Functions¶
Topology¶
Loading¶
This function should be avoided by the user if there is not a clear reason. When a new object of class msystem is initialized this function is called implicitly by construction.
- msystem.load_topol(name_file)¶
Parameters: name_file (str) – Name of input file with topology Returns: None
See topology formats for additional info.
Top_Par defined by user¶
AquaLab gives with this function the posibility to include user defined topologies and parameters. A python script as the one found in Aqua/top_par/top_par_template.py needs to be included in the working directory to be read with:
Selection¶
- msystem.selection(condition=None[, traj=0, frame='ALL', pbc=True])¶
Parameters: - condition (str) – Logical sentence with selection.
- traj (int) – Index of trajectory to analyse if a condition over coordinates needs to be evaluated.
- frame (list, int or str) – Index of frame to analyse if a condition over coordinates needs to be evaluated.
- pbc (bool) – Periodic Boundary Conditions if a condition over coordinates needs to be evaluated.
Returns: list of atom indexes.
Return type: list of integers.
Syntaxis¶
The syntaxis used by the function msystem.selection() is given by the classes atom, resid and chain. In addition, boolean operations can be done using the words: “AND”, “OR”, “NOT”, “IN”, “WITHIN”, “OF”; no matter if are written in capital or lower case, and the characters: “[”, “]”, “(”, ”)” and ”,”.
Some special words can be used although they have an easy translation:
- “backbone”: ‘(atom.name N CA C O)’
- “sidechain”: ‘(resid.type Protein and not atom.name N CA C O H1 H2)’
- “protein”: ‘(resid.type Protein)’
- “water”: ‘(resid.type Water)’
Find some examples in section Tutorial-Syntaxis.
See also
Donors and Acceptors¶
Writting pdb files¶
xxx
Trajectories¶
Load Trajectory¶
- msystem.load_traj(file_input=None[, frame=None, begin=None, end=None, increment=1, units='frames', verbose=False])¶
Parameters: - file_input (str) – Name of trajectory file in the following formats: pdb, gro, xtc, trr, dcd.
- frame (int or list.) – Index of frames to be loaded.
- begin (int.) – Frame to start the loading process.
- end (int.) – Frame to finish the loading process.
- increment (int.) – Interval to load frames.
- units (str.) – Units for “begin”, “end” and “increment”. [only units=’frames’ available]
- verbose (bool) – Prints out general information.
Returns: None
Prints out: general information if verbose=True.
Info Trajectories¶
- msystem.info_trajs()¶
Returns: None Prints out: General information of the whole set of trajectories loaded.
Delete Trajectory¶
- msystem.delete_traj(index='ALL')¶
Parameters: - index – index of trajectory to be deleted in the list msystem.traj
- index – int or ‘ALL’
Returns: None
Load Frames¶
To append a new frame to the list traj.frame:
- traj.upload_frame(frame='next'[, begin=None, end=None, increment=1, units=None])¶
Parameters: - frame (int or list or ‘next’ or ‘all’.) – Index of frames to be loaded.
- begin (int.) – Frame to start the loading process.
- end (int.) – Frame to finish the loading process.
- increment (int.) – Interval to load frames.
- units (str.) – Units for “begin”, “end” and “increment”. [only units=’frames’ available]
Returns: None
To rewrite an old frame of the traj.frame list with a new frame:
Info Frames¶
- traj.info()¶
Returns: None Prints out: General information of the whole set of the trajectory.
Delete Frames¶
- traj.delete_frame(frame='ALL'[, begin=None, end=None, increment=1, units=None])¶
Parameters: - frame (int or list or ‘ALL’.) – Index of frame in the list traj.frame to be deleted.
- begin (int.) – Frame to start the deleting process. [not available yet]
- end (int.) – Frame to finish the deleting process. [not available yet]
- increment (int.) – Interval to delete frames. [not available yet]
- units (str.) – Units for “begin”, “end” and “increment”. [only units=’frames’ available]
Returns: None
See also
.
