Re: [PyMOL] Placing pseudo atom on COM and saving it as pdb

[Subha K]

Oh yes, I am not familiar with the pymol options yet. So, couldn't figure
that out.

Thanks anyways for the quick help.

Cheers,
Subha

On Wed, Oct 12, 2016 at 2:02 PM, Tsjerk Wassenaar  wrote:

> Hi Subha,
>
> Sorry, my bad. It should've been object='pseudo' and not name='pseudo'.
> Should've tested it first.
>
> Cheers,
>
> Tsjerk
>
> On Wed, Oct 12, 2016 at 9:56 PM, Subha K  wrote:
>
>> Thanks David and Tsjerk for the kind reply and suggestion.
>>
>> I Figured a solution by combining both of your suggestions
>>
>> def center(selection, com=True):
>>
>> model = cmd.get_model(selection)
>>
>> xyz = np.array(model.get_coord_list())
>>
>> mass = [i.get_mass() for i in model.atom]
>>
>> xyz_m = xyz * np.array([mass]).T
>>
>> if com:
>>
>> return tuple(np.sum(xyz_m, 0)/model.get_mass())
>>
>> else:
>>
>> return tuple(np.average(xyz, 0))
>>
>>
>> with open("./out") as f:
>>
>> for line in f:
>>
>> in_pdb_file = line.strip()
>>
>> print in_pdb_file
>>
>> cmd.load(in_pdb_file, 'tmp')
>>
>> COM = center('resn UNK')
>>
>> cmd.pseudoatom('ligCOM', pos=COM)
>>
>> cmd.save(in_pdb_file[:-4] + "_dummy.pdb", "all")
>>
>> cmd.delete('ligCOM')
>>
>> cmd.delete('tmp')
>>
>>
>> @Tsjerk: Don't know why I got an error: Selector-Error: Invalid selection
>> name "pseudo".
>> pseudo<--
>>
>> Thanks again for the support.
>>
>> Best Regards,
>> Subha
>>
>>
>>
>>
>>
>> On Wed, Oct 12, 2016 at 12:53 PM, Tsjerk Wassenaar 
>> wrote:
>>
>>>
>>> Hi Subha,
>>>
>>> Probably this will get close:
>>>
>>> for pdb in open('./out').readlines():
>>> pdb = pdb.strip()
>>> cmd.load(pdb,'tmp')
>>> cmd.pseudoatom('tmp',name='pseudo')
>>> cmd.save(pdb[:-4]+'-pseudo.pdb','pseudo')
>>> cmd.delete('tmp')
>>> cmd.delete('pseudo')
>>>
>>> ... Just a bit too much for a oneliner ;)
>>>
>>> Hope it helps,
>>>
>>> Tsjerk
>>>
>>>
>>> On Wed, Oct 12, 2016 at 8:16 PM, Subha K  wrote:
>>>
 Hi There,

 I am looking to automate the calculation of centre of mass and placing
 a pseudo atom on the COM and save it as a pdb file . Going through the
 forum [https://sourceforge.net/p/pymol/mailman/message/34458943/] , I
 found some useful scripts for this, but, I am having trouble getting it
 done for all files in a directory. My script does what I need for the first
 file alone. Some looping or other is not correct. Or there could be an easy
 and better way to do it. I couldn't figure that out.  So, could some one
 please help me solve this?

 I have 100 files F01, F02, F100 ... in the directory dockout. I would
 like to calculate the COM and place a pseudo atom on the COM and save it as
 a pdb for all the 100 files.
 'out' in the script corresponds to the list of all the 100 files.

 import pymol

 from pymol import cmd

 pymol.finish_launching()

 import numpy as np

 import glob

 import fileinput

 def center(selection, com=True):

 model = cmd.get_model(selection)

 xyz = np.array(model.get_coord_list())

 mass = [i.get_mass() for i in model.atom]

 xyz_m = xyz * np.array([mass]).T

 if com:

 return tuple(np.sum(xyz_m, 0)/model.get_mass())

 else:

 return tuple(np.average(xyz, 0))


 def GetListOfFiles (filename):

 l = []

 for line in fileinput.input( filename ):

 tokens = line.split( )

 l.append(tokens)

 return l


 def Calculate_COM (list):

 for i in range (len(list)):

 print list[i][0]

