form

int eslc_biomolecule_range_find_allmonomers ( ehandle sourcebiomolecule_handle, ehandle targetbiomolecule_handle, float maxrange, ehandle *monomerlist )
input

sourcebiomolecule_handle

targetbiomolecule_handle

maxrange
output

monomerlist
return

count of all monomers

eslc_biomolecule_range_find_allmonomernumbers

Find and return a list of monomer (numbers) in the target biomolecule that are within "maxrange" of the atoms in the source biomolecule.

form

int eslc_biomolecule_range_find_allmonomernumbers ( ehandle sourcebiomolecule_handle, ehandle targetbiomolecule_handle, float maxrange, int *monomernumberlist )
input

sourcebiomolecule_handle

targetbiomolecule_handle

maxrange
output

monomernumberlist
return

count