Notebook04: Use buildH as a module
Contents
Notebook04: Use buildH as a module¶
buildH is intended to be used mainly in the Unix command line but also as a module to a lesser extent. The features available are minimal: you can just call the main function of buildH and result files will be written.
It is not a proper API but more a way to call buildH inside larger analysis python scripts.
Checking buildH activation¶
As explained in Notebook01, you should have activated buildH before launching this notebook.
[1]:
import buildh
print(buildh.__version__)
1.6.0
Download data files¶
We will use the same data files as the ones in Notebook01 : the Berger POPC test case.
[2]:
# Coordinate file
!wget https://raw.githubusercontent.com/patrickfuchs/buildH/master/docs/Berger_POPC_test_case/start_128popc.pdb
# Trajectory file
!wget https://raw.githubusercontent.com/patrickfuchs/buildH/master/docs/Berger_POPC_test_case/popc0-25ns_dt1000.xtc
# Def file
!wget https://raw.githubusercontent.com/patrickfuchs/buildH/master/def_files/Berger_POPC.def
--2022-01-17 16:11:16-- https://raw.githubusercontent.com/patrickfuchs/buildH/master/docs/Berger_POPC_test_case/start_128popc.pdb
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.109.133, 185.199.110.133, 185.199.111.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.109.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 2253759 (2.1M) [text/plain]
Saving to: ‘start_128popc.pdb’
start_128popc.pdb 100%[===================>] 2.15M --.-KB/s in 0.05s
2022-01-17 16:11:17 (44.2 MB/s) - ‘start_128popc.pdb’ saved [2253759/2253759]
--2022-01-17 16:11:17-- https://raw.githubusercontent.com/patrickfuchs/buildH/master/docs/Berger_POPC_test_case/popc0-25ns_dt1000.xtc
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.108.133, 185.199.109.133, 185.199.110.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.108.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 2725936 (2.6M) [application/octet-stream]
Saving to: ‘popc0-25ns_dt1000.xtc’
popc0-25ns_dt1000.x 100%[===================>] 2.60M --.-KB/s in 0.06s
2022-01-17 16:11:17 (41.9 MB/s) - ‘popc0-25ns_dt1000.xtc’ saved [2725936/2725936]
--2022-01-17 16:11:18-- https://raw.githubusercontent.com/patrickfuchs/buildH/master/def_files/Berger_POPC.def
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.111.133, 185.199.108.133, 185.199.109.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.111.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 2135 (2.1K) [text/plain]
Saving to: ‘Berger_POPC.def’
Berger_POPC.def 100%[===================>] 2.08K --.-KB/s in 0s
2022-01-17 16:11:18 (4.54 MB/s) - ‘Berger_POPC.def’ saved [2135/2135]
buildH as a module¶
The only function accessible is the main one of buildH: buildh.launch(). It has the same arguments than the buildH command line (see Command line options and api implementation):
[3]:
help(buildh.launch)
Help on function launch in module buildh.UI:
launch(coord_file, def_file, lipid_type, traj_file=None, out_file='OP_buildH.out', prefix_traj_ouput=None, begin=None, end=None, lipid_jsons=None, ignore_CH3s=False)
Launch BuildH calculations.
This is the only function which can be called inside a Python script to use BuildH as a module.
It checks the different arguments and call the main function.
Parameters
----------
coord_file : str
Coordinate file. Only .pdb and .gro files are currently supported.
def_file : str
Order parameter definition file.
lipid_type : str
Combinaison of ForceField name and residue name for the lipid to calculate the OP on (e.g. Berger_POPC).
It must match with the internal topology files or the one(s) supplied.
traj_file : str, optional
Trajectory file (could be in XTC, TRR or DCD format), by default None.
out_file : str, optional
Output file name for storing order parameters, by default "OP_buildH.out".
prefix_traj_ouput : str, optional
Base name for trajectory output with hydrogens.
File extension will be automatically added.
By default None.
begin : int, optional
The first frame (ps) to read from the trajectory, by default None.
end : int, optional
The last frame (ps) to read from the trajectory, by default None.
lipid_jsons : list, optional
User topology lipid json file(s), by default None.
ignore_CH3s: bool, optional
Ignore CH3s groups for the construction of hydrogens and the calculation of the OP.
Raises
------
FileNotFoundError
When either coord_file, def_file or the traj_file is missing.
TypeError
When lipid_jsons is not a list.
BuildHError
When something went wront during calculation.
Now, we can call launch() with the correct arguments:
[4]:
buildh.launch("start_128popc.pdb", "Berger_POPC.def", "Berger_POPC", traj_file="popc0-25ns_dt1000.xtc", out_file="OP_POPC.dat")
Constructing the system...
System has 28526 atoms
Dealing with frame 0 at 0.0 ps.