 X=1

 if (X<101):

 os.system("cp ./dockout/F"+ str(X).zfill(2)+ " ./lig.pdb")

 for pdb in glob.glob("lig.pdb"):

 cmd.load(pdb)

 COM = center('resn UNK')

 cmd.pseudoatom('ligCOM', pos=COM)

 cmd.save("complex_dummy.pdb", "all")

 os.system("mv complex_dummy.pdb complex_" +
 str(X).zfill(2) + "_dummy.pdb")

 os.system("rm lig.pdb")

 X=X+1

 else:

 break

 listofFiles = GetListOfFiles ("./out")

 print listofFiles

 Calculate_COM(listofFiles)



 Thanks,
 Subha


 
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 Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
 

Re: [PyMOL] Placing pseudo atom on COM and saving it as pdb

[Tsjerk Wassenaar]

Hi Subha,

Sorry, my bad. It should've been object='pseudo' and not name='pseudo'.
Should've tested it first.

Cheers,

Tsjerk

On Wed, Oct 12, 2016 at 9:56 PM, Subha K  wrote:

> Thanks David and Tsjerk for the kind reply and suggestion.
>
> I Figured a solution by combining both of your suggestions
>
> def center(selection, com=True):
>
> model = cmd.get_model(selection)
>
> xyz = np.array(model.get_coord_list())
>
> mass = [i.get_mass() for i in model.atom]
>
> xyz_m = xyz * np.array([mass]).T
>
> if com:
>
> return tuple(np.sum(xyz_m, 0)/model.get_mass())
>
> else:
>
> return tuple(np.average(xyz, 0))
>
>
> with open("./out") as f:
>
> for line in f:
>
> in_pdb_file = line.strip()
>
> print in_pdb_file
>
> cmd.load(in_pdb_file, 'tmp')
>
> COM = center('resn UNK')
>
> cmd.pseudoatom('ligCOM', pos=COM)
>
> cmd.save(in_pdb_file[:-4] + "_dummy.pdb", "all")
>
> cmd.delete('ligCOM')
>
> cmd.delete('tmp')
>
>
> @Tsjerk: Don't know why I got an error: Selector-Error: Invalid selection
> name "pseudo".
> pseudo<--
>
> Thanks again for the support.
>
> Best Regards,
> Subha
>
>
>
>
>
> On Wed, Oct 12, 2016 at 12:53 PM, Tsjerk Wassenaar 
> wrote:
>
>>
>> Hi Subha,
>>
>> Probably this will get close:
>>
>> for pdb in open('./out').readlines():
>> pdb = pdb.strip()
>> cmd.load(pdb,'tmp')
>> cmd.pseudoatom('tmp',name='pseudo')
>> cmd.save(pdb[:-4]+'-pseudo.pdb','pseudo')
>> cmd.delete('tmp')
>> cmd.delete('pseudo')
>>
>> ... Just a bit too much for a oneliner ;)
>>
>> Hope it helps,
>>
>> Tsjerk
>>
>>
>> On Wed, Oct 12, 2016 at 8:16 PM, Subha K  wrote:
>>
>>> Hi There,
>>>
>>> I am looking to automate the calculation of centre of mass and placing a