Writting dcd files¶
- traj.write(file_name=None, frame='ALL', begin=None, end=None, increment=1, units=None, action=None)¶
Parameters: - file_name (str) – Name of new trajectory file.
- frame (int or list or ‘ALL’) – Indexes of frames to be written in the new trajectory file.
- begin (int.) – Frame to start the deleting process. [not available yet]
- end (int.) – Frame to finish the deleting process. [not available yet]
- increment (int.) – Interval to delete frames. [not available yet]
- units (str.) – Units for “begin”, “end” and “increment”. [only units=’frames’ available]
- action (str.) – “OPEN” or “CLOSE” to open or close a file without writting, None to writte frames in the opened new trajectory file.
Returns: None
Analysis¶
Distances¶
- msystem.distance(sel1='ALL', sel2=None, traj=0, frame='ALL', legend=False, pbc=True)¶
Parameters: - sel1 (int, list[int], string.) – List or selection of atoms
- sel2 (int, list[int], string.) – List or selection of atoms
- traj (int) – Index of trajectory to be analysed.
- frame (int, list[int] or ‘ALL’) – List of frame indexes.
- legend (bool) – Key of distances as output if True.
- pbc (bool) – With periodic boundary conditions if True.
Returns: distances, keys1 [if legend], keys2 [if legend]
Return type: - distances:
- numpy.array[num_frames,atoms_sel1,atoms_sel2]
- numpy.array[atoms_sel1,atoms_sel2] (if num_frames=1)
- keys1:
- list[atoms_sel1]
- keys2:
- list[atoms_sel2]
See also
Ramachandran Map¶
The function computes the pairs of angles phi-psi for any list of residues and frames. Since each dihedral angle is computed with atoms from 2 different residues, the relationship between angle and residue is given by the atom ‘CA’.
- msystem.ramachandran_map(resid='ALL', traj=0, frame='ALL', pdb_index=False, legend=False)¶
Parameters: - resid (int, list[int] or ‘ALL’) – List of residue indexes or pdb indexes.
- traj (int) – Index of trajectory to be analysed.
- frame (int, list[int] or ‘ALL’) – List of frame indexes.
- pdb_index (bool) – Residues in input and output are identified by the pdb indexes if True.
- legend (bool) – Key of angles in output if True.
Returns: angles, keys [if legend]; List of pairs phi-psi (radians) for the corresponding residues and frames, and key legend if choosen.
Return type: - angles:
- numpy.array[num_frames,num_resids,2].
- numpy.array[num_resids,2] (if num_frames=1)
- numpy.array[num_frames,2] (if num_resids=1)
- numpy.array[2] (if num_frames=num_resids=1)
- keys:
- list[num_resids][2]
- list[num_resids][2] (if num_resids=1)
See also
Note
Depending on how this method is used, it can result with a low performance. Check msystem.dihedral_angle() for a better performance.
Covalent chains¶
- msystem.selection_covalent_chains(chain=None, select='protein')¶
Parameters: - chain (list[str]) – List of atom names to find as covalently bonded chains in “select”.
- select (str) – Selection or set of atoms where the method looks for covalent chains. (see: msystem.selection())
Returns: chains; List of chains found. Each chain is a list of the corresponding atom indexes.
Return type: - chains:
- list[num_chains][atom_indexes]
See also
Dihedral Angles¶
The method computes the value of any list of 4 atoms defining a dihedral angle. The output
- msystem.dihedral_angle(covalent_chain=None, traj=0, frame='ALL')¶
Parameters: - covalent_chain (list[int] or list[list[int]]) – List of 4 atoms defining the dihedral angle, or list of lists. (see: msystem.selection_covalent_chains())
- traj (int) – Index of traj to be analysed.
- frame (int, list[int] or ‘ALL’) – List of frame indexes.
Returns: angles; List of angle values (radians) in the same order found in input parameter covalent_chain.
Return type: - angles:
- numpy.array[num_frames,num_angs].
- numpy.array[num_angs] (if num_frames=1)
- numpy.array[num_frames] (if num_angs=1)
- float (if num_angs=1 and num_frames=1)
See also
