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1. Sorting and reordering It is possible to reorder the molecules in a System by using the method chemlab core System reorder_molecules that takes the new order as the first argument Re ordering can be useful for example to sort the molecules against a certain key If you use chemlab in conjunction with GROMACS you may use the chemlab core System sort to sort the molecules according to their molecular formulas before exporting The topology file expect to have a file with the same molecule type ordererd 2 3 3 Extending the base types Warning This part of chemlab is still in draft This first very brief implementation serves as a specification document As we collect more feedback and feature requests there will be an expansion and a refinement of the extension functionalities Differents applications of chemistry may require additional data attached to each atom molecule or system For example you may need the velocity of the system atomic charges or number of electrons Chemlab should be able to provide a way to simply attach this data while retaining the selection and sorting functionalities The management of the atomic and molecular properties within a System is done through specific handlers Those handlers are called attributes and fields In the following example we may see how it s possible to add a new field y to the Atom class and transmit this field as a v_array in the Molecule and System class I
2. chemlab graphics transformations random_rotation_matrix rand None Return uniform random rotation matrix rand array like Three independent random variables that are uniformly distributed between 0 and 1 for each returned quaternion gt gt gt R random_rotation_matrix gt gt gt numpy allclose numpy dot R T R numpy identity 4 True chemlab graphics transformations random_vector size Return array of random doubles in the half open interval 0 0 1 0 gt gt gt v random_vector 10000 gt gt gt numpy all v gt 0 and numpy all v lt 1 True gt gt gt v0 random_vector 10 gt gt gt vl random_vector 10 gt gt gt numpy any v0 vl False chemlab graphics transformations reflection_from_matrix matrix Return mirror plane point and normal vector from reflection matrix gt gt gt v0 numpy random random 3 0 5 gt gt gt vl numpy random random 3 0 5 gt gt gt MO reflection_matrix v0 v1 gt gt gt point normal reflection_from_matrix M0 gt gt gt M1 reflection_matrix point normal gt gt gt is_same_transform MO M1 True chemlab graphics transformations reflection_matrix point normal Return matrix to mirror at plane defined by point and normal vector gt gt gt v0 numpy random random 4 0 5 gt gt gt v0O 3 1 gt gt gt vl numpy random random 3 0 5 gt gt gt R reflection_matrix
3. classmethod from_arrays kwargs Initialize a System from its constituent arrays It is the fastest way to initialize a System well suited for reading one or more big System from data files Parameters The following parameters are required r_array type_array emol_indices 54 Chapter 3 Reference Documentation chemlab Documentation Release 0 4 To further speed up the initialization process you optionally pass the other derived arrays m_array emol_n_atoms eatom_export_array emol_export Example Our classic example of 3 water molecules r_array np random random 3 9 type_array O ve VHT OE Hy TH y VOW Uae es mol_indices 0 3 6 System from_arrays r_array r_array type_array type_array mol_indices mol_indices classmethod from_json string Create a System instance from a json string Such strings are produced from the method chemlab core System tojson get_molecule index Get the Molecule instance corresponding to the molecule at index This method is useful to use Molecule properties that are generated each time such as Molecule formula and Molecule center_of_mass guess_bonds Guess the bonds between the molecules constituent of the system mol_to_atom_indices indices Given the indices over molecules return the indices over atoms Parameters indices np ndarray N dtype int Array of integers between 0 and System n_mol Returns np ndarray N dt
4. gt gt gt q quaternion_from_matrix R gt gt gt numpy allclose q 0 82336615 0 13610694 0 46344705 0 29792603 True gt gt gt R random_rotation_matrix gt gt gt q quaternion_from_matrix R gt gt gt is_same_transform R quaternion_matrix q True 3 3 chemlab graphics 95 chemlab Documentation Release 0 4 chemlab graphics transformations quaternion_imag quaternion Return imaginary part of quaternion gt gt gt quaternion_imag 3 array 0 T Zak 0 1 2 7 r chemlab graphics transformations quaternion_inverse quaternion Return inverse of quaternion gt gt gt q0 gt gt gt ql random_quaternion quaternion_inverse q0 gt gt gt numpy allclose quaternion_multiply q0 True ql 1 0 0 0 chemlab graphics transformations quaternion_matrix quaternion Return homogeneous rotation matrix from quaternion gt gt gt M quaternion_matrix 0 99810947 0 06146124 0 0 gt gt gt numpy allclose M rotation_matrix 0 123 1 0 0 True gt gt gt M quaternion_matrix 1l 0 0 0 gt gt gt numpy allclose M numpy identity 4 True gt gt gt M quaternion_matrix 0 1 0 0 gt gt gt numpy allclose M numpy diag 1l l 1 1 True chemlab graphics transformations quaternion_multip y quaternion1 quaternion0 Return multiplication of two quaternions
5. gt gt gt q quaternion_multiply 4 gt gt gt numpy allclose q 28 44 True I 25 14 48 3 6 71 chemlab graphics transformations Return real part of quaternion quaternion_real quaternion gt gt gt quaternion_real 3 3 0 0 1 2 chemlab graphics transformations quaternion_slerp quat0 quatl fraction shortestpath True spin 0 Return spherical linear interpolation between two quaternions gt gt gt q0 random_quaternion gt gt gt ql random_quaternion gt gt gt q quaternion_slerp q0 ql 0 gt gt gt numpy allclose q q0 True gt gt gt q quaternion_slerp q0 ql 1 1 gt gt gt numpy allclose q ql Trug gt gt gt q quaternion_slerp q0 ql 0 5 gt gt gt angle math acos numpy dot q0 q gt gt gt numpy allclose 2 True math acos numpy dot q0 ql angle or numpy allclo se 2 math ac chemlab graphics transformations random_quaternion rand None Return uniform random unit quaternion rand array like or None Three independent random variables that are uniformly distributed between 0 and 1 96 Chapter 3 Reference Documentation chemlab Documentation Release 0 4 gt gt gt q random_quaternion gt gt gt numpy allclose l vector_norm q True gt gt gt q random_quaternion numpy random random 3 gt gt gt len q shape q shape 0 1 True
6. 3 4 chemlab db 101 chemlab Documentation Release 0 4 ekey str The key associated with the database entry By convention you can use dotted names to provide some kind of nested structure eargs kwargs Custom extra arguments 3 4 2 ChemlabDB class chemlab db ChemlabDB Chemlab default database This database contains some example molecules and some atomic data get self molecule key Retrieve a molecule from the database The included molecule keys are example water eexample norbornene gromacs spc gromacs spce gromacs nat gromacs cl get self data key Retrieve atomic data The available data is esymbols Atomic symbols in a list evdwdict Dictionary with per element Van Der Waals radii emassdict Dictionary of masses epaulingenegdict Dictionary with per element Pauling electronegativity earenegdict Dictionary with per element Allred Rochow electronegativity emaxbonddict Dictionary of maximum bond valences 6 if unknown ionpotdict Dictionary of ionisation potentials in eV eeaffdict Dictionary of electron affinities in eV Data was taken from the OpenBabel distribution 3 4 3 ChemSpiderDB class chemlab db ChemSpiderDB token None Retrieve data from the online Chemspider database by passing an string identifier Parameters token str None The chemspider security token When token is None chemlab will try to retrieve the token from a configuration file in HOME
7. 5 5 5 unit cell repetitions in each direction selection s r_array 0 gt 0 5 sub_s subsystem_from_atoms s selection display_system sub_s It is also possible to select a subsystem by selecting specific molecules in the following example we select the first 10 water molecules by using subsystem_from molecules from chemlab core import subsystem_from_molecules selection np array 0 1 2 3 4 5 6 7 8 9 sub_s subsystem_from_molecules s selection Note chemlab will provide other selection utilities in the future if you have a specific request file an issue on github 12 Chapter 2 User Manual chemlab Documentation Release 0 4 Merging systems You can also create a system by merging two different systems In the following example we will see how to make a NaCl H20 interface by using chemlab core merge_systems import numpy as np from chemlab core import Atom Molecule crystal from chemlab core import subsystem_from_atoms merge_systems from chemlab graphics import display_system Make water crystal wat Molecule Atom O 0 00 0 00 0 01 Atom H 0 00 0 08 0 05 Atom H 0 00 0 08 0 05 water_crystal crystal 0 0 0 0 0 0 wat 225 cellpar 54 54 54 90 90 90 unit cell parameters repetitions 5 5 5 unit cell repetitions in each direction Make nacl crystal na Molecule Atom Na 0 0
8. add_post_processing GammaCorrectionEffect color correction Effect 2 5 Graphics and Visualization 23 chemlab Documentation Release 0 4 Unfortunately on ATI cards with open source drivers can t apply multiple post processing effects I m investigating the issue but this can be potentially due to a bug in the drivers See also List of Post Processing Effects 2 5 4 Offline Rendering New in version 0 3 With chemlab you can produce renderings programmatically without having to display anything or tinkering with the user interface This feature comes pretty useful when generating reports with a lot of pictures Let s say you want to make a showcase of different chemical compounds such as the first four alkanes First of all we ll take a sample molecule to adjust the looks and then we ll adapt the code to render all of the alkanes in a sequence As an example we ll tweak our rendering on the norbornene molecule contained in the chemlab database from chemlab db import ChemlabDB cdb ChemlabDB norb cdb get molecule example norbornene 24 Chapter 2 User Manual chemlab Documentation Release 0 4 We want to do the rendering of this molecule using a space fill representation this can be achieved by using the AtomRenderer which will render each atom as a sphere with its Van Der Waals radius from chemlab graphics import QtViewer from chemlab gra
9. avail quantity gt gt gt datafile ener edr read avail quantities Temperature Pressure Potential To get the frame information for a certain quantity you may use the quantity property passing the quantity as additional argument this will return two arrays the first is an array of times in ps and the second are the corrisponding quantities gt gt gt time temp datafile ener edr read quantity Temperature gro class Features read quantity quant Return an array of times in ps and the corresponding quantities at that times read avail quantities Return the available quantities in the file read units Return a dictionary where the keys are the quantities and the value are the units in which that quantity is expressed read frames Return a dictionary where the keys are the quantities and the value are the units in which that quantity is expressed GROMACS coordinate files Extension gro chemlab io handlers GromacsIO fd Handler for gro file format Example at http manual gromacs org online gro html Features read system Read the gro file and return a System instance It also add the following exporting informations groname The molecule names indicated in the gro file This is added to each entry of Sys tem mol_export 3 2 chemlab io 59 chemlab Documentation Release 0 4 gr
10. this is the recommended way for automatically opening a file from chemlab io import datafile For reading sys datafile waterbox gro read system t coords datafile traj xtc read trajectory For writing datafile output gro w write system sys See also Supported File Formats chemlab io datafile 2 4 3 Implementing your own lOHandler Implementing or improving an existing IOHandler is a great way to participate in chemlab development Fortunately it s extremely easy to set one up 16 Chapter 2 User Manual chemlab Documentation Release 0 4 It boils down to a few steps 1 Subclass TOHandler 2 Define the class attributes can_read and can_write 3 Implement the write and read methods for the features that you added in can_read and can_write 4 Write the documentation for each feature Here is an example of the xyz handler import numpy as np from chemlab io handlers import IOHandler from chemlab core import Molecule class XyzIO IOHandler The XYZ format is described in this wikipedia article http en wikipedia org wiki XYZ_file_format x Featuresx method read molecule Read the coordinates in a py class chemlab core Molecule instance method write molecule mol Writes a py class chemlab core Molecule instance in the XYZ format re can_read molecule can_write molecule def read self feature self che
11. widget The parent QChemlabWidget positons np ndarray NPOINTS 3 dtype np float32 Positions of the points to draw colors np ndarray NPOINTS 4 dtype np uint8 or list of tuples Color of each point in the r g b a for mat in the interval 0 255 update_colors colors Update the colors update_positions vertices Update the point positions TriangleRenderer class chemlab graphics renderers TriangleRenderer widget vertices normals colors shad ing phong Renders an array of triangles A lot of renderers are built on this for example SohereRenderer The implementation is relatively fast since it s based on VertexBuffers Parameters 3 3 chemlab graphics 73 chemlab Documentation Release 0 4 widget The parent QChemlabWidget vertices np ndarray NTRIANGLES 3 3 dtype float The triangle vertices keeping in mind the unwind ing order If the face of the triangle is pointing outwards the vertices should be provided in clokckwise order normals np ndarray NTRIANGLES 3 3 dtype float The normals to each of the triangle vertices used for lighting calculations colors np ndarray NTRIANGLES 3 4 dtype np uint8 Color for each of the vertices in r g b a values in the interval 0 255 update_colors colors Update the triangle colors update_normals normals Update the triangle normals update_vertices vertices Update the triangle vertices BoxRenderer class chemlab
12. In the following code we prepare the QtViewer with the effects we call v widget initializeGL in place of v show and for each molecule we add an AtomRenderer and adjust the camera from chemlab db import CirDB from chemlab graphics import QtViewer from chemlab graphics renderers import AtomRenderer from chemlab graphics postprocessing import FXAAEffect SSAOEffect A series of compounds to display compounds methane ethane propane butane db CirDB Prepare the viewer v QtViewer v widget initalizeGL Needed if you don t call show v add_post_processing SSAOEffect kernel_size 128 kernel_radius 1 0 v add_post_processing FXAAEffect for compound in compounds mol db get molecule compound rend v add_renderer AtomRenderer mol r_array mol type_array lt widget camera autozoom mol r_array Give some extra zoom v widget camera mouse_zoom 1 0 se v widget toimage 300 300 save compound png Cleanup cremove_renderer rend lt 2 5 Graphics and Visualization 27 chemlab Documentation Release 0 4 28 Chapter 2 User Manual chemlab Documentation Release 0 4 This example is stored in the chemlab examples offline_rendering py file 2 5 Graphics and Visualization 29 chemlab Documentation Release 0 4 2 5 5 Tutorial TetrahedronRenderer Note This section is mainly for developer
13. It is useful to notice that with Viewer add_renderer we are not passing an instance of the renderer but we re passing the renderer class and its respective constructor arguments The method Viewer add_renderer returns the actual instance It is possible as well to overlay 2D elements to a scene in a similar fashion this will display a string at the screen position 300 300 from chemlab graphics uis import TextUI tui v add_ui TextUI 300 300 Hello World Anyway I encourage you to use the powerful Qt framework to provide interaction and widgets to your application 2 5 Graphics and Visualization 19 chemlab Documentation Release 0 4 2 5 2 Renderers Renderers are simply classes used to draw 3D objects They are tecnically required to provide just one method draw and they must take an instance of OChemlabWidget as their first argument check out the Abst ract Renderer class In this way they provide the maximum flexibility required to build efficient opengl routines Renderers may be subclass other renderers as well as use other renderers A very useful renderer is TriangleRenderer used to render efficiently a list of triangles it constitutes a basis for writing other renderers TriangleRenderer works like this you pass the vertices normals and colors of the triangles and it will display a set of triangles in the world from chemlab graphics import QtViewer from chemlab graphics renderers import
14. M1 compose_matrix scale shear angles trans persp gt gt gt is_same_transform M M1 True gt gt gt v0 vl random_vector 3 random_vector 3 gt gt gt M rotation_matrix angle_between_vectors v0 vl vector_product v0 v1 gt gt gt v2 numpy dot v0 M 3 3 T gt gt gt numpy allclose unit_vector vl unit_vector v2 True class chemlab graphics transformations Arcball initial None Virtual Trackball Control gt gt gt ball Arcball ball Arcball initial numpy identity 4 ball place 320 320 320 ball down 500 250 ball drag 475 275 R ball matrix numpy allclose numpy sum R gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt 3 90583455 True gt gt gt gt gt gt ball Arcball initial 1 ball place 320 320 320 ball setaxes 1 1 0 1 ball setconstrain True ball down 400 200 ball drag 200 400 R ball matrix numpy allclose numpy sum R 0 0 O gt gt gt 1 0 gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt 0 2055924 True gt gt gt ball next down point Set initial cursor window coordinates and pick constrain axis drag point Update current cursor window coordinates getconstrain Return state of constrain to axis mode matrix Return homogeneous rotation matrix next acceleration 0 0 Continue rotation in direct
15. The API is not stable yet and is expected to change between revisions This Python code is not optimized for speed Refer to the transformations c module for a faster implementation of some functions 86 Chapter 3 Reference Documentation chemlab Documentation Release 0 4 Documentation in HTML format can be generated with epydoc Matrices M can be inverted using numpy linalg inv M be concatenated using numpy dot MO M1 or transform homogeneous coordinate arrays v using numpy dot M v for shape 4 column vectors respectively numpy dot v M T for shape 4 row vectors array of points This module follows the column vectors on the right and row major storage C contiguous conventions The translation components are in the right column of the transformation matrix i e M 3 3 The transpose of the trans formation matrices may have to be used to interface with other graphics systems e g with OpenGL s glMultMatrixd See also 16 Calculations are carried out with numpy float64 precision Vector point quaternion and matrix function arguments are expected to be array like i e tuple list or numpy arrays Return types are numpy arrays unless specified otherwise Angles are in radians unless specified otherwise Quaternions w ix jy kz are represented as w x y z A triple of Euler angles can be applied interpreted in 24 ways which can be specified using a 4 character strin
16. This renderer serves as an example and can be used to access the textures used for the rendering through the texture attribute This texture can be used to dump the image being rendered OutlineEffect class chemlab graphics postprocessing OutlineEffect widget kind depthnormal Add a black cartoon like outline This effect analyzes each point to be drawn and check if it s at a point of discontinuity either because there s a change in surface normal an edge or because there s a change in depth a step You can customize the effect by applyning just the normal or the depth test 80 Chapter 3 Reference Documentation chemlab Documentation Release 0 4 nosetests OUTLINE OFF OUTLINE ON Parameters kind depthnormal depthonly normalonly Set the edge determination test to both depth and normal discontinuity or either one of the two SSAOEffect class chemlab graphics postprocessing SSAOEffect widget kernel_size 32 ker nel_radius 2 0 ssao_power 2 0 Screen space ambient occlusion This effect greatly enhances the perception of the shape of the molecules More occluded areas pockets are darkened to produce a more realistic illumination For each pixel to draw the algorithm randomly samples its neighbourhood to determine how occluded is the point The effect can be tweaked to increase the darkening the accuracy and the sensibility to small pockets 3 3 chemlab graphics
