Hey :)
Here is an all Python solution to load a .gro file, including the box
vectors. It simply converts to PDB format and calls cmd.read_pdbstr...
It supports multimodel files. I'll probably add a mechanism to
identify chains from breaks, as the .gro format does not use chain
identifiers, and may add gzip support. Later I'll also add MARTINI
coarse graining, while I'm at it :)
Hope it helps,
Tsjerk
###
from pymol import cmd
import math
_pdbline = "ATOM %5i %-3s %3s%2s%4i %8.3f%8.3f%8.3f%6.2f%6.2f
%1s \n"
_pdbBoxLine = "CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f P 1 1\n"
d2r = math.pi/180
def cos_angle(a,b):
p = sum([i*j for i,j in zip(a,b)])
q = math.sqrt(sum([i*i for i in a])*sum([j*j for j in b]))
return min(max(-1,p/q),1)
def norm2(a):
return sum([i*i for i in a])
def norm(a):
return math.sqrt(norm2(a))
def groBoxRead(a):
b = [10*float(i) for i in a.split()] + 6*[0] # Padding for rectangular boxes
return b[0],b[3],b[4],b[5],b[1],b[6],b[7],b[8],b[2]
def groAtom(a):
#012345678901234567890123456789012345678901234567890
# 1PRN N 1 4.168 11.132 5.291
## ===> atom name, res name, res id, chain
x, y, z
return (a[10:15].strip(),a[5:10].strip(),int(a[:5]),"
",10*float(a[20:28]),10*float(a[28:36]),10*float(a[36:44]))
# Simple GRO iterator
def groFrameIterator(stream):
while True:
title = stream.readline()
natoms = stream.readline().strip()
if not natoms:
break
natoms = int(natoms)
atoms = [groAtom(stream.readline()) for i in range(natoms)]
box = groBoxRead(stream.readline())
yield title, atoms, box
def pdbOut(atom,i=1):
return _pdbline%((i,) + (atom[0][:3],) + (atom[1],) + (atom[3],) +
(atom[2],) + atom[4:] + (1,40) + (atom[0][0],))
def pdbBoxString(box):
nu = math.sqrt(norm2(box[0:3]))
nv = math.sqrt(norm2(box[3:6]))
nw = math.sqrt(norm2(box[6:9]))
alpha = nv*nw == 0 and 90 or math.acos(cos_angle(box[3:6],box[6:9]))/d2r
beta = nu*nw == 0 and 90 or math.acos(cos_angle(box[0:3],box[6:9]))/d2r
gamma = nu*nv == 0 and 90 or math.acos(cos_angle(box[0:3],box[6:9]))/d2r
return _pdbBoxLine %
(norm(box[0:3]),norm(box[3:6]),norm(box[6:9]),alpha,beta,gamma)
def gro(filename):
objname = filename[1+filename.rfind("/"):filename.rfind(".")]
pdb = []
model = 1
for title, atoms, box in groFrameIterator(open(filename)):
pdb.append("MODEL %8d"%model)
pdb.append(pdbBoxString(box))
pdb.extend([pdbOut(atom,i) for atom, i in
zip(atoms,range(1,len(atoms)+1))])
pdb.append("ENDMDL")
model += 1
cmd.read_pdbstr("\n".join(pdb),objname)
cmd.extend("gro",gro)
###
On Wed, Aug 17, 2011 at 5:11 AM, Jason Vertrees
<jason.vertr...@schrodinger.com> wrote:
> Hi Michael,
>
> PyMOL knows about gromacs files, but needs to better handle .gro
> files, specifically. Currently you have to export to a PDB to read the
> topology.
>
> Please file this on the open-source tracker
> (https://sourceforge.net/tracker/?group_id=4546) and I'll get to it
> ASAP.
>
> Cheers,
>
> -- Jason
>
> On Mon, Aug 15, 2011 at 8:19 PM, Michael Daily <mdaily.w...@gmail.com> wrote:
>> Hi all,
>>
>> Is there a direct way to load a gromacs structure file (.gro) in PyMOL? I
>> know it's simple to convert them to pdb using editconf, but I want to load
>> gro files directly (as you can in vmd) because they permit higher max. atom
>> and residue numbers (100K vs. 10K for pdb) and permit longer residue names
>> (4 chars vs. 3 for vmd).
