amber_prmtop.h File Reference

#include <mylib.h>
#include <general.h>
#include <molecules.h>
#include <declarations.h>
#include <AMBER/amber_prmtop_structs.h>

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Functions
void	amber_prmtop_init (amber_prmtop *P)
void	read_amber_prmtop_asis (fileset F, amber_prmtop *P)
assembly	parse_amber_prmtop (amber_prmtop *P)
void	find_molecules_molbond_array (int nMB, molbond *MB, int NATOM, molindex *AT)
assembly	load_amber_prmtop (fileset F)
void	add_trajcrds_to_prmtop_assembly (fileset F, assembly *A, char ftype, int offset)
void	deallocateAmberPrmtopSection (amber_prmtop_section *aps)
void	deallocateAmberPrmtop (amber_prmtop *ap)

---

Detailed Description

Header file for functions that read amber prmtop files into the GLYLIB structures

begun on 20080622 by BLFoley

Definition in file amber_prmtop.h.

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Function Documentation

void add_trajcrds_to_prmtop_assembly	(	fileset	F,
		assembly *	A,
		char	ftype,
		int	offset
	)

< temporary char holders

< alternate coords or vectors allocated outgoing

< alternate coords or vectors allocated incoming

< for testing [f,s]scanf results

< atom index

< dummy coordinate index

< counter to test if there should be a newline

DO NOT RE/OPEN the file

See if we are at the start of the file or not

Don't make lots of silly checks -- just add coordinates to atom structures...

First, allocate space as needed, and clear any unused middle-space

Now scan through and add info to the structure

If this is type 'r', see if there is any more info in the file

Parameters:

F	The trajectory file containing the data *Must* be open
A	Assembly ("incoming") to which the crds should be added
ftype	'c' if coordinate ; 'v' if velocity ; 'r' if restart (might have both)
offset	read in the offset-th trajectory -- starts with zero=current

Definition at line 87 of file add_trajcrds_to_prmtop_assembly.c.

References assembly::a, assembly::BOX, boxinfo::C, vectormag_3D::d, coord_nD::D, fileset::F, coord_3D::i, vectormag_3D::i, coord_3D::j, vectormag_3D::j, coord_3D::k, vectormag_3D::k, mywhine(), assembly::na, atom::nalt, assembly::nBOX, boxinfo::nC, coord_nD::nD, atom::nvec, atom::v, and atom::xa.

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void amber_prmtop_init

(

amber_prmtop *

P

)

Definition at line 7 of file amber_prmtop_init.c.

References AMBER_PRMTOP_FLAGS, AMBER_PRMTOP_FORMATS, amber_prmtop::FLAGS, amber_prmtop::FORMATS, amber_prmtop::IFBOX, amber_prmtop::IFCAP, amber_prmtop::IFPERT, amber_prmtop::MBONA, amber_prmtop::MBPER, amber_prmtop::MDPER, amber_prmtop::MGPER, amber_prmtop::MPHIA, amber_prmtop::MTHETA, amber_prmtop::NATOM, amber_prmtop::NATYP, amber_prmtop::NBONA, amber_prmtop::NBONH, amber_prmtop::NBPER, amber_prmtop::NDPER, amber_prmtop::nES, amber_prmtop::NEXT, amber_prmtop::nFF, amber_prmtop::NGPER, amber_prmtop::NHPARM, amber_prmtop::NMXRS, amber_prmtop::NPARM, amber_prmtop::NPHB, amber_prmtop::NPHIA, amber_prmtop::NPHIH, amber_prmtop::NPTRA, amber_prmtop::NRES, amber_prmtop::nS, amber_prmtop::nSS, amber_prmtop::NTHETA, amber_prmtop::NTHETH, amber_prmtop::NTYPES, amber_prmtop::NUMANG, and amber_prmtop::NUMBND.

Referenced by load_amber_prmtop().

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void deallocateAmberPrmtop

(

amber_prmtop *

ap

)

Definition at line 59 of file deallocate_amber_structures.c.

