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First draft of a python wrapper for gromacs library

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Niels Müller
2016-03-16 13:07:02 +01:00
parent b49941595b
commit 58d5d3a6c4
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pygmx/topology.pxd Normal file
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from utility cimport *
from math cimport *
from mdtypes cimport *
cdef extern from "gromacs/topology/atoms.h":
ctypedef struct t_atom:
real m, q; # Mass and charge */
real mB, qB; # Mass and charge for Free Energy calc */
unsigned short type; # Atom type */
unsigned short typeB; # Atom type for Free Energy calc */
int ptype; # Particle type */
int resind; # Index into resinfo (in t_atoms) */
int atomnumber; # Atomic Number or 0 */
char elem[4]; # Element name */
ctypedef struct t_resinfo:
char **name; # Pointer to the residue name */
int nr; # Residue number */
unsigned char ic; # Code for insertion of residues */
int chainnum; # Iincremented at TER or new chain id */
char chainid; # Chain identifier written/read to pdb */
char **rtp; # rtp building block name (optional) */
ctypedef struct t_pdbinfo:
pass
ctypedef struct t_atoms:
int nr # Nr of atoms */
t_atom *atom # Array of atoms (dim: nr) */
# The following entries will not */
# always be used (nres==0) */
char ***atomname # Array of pointers to atom name */
# use: (*(atomname[i])) */
char ***atomtype # Array of pointers to atom types */
# use: (*(atomtype[i])) */
char ***atomtypeB # Array of pointers to B atom types */
# use: (*(atomtypeB[i])) */
int nres # The number of resinfo entries */
t_resinfo *resinfo # Array of residue names and numbers */
t_pdbinfo *pdbinfo # PDB Information, such as aniso. Bfac */
ctypedef struct t_atomtypes:
pass
#ctypedef t_atoms *t_atoms_ptr
cdef extern from "gromacs/topology/symtab.h":
ctypedef struct t_symtab:
pass
cdef extern from "gromacs/topology/block.h":
ctypedef struct t_block:
pass
ctypedef struct t_blocka:
pass
cdef extern from "gromacs/topology/idef.h":
ctypedef struct t_ilist:
pass
ctypedef struct gmx_ffparams_t:
pass
cdef extern from "gromacs/topology/topology.h":
ctypedef struct gmx_moltype_t:
char **name; # Name of the molecule type */
t_atoms atoms; # The atoms in this molecule */
t_ilist ilist[0]; # Interaction list with local indices */
t_block cgs; # The charge groups */
t_blocka excls; # The exclusions */
ctypedef struct gmx_molblock_t:
int type; # The molcule type index in mtop.moltype */
int nmol; # The number of molecules in this block */
int natoms_mol; # The number of atoms in one molecule */
int nposres_xA; # The number of posres coords for top A */
rvec *posres_xA; # The posres coords for top A */
int nposres_xB; # The number of posres coords for top B */
rvec *posres_xB; # The posres coords for top B */
ctypedef struct gmx_groups_t:
pass
ctypedef struct gmx_mtop_t:
char **name # Name of the topology */
gmx_ffparams_t ffparams
int nmoltype
gmx_moltype_t *moltype
int nmolblock
gmx_molblock_t *molblock
bint bIntermolecularInteractions # Are there intermolecular
# interactions? */
t_ilist *intermolecular_ilist # List of intermolecular interactions
# using system wide atom indices,
# either NULL or size F_NRE */
int natoms
int maxres_renum # Parameter for residue numbering */
int maxresnr # The maximum residue number in moltype */
t_atomtypes atomtypes # Atomtype properties */
t_block mols # The molecules */
gmx_groups_t groups
t_symtab symtab # The symbol table */
# cdef extern from "gromacs/topology/topology.h":
# generate a t_atoms struct for the system from gmx_mtop_t
# t_atoms* mtop2atoms(gmx_mtop_t *mtop)