BONDING

Functions
void	set_molecule_atom_nodes_from_bonds (molecule *m)
int	follow_molecule_atom_nodes_from_bonds (molecule *m, int iTree, atom *a)
void	set_molecule_residue_molbonds (molecule *m)
void	set_residue_atom_nodes_from_bonds (residue *r)
int	follow_residue_atom_nodes_from_bonds (residue *r, int iTree, atom *a)
void	set_molecule_residue_nodes_from_bonds (molecule *m)
int	follow_molecule_residue_nodes_from_bonds (molecule *m, int iTree, residue *r)
void	set_nbonds_for_atoms_in_assembly (assembly *A)

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Detailed Description

Purpose: Functions associated with bonding. Begin 20110417 BLFoley

Return values for follow functions: 0 : Made it all the way to the end. All ok. -1 : Made it to an appropriate end in the middle. Don't continue. -2 : Something else happened, but probably is ok.

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Function Documentation

int follow_molecule_atom_nodes_from_bonds	(	molecule *	m,
		int	iTree,
		atom *	a
	)

Definition at line 434 of file bonding_utilities.c.

References ensindex::a, residue::a, molecule::aT, copy_moli_to_ensi(), follow_molecule_atom_nodes_from_bonds(), ensindex::i, atom_node::i, atom_node::ID, is_consistent_ensi_moli(), molindex::m, atom::m, atom::mb, atom::mTi, mywhine(), molecule::na, atom_node::ni, atom::nmb, atom_node::no, atom_node::o, ensindex::r, molecule::r, and molbond::t.

Referenced by follow_molecule_atom_nodes_from_bonds(), and set_molecule_atom_nodes_from_bonds().

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int follow_molecule_residue_nodes_from_bonds	(	molecule *	m,
		int	iTree,
		residue *	r
	)

Definition at line 99 of file bonding_utilities.c.

References follow_molecule_residue_nodes_from_bonds(), molbond::i, is_consistent_molbond_molbond_inverse(), molindex::m, residue::m, residue_node::mbi, residue_node::mbo, residue::mTi, mywhine(), residue_node::nmbi, residue_node::nmbo, molecule::nr, residue::nrb, molindex::r, molecule::r, residue::rb, molecule::rT, and molbond::t.

Referenced by follow_molecule_residue_nodes_from_bonds(), and set_molecule_residue_nodes_from_bonds().

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int follow_residue_atom_nodes_from_bonds	(	residue *	r,
		int	iTree,
		atom *	a
	)

Definition at line 262 of file bonding_utilities.c.

References ensindex::a, residue::a, residue::aT, copy_moli_to_ensi(), follow_residue_atom_nodes_from_bonds(), ensindex::i, atom_node::i, atom_node::ID, is_consistent_ensi_moli(), atom::mb, mywhine(), residue::na, atom_node::ni, atom::nmb, atom_node::no, atom_node::o, molindex::r, atom::rTi, and molbond::t.

Referenced by follow_residue_atom_nodes_from_bonds(), and set_residue_atom_nodes_from_bonds().

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void set_molecule_atom_nodes_from_bonds

(

molecule *

m

)

Definition at line 387 of file bonding_utilities.c.

References residue::a, molecule::aT, copy_moli_to_ensi(), follow_molecule_atom_nodes_from_bonds(), ensindex::i, atom_node::ID, is_consistent_ensi_ensi(), atom_node::isorigin, atom::mTi, mywhine(), residue::na, molecule::na, molecule::nr, and molecule::r.

Referenced by load_amber_prmtop().

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void set_molecule_residue_molbonds

(

molecule *

m

)

Definition at line 18 of file bonding_utilities.c.

References residue::a, atom::mb, mywhine(), residue::na, atom::nmb, molecule::nr, residue::nrb, molindex::r, molecule::r, residue::rb, and molbond::t.

Referenced by load_amber_prmtop().

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void set_molecule_residue_nodes_from_bonds

(

molecule *

m

)

Definition at line 70 of file bonding_utilities.c.

References copy_moli_to_ensi(), follow_molecule_residue_nodes_from_bonds(), ensindex::i, residue_node::ID, is_consistent_ensi_ensi(), residue_node::isorigin, residue::mTi, mywhine(), molecule::nr, molecule::r, and molecule::rT.

Referenced by load_amber_prmtop().

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void set_nbonds_for_atoms_in_assembly

(

assembly *

A

)

void set_residue_atom_nodes_from_bonds

(

residue *

r

)

Definition at line 233 of file bonding_utilities.c.

References residue::a, residue::aT, copy_moli_to_ensi(), follow_residue_atom_nodes_from_bonds(), ensindex::i, atom_node::ID, is_consistent_ensi_ensi(), atom_node::isorigin, mywhine(), residue::na, and atom::rTi.

Referenced by load_amber_prmtop().

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