>>
>> Thanks,
>> Mike
>>
>> --
>> ====================================
>> Michael D. Daily
>> Postdoctoral research associate
>> Pacific Northwest National Lab (PNNL)
>> 509-375-4581
>> (formerly Qiang Cui group, University of Wisconsin-Madison)
>>
>> ------------------------------------------------------------------------------
>> uberSVN's rich system and user administration capabilities and model
>> configuration take the hassle out of deploying and managing Subversion and
>> the tools developers use with it. Learn more about uberSVN and get a free
>> download at: http://p.sf.net/sfu/wandisco-dev2dev
>>
>> _______________________________________________
>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120
>
> ------------------------------------------------------------------------------
> Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
> user administration capabilities and model configuration. Take
> the hassle out of deploying and managing Subversion and the
> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
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>
--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
from pymol import cmd
import math
_pdbline = "ATOM %5i %-3s %3s%2s%4i %8.3f%8.3f%8.3f%6.2f%6.2f %1s \n"
_pdbBoxLine = "CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f P 1 1\n"
d2r = math.pi/180
def cos_angle(a,b):
p = sum([i*j for i,j in zip(a,b)])
q = math.sqrt(sum([i*i for i in a])*sum([j*j for j in b]))
return min(max(-1,p/q),1)
def norm2(a):
return sum([i*i for i in a])
def norm(a):
return math.sqrt(norm2(a))
def groBoxRead(a):
b = [10*float(i) for i in a.split()] + 6*[0] # Padding for rectangular boxes
return b[0],b[3],b[4],b[5],b[1],b[6],b[7],b[8],b[2]
def groAtom(a):
#012345678901234567890123456789012345678901234567890
# 1PRN N 1 4.168 11.132 5.291
## ===> atom name, res name, res id, chain x, y, z
return (a[10:15].strip(),a[5:10].strip(),int(a[:5])," ",10*float(a[20:28]),10*float(a[28:36]),10*float(a[36:44]))
# Simple GRO iterator
def groFrameIterator(stream):
while True:
title = stream.readline()
natoms = stream.readline().strip()
if not natoms:
break
natoms = int(natoms)
atoms = [groAtom(stream.readline()) for i in range(natoms)]
box = groBoxRead(stream.readline())
yield title, atoms, box
def pdbOut(atom,i=1):
return _pdbline%((i,) + (atom[0][:3],) + (atom[1],) + (atom[3],) + (atom[2],) + atom[4:] + (1,40) + (atom[0][0],))
def pdbBoxString(box):
nu = math.sqrt(norm2(box[0:3]))
nv = math.sqrt(norm2(box[3:6]))
nw = math.sqrt(norm2(box[6:9]))
alpha = nv*nw == 0 and 90 or math.acos(cos_angle(box[3:6],box[6:9]))/d2r
beta = nu*nw == 0 and 90 or math.acos(cos_angle(box[0:3],box[6:9]))/d2r
gamma = nu*nv == 0 and 90 or math.acos(cos_angle(box[0:3],box[6:9]))/d2r
return _pdbBoxLine % (norm(box[0:3]),norm(box[3:6]),norm(box[6:9]),alpha,beta,gamma)
def gro(filename):
objname = filename[1+filename.rfind("/"):filename.rfind(".")]
pdb = []
model = 1
for title, atoms, box in groFrameIterator(open(filename)):
pdb.append("MODEL %8d"%model)
pdb.append(pdbBoxString(box))
pdb.extend([pdbOut(atom,i) for atom, i in zip(atoms,range(1,len(atoms)+1))])
pdb.append("ENDMDL")
model += 1
cmd.read_pdbstr("\n".join(pdb),objname)
cmd.extend("gro",gro)
------------------------------------------------------------------------------
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user administration capabilities and model configuration. Take
the hassle out of deploying and managing Subversion and the
tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
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