This package is a python library with tools for the Molecular Simulation - Software Gromos. It allows you to easily set up, manage and analyze simulations in python.
Home Page: https://rinikerlab.github.io/PyGromosTools/
License: MIT License
Data is not written to imd output file with the following code on line 37.
out_imd = imd.write(out_imd)
Would it make sense to support syntax that allows the following:
grom_system.imd.TITLE = "My new title"
in analogy to
grom_system.imd.STEP.NSTLIM = 3000
I feel like it would make the workflow more natural.
Implement some sub-sub-blocks which are missing at the moment:
Can somebody add a tre file which contains all these sub-sub-blocks to the example section for demonstration?
To be checked:
-[x] hpc_queuing
_submission_system
dummy
local
lsf
files
[ ]blocks
simulations
-[ ] utils
Some gromos++ functions take several arguments of the same category. For some functions, this is represented through the use of list, e.g. for com_top:
@gromosTypeConverter
def com_top(self, in_topo_paths:(str or List[str]), topo_multiplier:(int or List[int])=1, out_top_path:str= "combined_out.top",
take_topology_params_of_file:int=1, take_solvent_parameters_of_file:int=1,
_binary_name:str="com_top")->str: #Todo: also take lists as input ! bschroed
Other functions only support a concatenated string, e.g. ran_box. In that particular case, in_top_path, in_cnf_path, and nmolecule would be better represented by list:
@gromosTypeConverter
def ran_box(self, in_top_path:str, in_cnf_path:str, out_cnf_path:str= "",
periodic_boundary_condition: str = "r", nmolecule:int = 1, dens:float = 1.0, threshold:float=None, layer:bool = False,
boxsize:float=None, fixfirst:bool = False, seed:float=None, _binary_name="ran_box", verbose=False, return_command_only=False)->str:
Is that something we want to change?
In the new parallel GromosXX RE-EDS code, the format of the repdat output file changed slightly. The changes are related to the column names and the indices starting at 0 instead of 1. I described it in more detail here: rinikerlab/reeds#47
Once we make the switch to the new parallel code, we should also adapt the functions which depend on repdat s.t. the new format is the default, but the old format is still supported.
I have issues with lsf access on euler, when I want to check if a job is already submitted.
("bjobs -w") is not terminating some times.
Do you expierence this two?
We need to checkout the jupyter notebooks of the example folder for our relase :)
What needs to be done?
ToDos - Check:
Add:
add RMSD evaluation
Some blocks need special attention and should maybe override the eq methode the inherit from the generic_block
the labels in the imd files don't match the arguments order, I think NRES, NEOFF, NUMSTATES is the correct order
if a deepcopy is executed without all files being read in it fails with:
gromos_system.py:241 -->new_dict.update({key: attribute_dict[key]._asdict()})
'NoneType' object has no attribute '_asdict'maybe? ;)Automatic testing is important and the testing files are already present for this, but need to be filled with test.
The files you can find in pygromos/tests
Write tests:
Can we improve the speed of the unit test?
A few points possible points:
Add examples of how to use the OFF-Gromos-Topology creator
maybe? ;)
adding multiple tops together is very slow. Especially for easy task like multiplying a top for a condensed phase simulation this is not necessary. A lot of overhead could be avoided by adding a multiply option.
This would significantly speed up the creation of topologies
Adding solvation free energy calculations to release 3
I'm checking the trajectory example jupyter notebook at the moment.
I think this is probably now even an issue, but at the very beginning when the first instance of a traj_trc.Trc class is instantiated, there is the following warning:
/home/mlehner/anaconda3/envs/gromos/lib/python3.7/site-packages/pandas/core/generic.py:2621: PerformanceWarning:
your performance may suffer as PyTables will pickle object types that it cannot
map directly to c-types [inferred_type->mixed,key->block2_values] [items->Index(['POS_1', 'POS_2', 'POS_3', 'POS_4', 'POS_5', 'POS_6', 'POS_7', 'POS_8',
'POS_9', 'POS_10', 'POS_11', 'POS_12', 'POS_13', 'POS_14', 'POS_15',
'POS_16', 'POS_17', 'POS_18'],
dtype='object')]
encoding=encoding,
I thought I'd report it just to be thorough
At some ime point we need an MTB representation in pygromos :)
The NRE value of the FORCE Block is written out as a float resulting in an value error.
I believe this is due to it being read in as a float in the read_content_from_str function.