Dealing with frame 1 at 1000.0 ps.
Dealing with frame 2 at 2000.0 ps.
Dealing with frame 3 at 3000.0 ps.
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Results written to OP_POPC.dat
The order parameters are in OP_POPC.dat.
[5]:
!head OP_POPC.dat
# OP_name resname atom1 atom2 OP_mean OP_stddev OP_stem
#--------------------------------------------------------------------
gamma1_1 POPC C1 H11 0.01304 0.12090 0.01069
gamma1_2 POPC C1 H12 0.00666 0.09279 0.00820
gamma1_3 POPC C1 H13 -0.01531 0.09141 0.00808
gamma2_1 POPC C2 H21 0.01511 0.12080 0.01068
gamma2_2 POPC C2 H22 -0.02050 0.09386 0.00830
gamma2_3 POPC C2 H23 -0.00660 0.09137 0.00808
gamma3_1 POPC C3 H31 0.01430 0.11796 0.01043
gamma3_2 POPC C3 H32 -0.00513 0.08670 0.00766
[6]:
!tail OP_POPC.dat
oleoyl_C14b POPC C29 H292 -0.09232 0.08611 0.00761
oleoyl_C15a POPC C30 H301 -0.07331 0.08235 0.00728
oleoyl_C15b POPC C30 H302 -0.07558 0.08218 0.00726
oleoyl_C16a POPC C31 H311 -0.07262 0.08300 0.00734
oleoyl_C16b POPC C31 H312 -0.07200 0.08320 0.00735
oleoyl_C17a POPC CA1 HA11 -0.04622 0.07990 0.00706
oleoyl_C17b POPC CA1 HA12 -0.04141 0.08677 0.00767
oleoyl_C18a POPC CA2 HA21 0.03691 0.08420 0.00744
oleoyl_C18b POPC CA2 HA22 -0.04603 0.07979 0.00705
oleoyl_C18c POPC CA2 HA23 -0.04145 0.08636 0.00763
Here is another example where we use the option ignore_CH3s, which does not output the order parameters of methyl (CH3) groups even if they are present in the def file.
[7]:
buildh.launch("start_128popc.pdb", "Berger_POPC.def", "Berger_POPC", traj_file="popc0-25ns_dt1000.xtc", out_file="OP_POPC.dat", ignore_CH3s=True)
Constructing the system...
System has 28526 atoms
Building hydrogens and computing order parameters will be skipped on CH3 groups (--ignore-CH3s activated).
Dealing with frame 0 at 0.0 ps.
Dealing with frame 1 at 1000.0 ps.
Dealing with frame 2 at 2000.0 ps.
Dealing with frame 3 at 3000.0 ps.
Dealing with frame 4 at 4000.0 ps.
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Results written to OP_POPC.dat
[8]:
!head OP_POPC.dat
# OP_name resname atom1 atom2 OP_mean OP_stddev OP_stem
#--------------------------------------------------------------------
beta1 POPC C5 H51 0.04934 0.11999 0.01061
beta2 POPC C5 H52 0.07162 0.12108 0.01070
alpha1 POPC C6 H61 0.11839 0.15261 0.01349
alpha2 POPC C6 H62 0.13903 0.19003 0.01680
g3_1 POPC C12 H121 -0.28674 0.09135 0.00807
g3_2 POPC C12 H122 -0.16195 0.14832 0.01311
g2_1 POPC C13 H131 -0.15159 0.14511 0.01283
g1_1 POPC C32 H321 0.21133 0.22491 0.01988
[9]:
!tail OP_POPC.dat
oleoyl_C13a POPC C28 H281 -0.09307 0.07657 0.00677
oleoyl_C13b POPC C28 H282 -0.08427 0.08647 0.00764
oleoyl_C14a POPC C29 H291 -0.09291 0.07618 0.00673
oleoyl_C14b POPC C29 H292 -0.09232 0.08611 0.00761
oleoyl_C15a POPC C30 H301 -0.07331 0.08235 0.00728
oleoyl_C15b POPC C30 H302 -0.07558 0.08218 0.00726
oleoyl_C16a POPC C31 H311 -0.07262 0.08300 0.00734
oleoyl_C16b POPC C31 H312 -0.07200 0.08320 0.00735
oleoyl_C17a POPC CA1 HA11 -0.04622 0.07990 0.00706
oleoyl_C17b POPC CA1 HA12 -0.04141 0.08677 0.00767
We can see that all order parameters belonging to methyl (CH3) groups are not present in the output file OP_POPC.dat (such as those from gamma_* or oleoyl_C18 carbon atoms).
Conclusion¶
We showed you quickly how to launch buildH as a Python module which can be convenient in a Jupyter Notebook. If you want to plot the corresponding order parameters, you can have a look to Notebook01.