>>> pseudo atom on the COM and save it as a pdb file . Going through the forum [
>>> https://sourceforge.net/p/pymol/mailman/message/34458943/] , I found
>>> some useful scripts for this, but, I am having trouble getting it done for
>>> all files in a directory. My script does what I need for the first file
>>> alone. Some looping or other is not correct. Or there could be an easy and
>>> better way to do it. I couldn't figure that out.  So, could some one please
>>> help me solve this?
>>>
>>> I have 100 files F01, F02, F100 ... in the directory dockout. I would
>>> like to calculate the COM and place a pseudo atom on the COM and save it as
>>> a pdb for all the 100 files.
>>> 'out' in the script corresponds to the list of all the 100 files.
>>>
>>> import pymol
>>>
>>> from pymol import cmd
>>>
>>> pymol.finish_launching()
>>>
>>> import numpy as np
>>>
>>> import glob
>>>
>>> import fileinput
>>>
>>> def center(selection, com=True):
>>>
>>> model = cmd.get_model(selection)
>>>
>>> xyz = np.array(model.get_coord_list())
>>>
>>> mass = [i.get_mass() for i in model.atom]
>>>
>>> xyz_m = xyz * np.array([mass]).T
>>>
>>> if com:
>>>
>>> return tuple(np.sum(xyz_m, 0)/model.get_mass())
>>>
>>> else:
>>>
>>> return tuple(np.average(xyz, 0))
>>>
>>>
>>> def GetListOfFiles (filename):
>>>
>>> l = []
>>>
>>> for line in fileinput.input( filename ):
>>>
>>> tokens = line.split( )
>>>
>>> l.append(tokens)
>>>
>>> return l
>>>
>>>
>>> def Calculate_COM (list):
>>>
>>> for i in range (len(list)):
>>>
>>> print list[i][0]
>>>
>>> X=1
>>>
>>> if (X<101):
>>>
>>> os.system("cp ./dockout/F"+ str(X).zfill(2)+ " ./lig.pdb")
>>>
>>> for pdb in glob.glob("lig.pdb"):
>>>
>>> cmd.load(pdb)
>>>
>>> COM = center('resn UNK')
>>>
>>> cmd.pseudoatom('ligCOM', pos=COM)
>>>
>>> cmd.save("complex_dummy.pdb", "all")
>>>
>>> os.system("mv complex_dummy.pdb complex_" +
>>> str(X).zfill(2) + "_dummy.pdb")
>>>
>>> os.system("rm lig.pdb")
>>>
>>> X=X+1
>>>
>>> else:
>>>
>>> break
>>>
>>> listofFiles = GetListOfFiles ("./out")
>>>
>>> print listofFiles
>>>
>>> Calculate_COM(listofFiles)
>>>
>>>
>>>
>>> Thanks,
>>> Subha
>>>
>>>
>>> 
>>> --
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>>> ___
>>> 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
>>>
>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>>
>