This could be fixed by replacing the float by int.
setattr(self, self._order[0][1][1], list(map(int, content[3].split()[1:])))gromos_system simulation building blocks do not check if trajectories are written. If WRITETRAJ Block is set to 0 a error is thrown.
By @MTLehner
Can we please change the system information block that is shown when printing a gromos_system???
@bschroed when I simulate a simple Cyclohexane molecule it's not my ligand and I also don't expect to see a protein! If anything we should stick to the gromos convention of distinguishing between solute and solvent.
bash sub process does not spawn with the same conda enviroment if started from a jupyter notebook from vscode on wsl
We should check and make sure, that all types in our IMD and TOP classes.
@mlehner
we talked about this before, I just found, that I already started the automatic detection of the submission system:
from pygromos.hpc_queuing.submission_syste.Submission_System import SubmissionSystem
Hi,
I had a look at the trc-pandas coumn types, and wonder if the object types are good?
TIMESTEP_step int64
TIMESTEP_time float64
POS_1 object
POS_2 object
POS_3 object
...
POS_4580 object
POS_4581 object
POS_4582 object
POS_4583 object
POS_4584 object
Length: 4586, dtype: object
Hi
I found one issue with the lattice shifts.
If I have a coord. traj with a pbc, it results in issues when I want to write out the coordinates as pdb, as the system is not centered and the pbc was not removed.
Bring topo files
In the TI example notebook examples/example_TI_gromos_simulation.ipynb, the file /examples/example_files/TI_Calculation/TI_input/M030_6KET.disres is specified, but this file isn't in the repository. This leads to the following error:
---------------------------------------------------------------------------
OSError Traceback (most recent call last)
<ipython-input-13-14f2d2d90c97> in <module>
6 grom_system = Gromos_System(in_cnf_path=cnf_path, in_top_path=top_path,
7 in_disres_path=disres_path,
----> 8 system_name=sys_name, work_folder=input_dir)
9
10
/cluster/work/igc/wsalome/anaconda3/envs/pygromos/lib/python3.7/site-packages/PyGromos-0+untagged.176.g9b9886d-py3.7.egg/pygromos/files/gromos_system/gromos_system.py in __init__(self, work_folder, system_name, in_smiles, in_top_path, in_cnf_path, in_imd_path, in_disres_path, in_ptp_path, in_posres_path, in_refpos_path, in_gromosXX_bin_dir, in_gromosPP_bin_dir, rdkitMol, readIn, Forcefield, auto_convert, adapt_imd_automatically, verbose)
136 "refpos": in_refpos_path,
137 }
--> 138 self.parse_attribute_files(file_mapping, readIn=readIn, verbose=verbose)
139
140 ##System Information:
/cluster/work/igc/wsalome/anaconda3/envs/pygromos/lib/python3.7/site-packages/PyGromos-0+untagged.176.g9b9886d-py3.7.egg/pygromos/files/gromos_system/gromos_system.py in parse_attribute_files(self, file_mapping, readIn, verbose)
523 [check_file_paths.append(x) for k, x in file_mapping.items() if (not x is None)]
524 if (len(check_file_paths) > 0):
--> 525 bash.check_path_dependencies(check_file_paths, verbose=verbose)
526
527 # SET Attribute-FILES
/cluster/work/igc/wsalome/anaconda3/envs/pygromos/lib/python3.7/site-packages/PyGromos-0+untagged.176.g9b9886d-py3.7.egg/pygromos/utils/bash.py in check_path_dependencies(check_required_paths, check_warn_paths, verbose)
123 print("\n==================\nAUTSCH\n==================\n")
124 missing_str = "\n\t".join(map(str, missing))
--> 125 raise IOError("COULD NOT FIND all DEPENDENCY!\n\t Could not find path to: \n\t" + str(missing_str), "\n\n")
126 elif verbose:
127 print("All dependencies are correct!", "\n\n")
OSError: [Errno COULD NOT FIND all DEPENDENCY!
Could not find path to:
./example_files/TI_Calculation/TI_input/M030_6KET.disres]
@schroederb I think you originally wrote this tutorial. Do you still have the file on one of your local branches?