17. graphics transformations 97 RcsbDB class in chemlab db 104 read chemlab io handlers OHandler method 62 read CmlIO method 58 read EdrIO method 59 read GromacsIO method 59 read MolIO method 60 read PdbIO method 60 read XtcIO method 60 61 read XyzIO method 61 reflection_from_matrix in module chem lab graphics transformations 97 reflection_matrix in module chem lab graphics transformations 97 remotefile in module chemlab io 58 remove_atoms chemlab core System method 55 remove_molecules chemlab core System method 55 remove_post_processing chemlab graphics QtViewer method 65 Index 117 chemlab Documentation Release 0 4 remove_renderer chemlab graphics QtViewer method 65 renderers QChemlab Widget attribute 83 reorder_molecules chemlab core System method 55 restore chemlab graphics camera Camera method 86 rotation_from_matrix in module chem lab graphics transformations 97 rotation_matrix in module chem lab graphics transformations 98 run chemlab graphics QtViewer method 65 S scale_from_matrix in module chem lab graphics transformations 98 scale_matrix in module chem lab graphics transformations 98 schedule chemlab graphics QtViewer method 65 set_text chemlab graphics QtTrajectory Viewer method 66 setaxes chemlab graphics transformations Arcball method 89 setconstra
18. numpy identity 4 1 1 True gt gt gt point numpy random random 3 0 5 gt gt gt normal numpy random random 3 0 5 gt gt gt direct numpy random random 3 0 5 gt gt gt persp numpy random random 3 0 5 gt gt gt PO projection_matrix point normal gt gt gt Pl projection_matrix point normal direction direct gt gt gt P2 projection_matrix point normal perspective persp gt gt gt P3 projection_matrix point normal perspective persp pseudo True gt gt gt is_same_transform P2 numpy dot P0 P3 True gt gt gt P projection_matrix 3 0 0 1 1 0 1 0 01 gt gt gt v0 numpy random rand 4 5 0 5 gt 20 94 Chapter 3 Reference Documentation chemlab Documentation Release 0 4 gt gt gt v0 3 1 gt gt gt vl numpy dot P v0 gt gt gt numpy allclose vli 1 vO 1 True gt gt gt numpy allclose v1 0 3 v1 1 True chemlab graphics transformations quaternion_about_axis angle axis Return quaternion for rotation about axis gt gt gt q quaternion_about_axis 0 123 1 0 0 gt gt gt numpy allclose g 0 99810947 0 06146124 0 0 True chemlab graphics transformations quaternion_conjugate quaternion Return conjugate of quaternion gt gt gt q0 random_quaternion gt gt gt ql quaternion_conjugate q0 gt gt gt ql 0 q0 0 and all ql 1 q0
19. 2 0 0 0 2 O 2 0 01 gt gt gt vl 0 3 O 0 0 3 0 0 31 3 7 3 31 gt gt gt a angle_between_vectors v0 vl axis 1 gt gt gt numpy allclose a 1 5708 1 5708 1 5708 0 955327 True chemlab graphics transformations arcball_constrain_to_axis point axis Return sphere point perpendicular to axis 90 Chapter 3 Reference Documentation chemlab Documentation Release 0 4 chemlab graphics transformations arcball_map_to_sphere point center radius Return unit sphere coordinates from window coordinates chemlab graphics transformations arcball_nearest_axis point axes Return axis which arc is nearest to point chemlab graphics transformations clip_matrix left right bottom top near far perspec tive False Return matrix to obtain normalized device coordinates from frustrum The frustrum bounds are axis aligned along x left right y bottom top and z near far Normalized device coordinates are in range 1 1 if coordinates are inside the frustrum If perspective is True the frustrum is a truncated pyramid with the perspective point at origin and direction along z axis otherwise an orthographic canonical view volume a box Homogeneous coordinates transformed by the perspective clip matrix need to be dehomogenized divided by w coordinate gt gt gt frustrum numpy random rand 6 gt gt gt frustrum 1 frustrum 0 gt gt gt
20. 281 277 gt gt gt affine_matrix_from_points v0 v1 array 0 14549 0 00062 675 50008 0 00048 0 14094 53424971 0 0 1 11 gt gt gt T translation_matrix numpy random random 3 0 5 gt gt gt R random_rotation_matrix numpy random random 3 gt gt gt S scale_matrix random random gt gt gt M concatenate_matrices T R S gt gt gt v0 numpy random rand 4 100 0 5 20 gt gt gt v0 3 1 gt gt gt vl numpy dot M v0 gt gt gt v0 3 numpy random normal 0 le 8 300 reshape 3 1 gt gt gt M affine_matrix_from_points v0 3 vl 3 gt gt gt numpy allclose vl numpy dot M v0 True More examples in superimposition_matrix chemlab graphics transformations angle_between_vectors v0 vl directed True axis 0 Return angle between vectors If directed is False the input vectors are interpreted as undirected axes i e the maximum angle is pi 2 gt gt gt a angle_between_vectors 1 2 3 1 2 3 gt gt gt numpy allclose a math pi True gt gt gt a angle_between_vectors 1l 2 3 1 2 3 directed False gt gt gt numpy allclose a 0 True gt gt gt vO 2 0 0 2 0 2 0 2 0 0 2 ZJ gt gt gt vl 3 0 0 gt gt gt a angle_between_vectors v0 vl gt gt gt numpy allclose a 0 1 5708 1 5708 0 95532 True gt gt gt v0 2 0 0
21. Example screenshot screen png 1200 1200 3 7 chemlab qc This package contains quantum chemistry utilities Note this module is include mainly for illustration demo purposes If you wish to maintain a quantum chemistry section in chemlab post an issue on http github com chemlab chemlab issues chemlab qc molecular_orbital coords mocoeffs gbasis Return a molecular orbital given the nuclei coordinates as well as molecular orbital coefficients and basis set specification as given by the cclib library The molecular orbital is represented as a function that takes x y z coordinates in a vectorized fashion and returns a real number 3 8 chemlab notebook This package contains commands useful in the Python notebook chemlab notebook download_molecule name Fetch a molecule from the web by its common name chemlab notebook load_molecule name format None Read a chemlab core Molecule from a file See also chemlab io datafile chemlab notebook load_remote_molecule url format None Load a molecule from the remote location specified by url Example load_remote_molecule https raw github com chemlab chemlab testdata master benzenle mol chemlab notebook load_remote_systenm url format None Load a system from the remote location specified by url Example 3 7 chemlab qc 109 chemlab Documentation Release 0 4 load_remote_system https raw github
22. Markup Language cml extension chemlab db e New package to handle databases e CirDB to retrieve molecules from chemical identifier resolver e ChemlabDB to retrieve built in data e LocalDB to make personal databases chemlab ipython e Preliminary ipython notebook integration It can display Molecule and System instances by using out of screen rendering 6 Chapter 2 User Manual chemlab Documentation Release 0 4 chemlab utils e Implemented some periodic non periodic distance finding routines Table of Contents 2 2 Installation and Quickstart The easiest way to install chemlab is to use the Anaconda python distribution from the following link http continuum io downloads Then you can run the following command conda install c http conda binstar org gabrielelanaro chemlab You can also install chemlab on Ubuntu 14 04 using apt First install the dependencies sudo apt get install python numpy python scipy python openg cython python matplotlib python qt4 gl python qt4 Then install chemlab from the setup py included sudo python setup py install NOTE For python3 support install the corresponding python3 packages available in your distribution or use pip Once you re setup you re ready to to dig in chemlab s features You may start from the User Manual 2 2 1 Development After installing the dependencies grab the chemlab source from git git clone recursive https github com chemlab chemlab
23. SSAO Screen Space Ambient Occlusion e Renderers Implemented toon shading for different shapes chemlab Documentation Release 0 4 CylinderImpostorRenderer a really fast way to draw cylinders e Offline Rendering at any resolution supported by the video card e Started some work on user interaction for a full molecular viewer chemlab db e New Databases RCSB for protein structures ToxNetDB for properties ChemspiderDB 2 1 3 Version 0 2 chemlab core Serialization through json with from_json and tojson for Atom System and Molecule Removing atoms and molecules from System System remove_atoms System remove_molecules Experimental support for customized Atom Molecule System types Some indexing routines System atom_to_molecules_indices and System mol_to_atom_indices Custom sorting of systems throught System reorder_molecules Support for bonds in molecules and experimental support for bonds in Systems throught Molecule bonds and System get_bonds_array System merge_systems has a better overlap handling Removed boxsize attribute now you have to always specify box_vectors Implemented random_lattice_box to do random solvent boxes chemlab graphics e New Renderers BallAndStickRenderer BondRenderer WireframeRenderer e Implemented Camera autozoom for autoscaling e Reimplemented BondRenderer in cython chemlab io e New Handlers MDL molfile mol extension Chemical
24. The convention is that if we specify 3 triangle vertices in clockwise order this means that the face points outwards from the solid 30 Chapter 2 User Manual chemlab Documentation Release 0 4 V4 We can therefore write our vertices and colors vertices np array vl v4 v3 v3 v4 v2 vl v3 v2 we v4 wl colors green 12 All is left to do is write the normals to the surface at each vertex This is easily done by calculating the cross product of the vectors constituting two sides of a triangle remember that the normals should point outward and normalize the result nl np cross v4 vl v3 v1 nl np linalg norm n1 n2 np cross v4 v3 v2 v3 n2 np linalg norm n2 n3 np cross v3 vl v2 v1 n3 np linalg norm n3 n4 np cross v4 v2 vl v2 n4 np linalg norm n4 2 5 Graphics and Visualization 31 chemlab Documentation Release 0 4 normals nl nl nl n2 B2 B2 n3 n3 n3 n4 n4 n4 from chemlab graphics renderers import TriangleRenderer v add_renderer TriangleRenderer vertices normals colors v run Now that we ve got the basic shape in place we can code the actual Renderer class to be used directly with the viewer We will make a renderer that given a set of coordinates will display many tetrahedra We can start by defining a Renderer class inheriting from AbstractRenderer the main
25. There is also a chemlab core System guess_bonds method to automatically set the intramolecular bonds Building Systems Random Boxes It is possible to build boxes where atoms are placed randomly by _ using the chemlab core random_lattice_box function A set of template molecules are copied and trans lated randomly on the points of a 3d lattice This ensures that the spacing between molecules is consistent and to avoid overlaps 10 Chapter 2 User Manual chemlab Documentation Release 0 4 To make an example box from chemlab db import ChemlabDB from chemlab core import random_lattice_box Example water molecule water ChemlabDB get molecule example water s random_lattice_box water 1000 4 0 4 0 4 0 Crystals chemlab provides an handy way to build crystal structures from the atomic coordinates and the space group informa tion If you have the crystallographic data you can easily build a crystal from chemlab core import Atom Molecule crystal from chemlab graphics import display_system Molecule templates na Molecule Atom Na 0 0 Os 0 00AT cl Molecule Atom Cl 0 0 0 0 r 0 0 s crystal 0 0 0 0 0 0 0 5 0 5 0 5 Fractional Positions na cl Molecules 225 Space Group cellpar 54 54 54 90 90 90 unit cell parameters repetitions 5 5 5 unit cell repetitions in each direction display_system s See
26. This information is written by GROMACS in the edr file You can use the chemlab script to view that chemlab gromacs energy ener edr Pressur chemlab gromacs energy ener edr Temperatur chemlab gromacs energy ener edr Potential chemlab gromacs energy ener edr Density Warning The chemlab gromacs command is a work in progress the syntax may change in the future It is also possible to view and get the results by directly reading the files and have direct access to the xtc coordinates and the energy stored in the edr files Take a look at the reference for chemlab io handlers XtcIO and chemlab io handlers EdrIo The tutorial is over if you have any problem or want to know more just drop an email on the mailing list python chemlab googlegroups com or file an issue on github https github com chemlab chemlab issues 2 9 Using GROMACS with chemlab 47 chemlab Documentation Release 0 4 48 Chapter 2 User Manual CHAPTER 3 Reference Documentation Packages 3 1 chemlab core This package contains general functions and the most basic data containers such as Atom Molecule and System Plus some utility functions to create and edit common Systems 3 1 1 The Atom class class chemlab core Atom type r export None Create an Atom instance Atom is a generic container for particle data See also Atoms Molecules and Systems Parameters type str Atomic symbol r np nda
27. TriangleRenderer from chemlab graphics colors import green import numpy as np vertices np array 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 normals np array 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 colors np array green green green v QtViewer v add_renderer TriangleRenderer vertices normals colors v run qtviewer pyc 20 Chapter 2 User Manual chemlab Documentation Release 0 4 If you pass 6 vertices normals colors it will display 2 triangles and so on As a sidenote it is very efficient and in fact chemlab graphics renderers TriangleRenderer is used as a backend for a lot of other renderers such as SphereRenderer and CylinderRenderer If you can reduce a shape in triangles you can easily write a renderer for it In addition to that TriangleRenderer provides also a method to update vertices normals and colors We can demonstrate that from the last example by defining an update function that rotates our triangle from chemlab graphics transformations import rotation_matrix def update y_axis np array 0 0 1 0 0 0 We take the 3 3 part because rotation_matrix can be used to rotate homogeneous 4D coordinates rot rotation_matrix 3 14 32 y_axis 3 3 This is the numpy efficient way of applying rot to each coordinate vertices np dot vertices rot T normals np dot vertices rot T tr update_vertices vertices t
28. Xx symbol backend impostors polygons points You can choose the rendering method between the sphere im postors polygonal sphere and points color_scheme dict should contain the Xx key value pair A dictionary mapping atom types to colors By default it is the color scheme provided by chemlab graphics colors default_atom_map The Xx symbol value is taken as the default color radii_map dict should contain the Xx key value pair A dictionary mapping atom types to radii The de fault is the mapping contained in chemlab db vdw vdw_dict update_positions r_array Update the atomic positions BondRenderer class chemlab graphics renderers BondRenderer widget bonds r_array type_array radius 0 02 style cylinders shad ing phong Render chemical bonds as cylinders or lines Parameters widget The parent QChemlabWidget bonds np ndarray NBONDS 2 dtype int An array of integer pairs that represent the bonds r_array np ndarray NATOMS 3 dtype float The coordinate array type_array np ndarray NATOMS 3 dtype object An array containing all the atomic symbols like Ar H O If the atomic type is unknown use the Xx symbol radius float default 0 02 The radius of the bonds style cylinders lines Whether to render the bonds as cylinders or lines BallAndStickRenderer class chemlab graphics renderers BallAndStickRenderer widget r_array type_arra
29. also chemlab core crystal Note If you d like to implement a cif file reader you re welcome Drop a patch on github Manipulating Systems Selections You can manipulate systems by using some simple but flexible functions It is really easy to gen erate a system by selecting a part from a bigger system this is implemented in the functions chemlab core subsystem_from_atoms and chemlab core subsystem_from_molecules Those two functions take as the first argument the original System and as the second argument a selection A selection is either a boolean array that is True when we want to select that element and False otherwise or an integer array containing the elements that we want to select By using those two functions we can create a subsystem by building those selections The following example shows an easy way to take the molecules that contain atoms in the region of space x gt 0 5 by employing subsystem_from_atoms import numpy as np from chemlab core import crystal Molecule Atom subsystem_from_atoms from chemlab graphics import display_system 2 3 Atoms Molecules and Systems 11 chemlab Documentation Release 0 4 Template molecul wat Molecule Atom O 0 00 0 00 0 01 Atom H 0 00 0 08 0 05 Atom H 0 00 0 08 0 05 s crystal 0 0 0 0 0 0 wat 225 cellpar 54 54 54 90 90 90 unit cell parameters repetitions
30. frustrum 3 frustrum 2 gt gt gt frustrum 5 frustrum 4 gt gt gt M clip_matrix perspective False gt gt gt numpy dot M frustrum 0 frustrum 2 array l l bg lAy 1 frustrum 1 l gt gt gt numpy dot M array ley Loy Ley Le frustrum frustrum 3 frustrum 4 1 frustrum 5 1 gt gt gt M clip_matrix perspective True frustrum gt gt gt v numpy dot M frustrum 0 frustrum 2 frustrum 4 1 gt gt gt v v 3 array Iele Klvy Sle Laly gt gt gt v numpy dot M frustrum 1 frustrum 3 frustrum 4 1 gt gt gt v v 3 array 1 1 1 1 1 chemlab graphics transformations compose_matrix scale None shear None gles None _ translate None spective None an per Return transformation matrix from sequence of transformations This is the inverse of the decompose_matrix function Sequence of transformations scale vector of 3 scaling factors shear list of shear factors for x y x z y z axes angles list of Euler angles about static x y z axes translate translation vector along x y z axes perspective perspective partition of matrix gt gt gt scale numpy random random 3 0 5 gt gt gt shear numpy random random 3 0 5 gt gt gt angles numpy random random 3 0 5 2 math pi gt gt gt trans numpy random random 3 0 5 gt gt gt persp numpy random random
31. git Complile the included extensions python setup py build_ext inplace Just add the chemlab directory to the PYTHONPATH in your bashrc export PYTHONPATH SPYTHONPATH path to chemlab 2 3 Atoms Molecules and Systems In chemlab atoms can be represented using the chemlab core Atom data structure that contains some common information about our particles like type mass and position Atom instances are easily created by initializing them with data gt gt gt from chemlab core import Atom gt gt gt ar Atom Ar 0 0 0 0 0 0 gt gt gt ar type Ap gt gt gt ar r np array 0 0 0 0 0 01 2 2 Installation and Quickstart 7 chemlab Documentation Release 0 4 Note for the atomic coordinates you should use nanometers A chemlab core Molecule is an entity composed of more atoms and most of the Molecule properties are inherited from the constituent atoms To initialize a Molecule you can for example pass a list of atom instances to its constructor gt gt gt from chemlab core import Molecule gt gt gt mol Molecule fatl at2 at3 2 3 1 Manipulating Molecules Molecules are easily and efficiently manipulated through the use of numpy arrays One of the most useful arrays contained in Molecule is the array of coordinates Molecule r_array The array of coordinates is a numpy array of shape NA 3 where NA is the number of atoms in the molecu
32. graphics renderers BoxRenderer widget vectors origin lt Mock object gt color 0 0 0 255 Used to render one wireframed box Parameters widget The parent QChemlabWidget vectors np ndarray 3 3 dtype float The three vectors representing the sides of the box origin np ndarray 3 3 dtype float default to zero The origin of the box color 4 int tuple r g b a color in the range 0 255 update vectors Update the box vectors LineRenderer class chemlab graphics renderers LineRenderer widget startends colors width 1 5 Render a set of lines 74 Chapter 3 Reference Documentation chemlab Documentation Release 0 4 Parameters widget The parent QChemlabWidget startends np ndarray NLINES 2 3 dtype float Start and end position of each line in the form of an array sl 0 0 0 0 0 0 startends sl el s2 e2 colors np ndarray NLINES 2 4 dtype np uint8 The corresponding color of each extrema of each line update_colors colors Update the colors update_positions vertices Update the line positions 3 3 chemlab graphics 75 chemlab Documentation Release 0 4 CylinderRenderer class chemlab graphics renderers CylinderRenderer widget bounds radii colors Renders a set of cylinders The API is quite similar to LineRenderer Parameters widget The parent QChemlabWidget bounds np ndarray NCYL 2 3 dtype float Start and end poi
