Re: [gmx-users] numerical matrix from xpm file
Hi Tsjerk
It's very useful in my problem also.
thanks again.
regards
anupam
> Hi Anupam,
>
> I recently wrote a small python script to convert gromacs .xpm files
> to numbers. Maybe it'll be of some use to you:
>
> Cheers,
>
> Tsjerk
>
> ###
>
> #!/usr/bin/env python
>
> import sys
>
> def unquote(s):
> return s[1+s.find('"'):s.rfind('"')]
>
> def uncomment(s):
> return s[2+s.find('/*'):s.rfind('*/')]
>
> def col(c):
> color = c.split('/*')
> value = unquote(color[1])
> color = unquote(color[0]).split()
> sys.stderr.write("%s: %s %s %s\n"%(c.strip(),color[0], color[1], value))
> return color[0], value
>
> # Open the xpm file for reading
> xpm = open(sys.argv[1])
>
> # Read in lines until we fidn the start of the array
> meta = [xpm.readline()]
> while not meta[-1].startswith("static char *gromacs_xpm[]"):
> meta.append(xpm.readline())
>
> # The next line will contain the dimensions of the array
> dim = xpm.readline()
> # There are four integers surrounded by quotes
> nx, ny, nc, nb = [int(i) for i in unquote(dim).split()]
>
> # The next dim[2] lines contain the color definitions
> # Each pixel is encoded by dim[3] bytes, and a comment
> # at the end of the line contains the corresponding value
> colors = dict([col(xpm.readline()) for i in range(nc)])
>
> for i in xpm:
> if i.startswith("/*"):
> continue
> j = unquote(i)
> z = [colors[j[k:k+nb]] for k in range(0,nx,nb)]
> sys.stdout.write(" ".join(z)+"\n")
>
> ###
>
> On Mon, Oct 4, 2010 at 12:33 PM, Anupam Nath Jha
> wrote:
>>
>> right. I also came to see one of them but with no result.
>> and since it was done some time back so I thought if some one has come up
>> with
>> some method to get that.
>>
>> right now I wanted the matrix information obtained from command g_mdmat.
>> can you suggest some way to get that.
>>
>> thanks
>> anupam
>>
>>
>>> No, there's no ability to do this. I think there should be, though, and seem
>>> to
>>> recall discussion of it on one or other mailing list or the web page.
>>>
>>> Mark
>>>
>>> - Original Message -
>>> From: Anupam Nath Jha
>>> Date: Saturday, October 2, 2010 21:32
>>> Subject: [gmx-users] numerical matrix from xpm file
>>> To: gmx-users@gromacs.org
>>>
>>>>
>>>> Hi all
>>>>
>>>> Is it possible to obtain the matrix in numeric form from xpm
>>>> (obtained from
>>>> gromacs analysis) files.
>>>>
>>>> because it's not coming in options for ourput files.
>>>>
>>>> thanks with regards
>>>> anupam
>>>>
>>>> --
>>>>
>>>>
>>>> --
>>>> This message has been scanned for viruses and
>>>> dangerous content by MailScanner, and is
>>>> believed to be clean.
>>>>
>>>> --
>>>> gmx-users mailing list gmx-us...@gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>> Please don't post (un)subscribe requests to the list. Use the
>>>> www interface or send it to gmx-users-requ...@gromacs.org.
>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> --
>>> This message has been scanned for viruses and
>>> dangerous content by MailScanner, and is
>>> believed to be clean.
>>>
>>> --
>>> gmx-users mailing list gmx-us...@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search
>>> before posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-requ...@gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>> --
>> Science is facts; just as houses are made of stone, so is science is made of
>> facts; but a pile of stones is not a house, and a collection of facts is not
>> necessarily science.