-- 
Tsjerk A. Wassenaar, Ph.D.
--
Check out the vibrant tech community on one of the world's most 
engaging tech sites, SlashDot.org! http://sdm.link/slashdot_

Re: [PyMOL] Placing pseudo atom on COM and saving it as pdb

[Subha K]

Thanks David and Tsjerk for the kind reply and suggestion.

I Figured a solution by combining both of your suggestions

def center(selection, com=True):

model = cmd.get_model(selection)

xyz = np.array(model.get_coord_list())

mass = [i.get_mass() for i in model.atom]

xyz_m = xyz * np.array([mass]).T

if com:

return tuple(np.sum(xyz_m, 0)/model.get_mass())

else:

return tuple(np.average(xyz, 0))


with open("./out") as f:

for line in f:

in_pdb_file = line.strip()

print in_pdb_file

cmd.load(in_pdb_file, 'tmp')

COM = center('resn UNK')

cmd.pseudoatom('ligCOM', pos=COM)

cmd.save(in_pdb_file[:-4] + "_dummy.pdb", "all")

cmd.delete('ligCOM')

cmd.delete('tmp')


@Tsjerk: Don't know why I got an error: Selector-Error: Invalid selection
name "pseudo".
pseudo<--

Thanks again for the support.

Best Regards,
Subha





On Wed, Oct 12, 2016 at 12:53 PM, Tsjerk Wassenaar 
wrote:

>
> Hi Subha,
>
> Probably this will get close:
>
> for pdb in open('./out').readlines():
> pdb = pdb.strip()
> cmd.load(pdb,'tmp')
> cmd.pseudoatom('tmp',name='pseudo')
> cmd.save(pdb[:-4]+'-pseudo.pdb','pseudo')
> cmd.delete('tmp')
> cmd.delete('pseudo')
>
> ... Just a bit too much for a oneliner ;)
>
> Hope it helps,
>
> Tsjerk
>
>
> On Wed, Oct 12, 2016 at 8:16 PM, Subha K  wrote:
>
>> Hi There,
>>
>> I am looking to automate the calculation of centre of mass and placing a
>> pseudo atom on the COM and save it as a pdb file . Going through the forum [
>> https://sourceforge.net/p/pymol/mailman/message/34458943/] , I found
>> some useful scripts for this, but, I am having trouble getting it done for
>> all files in a directory. My script does what I need for the first file
>> alone. Some looping or other is not correct. Or there could be an easy and
>> better way to do it. I couldn't figure that out.  So, could some one please
>> help me solve this?
>>
>> I have 100 files F01, F02, F100 ... in the directory dockout. I would
>> like to calculate the COM and place a pseudo atom on the COM and save it as
>> a pdb for all the 100 files.
>> 'out' in the script corresponds to the list of all the 100 files.
>>
>> import pymol
>>
>> from pymol import cmd
>>
>> pymol.finish_launching()
>>
>> import numpy as np
>>
>> import glob
>>
>> import fileinput
>>
>> def center(selection, com=True):
>>
>> model = cmd.get_model(selection)
>>
>> xyz = np.array(model.get_coord_list())
>>
>> mass = [i.get_mass() for i in model.atom]
>>
>> xyz_m = xyz * np.array([mass]).T
>>
>> if com:
>>
>> return tuple(np.sum(xyz_m, 0)/model.get_mass())
>>
>> else:
>>
>> return tuple(np.average(xyz, 0))
>>
>>
>> def GetListOfFiles (filename):
>>
>> l = []
>>
>> for line in fileinput.input( filename ):
>>
>> tokens = line.split( )
>>
>> l.append(tokens)
>>
>> return l
>>
>>
>> def Calculate_COM (list):
>>
>> for i in range (len(list)):
>>
>> print list[i][0]
>>
>> X=1
>>
>> if (X<101):
>>
>> os.system("cp ./dockout/F"+ str(X).zfill(2)+ " ./lig.pdb")
>>
>> for pdb in glob.glob("lig.pdb"):
>>
>> cmd.load(pdb)
>>
>> COM = center('resn UNK')
>>
>> cmd.pseudoatom('ligCOM', pos=COM)
>>
>> cmd.save("complex_dummy.pdb", "all")
>>
>> os.system("mv complex_dummy.pdb complex_" + str(X).zfill(
>> 2) + "_dummy.pdb")
>>
>> os.system("rm lig.pdb")
>>
>> X=X+1
>>
>> else:
>>
>> break
>>
>> listofFiles = GetListOfFiles ("./out")
>>
>> print listofFiles
>>
>> Calculate_COM(listofFiles)
>>
>>
>>
>> Thanks,
>> Subha
>>
>>
>> 
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>> ___
>> 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
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
>
--
Check out the vibrant tech community on one of the world's most 
engaging tech sites, SlashDot.org! http://sdm.link/slashdot___
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Re: [PyMOL] Placing pseudo atom on COM and saving it as pdb

[David Hall]

Every time you loop through the list of files, you set X=1 ; you do your X=X+1 
in a loop that will only run once ( because glob.glob(“lig.pdb”) is only going 
to return a list of length 1 that has lig.pdb) , so you set X=1 , then X=2, 
then back to X=1 before you process the next entry. That is why you are only 
processing the first file, probably doing so 100 times.

you probably want something like

with open(“out") as f:
for line in f:
  in_pdb_file = line.strip()
  // code for processing in_pdb_file here

or

for X in range(1,101):
in_pdb_file = “dockout/F"+ str(X).zfill(2)
   // code for processing in_pdb_file here