33. gt gt numpy allclose vl numpy dot M v0 1 3 3 chemlab graphics 99 chemlab Documentation Release 0 4 True gt gt gt M superimposition_matrix v0 vl scale True usesvd False gt gt gt numpy allclose vl numpy dot M v0 True gt gt gt v numpy empty 4 100 3 gt gt gt vi 0 vO gt gt gt M superimposition_matrix v0 vl scale True usesvd False gt gt gt numpy allclose vl numpy dot M v 0 True chemlab graphics transformations translation_from_matrix matrix Return translation vector from translation matrix gt gt gt v0 numpy random random 3 0 5 gt gt gt vl translation_from_matrix translation_matrix v0 gt gt gt numpy allclose v0 v1 rue chemlab graphics transformations translation_matrix direction Return matrix to translate by direction vector gt gt gt v numpy random random 3 0 5 gt gt gt numpy allclose v translation_matrix v 3 3 True chemlab graphics transformations unit_vector data axis None out None Return ndarray normalized by length i e eucledian norm along axis gt gt gt v0 numpy random random 3 gt gt gt vl unit_vector v0 gt gt gt numpy allclose vl v0 numpy linalg norm v0 True gt gt gt v0 numpy random rand 5 4 3 gt gt gt vl unit_vector v0 axis 1 gt gt gt v2 v0 numpy expand
34. it to the renderers attribute from chemlab graphics import QChemlabWidget from chemlab graphics renderers import SphereRenderer widget QChemlabWidget widget renderers append SphereRenderer widget You can also add other elements for the scene such as user interface elements for example some text This is done in a way similar to renderers from chemlab graphics import QChemlabWidget from chemlab graphics uis import TextUI widget QChemlabWidget widget uis append TextUI widget 200 200 Hello world Warning At this point there is only one ui element available PyQt4 provides a lot of UI elements so there s the possibility that UI elements will be converted into renderers QChemlabWidget has its own mouse gestures eLeft Mouse Drag Orbit the scene Right Mouse Drag Pan the scene Wheel Zoom the scene renderers Type list of Abst ract Renderer subclasses It is a list containing the active renderers QChemlab Widget will call their draw method when appropriate camera Type Camera The camera encapsulates our viewpoint on the world That is where is our position and our orientation You should use on the camera to rotate move or zoom the scene light_dir Type np ndarray 3 dtype float Default np arrray 0 0 0 0 1 0 The light direction in camera space Assume you are in the space looking at a certain point your position is the origin now imagine you have a lamp
35. not linear in other words we perceive better dark tones than light tones As a result the image produced is usually too dark To offset this effect you can apply gamma correction The correct value is screen dependent but it is usually between 1 8 and 2 5 You can tweak this parameter through the parameter gamma 78 Chapter 3 Reference Documentation chemlab Documentation Release 0 4 GAMMA OFF GAMMA ON GlowEffect class chemlab graphics postprocessing GlowEffect widget Enhance objects with a glowing effect This effect can be used to illuminate objects like they were small lightbulbs It can be used for example to implement selection or special effects To setup the illumination strength you can use the color alpha value If the alpha value is zero the illumination will be maximum if the alpha is 255 no illumination will take place If you change this value at runtime the glowing will change accordingly For example if you re using a SohereImpostorRenderer to illuminate the sphere you have to setup the color like this Setup positions and radii Set the alpha value to 0 for max illumination colors np array 0 0 0 255 O uint8 v add_renderer positions radii colors 3 3 chemlab graphics 79 chemlab Documentation Release 0 4 GLOW OFF GLOW ON NoEffect class chemlab graphics postprocessing NoEffect widget Re render the object without implementing any effect
36. selections visible_atoms Return the indices of the currently visible atoms chemlab mviewer api selections visible_to_original visible_index Transform the indexes of the visible atoms to the indexes of the total atoms 3 6 chemlab mviewer api 107 chemlab Documentation Release 0 4 3 6 4 Appeareance Commands Those commands are for changing the appeareance of the object displayed by the molecular viewer chemlab mviewer api appeareance add_post_processing effect options Apply a post processing effect Parameters effect string The effect to be applied choose between ssao outline fxaa gamma options Options used to initialize the effect check the List of Post Processing Effects for a complete refer ence of all the options Returns A string identifier that can be used to reference the applied effect chemlab mviewer api appeareance change_background color Setup the background color to color Example change_background black change_background white change_background ffffff You can call this function interactively by using change_color interactive A new dialog will popup with a color chooser See also chemlab graphics colors parse_color chemlab mviewer api appeareance change_color color Change the color of the currently selected objects color is represented as a string Otherwise color can be passed as an rgba tuple of values between 0 255 Re
37. ssaol kernel_size 128 remove_post_processing fxaa2 clear_post_processing 2 7 Molecular Viewer 39 chemlab Documentation Release 0 4 2 7 3 Loading Data The Chemlab molecular viewer provides quite handy function to load some data into it load_system file gro load_molecule file cml1 You can also download the molecule from a web database by its common name download_molecule aspirine Or you can also download and open a file from a remote location using directly its URL load_remote_system https raw github com chemlab chemlab testdata master naclwater gr load_remote_molecule https raw github com chemlab chemlab testdata master benzene mo Loading Trajectories Chemlab supports the loading of trajectory files for example the xtc files from GROMACS After you load a system you can attach some trajectory data with load_trajectory or load_remote_trajectory load_system water gro load_trajectory traj xtc We can run a small test using the test files from chemlab load_remote_system https raw github com chemlab chemlab testdata master water gro load_remote_trajectory https github com chemlab chemlab testdata raw master trajout xtc A series of commands will appear and you can move through the trajectory by dragging the bar or the Play Stop button You can also move programmatically using the function goto_tim
38. 0 unproject chemlab graphics camera Camera method 86 update chem chemlab graphics renderers BoxRenderer method 74 update_bounds chem lab graphics renderers CylinderRenderer method 76 update_colors chem lab graphics renderers LineRenderer method 75 update_colors chem lab graphics renderers PointRenderer method 73 update_colors chem lab graphics renderers TriangleRenderer method 74 update_function chemlab graphics QtTrajectory Viewer method 67 update_normals lab graphics renderers TriangleRenderer method 74 update_positions chem lab graphics renderers AtomRenderer method 70 update_positions chem lab graphics renderers BallAndStickRenderer method 71 update_positions chem lab graphics renderers LineRenderer method 75 update_positions chem lab graphics renderers PointRenderer method 13 update_positions lab graphics renderers SphereRenderer method 69 update_vertices lab graphics renderers TriangleRenderer method 74 chem chem chem V vector_norm in module chem 118 Index chemlab Documentation Release 0 4 lab graphics transformations 100 vector_product in module chem lab graphics transformations 101 W WireframeRenderer class in chem lab graphics renderers 71 write chemlab io handlers OHandler method 62 write CmlIO method 58 write GromacsIO method 60 writ
39. 0 0 0 0 cl Molecule Atom Cl 0 0 0 0 0 0 nacl_crystal crystal 0 0 0 0 0 0 0 5 0 5 0 5 na cl 225 cellpar 54 54 54 90 90 90 repetitions 5 5 5 water_half subsystem_from_atoms water_crystal water_crystal r_array 0 gt 1 2 nacl_half subsystem from_atoms nacl_crystal nacl_crystal r_array 0 lt 1 2 interface merge_systems water_half nacl_half display_system interface 2 3 Atoms Molecules and Systems 13 chemlab Documentation Release 0 4 At the present time the merging will avoid overlapping by creating a bounding box around the two systems and removing the molecules of the first system that are inside the second system bounding box In the future there will be more clever ways to handle this overlaps Removing There are two methods used to remove specific atoms and molecules from a system chemlab core System remove_molecules and chemlab core System remove_atoms Taking from the previous NaCl example you may need to remove some excess ions to meet the electroneutrality condition n_na and n_cl are the number of Na and Cl molecules toremove Na if n_na gt n_cl else Cl nremove abs n_na n_cl Number of indices to be removed remove_indices s type_array toremove nonzero 0 nremove s remove_atoms rem_indices 14 Chapter 2 User Manual chemlab Documentation Release 0 4
40. 1 True chemlab graphics transformations quaternion_from_euler ai aj ak axes sxyz Return quaternion from Euler angles and axis sequence ai aj ak Euler s roll pitch and yaw angles axes One of 24 axis sequences as string or encoded tuple gt gt gt q quaternion_from_euler l 2 3 ryxz gt gt gt numpy allclose q 0 435953 0 310622 0 718287 0 444435 True chemlab graphics transformations quaternion_from_matrix matrix isprecise False Return quaternion from rotation matrix If isprecise is True the input matrix is assumed to be a precise rotation matrix and a faster algorithm is used gt gt gt q quaternion_from_matrix numpy identity 4 True gt gt gt numpy allclose q 1 0 0 0 True gt gt gt q quaternion_from_matrix numpy diag 1 l 1 1 gt gt gt numpy allclose q 0 1 0 0 or numpy allclose q 0 1 0 0 True gt gt gt R rotation_matrix 0 123 1 2 3 gt gt gt q quaternion_from_matrix R True gt gt gt numpy allclose q 0 9981095 0 0164262 0 0328524 0 0492786 True gt gt gt R 0 545 0 797 0 260 Ol 0 733 0 603 0 313 0J 0 407 0 021 0 913 0 CO 0 0 1 gt gt gt q quaternion_from_matrix R gt gt gt numpy allclose q 0 19069 0 43736 0 87485 0 083611 True gt gt gt R 0 395 On362 04843 Oly 0 626 0 796 0 056 0 0 677 O 498 0 529 0 0 0 0 1
41. 2 v4 v1 1 self _th_normals np array ml ni nil nz n2 2 32 Chapter 2 User Manual chemlab Documentation Release 0 4 m3 m3 n3 n4 n4 n4 self n_tetra len positions tot_vertices for pos in positions tot_vertices extend self _th_vertices pos Refer to numpy tile this simply repeats th lements of the array in an efficient manner tot_normals np tile self _th_normals self n_tetra 1 tot_colors green self n_tetra x 12 NOTICE that we have to pass widget as the first argument self tr TriangleRenderer widget tot_vertices tot_normals tot_colors def draw self self tr draw To demostrate let s draw a grid of 125 tetrahedra positions for x in range 5 for y in range 5 for z in range 5 positions append float x 2 float y 2 float z 2 v add_renderer TetrahedraRenderer positions v widget camera position np array 0 0 0 0 20 0 v run 2 5 Graphics and Visualization 33 chemlab Documentation Release 0 4 If you had any problem with the tutorial or you want to implement other kind of renderers don t exitate to contact me The full code of this tutorial is in chemlab examples tetrahedra_tutorial py 2 6 Database Support Typing every time your molecules and system is not fun nor efficient for this reason chemlab provides ready to use database utilities Data
42. 4 0 5 gt gt gt MO compose_matrix scale shear angles trans persp gt gt gt result decompose_matrix M0 gt gt gt M1 compose_matrix result gt gt gt is_same_transform MO M1 True chemlab graphics transformations concatenate_matrices matrices Return concatenation of series of transformation matrices 3 3 chemlab graphics 91 chemlab Documentation Release 0 4 gt gt gt M numpy random rand 16 reshape 4 4 0 5 gt gt gt numpy allclose M concatenate_matrices M True gt gt gt numpy allclose numpy dot M M T concatenate_matrices M M T True chemlab graphics transformations decompose_matrix matrix Return sequence of transformations from transformation matrix matrix array_like Non degenerative homogeneous transformation matrix Return tuple of scale vector of 3 scaling factors shear list of shear factors for x y x z y z axes angles list of Euler angles about static x y z axes translate translation vector along x y z axes perspective perspective partition of matrix Raise ValueError if matrix is of wrong type or degenerative gt gt gt TO translation_matrix 1l 2 3 gt gt gt scale shear angles trans persp decompose_matrix TO gt gt gt T1 translation_matrix trans gt gt gt numpy allclose TO T1 True gt gt gt S scale_matrix 0 123 gt gt gt scale shear angles trans pers
43. 5 chemlab notebook module 109 ChemlabDB class in chemlab db 102 ChemSpiderDB class in chemlab db 102 CirDB class in chemlab db 103 clip_matrix in module chem lab graphics transformations 91 CmlIO class in chemlab io handlers 58 compose_matrix in module chem lab graphics transformations 91 concatenate_matrices in module chem lab graphics transformations 9 1 copy chemlab core Atom method 50 copy chemlab core Molecule method 51 copy chemlab core System method 54 crystal in module chemlab core 57 current_frame in module chemlab mviewer api core 105 current_frame_times in lab mviewer api core 105 current_nframes in module chemlab mviewer api core 105 current_representation in lab mviewer api core 105 module chem module chem 115 chemlab Documentation Release 0 4 current_system in module chemlab mviewer api core 105 current_time in module chemlab mviewer api core 105 current_trajectory in lab mviewer api core 105 CylinderRenderer class in chemlab graphics renderers 76 module chem D datafile in module chemlab io 58 decompose_matrix in module lab graphics transformations 92 DefaultRenderer class in chemlab graphics renderers 67 directory LocalDB attribute 103 display_system in module chemlab graphics 62 display_trajectory in module chemlab graphics 63 distance in mo
44. 81 chemlab Documentation Release 0 4 nosetests SSAO OFF SSAO ON Parameters kernel_size int min 1 max 128 default 32 The number of random samples used to determine if an area is occluded At small values the perfor mance is good and the quality is bad at high value is the opposite is true kernel_radius float default 2 0 The maximum distances of the sampling neighbours It should be comparable with the pocket size you intend to see At small values it s smoother but will darken just small pockets at high values will reveal bigger pockets but the result would be more rough ssao_power float default 2 0 Elevate the darkening effect to a certain power This will make the dark areas darker for a more dramatic effect 3 3 5 Low level widgets The QChemlabWidget class This is the molecular viewer widget used by chemlab 82 Chapter 3 Reference Documentation chemlab Documentation Release 0 4 class chemlab graphics QChemlabWidget args kwargs Extensible and modular OpenGL widget developed using the Qt PyQt4 Framework This widget can be used in other PyQt4 programs The widget by itself doesn t draw anything it delegates the writing task to external components called render ers that expose the interface found in Abst ractRenderer Renderers are responsible for drawing objects in space and have access to their parent widget To attach a renderer to QChemlabWidget you can simply append
45. None Set the function to be called when it s time to display a frame func should be a function that takes one integer argument that represents the frame that has to be played def func index Update the renderers to match the current animation index 3 3 3 Renderers and Uls List of available renderers Interfaces class chemlab graphics renderers AbstractRenderer widget args kwargs AbstractRenderer is the standard interface for renderers Each renderer have to implement an initialization function __init__ and a draw method to do the actual drawing using OpenGL or by using other more basic renderers Usually the renderers have also some custom functions that they use to update themselves For example a Spher eRenderer implements the function update_positions to move the spheres around without having to regenerate all of the other properties See also Graphics and Visualization for a tutorial on how to develop a simple renderer Parameters widget chemlab graphics QChemlabWidget The parent OChemlabWidget Renderers can use the widget to access the camera lights and other informations args kwargs Any other argument that they may use draw Generic drawing function to be implemented by the subclasses class chemlab graphics renderers ShaderBaseRenderer widget vertex fragment Bases chemlab graphics renderers base AbstractRenderer Instruments OpenGL with a vertex and a fragment shader This
46. You can also select hidden objects and show them select_hidden show 2 7 6 Writing your own commands The built in commands provide a quick and easy way to operate on your molecules and they provide basic functionality The true power of chemlab relies in the possibility to write and load your commands using the power and simplicity of Python For example we can write a command that calculates automatically the distance between two selected atoms We can open a file utils py and put the following code in it import numpy as np def distance sel selected_atoms if len sel 2 print Only two atoms must be selected return else Here we use numpy fancy indexing a b current_system r_array sel return np linalg norm b a How can we access this function from a chemlab session The chemlab shell is just a regular Python shell so one solution will be to simply add the directory to your PYTHONPATH and import it manually However chemlab provides an init file that lets you write some code that will be called at initialization time 2 7 Molecular Viewer 41 chemlab Documentation Release 0 4 The file is stored in the path chemlab scripts __init__ py To automatically load the command distance we have to first put the file utils py in the directory chemlab scripts and add the following line to the __ init __ file from utils import distance You can e
47. _dims numpy sqrt numpy sum vO v0 axis 2 2 gt gt gt numpy allclose vl v2 True gt gt gt vl unit_vector v0 axis 1 gt gt gt v2 v0 numpy expand_dims numpy sqrt numpy sum v0 v0 axis 1 1 gt gt gt numpy allclose vl v2 True gt gt gt vl numpy empty 5 4 3 gt gt gt unit_vector v0 axis 1 out vl1 gt gt gt numpy allclose vl v2 True gt gt gt list unit_vector gt gt gt list unit_vector 1 1 0 chemlab graphics transformations vector_norm data axis None out None Return length i e eucledian norm of ndarray along axis gt gt gt v numpy random random 3 gt gt gt n vector_norm v gt gt gt numpy allclose n numpy linalg norm v True gt gt gt v numpy random rand 6 5 3 gt gt gt n vector_norm v axis 1 gt gt gt numpy allclose n numpy sqrt numpy sum v v axis 2 100 Chapter 3 Reference Documentation chemlab Documentation Release 0 4 True gt gt gt n vector_norm v axis 1 gt gt gt numpy allclose n numpy sqrt numpy sum v v axis 1 True gt gt gt v numpy random rand 5 4 3 gt gt gt n numpy empty 5 3 gt gt gt vector_norm v axis l1 out n gt gt gt numpy allclose n numpy sqrt numpy sum v v axis 1 True gt gt gt vector_norm 0 0 gt gt gt vector_norm 1 1 0 chemlab graphics transformations ve
48. ale_matrix factor origin gt gt gt factor origin direction scale_from_matrix S0 gt gt gt S1 scale_matrix factor origin direction gt gt gt is_same_transform S0O S1 True gt gt gt SO scale_matrix factor origin direct gt gt gt factor origin direction scale_from_matrix S0 gt gt gt S1 scale_matrix factor origin direction gt gt gt is_same_transform S0O S1 True chemlab graphics transformations scale_matrix factor origin None direction None Return matrix to scale by factor around origin in direction Use factor 1 for point symmetry gt gt gt v numpy random rand 4 5 0 5 20 gt gt gt v 3 1 gt gt gt S scale_matrix 1 234 gt gt gt numpy allclose numpy dot S v 3 1 234 v 3 True gt gt gt factor random random 10 5 gt gt gt origin numpy random random 3 0 5 gt gt gt direct numpy random random 3 0 5 gt gt gt S scale_matrix factor origin gt gt gt S scale_matrix factor origin direct chemlab graphics transformations shear_from_matrix matrix Return shear angle direction and plane from shear matrix gt gt gt angle random random 0 5 4 math pi gt gt gt direct numpy random random 3 0 5 gt gt gt point numpy random random 3 0 5 gt gt gt normal numpy cross direct numpy random random 3 gt gt gt SO shear_matrix angle dir