>>
>> Anupam Nath Jha
>> Ph. D. Student
>> Saraswathi Vishveshwara Lab
>> Molecular Biophysics Unit
>>
Re: [gmx-users] numerical matrix from xpm file
right. I also came to see one of them but with no result. and since it was done some time back so I thought if some one has come up with some method to get that. right now I wanted the matrix information obtained from command g_mdmat. can you suggest some way to get that. thanks anupam > No, there's no ability to do this. I think there should be, though, and seem > to > recall discussion of it on one or other mailing list or the web page. > > Mark > > - Original Message - > From: Anupam Nath Jha > Date: Saturday, October 2, 2010 21:32 > Subject: [gmx-users] numerical matrix from xpm file > To: gmx-users@gromacs.org > >> >> Hi all >> >> Is it possible to obtain the matrix in numeric form from xpm >> (obtained from >> gromacs analysis) files. >> >> because it's not coming in options for ourput files. >> >> thanks with regards >> anupam >> >> -- >> >> >> -- >> This message has been scanned for viruses and >> dangerous content by MailScanner, and is >> believed to be clean. >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search > before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Science is facts; just as houses are made of stone, so is science is made of facts; but a pile of stones is not a house, and a collection of facts is not necessarily science. Anupam Nath Jha Ph. D. Student Saraswathi Vishveshwara Lab Molecular Biophysics Unit IISc,Bangalore-560012 Karnataka Ph. no.-22932611 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] numerical matrix from xpm file
Hi Anupam,
I recently wrote a small python script to convert gromacs .xpm files
to numbers. Maybe it'll be of some use to you:
Cheers,
Tsjerk
###
#!/usr/bin/env python
import sys
def unquote(s):
return s[1+s.find('"'):s.rfind('"')]
def uncomment(s):
return s[2+s.find('/*'):s.rfind('*/')]
def col(c):
color = c.split('/*')
value = unquote(color[1])
color = unquote(color[0]).split()
sys.stderr.write("%s: %s %s %s\n"%(c.strip(),color[0], color[1], value))
return color[0], value
# Open the xpm file for reading
xpm = open(sys.argv[1])
# Read in lines until we fidn the start of the array
meta = [xpm.readline()]
while not meta[-1].startswith("static char *gromacs_xpm[]"):
meta.append(xpm.readline())
# The next line will contain the dimensions of the array
dim = xpm.readline()
# There are four integers surrounded by quotes
nx, ny, nc, nb = [int(i) for i in unquote(dim).split()]
# The next dim[2] lines contain the color definitions
# Each pixel is encoded by dim[3] bytes, and a comment
# at the end of the line contains the corresponding value
colors = dict([col(xpm.readline()) for i in range(nc)])
for i in xpm:
if i.startswith("/*"):
continue
j = unquote(i)
z = [colors[j[k:k+nb]] for k in range(0,nx,nb)]
sys.stdout.write(" ".join(z)+"\n")
###
On Mon, Oct 4, 2010 at 12:33 PM, Anupam Nath Jha
wrote:
>
> right. I also came to see one of them but with no result.
> and since it was done some time back so I thought if some one has come up with
> some method to get that.
>
> right now I wanted the matrix information obtained from command g_mdmat.
> can you suggest some way to get that.
>
> thanks
> anupam
>
>
>> No, there's no ability to do this. I think there should be, though, and seem
>> to
>> recall discussion of it on one or other mailing list or the web page.
>>
>> Mark
>>
>> - Original Message -
>> From: Anupam Nath Jha
>> Date: Saturday, October 2, 2010 21:32
>> Subject: [gmx-users] numerical matrix from xpm file
>> To: gmx-users@gromacs.org
>>
>>>
>>> Hi all
>>>
>>> Is it possible to obtain the matrix in numeric form from xpm
>>> (obtained from
>>> gromacs analysis) files.
>>>
>>> because it's not coming in options for ourput files.
>>>
>>> thanks with regards
>>> anupam
>>>
>>> --
>>>
>>>
>>> --
>>> This message has been scanned for viruses and
>>> dangerous content by MailScanner, and is
>>> believed to be clean.
>>>
>>> --
>>> gmx-users mailing list gmx-us...@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-requ...@gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> --
>> This message has been scanned for viruses and
>> dangerous content by MailScanner, and is
>> believed to be clean.
>>
>> --
>> gmx-users mailing list gmx-us...@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search
>> before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
> --
> Science is facts; just as houses are made of stone, so is science is made of
> facts; but a pile of stones is not a house, and a collection of facts is not
> necessarily science.
>
> Anupam Nath Jha
> Ph. D. Student
> Saraswathi Vishveshwara Lab
> Molecular Biophysics Unit
> IISc,Bangalore-560012
> Karnataka
> Ph. no.-22932611
>
>
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
> --
> gmx-users mailing list gmx-us...@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
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
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] numerical matrix from xpm file
No, there's no ability to do this. I think there should be, though, and seem to recall discussion of it on one or other mailing list or the web page. Mark - Original Message - From: Anupam Nath Jha Date: Saturday, October 2, 2010 21:32 Subject: [gmx-users] numerical matrix from xpm file To: gmx-users@gromacs.org > > Hi all > > Is it possible to obtain the matrix in numeric form from xpm > (obtained from > gromacs analysis) files. > > because it's not coming in options for ourput files. > > thanks with regards > anupam > > -- > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] numerical matrix from xpm file
Hi all Is it possible to obtain the matrix in numeric form from xpm (obtained from gromacs analysis) files. because it's not coming in options for ourput files. thanks with regards anupam -- -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