We should introduce a copy and a __deepcopy__function to all files and trajs, so we are able to copy the obj:
lam_system = copy.deepcopy(sd_gromos_system)
to be implemented in :
In tutorial_gromos_pipeline.ipynb, template files are not consequently copied with rebase_files(). As a consequence, the templates are overwritten. I opened a PR with a fix.
in the FORCE class in files/blocks/imd_blocks.py (probably also in the other classes, I didn't check further) there is a conversion of parameters to booleans, but the parameters seem to be strings instead of integers and in my case both "1" and "0" are converted to "True"
We need to implement dealing with periodic boundary conditions.
Location of choice would be in the analysis module coordinate_analysis.
in_imd_path Argument in pygromos.simulattion.modules.general_simulation_modules::simulation does not work or is counter intuitive. The Argument is only used if the gromos_system.imd is a future_file.
This should either be explicitly written in the documentation or changed (always used if not None). Alternatively a force_imd_override option would be nice.
Write Jupyter Example Notebook for the new Submission System (with gromos_system)
Repdate got modified with the change to the new trajectories (pandas) and needs some rework
the gromosXX/gromos++ paths are not passed from gromos_system to the simulations blocks
I noticed this package was using the slightly older openforcefield namespace, which is no longer being updated. I'm unaware of anything glaringly incorrect with v0.8.3, but migrating to the new namespace will allow for new features and fixes to be applied with new versions of the toolkit.
If making this change, the omnia channel can be dropped from the environment. This might make solving environments quicker. Also, omnia in general is out of service so dropping it would avoid accidentally pulling in old package.
In my experience, it's as simple as replacing every openforcefield in code with openff.toolkit. I'd be happy to help with or directly submit a patch myself if any issues arise.
@mlehner
we talked about this before, I just found, that I already started the automatic detection of the submission system:
from pygromos.hpc_queuing.submission_syste.Submission_System import SubmissionSystem
Topo offers many helper functions, to create and modify the files (add atoms, change solvent, change LJ Parameters, ....)
Write a Example Notebook with all these functions Documented
In tutorial_gromos_pipeline.ipynb, cell 16 causes an error:
cnf = Cnf(cnf_eq_NVP)
trc = Trc(out_eq_NVP+".trc")
trc.cog_reframe(cnf)
trc.visualize(cnf)
The error reads:
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
/tmp/ipykernel_31664/325201585.py in <module>
1 cnf = Cnf(cnf_eq_NVP)
2 trc = Trc(out_eq_NVP+".trc")
----> 3 trc.cog_reframe(cnf)
4 trc.visualize(cnf)
~/Documents/repos/PyGromosTools/pygromos/files/trajectory/trc.py in cog_reframe(self, cnf, index_list)
316
317 # cog calculation: select POS -> apply pbc -> average all positions
--> 318 pbc_pos = self.database[col_list].applymap(lambda x: ca._periodic_distance(x, grid))
319 cog = pbc_pos.sum(axis=1) / len(col_list)
320 #print("COG:", cog)
~/miniconda3/envs/pultar-dev/lib/python3.9/site-packages/pandas/core/frame.py in applymap(self, func, na_action, **kwargs)
8823 return lib.map_infer(x.astype(object)._values, func, ignore_na=ignore_na)
8824
-> 8825 return self.apply(infer).__finalize__(self, "applymap")
8826
8827 # ----------------------------------------------------------------------
~/miniconda3/envs/pultar-dev/lib/python3.9/site-packages/pandas/core/frame.py in apply(self, func, axis, raw, result_type, args, **kwargs)
8738 kwargs=kwargs,
8739 )
-> 8740 return op.apply()
8741
8742 def applymap(
~/miniconda3/envs/pultar-dev/lib/python3.9/site-packages/pandas/core/apply.py in apply(self)
686 return self.apply_raw()
687
--> 688 return self.apply_standard()
689
690 def agg(self):
~/miniconda3/envs/pultar-dev/lib/python3.9/site-packages/pandas/core/apply.py in apply_standard(self)
810
811 def apply_standard(self):
--> 812 results, res_index = self.apply_series_generator()
813
814 # wrap results