49. are many ways to generate a box of water in our example we will place 512 water molecules in a cubic grid The advantages of doing that is the simplicity of the approach and the fact that we are naturally avoid any overlap between adiacent molecules To generate such a box we will 1 Create a template water Molecule 2 Translate this molecule on the grid points 3 Add the molecule to a preinitialized System import numpy as np from chemlab core import Atom Molecule System from chemlab graphics import display_system Spacing between two grid points spacing 0 3 an 8x8x8 grid for a total of 512 points grid_size 8 8 8 Preallocate the system 512 molecules and 512 3 atoms s System empty 512 5123 Water template it contains export informations for gromacs more about export later water_tmp Molecule Atom O 0 0 0 0 0 0 export grotype OW Atom H 0 1 0 0 0 0 export grotype HW1 Atom H 0 03333 0 09428 0 0 export grotype HW2 export groname SOL for a in range grid_size 0 for b in range grid_size 1 for c in range grid_size 2 grid_point np array a b c spacing array operation water_tmp move_to grid_point s add water_tmp Adjust boxsize for periodic boundary conditions s box_vectors np eye 3 8 spacing Visualize to verify that the system was setup correctly display_system s If you run this it will
50. asily write and hook in a lot of extensions Please write something useful You will and attach your code on the chemlab github page https github com chemlab chemlab issues labels extension amp milestone amp state open Select within a radius In this section we ll see another example on how to implement a new function in chemlab We want to select all the atoms within a certain distance from the currently selected atoms We can create a file in the directory chem lab scripts distances py and we will implement a function like this that will operate on the current selection def select_within radius pass The implementation will be as follows for each atom find the neighbours atoms select them In chemlab term we have to do this the implementation is a bit inefficient but it s more readable from chemlab mviewer toolboxes selection import selected_atoms def select_within radius neighbours for i_central in selected_atoms r_central current_system r_array i_central for r in current_system r_array dist np linalg norm r r_central if dist lt radius neighbours append i select_atoms np unique neighbours Now let s test how this works in a chemlab session First of all let s add automatically the function to the file chem lab scripts __init__ py from myutils import select_within Now when you start chemlab this command will be made availabl
51. ay NSPHERES dtype float An array with the radius of each sphere colorlist np ndarray NSPHERES 4 or list of tuples An array with the color of each sphere Suitable colors are those found in chemlab graphics colors or any tuple with values r g b a in the range 0 255 update_positions positions Update the sphere positions SpherelmpostorRenderer class chemlab graphics renderers SphereImpostorRenderer viewer poslist radiuslist colorlist transparent False shading phong The interface is identical to SohereRenderer but uses a different drawing method The spheres are squares that always face the user Each point of the sphere along with the lighting is calculated in the fragment shader resulting in a perfect sphere SphereImpostorRenderer is an extremely fast rendering method it is perfect for rendering a lot of spheres gt 50000 and for animations AtomRenderer class chemlab graphics renderers AtomRenderer widget r_array type_array backend impostors color_scheme colors default_atom_map radii_map vdw_dict Render atoms by using different rendering methods 3 3 chemlab graphics 69 chemlab Documentation Release 0 4 Parameters widget The parent QChemlabWidget r_array np ndarray NATOMS 3 dtype float The atomic coordinate array type_array np ndarray NATOMS 3 dtype object An array containing all the atomic symbols like Ar H O If the atomic type is unknown use the
52. b db base AbstractDB method 101 get ChemlabDB method 102 get ChemSpiderDB method 102 103 get CirDB method 103 get Q LocalDB method 104 get RcsbDB method 104 get_molecule chemlab core System method 55 getconstrain chemlab graphics transformations Arcball method 89 GlowEffect class in chemlab graphics postprocessing 19 GromacsIO class in chemlab io handlers 59 guess_bonds chemlab core Molecule method 52 guess_bonds chemlab core System method 55 H has_renderer chemlab graphics QtViewer method 65 chem identity_matrix in module chem lab graphics transformations 93 inverse_matrix in module chem lab graphics transformations 93 IOHandler class in chemlab io handlers 61 is_same_transform in module chem lab graphics transformations 93 L light_dir QChemlabWidget attribute 83 LineRenderer class in chemlab graphics renderers 74 load_molecule in module chemlab notebook 109 load_remote_molecule in module chemlab notebook 109 load_remote_system in module chemlab notebook 109 load_remote_trajectory in module chemlab notebook 110 load_system in module chemlab notebook 110 load_trajectory in module chemlab notebook 110 LocalDB class in chemlab db 103 M m_array Molecule attribute 51 116 Index chemlab Documentation Release 0 4 m_array System attribute 52 mass Atom attribut
53. bases in chemlab can store arbitrary data that can be retrieved by using the get method The following is an example retrieving a molecular structure from CIR http cactus nci nih gov chemical structure the chemical resolve identifier website from chemlab db cirdb import CirDB mol CirDB get molecule aspirine Note CirDB uses internally the CirPy wrapper https github com mcs07 CIRpy all credits go to the author Chemlab includes also his own database for data as well as some molecules For example to get the vdw radii the data was taken from OpenBabel you can 34 Chapter 2 User Manual chemlab Documentation Release 0 4 from chemlab db import ChemlabDB cdb ChemlabDB vdw cdb get data vdwdict vdw He For more information refer to the chemlab db ChemlabDB documentation See also chemlab db 2 6 1 Having your own molecular database It may happen that you have your most frequently used collection of molecules and systems Chemlab provides a serialization system that let you easily dump your objects in a directory and retrieve them by using a local database This is achieved by the class chemlab db Loca1lDB from chemlab db import LocalDB ldb LocalDB path to yourdb Generate retrieve some molecule ldb store molecule examplemol mol ldb store system examplesys sys The method chemlab db LocalDB store takes a first argument
54. cel_selection Reset the current selection chemlab mviewer api selections clear_selection Clear the current selection chemlab mviewer api selections hide_selected Hide the selected objects chemlab mviewer api selections hide_water Conveniency command to hide water molecules chemlab mviewer api selections invert_selection Invert the current selection Select the currently unselected atoms chemlab mviewer api selections select_all Select all the visible atoms chemlab mviewer api selections select_atom_type name Select atoms by their type You can select all the hydrogen atoms as follows select_atom_type H chemlab mviewer api selections select_atoms indices Select atoms by their indices You can select the first 3 atoms as follows select_atoms 0 1 2 Return the current selection dictionary chemlab mviewer api selections select_connected_bonds Select the bonds connected to the currently selected atoms chemlab mviewer api selections select_molecules name Select all the molecules corresponding to the formulas chemlab mviewer api selections select_selection selection Select a Selection object chemlab mviewer api selections selected_atoms The indices of the currently selected atoms chemlab mviewer api selections unhide_all Unhide all the objects chemlab mviewer api selections unhide_selected Unhide the selected objects chemlab mviewer api
55. ces Atoms that constitute the Molecule Beware that the data gets copied and sub sequend changes in the Atom instances will not reflect in the Molecule export dict optional Export information for the Molecule r_array Type np ndarray N 3 dtype float Derived from Atom An array with the coordinates of each Atom 50 Chapter 3 Reference Documentation chemlab Documentation Release 0 4 type_array numpy array N of str Type np ndarray N dtype str Derived from Atom An array containing the chemical symbols of the constituent atoms m_array Type np ndarray N dtype float Derived from Atom Atray of masses charge_array Type np ndarray N dtype float Derived from Atom Array of the charges present on the atoms atom_export_array Type np ndarray N dtype object array of dicts Derived from Atom Atray of Atom export dicts n_atoms Type int Number of atoms present in the molecule export Type dict Export information for the whole Molecule bonds Type np ndarray NBONDS 2 dtype int A list containing the indices of the atoms connected by a bond Example 0 1 0 2 3 4 mass Type float Mass of the whole molecule in amu center_of_mass Type float geometric_center Type float formula Type str The brute formula of the Molecule i e H20 chemlab core 51 chemlab Documentation Release 0 4 copy Return a copy of the molecule instance classmethod from_arrays kwargs Create a Molecule f
56. change_color 0 0 0 255 Similarly you can change the radius of certain atoms or scale them select_all scale_atoms 2 0 Scale Factor change_radius 0 15 Exact value in nm Perhaps the most interesting feature are the post processing effects the most interesting is called ssao or Screen Space Ambient Occlusion It enhances the picture by giving nice shadows in the more occluded areas take a look at the picture generated by this code download_molecule testosterone select_all scale_atoms 2 0 We make the colors brighter ssao works best on light colors select_atom_type C change_color 210 210 210 0 That s a very light gray select_atom_type O change_color 255 163 163 255 change_background white pp_id add_post_processing ssao For max quality add_post_processing ssao kernel_size 128 38 Chapter 2 User Manual chemlab Documentation Release 0 4 There is a good amount of shadows you can also setup other effects such as anti aliasing and gamma correction add_post_processing fxaa add_post_processing gamma The function add_post_processing returns a string id that you can use to remove the effect or to change its options To list all the available post processing effects use the function List_post_processing list_post_processing ssaol fxaa2 gamma3 change_post_processing_options
57. chemlab Documentation Release 0 4 chemlab graphics transformations euler_matrix ai aj ak axes sxyz Return homogeneous rotation matrix from Euler angles and axis sequence ai aj ak Euler s roll pitch and yaw angles axes One of 24 axis sequences as string or encoded tuple gt gt gt R euler_matrix 1l 2 3 syxz gt gt gt numpy allclose numpy sum R 0 1 34786452 True gt gt gt R euler_matrix l 2 3 0 1 0 1 gt gt gt numpy allclose numpy sum R 0 0 383436184 True gt gt gt ai aj ak 4xmath pi numpy random random 3 0 5 gt gt gt for axes in _AXES2TUPLE keys i oe R euler_matrix ai aj ak axes gt gt gt for axes in _TUPLE2AXES keys R euler_matrix ai aj ak axes chemlab graphics transformations identity matrix Return 4x4 identity unit matrix gt gt gt I identity_matrix gt gt gt numpy allclose I numpy dot I I True gt gt gt numpy sum I numpy trace I 4 0 4 0 gt gt gt numpy allclose I numpy identity 4 True chemlab graphics transformations inverse_matrix matrix Return inverse of square transformation matrix gt gt gt MO random_rotation_matrix gt gt gt M1 inverse_matrix MO T gt gt gt numpy allclose M1 numpy linalg inv MO T True gt gt gt for size in range l 7 MO numpy random rand size size M1 inverse_matrix M0 if n
58. chemlab Documentation Release 0 4 Gabriele Lanaro August 10 2015 Contents 1 Current Status 2 User Manual 2A What sMew 2c 4 2 44 OS oe eee eS REE EAR RY eS 2 2 Installation and Quickstart 2 000 2 3 Atoms Molecules and Systems 2 4 Input and Output Routines 00 0 2 5 Graphics and Visualization 2 6 Database Supports os 04 sete eee ae ood be eas 2 1 Molecular Viewer lt 5 2 04 cease ee ga Se eee 2 8 Python integration i lt 23 4 4 2405 44444 240 a iN 2 9 Using GROMACS with chemlab 3 Reference Documentation Sill vehemilab cone o 3 25 bo Sa Kee ee eee ee eb oA Sid CMe mMlabao y sasa ce oe ep dy Se Gerd Qe Gs Goede ego a AL ak dy Ge 3 3 chemlab eraphics sst raea 4 oe a ee ew ee a ey 34 chemlab db s iara Aho ed ae whe aa AG ee S 35 chemlabutils sca 2 ona p oun ite See Rae ee ee a 36 chemlab mviewenapls 254 664 2085 oh bch oe 4b bi pee 3 7 AChemlabge s maceraya Ae SR eS ER Ree RS e Ae 3 8 chemlabnotebook 2 45 6 2405 888 5 ees 4 ee aes 4 License Python Module Index chemlab Documentation Release 0 4 Author Gabriele Lanaro Contributors Yotam Y Avital Adam Jackson Webpage https chemlab github com chemlab Project Page https github com chemlab chemlab Mailing List python chemlab googlegroups com Downloads https chemlab github com chemlab Chemlab is a library that can help the user with chemistry relevant calc
59. chemlab db CirDB Get 3D structure of arbitrary molecules given a string identifier get self molecule key Retrieve a molecule from the online CIR database by passing an identifier A key can be for instance the common name of a certain chemical a SMILES string or an InChi identifier This is just an adapter on the CirPy library Returns a Molecule instance 3 4 5 LocalDB class chemlab db LocalDB directory Store serialized molecules and systems in a directory tree See Having your own molecular database for an example of usage directory Directory where the database is located 3 4 chemlab db 103 chemlab Documentation Release 0 4 get self molecule key Get an entry from the database Key is the filename without extension of the serialized molecule Molecules are stored in the subdirectory get self system key Get an entry from the database Key is the filename without extension of the serialized system store self molecule key value store self system key value Store a Molecule or a System passed as value in the directory structure The objects are dumped to disk after being serialized to json 3 4 6 RcesbDB class chemlab db RcsbDB Access to the RCSB database for proteins To download a protein just write its PDB id that you can check on the website from chemlab db import RcsbDB mol RcsbDB get molecule 3ZJE get self mole
60. chemlabrc that has the entry chemspider token YOUR SECURITY TOKEN The get method requires a key argument to retrieve a database entry A valid key can be for instance the common name of a certain chemical a SMILES string or an InChi identifier This is just an adapter on the chemspipy library 102 Chapter 3 Reference Documentation chemlab Documentation Release 0 4 get self molecule key Retrieve a molecule 3D structure Returns a Molecule instance get self inchi key Retrieve the InChi string for the compound get self molecularformula key Retrieve the molecular formula as a LaTeX string get self imageurl key Retrieve the url of a 2D image representation of the compound get self smiles key Retrieve the SMILES string for the compound get self averagemass key Retrieve the average mass get self nominalmass key Retrieve the nominal mass get self inchikey key Return the InChi key get self alogp key Predicted LogP partition coefficient using the ACD LogP algorithm get self xlogp key Predicted LogP using the XLogP algorithm get self image key PNG image of the compound as a data string get self mol2d key MOL md file containing 2D coordinates of the compound get self commonname key Retrieve the common name of the compound 3 4 4 CirDB class
61. ck_feature feature read lines self fd readlines num int lines 0 title lines 1 if feature title return title if feature molecule type_array r_array for 1 in lines 2 type X yY Zz 1 split r_array append float x float y float z type_array append type r_array np array r_array 10 To nm type_array np array type_array return Molecule from_arrays r_array r_array type_array type_array def write self feature mol self check_feature feature write lines 2 4 Input and Output Routines 17 chemlab Documentation Release 0 4 if feature molecule lines append str mol n_atoms lines append Generated by chemlab for t x y Zz in zip mol type_array mol r_array lines append 3S 2 6f 6f t x 10 yx x1l0 z 10 L F AF CF Q OIL OL 6f self fd write n join lines A few remarks It is recommended to use the method check_feature before performing read write This will check that the feature is present in the can_read can_write list If you want to squeeze out performance you should use Molecule from_arrays and System from_arrays e You can read whatever data you wish for example the drJO handler does not read Molecule or System at all e You can definitely take inspiration from the handlers included in chemlab Supported File Formats 2 5 Graphics an
62. com chemlab chemlab testdata master naclwater gro chemlab notebook load_remote_trajectory url format None skip 1 Load a trajectory file from a remote location specified by url See also load_remote_system chemlab notebook load_system name format None Read a chemlab core System from a file See also chemlab io datafile chemlab notebook load_trajectory name format None skip 1 Read a trajectory from a file See also chemlab io datafile 110 Chapter 3 Reference Documentation CHAPTER 4 License Chemlab is released under the GNU GPLv3 and its main developer is Gabriele Lanaro 111 chemlab Documentation Release 0 4 112 Chapier 4 License Python Module Index chemlab graphics transformations 86 chemlab mviewer api core 105 chemlab notebook 109 113 chemlab Documentation Release 0 4 114 Python Module Index Index A AbstractDB class in chemlab db base 101 AbstractRenderer class in chemlab graphics renderers 67 add chemlab core System method 54 add_post_processing chemlab graphics QtViewer method 64 add_renderer chemlab graphics QtTrajectory Viewer method 66 add_renderer chemlab graphics QtViewer method 64 add_ui chemlab graphics QtTrajectory Viewer method 66 add_ui chemlab graphics QtViewer method 65 affine_matrix_from_points in module chem lab graphics transformations 89 angle_betwee
63. ctor_product v0 vl axis 0 Return vector perpendicular to vectors gt gt gt v vector_product 2 0 0 0 3 0 gt gt gt numpy allclose v 0 0 6 True gt gt gt v0 12 0 0 2 y DOr 2 0p 21y T0 0 25 211 gt gt gt v1 3 0 0 gt gt gt v vector_product v0 v1 gt gt gt numpy allclose v 0 0 0 0 0 0 6 6 0 6 0 6 True gt gt gt v0 12 0 0 2 0 O CO 2 07 27 0 01 gt gt gt vi 10 3 01 0y 0 31 E0 0 3J T3 37 31 gt gt gt v vector_product v0 vl axis 1 gt gt gt numpy allclose v 0 0 6 0 6 0 6 0 0 0 6 6 True 3 4 chemlab db 3 4 1 AbstractDB class chemlab db base AbstractDB Interface for a generic database A typical database can be used to retrieve molecules by calling the get method water db get molecul u water exampl A database can also provide custom functionalities to store or search for entries Those are implemented in custom methods See the other implementations for more relevant examples get feature key args kwargs Get a data entry from the database Subclasses are required to implement this method to provide access to the database Parameters efeature str An identifier that represents the kind of data that we want to extract Examples of such identifier are system molecule data etc ry
64. cule key The 4 alphanumeric PDB entry that you can get from the RCSB website 3 5 chemlab utils chemlab utils distances_within coords_a coords_b cutoff periodic False method simple Calculate distances between the array of coordinates coord_a and coord_b within a certain cutoff This function is a wrapper around different routines and data structures for distance searches It return a np ndarray containing the distances Parameters coords_a np ndarray N 3 dtype float First coordinate array coords_b np ndarray N 3 dtype float Second coordinate array cutoff float Maximum distance to search for periodic False or np ndarray 3 dtype float If False don t consider periodic images Otherwise periodic is an array containing the periodicity in the 3 dimensions method simple cell lists The method to use simple is a brute force distance search kdtree uses scipy ckdt ree module periodic not available and cell lists uses the cell linked list method 3 6 chemlab mviewer api Those are the default commands included in the chemlab molecular viewer 104 Chapter 3 Reference Documentation chemlab Documentation Release 0 4 3 6 1 Basic Commands Those commands are used to retrieve the basic objects that are currently displayed Basic functions to retrieve information on what s currently displayed in the molecular viewer chemlab mviewer api core current_frame Return the in