References deallocateAmberPrmtopSection(), amber_prmtop::nFF, and amber_prmtop::nS.

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void deallocateAmberPrmtopSection

(

amber_prmtop_section *

aps

)

Definition at line 44 of file deallocate_amber_structures.c.

References amber_prmtop_section::nt.

Referenced by deallocateAmberPrmtop().

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void find_molecules_molbond_array	(	int	nMB,
		molbond *	MB,
		int	NATOM,
		molindex *	AT
	)

Definition at line 37 of file find_molecules.c.

References follow_find_molecule_amber_prmtop_bond_target(), tempintset::i, molindex::i, molbond::i, molindex::m, mywhine(), tempintset::n, molbond::s, and molbond::t.

Referenced by parse_amber_prmtop().

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assembly load_amber_prmtop

(

fileset

F

)

Definition at line 7 of file load_amber_prmtop.c.

References amber_prmtop_init(), assembly::m, assembly::nm, molecule::nr, parse_amber_prmtop(), molecule::r, read_amber_prmtop_asis(), set_assembly_molindexes(), set_molecule_atom_nodes_from_bonds(), set_molecule_residue_molbonds(), set_molecule_residue_nodes_from_bonds(), and set_residue_atom_nodes_from_bonds().

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assembly parse_amber_prmtop

(

amber_prmtop *

P

)

Drop the contents of the original file in the void pointer space

< One for the "boxang" and the other for the x,y,z values

< Just an angle ("BETA" in the amber file specs)

< 3-D coordinate

< Record value of BETA

< Record BOX X

< Record BOX Y

< Record BOX Z

Definition at line 9 of file parse_amber_prmtop.c.