Generally, I would recommend strongly against using os.system for performing 
file operations. You should look into shutil.copy , shutil.move , and os.remove 


> On Oct 12, 2016, at 2:16 PM, Subha K  wrote:
> 
> Hi There,
> 
> I am looking to automate the calculation of centre of mass and placing a 
> pseudo atom on the COM and save it as a pdb file . Going through the forum 
> [https://sourceforge.net/p/pymol/mailman/message/34458943/ 
> ] , I found some 
> useful scripts for this, but, I am having trouble getting it done for all 
> files in a directory. My script does what I need for the first file alone. 
> Some looping or other is not correct. Or there could be an easy and better 
> way to do it. I couldn't figure that out.  So, could some one please help me 
> solve this?
> 
> I have 100 files F01, F02, F100 ... in the directory dockout. I would like to 
> calculate the COM and place a pseudo atom on the COM and save it as a pdb for 
> all the 100 files. 
> 'out' in the script corresponds to the list of all the 100 files.
> 
> import pymol
> from pymol import cmd
> pymol.finish_launching()
> import numpy as np
> import glob
> import fileinput
> def center(selection, com=True):
> model = cmd.get_model(selection)
> xyz = np.array(model.get_coord_list())
> mass = [i.get_mass() for i in model.atom]
> xyz_m = xyz * np.array([mass]).T
> if com:
> return tuple(np.sum(xyz_m, 0)/model.get_mass())
> else:
> return tuple(np.average(xyz, 0))
> 
> def GetListOfFiles (filename):
> l = []
> for line in fileinput.input( filename ):
> tokens = line.split( )
> l.append(tokens)
> return l
> 
> def Calculate_COM (list):
> for i in range (len(list)):
> print list[i][0]
> X=1
> if (X<101):
> os.system("cp ./dockout/F"+ str(X).zfill(2)+ " ./lig.pdb")
> for pdb in glob.glob("lig.pdb"):
> cmd.load(pdb)
> COM = center('resn UNK')
> cmd.pseudoatom('ligCOM', pos=COM)
> cmd.save("complex_dummy.pdb", "all")
> os.system("mv complex_dummy.pdb complex_" + str(X).zfill(2) + 
> "_dummy.pdb")
> os.system("rm lig.pdb")
> X=X+1
> else:
> break
> listofFiles = GetListOfFiles ("./out")
> print listofFiles
> Calculate_COM(listofFiles)
> 
> 
> Thanks,
> Subha 
> 
> --
> Check out the vibrant tech community on one of the world's most 
> engaging tech sites, SlashDot.org! 
> http://sdm.link/slashdot___
> 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

--
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Re: [PyMOL] Placing pseudo atom on COM and saving it as pdb

[Tsjerk Wassenaar]

Hi Subha,

Probably this will get close:

for pdb in open('./out').readlines():
pdb = pdb.strip()
cmd.load(pdb,'tmp')
cmd.pseudoatom('tmp',name='pseudo')
cmd.save(pdb[:-4]+'-pseudo.pdb','pseudo')
cmd.delete('tmp')
cmd.delete('pseudo')

... Just a bit too much for a oneliner ;)

Hope it helps,

Tsjerk


On Wed, Oct 12, 2016 at 8:16 PM, Subha K  wrote:

> Hi There,
>
> I am looking to automate the calculation of centre of mass and placing a
> pseudo atom on the COM and save it as a pdb file . Going through the forum [
> https://sourceforge.net/p/pymol/mailman/message/34458943/] , I found some
> useful scripts for this, but, I am having trouble getting it done for all
> files in a directory. My script does what I need for the first file alone.
> Some looping or other is not correct. Or there could be an easy and better
> way to do it. I couldn't figure that out.  So, could some one please help
> me solve this?
>
> I have 100 files F01, F02, F100 ... in the directory dockout. I would like
> to calculate the COM and place a pseudo atom on the COM and save it as a
> pdb for all the 100 files.
> 'out' in the script corresponds to the list of all the 100 files.
>
> import pymol
>
> from pymol import cmd
>
> pymol.finish_launching()
>
> import numpy as np
>
> import glob
>
> import fileinput
>
> def center(selection, com=True):
>
> model = cmd.get_model(selection)
>
> xyz = np.array(model.get_coord_list())
>
> mass = [i.get_mass() for i in model.atom]
>
> xyz_m = xyz * np.array([mass]).T
>
> if com:
>
> return tuple(np.sum(xyz_m, 0)/model.get_mass())
>
> else:
>
> return tuple(np.average(xyz, 0))
>
>
> def GetListOfFiles (filename):
>
> l = []
>
> for line in fileinput.input( filename ):
>
> tokens = line.split( )
>
> l.append(tokens)
>
> return l
>
>
> def Calculate_COM (list):
>
> for i in range (len(list)):
>
> print list[i][0]
>
> X=1
>
> if (X<101):
>
> os.system("cp ./dockout/F"+ str(X).zfill(2)+ " ./lig.pdb")
>
> for pdb in glob.glob("lig.pdb"):
>
> cmd.load(pdb)
>
> COM = center('resn UNK')
>
> cmd.pseudoatom('ligCOM', pos=COM)
>
> cmd.save("complex_dummy.pdb", "all")
>
> os.system("mv complex_dummy.pdb complex_" + str(X).zfill(2)
> + "_dummy.pdb")
>
> os.system("rm lig.pdb")
>
> X=X+1
>
> else:
>
> break
>
> listofFiles = GetListOfFiles ("./out")
>
> print listofFiles
>
> Calculate_COM(listofFiles)
>
>
>
> Thanks,
> Subha
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> ___
> 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
>



-- 
Tsjerk A. Wassenaar, Ph.D.
--
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engaging tech sites, SlashDot.org! http://sdm.link/slashdot___
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[PyMOL] Placing pseudo atom on COM and saving it as pdb

[Subha K]

Hi There,

I am looking to automate the calculation of centre of mass and placing a
pseudo atom on the COM and save it as a pdb file . Going through the forum [
https://sourceforge.net/p/pymol/mailman/message/34458943/] , I found some
useful scripts for this, but, I am having trouble getting it done for all
files in a directory. My script does what I need for the first file alone.
Some looping or other is not correct. Or there could be an easy and better
way to do it. I couldn't figure that out.  So, could some one please help
me solve this?

I have 100 files F01, F02, F100 ... in the directory dockout. I would like
to calculate the COM and place a pseudo atom on the COM and save it as a
pdb for all the 100 files.
'out' in the script corresponds to the list of all the 100 files.

import pymol

from pymol import cmd

pymol.finish_launching()

import numpy as np

import glob

import fileinput

def center(selection, com=True):

model = cmd.get_model(selection)

xyz = np.array(model.get_coord_list())

mass = [i.get_mass() for i in model.atom]

xyz_m = xyz * np.array([mass]).T

if com:

return tuple(np.sum(xyz_m, 0)/model.get_mass())

else:

return tuple(np.average(xyz, 0))


def GetListOfFiles (filename):

l = []

for line in fileinput.input( filename ):

tokens = line.split( )

l.append(tokens)

return l


def Calculate_COM (list):

for i in range (len(list)):

print list[i][0]

X=1

if (X<101):

os.system("cp ./dockout/F"+ str(X).zfill(2)+ " ./lig.pdb")

for pdb in glob.glob("lig.pdb"):

cmd.load(pdb)

COM = center('resn UNK')

cmd.pseudoatom('ligCOM', pos=COM)

cmd.save("complex_dummy.pdb", "all")

os.system("mv complex_dummy.pdb complex_" + str(X).zfill(2)
+ "_dummy.pdb")

os.system("rm lig.pdb")

X=X+1

else:

break

listofFiles = GetListOfFiles ("./out")

print listofFiles

Calculate_COM(listofFiles)



Thanks,
Subha
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