65. d Visualization 2 5 1 Intro The chemlab graphics package is one of the most interesting aspects of chemlab that sets him apart from similar programs The purpose of the package is to provide a solid library to develop 3D applications to display chemical data in an flexible way For example it s extremely easy to build a molecular viewer and add a bunch of custom features to it The typical approach when developing a graphics application is to create a Ot Viewer instance and add 3D features to it gt gt gt from chemlab graphics import QtViewer gt gt gt v OtViewer now let s define a molecule We can use the chemlab db module to get a water template gt gt gt from chemlab graphics renderers import AtomRenderer gt gt gt from chemlab db import ChemlabDB gt gt gt water ChemlabDB get molecule example water gt gt gt ar v add_renderer AtomRenderer water r_array water type_array gt gt gt v run 18 Chapter 2 User Manual chemlab Documentation Release 0 4 qtviewer pyc In this way you should be able to visualize a molecule where each atom is represented as a sphere There are also a set of viewing controls Mouse Drag Left Click or Left Right Up Down Rotate the molecule e Mouse Drag Right Click Pan the view e Mouse Wheel or Zoom in out In a similar fashion it is possible to display other features such as boxes cylinders lines etc
66. display the following window 44 Chapter 2 User Manual chemlab Documentation Release 0 4 qtviewer pyc Awesome Now we can write the gro file Notice that when we defined our water molecule we had to pass an export dictionary to the atoms and molecules The export mechanism is the way used by chemlab to handle all the variety of different file formats In this specific case gromacs defines its own atom and molecule names in the top file and then matches those to the gro file to infer the bonds and interactions TODO Add picture of the export dictionary How do we write the gro file Since we ve already setup our export information this is an one liner from chemlab io import datafile datafile start gro w write system s 2 9 4 top and mdp files I ll give you directly the gromacs input files to do an NPT simulation of water just create those files in your working directory topol top 2 9 Using GROMACS with chemlab 45 chemlab Documentation Release 0 4 molecul We simply import ready made definitions for th SOL and the atom types OW HW1 and HW2 include ffoplsaa itp include spce itp system Simple box of water molecules SOL 512 typ run mdp integrator md dt 0 001 nsteps 200000 nstxtcout 100 rlist 0 9 coulombtype pme rcoulomb 0 9 rvdw 0 9 dispcorr enerpres tcoupl
67. dule chemlab graphics transformations 92 distances_within in module chemlab utils 104 chem down chemlab graphics transformations Arcball method 89 download_molecule in module chemlab notebook 109 drag chemlab graphics transformations Arcball method 89 draw chemlab graphics renderers AbstractRenderer method 67 draw_vertices chem lab graphics renderers DefaultRenderer method 68 draw_vertices chem lab graphics renderers ShaderBaseRenderer method 67 E EdrIO class in chemlab io handlers 59 empty chemlab core System class method 54 euler_from_matrix in module chem lab graphics transformations 92 euler_from_quaternion in module chem lab graphics transformations 92 euler_matrix in module chem lab graphics transformations 92 export Atom attribute 50 export Molecule attribute 51 F fd IOHandler attribute 61 fields Atom attribute 50 formula Molecule attribute 51 fov Camera attribute 85 frames in module chemlab mviewer api core 105 from_arrays chemlab core Molecule class method 52 from_arrays chemlab core System class method 54 from_fields chemlab core Atom class method 50 from_json chemlab core System class method 55 FXAAEffect class in chemlab graphics postprocessing TI G GammaCorrectionEffect class in lab graphics postprocessing 78 geometric_center Molecule attribute 51 get chemla
68. e XyzIO method 61 X XtcIO class in chemlab io handlers 60 XyzlO class in chemlab io handlers 61 Index 119
69. e 49 mass Molecule attribute 51 matrix Camera attribute 85 matrix chemlab graphics transformations Arcball method 89 merge_systems in module chemlab core 57 mol_export System attribute 53 mol_indices System attribute 53 mol_n_atoms System attribute 54 mol_to_atom_indices chemlab core System method 55 molecular_orbital in module chemlab qc 109 Molecule class in chemlab core 50 MollO class in chemlab io handlers 60 mouse_rotate chemlab graphics camera Camera method 85 mouse_zoom method 85 move_to chemlab core Molecule method 52 msg in module chemlab mviewer api core 105 N n_atoms Molecule attribute 51 n_atoms System attribute 53 n_mol System attribute 53 next chemlab graphics transformations Arcball method 89 NoEffect class in chemlab graphics postprocessing 80 normalized in module chem lab graphics transformations 93 chemlab graphics camera Camera O orbit_x chemlab graphics camera Camera method 85 orbit_yQ chemlab graphics camera Camera method 86 orthogonalization_matrix in module chem lab graphics transformations 93 OutlineEffect class in chemlab graphics postprocessing 80 P paintGL chemlab graphics QChemlabWidget method 84 PdbIO class in chemlab io handlers 60 pivot Camera attribute 85 placeQ chemlab graphics transformations Arcball method 89 PointRenderer class in chemlab gra
70. e and goto_frame and inspect with the functions current_time and current_ frame 2 7 4 Selections In Chemlab you select and operate on atoms and bonds You can use the built in functions to select according to various types select_atoms 0 1 2 select_atom_type Na select_molecules H20 select_all select_within 0 1 0 2 You can also act on the selection in different ways invert_selection clear_selection Each selection routine returns a Selection object that contains information on the selection state so you can use it later select_atoms 0 1 2 Selection 0 1 2 tot 6 40 Chapter 2 User Manual chemlab Documentation Release 0 4 The Selection Selection objects have an API to be combined For example if you want to select Na and Cl atoms you can do in this way using the function select_selection na_at select_atoms Na cl_at select_atoms Cl1 select_selection atoms na_at add cl_at You can retrieve the currently selected atoms and bonds indices in the following way selected_atoms selected_bonds 2 7 5 Hiding and Showing Sometimes you want to hide certain objects from the current view to remove clutter For example if you want to select all the water molecules and hide them select_molecules H20 hide There s also a conveniency function to do this hide_water
71. e immediately Distance between two atoms In this section we will see how to use chemlab to find the interatomic distance between two selected atoms using the core functions Chemlab gives you some basic functions to change and retrieve information of what s currently displayed in the view For example to get the current System instance being displayed you can type 42 Chapter 2 User Manual chemlab Documentation Release 0 4 current_system If you want to know which are the indexes of the atoms currently selected you can type the following command selected_atoms array 0 1 You can also do the reverse given the indexes you can select two atoms the interface will update accordingly select_atoms 0 1 To calculate the distance between the selected atoms we have to first retrieve their indexes and then use the System to retrieve their coordinates At that point we can use them to find the distance it s the norm of the difference between the two coordinates selected selected_atoms s current_system a b s r_array selected import numpy as np distance np linalg norm a b 2 8 IPython integration There is some preliminary integration between chemlab and ipython notebook that will be extended and generalized in future releases To see it in action head over the example notebook 2 9 Using GROMACS with chemlab GROMACS is one of th
72. e most used packages for molecular simulations chemlab can provide a modern and intuitive interface to generate input and analyze the output of GROMACS calculations To illustrate the concepts we ll perform a very simple simulation of liquid water 2 9 1 Installing GROMACS This depends on the system you re using but I believe that GROMACS is already packaged for most linux distributions and also for other operating systems In Ubuntu sudo apt get install gromacs 2 9 2 What GROMACS needs In order to run a minimum simulation GROMACS requires to know some basic properties of the system we intend to simulate This boils down to basically 3 ingredients 1 The starting composition and configuration of our system This is provided by a gro file that contains the atom and molecule types and their position in space 2 Information about the connectivity and interactions between our particles This is called topology file and it is provided by writing a top file 2 8 IPython integration 43 chemlab Documentation Release 0 4 3 Simulation method This will require us to give parameters on how we want to make the system evolve This is provided by an mdp file chemlab can help us to build any system that we want and we ll use it to write a gro file Then we will use chemlab to visualize and analyze the result of the GROMACS simulation 2 9 3 Crafting a box of water There
73. ect numpy random random 3 0 5 gt gt gt persp numpy random random 3 0 5 gt gt gt PO projection_matrix point normal gt gt gt result projection_from_matrix P0 gt gt gt P1 projection_matrix result gt gt gt is_same_transform PO P1 True gt gt gt PO projection_matrix point normal direct gt gt gt result projection_from_matrix P0 gt gt gt P1 projection_matrix result gt gt gt is_same_transform PO P1 True gt gt gt PO projection_matrix point normal perspective persp pseudo False gt gt gt result projection_from_matrix P0 pseudo False gt gt gt Pl projection_matrix result gt gt gt is_same_transform PO P1 True gt gt gt PO projection_matrix point normal perspective persp pseudo True gt gt gt result projection_from_matrix P0O pseudo True gt gt gt Pl projection_matrix xresult gt gt gt is_same_transform PO P1 True chemlab graphics transformations projection_matrix point normal direc tion None perspective None pseudo False Return matrix to project onto plane defined by point and normal Using either perspective point projection direction or none of both If pseudo is True perspective projections will preserve relative depth such that Perspective dot Orthogonal PseudoPerspective gt gt gt P projection_matrix 0 0 0 1 0 0 gt gt gt numpy allclose P 1l 1
74. ect point normal gt gt gt angle direct point normal shear_from_matrix S0 gt gt gt S1 shear_matrix angle direct point normal 98 Chapter 3 Reference Documentation chemlab Documentation Release 0 4 gt gt gt is_same_transform S0O S1 True chem Return matrix to shear by angle along direction vector on shear plane lab graphics transformations shear_matrix angle direction point normal The shear plane is defined by a point and normal vector The direction vector must be orthogonal to the plane s normal vector A point P is transformed by the shear matrix into P such that the vector P P is parallel to the direction vector and its extent is given by the angle of P P P where P is the orthogonal projection of P onto the shear plane gt gt gt angle random random 0 5 4 math pi gt gt gt direct numpy random random 3 0 5 gt gt gt point numpy random random 3 0 5 gt gt gt normal numpy cross direct numpy random random 3 gt gt gt S shear_matrix angle direct point normal gt gt gt numpy allclose 1l numpy linalg det S True chemlab graphics transformations simple_clip_ matrix scale znear Zfar aspectra tio 1 0 Given the parameters for a frustum returns a 4x4 perspective projection matrix Parameters float scale float znear zfar near far plane z float Return a 4x4 perspective mat
75. ends bond_starts We sum the squares along the axis 1 this is equivalent of doint x 2 yee2 zxx2 for each row of the bond_vectors array gt gt gt distances np sqrt bond_vectors 2 sum axis 1 gt gt gt print distances 0 1 0 09999803 Sometimes you don t want to manually input the bonds but want to have them automatically generated In this case you may use the chemlab core Molecule guess_bonds method 2 3 2 Systems In context such as molecular simulations it is customary to introduce a new data structure called System A System represents a collection of molecules and optionally but recommended you can pass also periodic box information gt gt gt from chemlab core import System molecule a list of Molecule instances gt gt gt s System molecules boxsize 2 0 A System does not directly take Atom instances as its constituents therefore if you need to simulate a system made of single atoms say a box of liquid Ar you need to wrap the atoms into a Molecule gt gt gt ar Atom Ar 0 0 0 0 0 0 gt gt gt mol Molecule ar System similarly to Molecule can expose data by using arrays and it inherits atomic data from the con stituent molecules For instance you can easily and efficiently access all the atomic coordinates by using the attribute System r_array To understand the relation between Atom r Molecule r_array and System r_array you can refer
76. es can extend the methods __init__ read and write to implement their reading and writing routines Attributes fd can_read 3 2 chemlab io 61 chemlab Documentation Release 0 4 Type list of str A list of features that the handler can read can_write Type list of str A list of features that IOHandler can write check_feature feature readwrite Check if the feature is supported in the handler and raise an exception otherwise Parameters feature str Identifier for a certain feature readwrite read or write Check if the feature is available for reading or writing read feature args kwargs Read and return the feature feature It should raise an ValueError if the feature is not present in the handler can_read attribute use the method OHandler check_feature to provide this behaviour Certain features may require additional arguments and it is possible to pass those as well Example Subclasses can reimplement this method to add functionality class XyzIO IOHandler can_read molecule def read self feature xargs xkwargs self check_feature feature read if feature molecule Do stuff return geom write feature value args kwargs Same as read You have to pass also a value to write and you may pass any additional arguments Example class XyzIO IOHandler can_write molecule def write self feature value xargs xkwa
77. eveloped by Jesper Frills chemlab core random_lattice_box mol_list mol_number size spacing lt Mock object gt Make a box by placing the molecules specified in mol_list on random points of an evenly spaced lattice Using a lattice automatically ensures that no two molecules are overlapping Parameters mol_list list of Molecule instances A list of each kind of molecules to add to the system mol_number list of int The number of molecules to place for each kind size np ndarray 3 float The box size in nm spacing np ndarray 3 float 0 3 0 3 0 3 The lattice spacing in nm 3 1 chemlab core 57 chemlab Documentation Release 0 4 Returns A System instance Example Typical box with 1000 water molecules randomly placed in a box of size 2 0 2 0 2 0 from chemlab db import ChemlabDB Example water molecule water ChemlabDB get molecule example water s random_water_box water 1000 2 0 2 0 2 0 3 2 chemlab io This package contains utilities to read write a variety of chemical file formats chemlab io datafile filename mode rb format None Initialize the appropriate TOHand1ler for a given file extension or file format The datafile function can be conveniently used to quickly read or write data in a certain format gt gt gt handler datafile molecule pdb gt gt gt mol handler read molecule You can also use this shortcut gt gt
78. from which point we re seeing the scene It also handle the projection matrix the matrix we apply to project 3d points onto our 2d screen position Type np ndarray 3 float Default np array 0 0 0 0 5 0 The position of the camera You can modify this attribute to move the camera in various directions using the absoule x y and z coordinates a b c Type np ndarray 3 np ndarray 3 np ndarray 3 dtype float Default a np ndarray 1 0 0 0 0 0 b np ndarray 0 0 1 0 0 0 c np ndarray 0 0 0 0 1 0 84 Chapter 3 Reference Documentation chemlab Documentation Release 0 4 Those three vectors represent the camera orientation The a vector points to our right the b points upwards and c in front of us By default the camera points in the negative z axis direction pivot Type np ndarray 3 dtype float Default np array 0 0 0 0 0 0 The point we will orbit around by using Camera orbit_x and Camera orbit_y matrix Type np ndarray 4 4 dtype float Camera matrix it contains the rotations and translations needed to transform the world according to the camera position It is generated from the a b c vectors projection Type np ndarray 4 4 dtype float Projection matrix generated from the projection parameters z near z_far Type float float Near and far clipping planes For more info refer to http www lighthouse3d com tutorials view frustum culling fov Type f
79. g The previous snippet will stop at every frame from 0 to 10 ns with a step of 0 1 ns 3 6 2 Loading Commands Those commands are used to load write display or download structures from files or any other source chemlab mviewer api display autozoom Find optimal camera zoom level for the current view chemlab mviewer api display autozoom_ Find optimal camera zoom level for the current view chemlab mviewer api display display_molecule mol autozoom True Display a chemlab core Molecule instance in the viewer 3 6 chemlab mviewer api 105 chemlab Documentation Release 0 4 This function wraps the molecule in a system before displaying it chemlab mviewer api display display_ system system autozoom True Display a chemlab core System instance at screen chemlab mviewer api display download_molecule name Download a molecule by name chemlab mviewer api display goto_frame frame Go to a specific frame in the current trajectory chemlab mviewer api display goto_time timeval Go to a specific time in nanoseconds in the current trajectory chemlab mviewer api display guess_bonds Guess the bonds in the current system chemlab mviewer api display load_molecule name format None Read a chemlab core Molecule from a file See also chemlab io datafile chemlab mviewer api display load_remote_molecule url format None Load a molecule from the remote location specified by u
80. g or encoded 4 tuple Axes 4 string e g sxyz or tyxy e first character rotations are applied to s tatic or rotating frame e remaining characters successive rotation axis X y or z Axes 4 tuple e g 0 0 0 0 or 1 1 1 1 e inner axis code of axis x 0 y 1 z 2 of rightmost matrix b i e parity even 0 if inner axis x is followed by y y is followed by z or z is followed by x Otherwise odd 1 e repetition first and last axis are same 1 or different 0 e frame rotations are applied to static 0 or rotating 1 frame References Matrices and transformations Ronald Goldman In Graphics Gems I pp 472 475 Morgan Kaufmann 1990 2 More matrices and transformations shear and pseudo perspective Ronald Goldman In Graphics Gems IT pp 320 323 Morgan Kaufmann 1991 3 Decomposing a matrix into simple transformations Spencer Thomas In Graphics Gems II pp 320 323 Morgan Kaufmann 1991 4 Recovering the data from the transformation matrix Ronald Goldman In Graphics Gems II pp 324 331 Morgan Kaufmann 1991 Euler angle conversion Ken Shoemake In Graphics Gems IV pp 222 229 Morgan Kaufmann 1994 Arcball rotation control Ken Shoemake In Graphics Gems IV pp 175 192 Morgan Kaufmann 1994 Representing attitude Euler angles unit quaternions and rotati
81. gt mol datafile molecule pdb read molecule Parameters filename str Path of the file to open format str or None When different from None can be used to specify a format identifier for that file It should be used when the extension is ambiguous or when there isn t a specified filename See below for a list of the formats supported by chemlab chemlab io remotefile url format None The usage of remotefile is equivalent to chemlab io datafile except you can download a file from a remote url Example mol remotefile https github com chemlab chemlab testdata blob master 3ZJE pdb read molecule 3 2 1 Supported File Formats cml Chemical Markup Language Extension cml class chemlab io handlers Cml1IO0 fd The CML format is described in http www xml cml org Features read molecule Read the coordinates in a Molecule instance 58 Chapter 3 Reference Documentation chemlab Documentation Release 0 4 edr class write molecule mol Writes a Molecule instance in the CML format GROMACS energy file Extension edr chemlab io handlers EdrI0 fd EDR files store per frame information for gromacs trajectories Examples of properties obtainable from EDR files are temperature pressure density potential energy total energy eters To know which quantities are available in a certain edr file you can access the feature