~/miniconda3/envs/pultar-dev/lib/python3.9/site-packages/pandas/core/apply.py in apply_series_generator(self)
826 for i, v in enumerate(series_gen):
827 # ignore SettingWithCopy here in case the user mutates
--> 828 results[i] = self.f(v)
829 if isinstance(results[i], ABCSeries):
830 # If we have a view on v, we need to make a copy because
~/miniconda3/envs/pultar-dev/lib/python3.9/site-packages/pandas/core/frame.py in infer(x)
8821 if x.empty:
8822 return lib.map_infer(x, func, ignore_na=ignore_na)
-> 8823 return lib.map_infer(x.astype(object)._values, func, ignore_na=ignore_na)
8824
8825 return self.apply(infer).__finalize__(self, "applymap")
~/miniconda3/envs/pultar-dev/lib/python3.9/site-packages/pandas/_libs/lib.pyx in pandas._libs.lib.map_infer()
~/Documents/repos/PyGromosTools/pygromos/files/trajectory/trc.py in <lambda>(x)
316
317 # cog calculation: select POS -> apply pbc -> average all positions
--> 318 pbc_pos = self.database[col_list].applymap(lambda x: ca._periodic_distance(x, grid))
319 cog = pbc_pos.sum(axis=1) / len(col_list)
320 #print("COG:", cog)
AttributeError: module 'pygromos.analysis.coordinate_analysis' has no attribute '_periodic_distance'
The same error occurs in cell 20:
trc = Trc(out_md+".trc")
trc.TITLE = "\n".join(trc.TITLE)
trc.cog_reframe(cnf)
trc.visualize(cnf)
The error message reads:
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
/tmp/ipykernel_31664/153322794.py in <module>
1 trc = Trc(out_md+".trc")
2 trc.TITLE = "\n".join(trc.TITLE)
----> 3 trc.cog_reframe(cnf)
4 trc.visualize(cnf)
~/Documents/repos/PyGromosTools/pygromos/files/trajectory/trc.py in cog_reframe(self, cnf, index_list)
316
317 # cog calculation: select POS -> apply pbc -> average all positions
--> 318 pbc_pos = self.database[col_list].applymap(lambda x: ca._periodic_distance(x, grid))
319 cog = pbc_pos.sum(axis=1) / len(col_list)
320 #print("COG:", cog)
~/miniconda3/envs/pultar-dev/lib/python3.9/site-packages/pandas/core/frame.py in applymap(self, func, na_action, **kwargs)
8823 return lib.map_infer(x.astype(object)._values, func, ignore_na=ignore_na)
8824
-> 8825 return self.apply(infer).__finalize__(self, "applymap")
8826
8827 # ----------------------------------------------------------------------
~/miniconda3/envs/pultar-dev/lib/python3.9/site-packages/pandas/core/frame.py in apply(self, func, axis, raw, result_type, args, **kwargs)
8738 kwargs=kwargs,
8739 )
-> 8740 return op.apply()
8741
8742 def applymap(
~/miniconda3/envs/pultar-dev/lib/python3.9/site-packages/pandas/core/apply.py in apply(self)
686 return self.apply_raw()
687
--> 688 return self.apply_standard()
689
690 def agg(self):
~/miniconda3/envs/pultar-dev/lib/python3.9/site-packages/pandas/core/apply.py in apply_standard(self)
810
811 def apply_standard(self):
--> 812 results, res_index = self.apply_series_generator()
813
814 # wrap results
~/miniconda3/envs/pultar-dev/lib/python3.9/site-packages/pandas/core/apply.py in apply_series_generator(self)
826 for i, v in enumerate(series_gen):
827 # ignore SettingWithCopy here in case the user mutates
--> 828 results[i] = self.f(v)
829 if isinstance(results[i], ABCSeries):
830 # If we have a view on v, we need to make a copy because
~/miniconda3/envs/pultar-dev/lib/python3.9/site-packages/pandas/core/frame.py in infer(x)
8821 if x.empty:
8822 return lib.map_infer(x, func, ignore_na=ignore_na)
-> 8823 return lib.map_infer(x.astype(object)._values, func, ignore_na=ignore_na)
8824
8825 return self.apply(infer).__finalize__(self, "applymap")
~/miniconda3/envs/pultar-dev/lib/python3.9/site-packages/pandas/_libs/lib.pyx in pandas._libs.lib.map_infer()
~/Documents/repos/PyGromosTools/pygromos/files/trajectory/trc.py in <lambda>(x)
316
317 # cog calculation: select POS -> apply pbc -> average all positions
--> 318 pbc_pos = self.database[col_list].applymap(lambda x: ca._periodic_distance(x, grid))
319 cog = pbc_pos.sum(axis=1) / len(col_list)
320 #print("COG:", cog)
AttributeError: module 'pygromos.analysis.coordinate_analysis' has no attribute '_periodic_distance'
Conversion from trc/cnf to
and back
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