References molindex::a, ensindex::A, ensindex::a, angle_index::a, torsion_index::a, residue::a, molecule::a, assembly::a, amber_prmtop::ALMPER, amber_prmtop::AMASS, assembly::ANG, parameter_set::ANT, amber_prmtop::ASOL, parameter_set::AT, amber_prmtop::ATPOL, amber_prmtop::ATPOL1, angle_index::b, torsion_index::b, assembly::b, amber_prmtop::BETA, amber_prmtop::BOX, assembly::BOX, amber_prmtop::BSOL, parameter_set::BT, boxinfo::C, angle_index::c, torsion_index::c, boxinfo::CD, amber_prmtop::CGPER, atom::ch, amber_prmtop::CHRG, amber_prmtop::CN1, amber_prmtop::CN2, amber_prmtop::CUTCAP, coord_nD::D, amber_prmtop_section::D, molbond::D, angle_index::D, torsion_index::d, torsion_index::D, molecule::D, assembly::D, ensindex::E, atom::ensi, residue::ensi, molecule::ensi, find_molecules_molbond_array(), boxinfo::GTYPE, amber_prmtop::HBCUT, parameter_set::HBT, molindex::i, molbond::i, angle_index::i, torsion_index::i, amber_prmtop::IAC, amber_prmtop::IACPER, amber_prmtop::IAPER, amber_prmtop::IB, amber_prmtop::IBH, amber_prmtop::IBPER, amber_prmtop::ICB, amber_prmtop::ICBH, amber_prmtop::ICBPER, amber_prmtop::ICO, amber_prmtop::ICP, amber_prmtop::ICPH, amber_prmtop::ICPPER, amber_prmtop::ICT, amber_prmtop::ICTH, amber_prmtop::ICTPER, amber_prmtop::IGRAPH, amber_prmtop::IGRPER, amber_prmtop::IP, amber_prmtop::IPH, amber_prmtop::IPPER, amber_prmtop::IPRES, amber_prmtop::IPTER, amber_prmtop::IPTRES, amber_prmtop::IRES, amber_prmtop::IROTAT, amber_prmtop_section::is_standard, amber_prmtop::ISMPER, amber_prmtop::ISYMBL, amber_prmtop::IT, amber_prmtop::ITH, amber_prmtop::ITITL, amber_prmtop::ITREE, amber_prmtop::JB, amber_prmtop::JBH, amber_prmtop::JBPER, amber_prmtop::JOIN, amber_prmtop::JP, amber_prmtop::JPH, amber_prmtop::JPPER, amber_prmtop::JT, amber_prmtop::JTH, amber_prmtop::JTPER, bond_type::k, angle_type::k, torsion_type::k, amber_prmtop::KP, amber_prmtop::KPH, amber_prmtop::KPPER, amber_prmtop::KT, amber_prmtop::KTH, amber_prmtop::KTPER, bond_type::l, angle_type::l, amber_prmtop::LABRES, bond_type::LJ10_1012, bond_type::LJ12_1012, bond_type::LJ12_612, bond_type::LJ6_612, amber_prmtop::LP, amber_prmtop::LPH, amber_prmtop::LPPER, molindex::m, ensindex::m, atom::m, assembly::m, atom::mb, amber_prmtop::MBONA, atom::moli, residue::moli, amber_prmtop::MPHIA, amber_prmtop::MTHETA, mywhine(), torsion_type::n, torsion_type::N, atype::N, atom::n, atom::N, residue::n, residue::N, molecule::N, residue::na, molecule::na, assembly::na, assembly::nANG, parameter_set::nANT, parameter_set::nAT, amber_prmtop::NATCAP, amber_prmtop::NATEX, amber_prmtop::NATOM, assembly::nb, amber_prmtop::NBONA, amber_prmtop::NBONH, assembly::nBOX, parameter_set::nBT, parameter_set::NBT, amber_prmtop_section::nc, boxinfo::nC, boxinfo::nCD, atom::nch, coord_nD::nD, atom::nensi, residue::nensi, molecule::nensi, parameter_set::nHBT, assembly::nm, atom::nmb, parameter_set::nNBT, amber_prmtop::NPHB, amber_prmtop::NPHIA, amber_prmtop::NPHIH, assembly::nPRM, amber_prmtop::NPTRA, molecule::nr, assembly::nr, amber_prmtop::NRES, amber_prmtop::nS, amber_prmtop::NSP, amber_prmtop::NSPM, amber_prmtop::NSPSOL, bond_type::NT, amber_prmtop_section::nt, amber_prmtop::NTHETA, amber_prmtop::NTHETH, assembly::nTOR, parameter_set::nTRT, amber_prmtop::NTYPES, amber_prmtop::NUMANG, amber_prmtop::NUMBND, amber_prmtop::NUMEX, assembly::nVP, torsion_type::P, amber_prmtop::PHASE, amber_prmtop::PK, amber_prmtop::PN, amber_prmtop::POINTERS, assembly::PRM, prune_string_whitespace(), molindex::r, ensindex::r, molecule::r, assembly::r, amber_prmtop::REQ, amber_prmtop::RK, amber_prmtop::S, molbond::s, amber_prmtop::SOLTY, boxinfo::STYPE, molbond::t, atom::T, atom::t, amber_prmtop::TEQ, amber_prmtop::TK, assembly::TOR, parameter_set::TRT, assembly::VP, amber_prmtop::XCAP, amber_prmtop::YCAP, and amber_prmtop::ZCAP.

Referenced by load_amber_prmtop().

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void read_amber_prmtop_asis	(	fileset	F,
		amber_prmtop *	P
	)

Definition at line 17 of file read_amber_prmtop.c.

References amber_prmtop_section::D, amber_prmtop_section::desc, fileset::F, amber_prmtop::FN, amber_prmtop_section::FORMAT, amber_prmtop_section::is_standard, line, myfopen(), mywhine(), fileset::N, amber_prmtop_section::N, amber_prmtop_section::nc, amber_prmtop_section::npl, amber_prmtop_section::ns, amber_prmtop::nS, amber_prmtop_section::nt, amber_prmtop_section::nu, read_eek(), read_fneek(), amber_prmtop::S, amber_prmtop::SN, amber_prmtop_section::TYPE, and amber_prmtop::VERSION.

Referenced by load_amber_prmtop().

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