82. h differences 2 4 2 Reading and writing data The classes responsible for the I O are subclasses of chemlab io handlers IOHandler These handlers take a file like object as the first argument and they work all in the same way here is an example of GroHandler from chemlab io handlers import GromacsIO fd open waterbox gro rb infile GromacsI0O fd system infile read system Modify system as you wish fd open waterbox_out gro w outfile GromacsI0O fd outfile write system system You first create the handler instance for a certain format and then you can read a certain feature provided by the handler In this example we read and write the system feature Some file formats may have some extra data for each atom molecule or system For example the gro file formats have his own way to call the atoms in a water molecule OW HW1 HW2 To handle such issues you can write this information in the export arrays contained in the data structures such as Atom export Molecule export and their array based counterparts Molecule atom_export_array System mol_export and System atom_export_array Those attributes are especially important where you write in some data format since you may have to provide those attribute when you initialize your Atom Molecule and System You can easily open a data file without even having to search his format handler by using the utility function chemlab io datafile
83. h limits side effects and makes the code more predictable and easy to follow Bonds between atoms can be set or retrieved by using the bonds attribute It s an array of integers of dimensions nbonds 2 where the integer value corresponds to the atomic indices gt gt gt from chemlab db import ChemlabDB gt gt gt water ChemlabDB get molecule example water gt gt gt water bonds array 0 1 0 2 8 Chapter 2 User Manual chemlab Documentation Release 0 4 By using the numpy take function it s very easy to extract properties relative to the bonds numpy take lets you index an array using another array as a source of indices for example we can extract the bonds extrema in this way gt gt gt import numpy as np gt gt gt np take water type_array n bonds array O H O H dtype object If the array is not flat like r_array you can also specify the indexing axis the following snippet can be used to retrieve the bond distances With water bonds 0 we take an array with the indices of the first element of the bond And we use numpy take to use this array to index r_array We index along the axis 0 along this axis th lements are 3D vectors gt gt gt bond_starts np take water r_array water bonds 0 axis 0 gt gt gt bond_ends np take water r_array water bonds 1 axis 0 gt gt gt bond_vectors bond_
84. in chemlab graphics transformations Arcball method 89 ShaderBaseRenderer class in chem lab graphics renderers 67 shear_from_matrix in module chem lab graphics transformations 98 shear_matrix in module chem lab graphics transformations 99 simple_clip_matrix in module chem lab graphics transformations 99 sort chemlab core System method 56 SphereImpostorRenderer class in chem lab graphics renderers 69 SphereRenderer class in chemlab graphics renderers 68 SSAOEffect class in chemlab graphics postprocessing 81 state chemlab graphics camera Camera method 86 store LocalDB method 104 subsystem_from_atoms in module chemlab core 56 subsystem_from_molecules in module chemlab core 56 superimposition_matrix in module lab graphics transformations 99 System class in chemlab core 52 T TextUI class in chemlab graphics uis 77 toimage chemlab graphics QChemlabWidget method 84 tojson chemlab core Molecule method 52 tojson chemlab core System method 56 trajectory in module chemlab mviewer api core 105 chem translation_from_matrix in module chem lab graphics transformations 100 translation_matrix in module chem lab graphics transformations 100 TriangleRenderer class in chemlab graphics renderers 13 type Atom attribute 49 type_array System attribute 52 U unit_vector in module lab graphics transformations 10
85. in your hand light_dir is the direction this lamp is pointing And if you move jump or rotate the lamp will move with you Note With the current lighting mode there isn t a light position The light is assumed to be infinitely distant and light rays are all parallel to the light direction background_color 3 3 chemlab graphics 83 chemlab Documentation Release 0 4 Type tuple Default 255 255 255 255 white A 4 element r g b a tuple that specity the background color Values for r g b a are in the range 0 255 You can use the colors contained in chemlab graphics colors paintGL GL function called each time a frame is drawn toimage width None height None Return the current scene as a PIL Image Example You can build your molecular viewer as usual and dump an image at any resolution supported by the video card up to the memory limits v QtViewer Add the renderers v add_renderer Add post processing effects add_post_processing lt Move the camera widget camera autozoom widget camera orbit_x widget camera orbit_y aga lt Save the image image v widget toimage 1024 768 image save mol png See also https pillow readthedocs org en latest PIL html module PIL Image The Camera class class chemlab graphics camera Camera Our viewpoint on the 3D world The Camera class can be used to access and modify
86. ion of last drag place center radius Place Arcball e g when window size changes center sequence 2 Window coordinates of trackball center radius float Radius of trackball in window coordinates setaxes axes Set axes to constrain rotations setconstrain constrain Set state of constrain to axis mode chemlab graphics transformations affine_matrix_from_points v0 vl shear True scale True us esvd True 3 3 chemlab graphics 89 chemlab Documentation Release 0 4 Return affine transform matrix to register two point sets vO and v1 are shape ndims arrays of at least ndims non homogeneous coordinates where ndims is the dimensionality of the coordinate space If shear is False a similarity transformation matrix is returned If also scale is False a rigid Eucledian transfor mation matrix is returned By default the algorithm by Hartley and Zissermann 15 is used If usesvd is True similarity and Eucledian transformation matrices are calculated by minimizing the weighted sum of squared deviations RMSD accord ing to the algorithm by Kabsch 8 Otherwise and if ndims is 3 the quaternion based algorithm by Horn 9 is used which is slower when using this Python implementation The returned matrix performs rotation translation and uniform scaling if specified gt gt gt vO 0 1031 1031 0 0 0 1600 1600 gt gt gt vl 675 826 826 677 55 52
87. le According to the numpy broadcasting rules if you sum two arrays with shapes NA 3 and 3 each row of the first array gets summed with the second array Let s say we have a water molecule and we want to displace it randomly in a box this is easily accomplished by initializing a Molecule at the origin and summing its coordinates with a random displacement import numpy as np wat Molecule Atom H 0 0 0 Atom H 0 0 1 3 Atom O 0 0 0 0 bonds 2 0 2 1 Shapes NA 3 and 3 wat r_array np random rand 3 Using the same principles you can also apply other kinds of transformations such as matrices You can for example rotate the molecule by 90 degrees around the z axis from chemlab graphics transformations import rotation_matrix The transformation module returns 4x4 matrices M rotation_matrix np pi 2 np array 0 0 0 0 1 0 3 3 slow readable way for i r in enumerate wat r_array wat r_array i np dot M r numpy efficient way to do the same wat r_array np dot wat r_array M T The array based API provides a massive increase in performance and a more straightforward integration with C li braries thanks to the numpy arrays This feature comes at a cost the data is copied between atoms and molecules in other words the changes in the costituents atoms are not reflected in the Molecule and vice versa Even if it may look a bit unnatural this approac
88. loat field of view in degrees used to generate the projection matrix aspectratio Type float Aspect ratio for the projection matrix this should be adapted when the application window is resized autozoom points Fit the current view to the correct zoom level to display all points The camera viewing direction and rotation pivot match the geometric center of the points and the distance from that point is calculated in order for all points to be in the field of view This is currently used to provide optimal visualization for molecules and systems Parameters points np ndarray N 3 Array of points mouse_rotate dx dy Convenience function to implement the mouse rotation by giving two displacements in the x and y direc tions mouse_zoom inc Convenience function to implement a zoom function This is achieved by moving Camera position in the direction of the Camera c vector orbit_x angle Same as orbit_y but the axis of rotation is the Camera b vector 3 3 chemlab graphics 85 chemlab Documentation Release 0 4 We rotate around the point like if we sit on the side of a salad spinner orbit_y angle Orbit around the point Camera pivot by the angle angle expressed in radians The axis of rotation is the camera right vector Camera a In practice we move around a point like if we were on a Ferris wheel restore state Restore the camera state passed as a state dictionary You can obtain a previo
89. m Original system selection np ndarray of int or np ndarray NA of bool A boolean array that is True when the ith atom has to be selected or a set of atomic indices to be included Returns A new System instance chemlab core merge_systems sysa sysb bounding 0 2 Generate a system by merging sysa and sysb Overlapping molecules are removed by cutting the molecules of sysa that have atoms near the atoms of sysb The cutoff distance is defined by the bounding parameter Parameters sysa System First system sysb System Second system bounding float or False Extra space used when cutting molecules in sysa to make space for sysb If it is False no overlap handling will be performed 3 1 5 Routines to create Systems chemlab core ecrystal positions molecules group cellpar 1 0 1 0 1 0 90 90 90 repetitions 1 1 1 Build a crystal from atomic positions space group and cell parameters Parameters positions list of coordinates A list of the atomic positions molecules list of Molecule The molecules corresponding to the positions the molecule will be translated in all the equivalent positions group int str Space group given either as its number in International Tables or as its Hermann Mauguin symbol repetitions Repetition of the unit cell in each direction cellpar Unit cell parameters This function was taken and adapted from the spacegroup module found in ASE The module spacegroup module was originally d
90. n those cases they basically take as their argument the attribute field name the type and a function that return the default value for the field attribute from chemlab core attributes import MArrayAttr NDArrayAttr from chemlab core fields import AtomicField class MyAtom Atom fields Atom fields AtomicField v default lambda at np zeros 3 np float class MyMolecule Molecule attributes Molecule attributes MArrayAttr v_array v np float default lambda mol np zeros mol n class MySystem System attributes System attributes NDArrayAttr v_array v_array np float 3 atoms Those class are ready to use You may want to create new instances with the Atom from_fields Molecule from_arrays and System from_arrays Once you ve done your field specific job with MyAtom MyMolecule MySystem you can convert back to a chemlab default class class by using the astype methods at myat astype Atom mol mymol astype Molecule sys mysys astype System 2 3 Atoms Molecules and Systems 15 3 7 n chemlab Documentation Release 0 4 2 4 Input and Output Routines 2 4 1 The jungle of file formats There are a lot of file formats used and produced by chemistry applications Each program has his way to store geometries trajectories energies and properties etc chemlab tries to encompass all of those different properties by using a lightweight way to handle suc
91. n_vectors in module chem lab graphics transformations 90 Arcball class in chemlab graphics transformations 89 arcball_constrain_to_axis in module chem lab graphics transformations 90 arcball_map_to_sphere in module chem lab graphics transformations 90 arcball_nearest_axis in module chem lab graphics transformations 91 aspectratio Camera attribute 85 Atom class in chemlab core 49 atom_export_array Molecule attribute 51 atom_export_array System attribute 53 atom_to_molecule_indices chemlab core System method 54 AtomRenderer class in chemlab graphics renderers 69 autozoom chemlab graphics camera Camera method 85 B background_color QChemlabWidget attribute 83 BallAndStickRenderer class in lab graphics renderers 70 BondRenderer class in chemlab graphics renderers 70 bonds Molecule attribute 51 chem bonds System attribute 53 box_vectors System attribute 53 BoxRenderer class in chemlab graphics renderers 74 C Camera class in chemlab graphics camera 84 camera QChemlabWidget attribute 83 can_read IOHandler attribute 61 can_write IOHandler attribute 62 center_of_mass Molecule attribute 51 charge Atom attribute 50 charge_array Molecule attribute 51 charge_array System attribute 52 check_feature chemlab io handlers OHandler method 62 chemlab graphics transformations module 86 chemlab mviewer api core module 10
92. nt Number of molecules n_atoms Type int Number of atoms chemlab core 53 chemlab Documentation Release 0 4 mol_indices Type np ndarray N dtype int Gives the starting index for each molecule in the atomic arrays For example in a System comprised of 3 water molecules gt gt gt s mol_indices 0 3 6 gt gt gt s type_array 0 3 Peo H HY This array is used internally to retrieve all the Molecule derived data Do not modify unless you know what you re doing mol_n_ atoms Type np ndarray N dtype int Contains the number of atoms present in each molecule add mol Add the molecule mol to a System initialized through System empty atom_to_molecule_indices selection Given the indices over atoms return the indices over molecules If an atom is selected all the containing molecule is selected too Parameters selection np ndarray N dtype int np ndarray NATOMS dtype book Either an index array or a boolean selection array over the atoms Returns np ndarray N dtype int an array of molecular indices copy Return a copy of the current system classmethod empty _mol n_atoms box_vectors None Initialize an empty System containing n_mol Molecules and n_atoms Atoms The molecules can be added by using the method add Example How to initialize a system of 3 water molecules s System empty 3 9 for i in range 3 s add water
93. nts of the cylinder colors np ndarray NYCL 4 dtype np uint8 The color for each cylinder update_bounds bounds Update cylinders start and end positions 76 Chapter 3 Reference Documentation chemlab Documentation Release 0 4 List of available Uls TextUl class chemlab graphics uis TextUI widget x y text Display an overlay text at the point x y in screen space Warning The API for this element and uis in general is not yet finalized Parameters widget The parent OChemlabWidget x y int Points in screen coordinates x pixels from left y pixels from top text str String of text to display 3 3 4 Post Processing Effects List of Post Processing Effects FXAAEffect class chemlab graphics postprocessing FXAAEffect widget span_max 4 0 reduce_mul 0 125 re duce_min 0 0078125 Fast Approximate Anti Aliasing It is an efficient way to add anti aliasing to your scenes The reason to have it is to reduce jagged lines The parameters span_max reduce_mul reduce_min are tweakable even if it is suggested to keep them at their default value 3 3 chemlab graphics 77 chemlab Documentation Release 0 4 nosetests FXAA OFF FXAA ON GammacCorrectionEffect class chemlab graphics postprocessing GammaCorrectionEffect widget gamma 2 2 Add gamma correction to the current scene Scenes displayed by OpenGL are in RGB color space The response to colors by our eyes and by old CRT screens is
94. o programmatically download and generate geometries The molecular viewer is very fast it can easily animate 100000 spheres and the design is simple and flexible For more information about the newest features check out the release notes in the What s new document Chemlab is developer friendly it provides good documentation and has an easy structure to get in Feel free to send me anything that you may do with chemlab like supporting a new file format a new graphic renderer a nice example even if you don t think it s perfect Send an email to the mailing list or file an issue on the github page to discuss any idea that comes to your mind Get involved chemlab Documentation Release 0 4 4 Chapter 1 Current Status CHAPTER 2 User Manual 2 1 What s new 2 1 1 Version 0 4 chemlab mviewer e Added a full fledged molecular viewer But it will be gone in favor of the notebook based chemview chemlab io e Added cclib integration chemlab notebook e New module with functions for the Python notebook Requires chemview chemlab qe e Example module for quantum chemistry calculation Please file an issue on GitHub if you want to maintain it 2 1 2 Version 0 3 chemlab core e New bond handling with the Molecule bonds and System bonds attributes e Possibility to add charges chemlab graphics e Post Processing Effects FXAA Fast Approximate Antialiasing Gamma Correction Glow Outline
95. om chemlab graphics import QtViewer from chemlab graphics renderers import PointRenderer from chemlab graphics uis import TextUI vertices 0 0 0 0 0 0 0 0 1 0 0 0 2 0 0 0 0 0 blue 0 255 255 255 colors blue 3 v QtViewer pr v add_renderer PointRenderer vertices colors tu v add_ui TextUI 100 100 Hello world v run add_post_processing klass args kwargs Add a post processing effect to the current scene The usage is as following from chemlab graphics import QtViewer from chemlab graphics postprocessing import SSAOEffect v QtViewer effect v add_post_processing SSAOEffect See also List of Post Processing Effects Return an instance of AbstractEffect New in version 0 3 add_renderer klass args kwargs Add a renderer to the current scene Parameter 64 Chapter 3 Reference Documentation chemlab Documentation Release 0 4 klass renderer class The renderer class to be added args kwargs Arguments used by the renderer constructor except for the widget argument See also AbstractRenderer See also List of available renderers Return The istantiated renderer You should keep the return value to be able to update the renderer at run time add_ui klass args kwargs Add an UI element for the current scene The approach is the same as renderers Warning The UI api is not yet finalized has_
96. on vectors James Diebel 2006 on A U A discussion of the solution for the best rotation to relate two sets of vectors W Kabsch Acta Cryst 1978 A34 827 828 3 3 chemlab graphics 87 chemlab Documentation Release 0 4 9 Closed form solution of absolute orientation using unit quaternions BKP Horn J Opt Soc Am A 1987 4 4 629 642 10 Quaternions Ken Shoemake http www sfu ca jwa3 cmpt461 files quatut pdf 11 From quaternion to matrix and back JMP van Waveren 2005 http www intel com cd ids developer asmo na eng 293748 htm 12 Uniform random rotations Ken Shoemake In Graphics Gems IIT pp 124 132 Morgan Kaufmann 1992 13 Quaternion in molecular modeling CFF Karney J Mol Graph Mod 25 5 595 604 14 New method for extracting the quaternion from a rotation matrix Itzhack Y Bar Itzhack J Guid Contr Dynam 2000 23 6 1085 1087 15 Multiple View Geometry in Computer Vision Hartley and Zissermann Cambridge University Press 2nd Ed 2004 Chapter 4 Algorithm 4 7 p 130 16 Column Vectors vs Row Vectors http steve hollasch net cgindex math matrix column vec html Examples gt gt gt alpha beta gamma 0 123 1 234 2 345 gt gt gt origin xaxis yaxis zaxis 0 0 OJ 1 0 0 0 1 0 0 0 1 gt gt gt I identity_matrix gt gt gt Rx rotation_matrix alpha xaxis gt gt gt Ry rotation_matrix beta yaxis gt gt gt Rz rotation_matri
97. ot numpy allclose M1 numpy linalg inv M0O print size chemlab graphics transformations is_same_transform matrix0 matrix Return True if two matrices perform same transformation gt gt gt is_same_transform numpy identity 4 numpy identity 4 True gt gt gt is_same_transform numpy identity 4 random_rotation_matrix False chemlab graphics transformations normalized x Return the x vector normalized chemlab graphics transformations orthogonalization_matrix lengths angles Return orthogonalization matrix for crystallographic cell coordinates Angles are expected in degrees The de orthogonalization matrix is the inverse gt gt gt O orthogonalization_matrix 10 10 10 90 90 90 gt gt gt numpy allclose O 3 3 numpy identity 3 float 10 True 3 3 chemlab graphics 93 chemlab Documentation Release 0 4 gt gt gt O orthogonalization_matrix 9 8 12 0 15 5 87 2 80 7 69 7 gt gt gt numpy allclose numpy sum 0O 43 063229 True chemlab graphics transformations projection_from_matrix matrix pseudo False Return projection plane and perspective point from projection matrix Return values are same as arguments for projection_matrix function point normal direction perspective and pseudo gt gt gt point numpy random random 3 0 5 gt gt gt normal numpy random random 3 0 5 gt gt gt dir
98. otype The atom names as indicated in the gro file This is added to each entry of Sys tem atom_export_array write system syst Write the syst System instance to disk The export arrays should have the groname and grotype entries as specified in the read system method Example Export informations for water SPC Molecule Atom O 0 0 0 0 0 0 export grotype OW Atom H 0 1 0 0 0 0 export grotype HW1 Atom H 0 033 0 094 0 0 export grotype HW2 export groname SOL mol MDL Coordinate files Extension mol class chemlab io handlers Mol1I0 fd pdb Reader for MDL molfile http en wikipedia org wiki Chemical_table_file Features read molecule Read the molecule in a Molecule instance Protein Data Bank format Extension pdb class chemlab io handlers PdbI0 fd Starting implementation of a PDB file parser Note This handler was developed as an example If you like to contribute by implementing it you can write an email to the mailing list Features read molecule Read the pdb file as a huge Molecule read system Read the pdb file as a System where each residue is a molecule xtc GROMACS compressed trajectory file Extension xtc class chemlab io handlers XtcI0 fd Reader for GROMACS XTC trajectories Features read trajectory Read the frames from the file and returns the trajectory a
99. p decompose_matrix S gt gt gt scale 0 0 123 gt gt gt RO euler_matrix l 2 3 gt gt gt scale shear angles trans persp decompose_matrix R0 gt gt gt R1 euler_matrix xangles gt gt gt numpy allclose RO R1 True chemlab graphics transformations distance x x2 Distance between two points in space chemlab graphics transformations euler_from_matrix matrix axes sxyz Return Euler angles from rotation matrix for specified axis sequence axes One of 24 axis sequences as string or encoded tuple Note that many Euler angle triplets can describe one matrix gt gt gt RO euler_matrix l 2 3 syxz gt gt gt al be ga euler_from_matrix RO syxz gt gt gt R1 euler_matrix al be ga syxz gt gt gt numpy allclose RO R1 True gt gt gt angles 4 math pi numpy random random 3 0 5 gt gt gt for axes in _AXES2TUPLE keys RO euler_matrix axes axes xangles R1 euler_matrix axes axes xeuler_from_matrix RO axes if not numpy allclose RO R1 print axes failed chemlab graphics transformations euler_from_quaternion quaternion axes sxyz Return Euler angles from quaternion for specified axis sequence gt gt gt angles euler_from_quaternion 0 99810947 0 06146124 0 0 gt gt gt numpy allclose angles 0 123 0 0 True Chapter 3 Reference Documentation
100. phics renderers 72 position Camera attribute 84 projection Camera attribute 85 projection_from_matrix in module chem lab graphics transformations 94 projection_matrix in module chem lab graphics transformations 94 Q QChemlabWidget class in chemlab graphics 82 QtTrajectory Viewer class in chemlab graphics 66 QtViewer class in chemlab graphics 64 quaternion_about_axis in module chem lab graphics transformations 95 quaternion_conjugate in module chem lab graphics transformations 95 quaternion_from_euler in module chem lab graphics transformations 95 quaternion_from_matrix in module chem lab graphics transformations 95 quaternion_imag in module chem lab graphics transformations 95 quaternion_inverse in module chem lab graphics transformations 96 quaternion_matrix in module chem lab graphics transformations 96 quaternion_multiplyQ in module chem lab graphics transformations 96 quaternion_real in module chem lab graphics transformations 96 quaternion_slerp in module chem lab graphics transformations 96 R r Atom attribute 49 r_array Molecule attribute 50 r_array System attribute 52 random_lattice_box in module chemlab core 57 random_quaternion in module chem lab graphics transformations 96 random_rotation_matrix in module chem lab graphics transformations 97 random_vector in module chem lab
101. phics renderers import AtomRenderer v QtViewer atom_rend v add_renderer AtomRenderer norb r_array norb type_array After we ve got the renderer in place we can programmatically manipulate the camera to adjust at the right zoom level You can for instance use the chemlab graphics camera Camera autozoom method to automatically adjust the scene but you are free to use any other method present in the Camera class v widget camera autozoom norb r_array v run 2 5 Graphics and Visualization 25 chemlab Documentation Release 0 4 At this point you are free experiment with different effects and combinations In our case we ll add SSAO and anti aliasing to add more depth and smoothness to the rendering from chemlab graphics postprocessing import SSAOEffect FXAAEffect v add_post_processing SSAOEffect kernel_size 128 kernel_radius 1 0 v add_post_processing FXAAEffect v run To actually save the image you can now use the chemlab graphics OQChemlabWidget toimage method and select a resolution of 800x800 pixels This will return a PIL image that has a save method to store it as a png img v widget toimage 800 800 img save norb png 26 Chapter 2 User Manual chemlab Documentation Release 0 4 Once we ve got the sample molecule up and running it s very easy to automatize the process to produce images of different molecules
102. r update_normals normals v widget update v schedule update 10 v run 2 5 3 Post Processing Effects New in version 0 3 Post processing effects are a great way to increase the visual quality of your representations Those effects are applied after the scene is rendered and they can be applied one after each other to achieve a combination of effects Applying a post processing effect is extremely easy Let s see we are viewing a big molecule with lots of pockets such as a protein Grab the protein 3ZJE load it into chemlab and display it using a simple Van der Waals representation from chemlab graphics import QtViewer from chemlab graphics renderers import AtomRenderer from chemlab io import datafile protein datafile 32ZJE pdb read molecule v QtViewer v add_renderer AtomRenderer protein r_array protein type_array v run You ll get a representation like this 2 5 Graphics and Visualization 21 chemlab Documentation Release 0 4 This representation doesn t really show the molecule surface features plus it looks dull and plasticky We can add the screen space ambient occlusion effect to improve its visual quality Screen space ambient occlusion SSAO is a very powerful technique used by numerous videogames to make the illumination much more realistic by darkening the more occluded areas of the objects such as pockets and surface features Chemlab implements
103. renderer rend Return True if the renderer is present in the widget renderers remove_post_processing pp Remove a post processing effect versionadded 0 3 remove_renderer rend Remove a renderer from the current view Example rend v add_renderer AtomRenderer v remove_renderer rend New in version 0 3 run Display the QtViewer schedule callback timeout 100 Schedule a function to be called repeated time This method can be used to perform animations Example This is a typical way to perform an animation just from chemlab graphics import QtViewer from chemlab graphics renderers import SphereRenderer v QtViewer sr v add_renderer SphereRenderer centers radii colors def update calculate new_positions sr update_positions new_positions v widget repaint v schedule update v run 3 3 chemlab graphics 65 chemlab Documentation Release 0 4 Note remember to call QtViewer widget repaint each once you want to update the display Parameters callback function A function that takes no arguments that will be called at intervals timeout int Time in milliseconds between calls of the callback function Returns a QTimer to stop the animation you can use Qfimer stop The QtTrajectoryViewer class class chemlab graphics QtTrajectoryViewer Bases PyQt4 QtGui QMainWindow Interface for viewing trajectory It provides interface elemen
104. renderer automatically binds light and camera information Subclasses should not reimplement the draw method but the draw_vert ices method where you can bind and draw the objects Parameters widget The parent OChemlabWidget vertex str Vertex program as a string fragment str Fragment program as a string draw_vertices Method to be reimplemented by the subclasses 3 3 chemlab graphics 67 chemlab Documentation Release 0 4 class chemlab graphics renderers DefaultRenderer widget Bases chemlab graphics renderers base ShaderBaseRenderer Same as ShaderBaseRenderer with the default shaders You can find the shaders in chemlab graphics renderers shaders under the names of default_persp vert and default_persp frag draw_vertices Subclasses should reimplement this method SphereRenderer class chemlab graphics renderers SphereRenderer widget poslist radiuslist colorlist shad ing phong Renders a set of spheres The method used by this renderer is approximating a sphere by using triangles While this is reasonably fast for best performance and animation you should use Sphere ImpostorRenderer Parameters widget The parent QOChemlabWidget 68 Chapter 3 Reference Documentation chemlab Documentation Release 0 4 poslist np ndarray NSPHERES 3 dytpe float A position array While there aren t dimensions in the context of chemlab 1 unit of space equals 1 nm radiuslist np ndarr
105. rgs self check_feature feature write if feature molecule Do stuff return geom 3 3 chemlab graphics This package contains the features related to the graphic capabilities of chemlab 3 3 1 Ready to use functions The two following functions are a convenient way to quickly display and animate a System in chemlab 62 Chapter 3 Reference Documentation chemlab Documentation Release 0 4 chemlab graphics display_system sys style vdw Display the system sys with the default viewer chemlab graphics display_ trajectory sys times coords _list box_vectors None style spheres Display the the system sys and instrument the trajectory viewer with frames information qtviewer pyc gt Parameters sys System The system to be displayed times np ndarray NFRAMES dtype float The time corresponding to each frame This is used only for feedback reasons 3 3 chemlab graphics 63 chemlab Documentation Release 0 4 coords _list list of np ndarray NFRAMES 3 dtype float Atomic coordinates at each frame 3 3 2 Builtin 3D viewers The QtViewer class class chemlab graphics QtViewer Bases PyQt4 QtGui QMainWindow View objects in space This class can be used to build your own visualization routines by attaching renderers and uis to it See also Graphics and Visualization Example In this example we can draw 3 blue dots and some overlay text fr
106. rix Return matrix to transform given 3D point set into second point set vO and v1 are shape 3 or 4 arrays of at least 3 points chemlab graphics transformations superimposition_matrix v0 vl scale False us esvd True The parameters scale and usesvd are explained in the more general affine_matrix_from_points function The returned matrix is a similarity or Eucledian transformation matrix This function has a fast C implementation in transformations c gt gt gt v0 numpy random rand 3 10 gt gt gt M superimposition_matrix v0 v0 gt gt gt numpy allclose M numpy identity 4 True gt gt gt R random_rotation_matrix numpy random random 3 gt gt gt vO 1 0 0 0 1 0 0 0 1 1 1 1 gt gt gt vl numpy dot R v0 gt gt gt M superimposition_matrix v0 vl gt gt gt numpy allclose vl numpy dot M v0 True gt gt gt v0 numpy random rand 4 100 0 5 x 20 gt gt gt vO 3 1 gt gt gt vl numpy dot R v0 gt gt gt M superimposition_matrix v0 vl gt gt gt numpy allclose vl numpy dot M v0 True gt gt gt S scale_matrix random random gt gt gt T translation_matrix numpy random random 3 0 5 gt gt gt M concatenate_matrices T R S gt gt gt vl numpy dot M v0 gt gt gt v0 3 numpy random normal 0 le 9 300 reshape 3 gt gt gt M superimposition_matrix v0 vl scale True gt
107. rl Example load_remote_molecule https raw github com chemlab chemlab testdata master benzenl chemlab mviewer api display load_remote_system url format None Load a system from the remote location specified by url Example load_remote_system https raw github com chemlab chemlab testdata master naclwate chemlab mviewer api display load_remote_trajectory url format None Load a trajectory file from a remote location specified by url See also load_remote_system chemlab mviewer api display load_system name format None Read a chemlab core System from a file See also chemlab io datafile chemlab mviewer api display load_trajectory name skip 1 format None Load a trajectory file into chemlab You should call this command after you load a chemlab core System through load_system or load_remote_system chemlab mviewer api display reload_system Reload the current system in the viewer chemlab mviewer api display write_molecule filename format None Write the system displayed in a file as a molecule chemlab mviewer api display write_system filename format None Write the system currently displayed to a file 106 Chapter 3 Reference Documentation e mol r egro chemlab Documentation Release 0 4 3 6 3 Selection Commands Those commands are for selecting objects in the molecular viewer before performing operations on them chemlab mviewer api selections can
108. rom a set of Atom derived arrays Please refer to the Molecule Atom Derived At tributes Only r_array and type_array are absolutely required the others are optional gt gt gt Molecule from_arrays r_array np array 0 0 0 0 0 0 1 0 0 0 0 0 LOO WeO O20 1 type_array np array O H H molecule H20 Initializing a molecule in this way can be much faster than the default initialization method guess_bonds Guess the molecular bonds by using covalent radii information move_to r Translate the molecule to a new position r tojson Return a json string representing the Molecule This is useful for serialization 3 1 3 The System class class chemlab core System molecules box_vectors None A data structure containing information of a set of N Molecules and NA Atoms Parameters molecules list of molecules Molecules that constitute the System The data gets copied to the System subse quent changes to the Molecule are not reflected in the System box_vectors np ndarray 3 3 dtype float optional You can specify a periodic box of another shape by giving 3 box vectors The System class has attributes derived both from the Molecule and the Atom class r_array Type np ndarray NA 3 dtype float Derived from Atom Atomic coordinates m_array Type np ndarray NA dtype float Derived from Atom Atomic masses type_array Type np ndarray NA dtype object array of str Derived from Atom A
109. rray 3 list 3 Atomic coordinates in nm export dict optional Additional export information Example gt gt gt Atom H 0 0 0 0 0 0 In this example we re attaching additional data to the Atom instance The chemlab io GroIO can use this infor mation when exporting in the gro format gt gt gt Atom H 0 0 0 0 0 0 groname HW1 type Type str The atomic symbol e g Ar H O Type np ndarray 3 of floats Atomic position in nm 49 chemlab Documentation Release 0 4 mass Type float Mass in atomic mass units charge Type float Charge in electron charge units export Type dict Dictionary containing additional information when importing data from various formats See also chemlab io gro GroIO fields Type tuple This is a class attribute The list of attributes that constitute the Atom This is used to iterate over the Atom attributes at runtime copy Return a copy of the original Atom classmethod from_fields kwargs Create an Atom instance from a set of fields This is a slightly faster way to initialize an Atom Example gt gt gt Atom from_fields type Ar r_array np array 0 0 0 0 0 0 mass 39 948 export 3 1 2 The Molecule class class chemlab core Molecule atoms bonds None export None Molecule is a data container for a set of N Atoms See also Atoms Molecules and Systems Parameters atoms list of Atominstan
110. rray of all the atomic symbols It can be used to select certain atoms in a system charge_array 52 Chapter 3 Reference Documentation chemlab Documentation Release 0 4 Type np ndarray N dtype float Derived from Atom Array of the charges present on the atoms Example Suppose you have a box of water defined by the System s to select all oxygen atoms you can use the numpy selection rules gt gt gt oxygens s type_array 0 oxygens is an array of booleans of length NA where each True corresponds to an oxygen atom i e True False False True False False You can use the oxygen array to access other properties gt gt gt o_coordinates s r_array oxygens gt gt gt o_indices np arange s n_atoms oxygens bonds Type np ndarray NBONDS 2 dtype int Derived from Molecule An array of 2d indices that specify the index of the bonded atoms atom_export_array Type np ndarray NA dtype object array of dict Derived from Atom mol_export Type np ndarray N dtype object array of dict Derived from Molecule Export information relative to the molecule box_vectors Type np ndarray 3 3 dtype float or None Those are the three vectors that define of the periodic box of the system Example To define an orthorombic box of size 3 4 5 nm gt gt gt np array 3 0 0 0 0 0 Vector a O 0 4 0 04 0 Vector b 0 0 0 0 5 0 Vector c n_mol Type i
111. s In this section we ll see how to write a renderer that will display several tetrahedrons We will write our Tetrahedron Renderer based on TriangleRenderer To do that we first need to understand how a tetrahedron is made and how can we define the vertices that make the tetrahedron First of all we need to have the 4 coordinates that represents a tetrahedron Without even trying to visualize it just pick the values straight from Wikipedia import numpy as np vl np array 1 0 0 0 1 0 np sqrt 2 v2 np array 1 0 0 0 1 0 np sqrt 2 v3 np array 0 0 1 0 1 0 np sqrt 2 v4 np array 0 0 1 0 1 0 np sqrt 2 1 1 We can quickly verify if this is correcty by using a PointRenderer from chemlab graphics import QtViewer from chemlab graphics renderers import PointRenderer from chemlab graphics colors import black green blue red colors black green blue red v QOtViewer v add_renderer PointRenderer np array vl v2 v3 v4 colors v run We ve got 4 boring points that look like they re at the vertices of a tetrahedron Most importantly we learned that we can use PointRenderer to quickly test shapes Now let s define the four triangles 12 vertices that represent a solid tetrahedron It is good practice to put the triangle vertices in a certain order to estabilish which face is pointing outside and which one is pointing inside for optimization reasons
112. s an array of times and an array of atomic positions 60 Chapter 3 Reference Documentation chemlab Documentation Release 0 4 gt gt gt times positions datafile traj xtc read trajectory tl t2 t3 posl pos2 positions is a list of np ndarray n_atoms 3 read boxes After reading the trajectory feature you can call read boxes that will return a list of box_vectors correspoiding to each frame xyz XYZ coordinate format Extension xyz class chemlab io handlers XyzI0 fd The XYZ format is described in this wikipedia article http en wikipedia org wiki X YZ_file_format Features read molecule Read the coordinates in a Molecule instance write molecule mol Writes a Molecule instance in the XYZ format 3 2 2 cclib integration Those handlers are based on the cclib library The feature names extracted match those of the one included in the cclib documentation Chemlab also extract a chemlab core Molecu_e instance from the file through the feature named molecule List of file formats e gamess e gamessuk e gaussian e jaguar e molpro orca You can also use the method available_properties to get the available properties dynamically 3 2 3 The class lOHandler class chemlab io handlers IOHandler fd Generic base class for file readers and writers The initialization function takes a file like object fd as an argument Subclass
113. set the color by passing color None You can call this function interactively by using change_color interactive A new dialog will popup with a color chooser chemlab mviewer api appeareance change_default_radii def_map Change the default radii chemlab mviewer api appeareance change_post_processing_options str_id op tions Change the options of the post processing effect referred by its string id chemlab mviewer api appeareance change_radius value Change the radius of the currently selected atoms by a certain value If value is None set the radius to the default value chemlab mviewer api appeareance clear_post_processing Remove all post processing effects chemlab mviewer api appeareance list_post_processing List all the post processing effects by name 108 Chapter 3 Reference Documentation chemlab Documentation Release 0 4 chemlab mviewer api appeareance remove_post_processing str_id Remove a post processing effect by passing its string id provided by add_post_processing chemlab mviewer api appeareance scale_atoms fac Scale the currently selected atoms atoms by a certain factor fac Use the value fac 1 0 to reset the scale chemlab mviewer api appeareance screenshot filename width None height None Make a screenshot of the current view You can tweak the resolution up to what your GPU memory supports By defaults it uses the current window resolution
114. tart You can start the chemlab molecular viewer by typing chemlab view This will load the user interface consisting of the viewer and an Python shell o K object gt Details about object use object for extra details guiref gt A brief reference about the graphical user interface In 1 You can start typinc commands in the IPython shell and changes will appear immediately in the viewer Downloading a molecule from the web is really easy with the command chemlab mviewer api download_molecule 36 Chapter 2 User Manual chemlab Documentation Release 0 4 download_molecule aspirine You can select atoms by clicking on them The selection effect is a white glow E x download_molecule aspirin The molecular viewer can be used to perform some simple tasks programmatically 2 7 2 Changing the Appeareance Chemlab can make seriously good looking pictures The general way the appeareance related function work is that they apply on selections Say you want the change all the Carbon atom colors to black This is really easy to do 2 7 Molecular Viewer 37 chemlab Documentation Release 0 4 select_atom_type C change_color black The colors available as string are the standard HTML colors written in underscore You can also pass rgba tuples in the range 0 255 Please leave the alpha value to 255 select_atom_type C
115. teger corresponding to the current frame in the trajectory chemlab mviewer api core current_frame_times Return the list of times associated with the current trajectory chemlab mviewer api core current_nframes Return the number of frames in the current trajectory chemlab mviewer api core current_representation Return the current Representation instance Representations are a way to interact with the displayed chemical data chemlab mviewer api core current_system The chemlab core System that is currently being displayed chemlab mviewer api core current_time Return the floating point number corresponding to the current time in the trajectory in ns chemlab mviewer api core current_trajectory Return the current trajectory A trajectory is a set of frames chemlab mviewer api core frames skip Useful command to iterate on the trajectory frames It can be used in a for loop for i in frames coords current_trajectory i Do operation on coords You can use the option skip to take every i frame chemlab mviewer api core msg lt chemlab mviewer api core _Msg object gt Update the message in the status bar chemlab mviewer api core trajectory start None stop None step None Useful command to iterate on the trajectory frames by time in ns It is meant to be used in a for loop for i in trajectory 0 10 0 1 coords current_frame t current_time Do somethin
116. tem from where to extract the subsystem selection np ndarray of int or np ndarray N of bool selection can be either a list of molecular indices to select or a boolean array whose elements are True in correspondence of the molecules to select it is usually the result of a numpy comparison operation Example In this example we can see how to select the molecules whose center of mass that is in the region of space x gt 0 1 s System It is a set of 10 water molecules select for i range s n_mol if s get_molecule i center_of_mass 0 gt 0 1 select append i subs subsystem_from_molecules s np ndarray select Note The API for operating on molecules is not yet fully developed In the future there will be smarter ways to filter molecule attributes instead of looping and using System get_molecule chemlab core subsystem_from_atoms orig selection Generate a subsystem containing the atoms specified by selection If an atom belongs to a molecule the whole molecule is selected Example This function can be useful when selecting a part of a system based on positions For example in this snippet you can see how to select the part of the system a set of molecules whose x coordinates is bigger than 1 0 nm s System subs subsystem_from_atoms s r_array 0 gt 1 0 Parameters 56 Chapter 3 Reference Documentation chemlab Documentation Release 0 4 orig Syste
117. that can be ither molecule or system as a second argument the key used to store retrieve the entry and finally the object to store You can at a later time retrieve the entries in this way from chemlab db import LocalDB ldb LocalDB path to yourdb mol ldb get molecule examplemol s ldb get system examplesys The molecules files are serialized using the json format and stored in a very simple directory structure For the previous example the database directory would look like this path to yourdb molecule examplemol json system examplesys json The reason for such a simple structure is that in the future it will be easy to define custom made remote database for example you could have a community mantained github repo with commonly used molecules and data that can be directly accessed by chemlab everybody is welcome to develop such an extension On top of that you can copy paste json molecule files without having to do any migration See also chemlab db 2 6 Database Support 35 chemlab Documentation Release 0 4 2 7 Molecular Viewer The Chemlab molecular viewer is novel way for interacting editing and analyzing chemical data The chemlab philosophy is that the program should be really easy to extend there are so many applications in chemistry and physics and the user shouldn t be limited to the built in functionalities of the program 2 7 1 Quick S
118. thing you should notice is that you need an additional argument widget that will be passed when you use the method QtViewer add_renderer from chemlab graphics renderers import AbstractRenderer class TetrahedraRenderer AbstractRenderer def __init__ self widget positions super TetrahedraRenderer self __init__ widget The strategy to implement a multiple tetrahedron renderer will be like this e store the triangle vertices and normals of a single tetrahedra e for each position that we pass translate the vertices of the single tetrahedra and accumulate the obtained vertices in a big array e repeat the normals of a single tetrahedra for the number of tetrahedra we re going to render e generate the per vertex colors green for simplicity e create a TriangleRenderer as an attribute and initialize him with the accumulated vertices normals and colors e reimplement the draw method by calling the draw method of our trianglerenderer You can see the code in this snippet class TetrahedraRenderer AbstractRenderer def __init_ self widget positions super TetrahedraRenderer self __init__ widget vl np array 1 0 0 0 1 0 np sqrt 2 v2 np array 1 0 0 0 1 0 np ga v3 np array 0 0 1 0 1 0 np sqrt 2 v4 np array 0 0 1 0 1 0 np am 2 positions np array positions Vertices of a single tetrahedra self _th_vertices np array vl v4 v3 v3 v4 v2 vl v3 v2 v
119. this effect in the SSAOEffect class To apply it to the scene it s sufficient to add this simple line from chemlab graphics postprocessing import SSAOEffect v add_post_processing SSAOEf fect v run What you ll get is this with a much improved visual quality 22 Chapter 2 User Manual chem lab Documentation Release 0 4 Post processing effects can be customized with arguments The SSAO effect may have a dirty look you can fix that by changing the parameter kernel_size which default to 32 with a max value of 128 v add_post_processing SSAO Effect kernel_size 128 This will improve the visual quality at the cost of decreased performance To see all the options available take look at the api documentation List of Post Processing Effects Post processing effects can also be stacked on top of each other If your computer is powerful enough you can load your scene with a stack of effects that will be applied in turn from chemlab graphics postprocessing import SSAO I from chemlab graphics postprocessing from chemlab graphics postprocessing import FXAAI from chemlab graphics postprocessing add_post_processing SSAO add_post_processing FXAA cass lt run Effect import OutlineEffect Effect import GammaCorrection Effect better illumination add_post_processing OutlineEffect black outlines Effect fast antialiasing
120. to the picture below 2 3 Atoms Molecules and Systems 9 chemlab Documentation Release 0 4 Atom type Molecule type_array BEM System type_aray SEB EH You can preallocate a System by using the classmethod System empty pretty much like you can preallocate numpy arrays with np empty or np zeros and then add the molecules one by one import numpy as np from chemlab core import Atom Molecule System from chemlab graphics import display_system Template molecule wat Molecule Atom O 0 00 0 00 0 01 Atom H 0 00 0 08 0 05 Atom H 0 00 0 08 0 05 Initialize a system with four water molecules s System empty 4 12 4 molecules 12 atoms for i in range 4 wat move_to np random rand 3 randomly displace the water molecule s add wat data gets copied each time display_system s Since the data is copied the wat molecule acts as a template so you can move it around and keep adding it to the System Preallocating and adding molecules is a pretty fast way to build a System but the fastest way in terms of processing time is to build the system by passing ready made arrays this is done by using chemlab core System from_arrays Most of the chemlab core Molecule array attributes are still present in chemlab core System including System bonds bonds between molecules are currently not supported and setting them will result in an unex pected behaviour
121. ts to play pause and set the speed of the animation Example To set up a QtTrajectory Viewer you have to add renderers to the scene set the number of frames present in the animation by calling py meth chemlab graphics QtTrajectory Viewer set_ticks and define an update function Below is an example taken from the function chemlab graphics display_trajectory from chemlab graphics import QtTrajectoryViewer sys some System coords_list some list of atomic coordinates v QtTrajectoryViewer sr v add_renderer AtomRenderer sys r_array sys type_array backend impostors br v add_renderer BoxRenderer sys box_vectors v set_ticks len coords_list Q v update_function def on_update index sr update_positions coords_list index br update sys box_vectors v set_text format_time times index v widget repaint v run Warning Use with caution the API for this element is not fully stabilized and may be subject to change add_renderer klass args kwargs The behaviour of this function is the same as chemlab graphics QtViewer add_renderer add_ui klass args kwargs Add an UI element for the current scene The approach is the same as renderers Warning The UI api is not yet finalized 66 Chapter 3 Reference Documentation chemlab Documentation Release 0 4 set_text fext Update the time indicator in the interface update_function func frames
122. ulations using the flexibility and power of the python programming language It aims to be well designed and pythonic taking inspiration from projects such as numpy and scipy Chemlab s long term goal is to be General Chemistry is a huge field chemlab wants to provide a general ground from where to build domain specific tools and apps Array oriented Most operations and data structures are based on numpy arrays This let you write compact and efficient code Graphic chemlab integrates a 3D molecular viewer that is easily extendable and lets you write your own visu alization tools Interoperable chemlab wants to be interoperable with other chemistry programs by reading and writing differ ent file formats and using flexible data structures Fast Even if python is known to be slow every effort should be made to make chemlab fast enough by using effectively numpy arrays and efficient data structures When everything else fails we can still write the hard bits in C with the help of cython Contents 1 chemlab Documentation Release 0 4 2 Contents CHAPTER 1 Current Status Computational and theoretical chemistry is a huge field and providing a program that encompasses all aspects of it is an impossible task The spirit of chemlab is to provide a common ground from where you can build specific programs For this reason it includes a fully programmable molecular viewer Chemlab includes a lot of utilities t
123. us state from the method Camera state state Return the current camera state as a dictionary it can be restored with Camera restore unproject x y z 0 Receive x and y as screen coordinates and returns a point in world coordinates This function comes in handy each time we have to convert a 2d mouse click to a 3d point in our space Parameters x float in the interval 1 0 1 0 Horizontal coordinate 1 0 is leftmost 1 0 is rightmost y float in the interval 1 0 1 0 Vertical coordinate 1 0 is down 1 0 is up z float in the interval 1 0 1 0 Depth 1 0 is the near plane that is exactly behind our screen 1 0 is the far clipping plane Return type np ndarray 3 dtype float Returns The point in 3d coordinates world coordinates 3 3 6 Transformations Homogeneous Transformation Matrices and Quaternions A library for calculating 4x4 matrices for translating rotating reflecting scaling shearing projecting orthogonaliz ing and superimposing arrays of 3D homogeneous coordinates as well as for converting between rotation matrices Euler angles and quaternions Also includes an Arcball control object and functions to decompose transformation matrices Authors Christoph Gohlke Laboratory for Fluorescence Dynamics University of California Irvine Version 2012 10 14 Requirements e CPython 2 7 or 3 2 e Numpy 1 6 e transformations c 2012 01 01 optional implementation of some functions in C Notes
124. v rescale tc grps System ref_t 300 tau_t 0 1 pcoupl berendsen compressibility 4 5e 5 ref_p 1 0 gen_vel yes gen_temp 300 constraints all bonds 2 9 5 Running the simulation To run the simulation with gromacs we have to do two steps 1 Generate a parameter input this will check that our input make sense before running the simulation grompp_d f run mdp c start gro p topol top This will generate a bunch of files in your working directory 2 Now we run the simulation in the meantime go grab coffee mdrun_d v This will take a while depending on your machine If you are not a coffee drinker don t worry you can stop the simulation by pressing Ctrl C The good news is that chemlab can read files from partial runs 46 Chapter 2 User Manual chemlab Documentation Release 0 4 2 9 6 Viewing the results the command line way To quickly preview trajectories and system energies you can use the script chemlab included in the distribution in scripts chemlab GROMACS can store the trajectory in the form of atomic coordinates in the xtc file To play the trajectory you can use the command chemlab view start gro traj traj xtc Note the nstxtcout 100 option in the mdp file sets the output frequency in the xtc file You may also be interested to look at some other properties such as the potential energy pressure temperature and density
125. v0 v1 gt gt gt numpy allclose 2 numpy trace R True gt gt gt numpy allclose v0 numpy dot R v0 True gt gt gt v2 v0 copy gt gt gt v2 3 vl gt gt gt v3 v0 copy gt gt gt v2 3 vl gt gt gt numpy allclose v2 numpy dot R v3 True chemlab graphics transformations rotation_from_matrix matrix Return rotation angle and axis from rotation matrix 3 3 chemlab graphics 97 chemlab Documentation Release 0 4 gt gt gt angle random random 0 5 2 math pi gt gt gt direc numpy random random 3 0 5 gt gt gt point numpy random random 3 0 5 gt gt gt RO rotation_matrix angle direc point gt gt gt angle direc point rotation_from_matrix RO gt gt gt R1 rotation_matrix angle direc point gt gt gt is_same_transform RO R1 True chemlab graphics transformations rotation_matrix angle direction Create a rotation matrix corresponding to the rotation around a general axis by a specified angle R dd T cos a I dd T sin a skew d Parameters angle float a direction array d chemlab graphics transformations scale_from_matrix matrix Return scaling factor origin and direction from scaling matrix gt gt gt factor random random 10 5 gt gt gt origin numpy random random 3 0 5 gt gt gt direct numpy random random 3 0 5 gt gt gt SO sc
126. x gamma zaxis gt gt gt R concatenate_matrices Rx Ry Rz gt gt gt euler euler_from_matrix R rxyz gt gt gt numpy allclose alpha beta gamma euler True gt gt gt Re euler_matrix alpha beta gamma rxyz gt gt gt is_same_transform R Re True gt gt gt al be ga euler_from_matrix Re rxyz gt gt gt is_same_transform Re euler_matrix al be ga rxyz True gt gt gt qx quaternion_about_axis alpha xaxis gt gt gt qy gquaternion_about_axis beta yaxis gt gt gt qz quaternion_about_axis gamma zaxis gt gt gt q quaternion_multiply qx qy gt gt gt q quaternion_multiply q qz gt gt gt Rq quaternion_matrix q gt gt gt is_same_transform R Rq True gt gt gt S scale_matrix 1 23 origin gt gt gt T translation_matrix 1l 2 3 gt gt gt Z shear_matrix beta xaxis origin zaxis gt gt gt R random_rotation_matrix numpy random rand 3 gt gt gt M concatenate_matrices T R Z 8 gt gt gt scale shear angles trans persp decompose_matrix M gt gt gt numpy allclose scale 1 23 True gt gt gt numpy allclose trans 1 2 3 True gt gt gt numpy allclose shear 0 math tan beta 0 True gt gt gt is_same_transform R euler_matrix axes sxyz xangles True 88 Chapter 3 Reference Documentation chemlab Documentation Release 0 4 gt gt gt
127. y bonds shading phong Render a ball and stick representation of a series of coordinates and bonds 70 Chapter 3 Reference Documentation chemlab Documentation Release 0 4 Parameters widget The parent QChemlabWidget r_array np ndarray NATOMS 3 dtype float The coordinate array type_array np ndarray NATOMS 3 dtype object An array containing all the atomic symbols like Ar H O If the atomic type is unknown use the Xx symbol bonds np ndarray NBONDS 2 dtype int An array of integer pairs that represent the bonds update_positions r_array Update the coordinate array r_array WireframeRenderer class chemlab graphics renderers WireframeRenderer widget r_array type_array bonds Render a wireframe representation of a series of coordinates and bonds 3 3 chemlab graphics 71 chemlab Documentation Release 0 4 Parameters widget The parent QChemlabWidget r_array np ndarray NATOMS 3 dtype float The coordinate array type_array np ndarray NATOMS 3 dtype object An array containing all the atomic symbols like Ar H O If the atomic type is unknown use the Xx symbol bonds np ndarray NBONDS 2 dtype int An array of integer pairs that represent the bonds PointRenderer class chemlab graphics renderers PointRenderer widget positions colors Render colored points Parameters 72 Chapter 3 Reference Documentation chemlab Documentation Release 0 4
128. ype int the indices of all the atoms belonging to the selected molecules remove_atoms indices Remove the atoms positioned at indices The molecule containing the atom is removed as well If you have a system of 10 water molecules and 30 atoms if you remove the atoms at indices 0 1 and 29 you will remove the first and last water molecules Parameters indices np ndarray N dtype int Array of integers between 0 and System n_atoms remove_molecules indices Remove the molecules positioned at indices For example if you have a system comprised of 10 water molecules you can remove the first fifth and nineth by using system remove_molecules 0 4 8 Parameters indices np ndarray N dtype int Array of integers between 0 and System n_mol 3 1 chemlab core 55 chemlab Documentation Release 0 4 reorder_molecules new_order Reorder the molecules in the system according to new_order Parameters new_order np ndarray NMOL dtype int An array of integers containing the new order of the sys tem sort Sort the molecules in the system according to their brute formula tojson Serialize a System instance using json See also chemlab core System from_json 3 1 4 Routines to manipulate Systems chemlab core subsystem_from_molecules orig selection Create a system from the orig system by picking the molecules specified in selection Parameters orig System The sys

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