i63dZddlZddlmZddlmZddlmZGdd ej Z Gd d ej Z dS) a MOL2 file format --- :mod:`MDAnalysis.coordinates.MOL2` ======================================================== Classes to work with Tripos_ molecule structure format (MOL2_) coordinate and topology files. Used, for instance, by the DOCK_ docking code. Example for working with mol2 files ----------------------------------- To open a mol2, remove all hydrogens and save as a new file, use the following:: u = Universe("Molecule.mol2") gr = u.select_atoms("not name H*") print(len(u.atoms), len(gr)) gr.write("Molecule_noh.mol2") .. _MOL2: http://www.tripos.com/data/support/mol2.pdf .. _Tripos: http://www.tripos.com/ .. _DOCK: http://dock.compbio.ucsf.edu/ See Also -------- rdkit: rdkit_ is an open source cheminformatics toolkit with more mol2 functionality .. _rdkit: http://www.rdkit.org/docs/GettingStartedInPython.html Classes ------- .. autoclass:: MOL2Reader :members: .. autoclass:: MOL2Writer :members: Notes ----- * The MDAnalysis :class:`MOL2Reader` and :class:`MOL2Writer` only handle the MOLECULE, SUBSTRUCTURE, ATOM, and BOND record types. Other records are not currently read or preserved on writing. * As the CRYSIN record type is not parsed / written, MOL2 systems always have dimensions set to ``None`` and dimensionless MOL2 files are written. MOL2 format notes ----------------- * MOL2 Format Specification: (http://www.tripos.com/data/support/mol2.pdf) * Example file (http://www.tripos.com/mol2/mol2_format3.html):: # Name: benzene # Creating user name: tom # Creation time: Wed Dec 28 00:18:30 1988 # Modifying user name: tom # Modification time: Wed Dec 28 00:18:30 1988 @MOLECULE benzene 12 12 1 0 0 SMALL NO_CHARGES @ATOM 1 C1 1.207 2.091 0.000 C.ar 1 BENZENE 0.000 2 C2 2.414 1.394 0.000 C.ar 1 BENZENE 0.000 3 C3 2.414 0.000 0.000 C.ar 1 BENZENE 0.000 4 C4 1.207 -0.697 0.000 C.ar 1 BENZENE 0.000 5 C5 0.000 0.000 0.000 C.ar 1 BENZENE 0.000 6 C6 0.000 1.394 0.000 C.ar 1 BENZENE 0.000 7 H1 1.207 3.175 0.000 H 1 BENZENE 0.000 8 H2 3.353 1.936 0.000 H 1 BENZENE 0.000 9 H3 3.353 -0.542 0.000 H 1 BENZENE 0.000 10 H4 1.207 -1.781 0.000 H 1 BENZENE 0.000 11 H5 -0.939 -0.542 0.000 H 1 BENZENE 0.000 12 H6 -0.939 1.936 0.000 H 1 BENZENE 0.000 @BOND 1 1 2 ar 2 1 6 ar 3 2 3 ar 4 3 4 ar 5 4 5 ar 6 5 6 ar 7 1 7 1 8 2 8 1 9 3 9 1 10 4 10 1 11 5 11 1 12 6 12 1 @SUBSTRUCTURE 1 BENZENE 1 PERM 0 **** **** 0 ROOT N)base)util)store_init_argumentscZeZdZdZdZdddZefdZdZd dZ d Z d Z xZ S) MOL2ReaderaReader for MOL2 structure format. .. versionchanged:: 0.11.0 Frames now 0-based instead of 1-based. MOL2 now reuses the same Timestep object for every frame, previously created a new instance of Timestep each frame. .. versionchanged:: 0.20.0 Allows for comments at top of file. Ignores status bit strings .. versionchanged:: 2.0.0 Bonds attribute is not added if no bonds are present in MOL2 file .. versionchanged:: 2.2.0 Read MOL2 files with optional columns omitted. MOL2NAngstromtimelengthc tt|j|fi|d|_g}t j|5}t |D]Q\}}d|vr||gdt|r!|dd|R dddn #1swxYwYt||_ ||_ | |d\}}t||_|j |jfi|j |_|d|_dS)zRead coordinates from `filename`. Parameters ---------- filename : str or NamedStream name of the mol2 file or stream Nz@MOLECULE) start_linelinesrr)superr __init__n_atomsropenany enumerateappendlenn_framesframes parse_block _Timestep _ts_kwargsts _read_frame) selffilenamekwargsblocksfilinesectionscoords __class__s e/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/coordinates/MOL2.pyrzMOL2Reader.__init__s~ )j$(<r# atomz2The mol2 (starting at line {0}) block has no atomsrzMOL2Reader assumes that the number of atoms remains unchanged between frames; the current frame has {0}, the next frame has {1} atomsdtype)splitstriplower startswithrr Exceptionformatr ValueErrornpzerosfloat32r)r!blockr(cursorr' atom_linesr)r&aaidnamexyz atom_types r+rzMOL2Reader.parse_blocks'N * *Dd""K00399;;AACC#% %%  V  # #D ) ) ) )f% : 6% -.. \ !z??DLL __ , ,6$,J88  4<+2:>>>j)) # #DAq,-GGIIbqbM )Cq!Q a7F1aaa4LLcr||j}ntd|jdz}||S)Nz&MOL2Reader cannot assign to a timestepr)rNotImplementedErrorframer )r!rrKs r+_read_next_timestepzMOL2Reader._read_next_timesteps@ :BB&&NOO O Q&&&rHc |j|}n3#t$r&d|dt|}t|dwxYw||\}}dD](} |||jj|<#t$rY%wxYwtj |tj |j_ |j r| |jj||j_|jS)NzInvalid frame z for trajectory with length )molecule substructurer1)r IndexErrorrIOErrorrrdataKeyErrorr;arrayr= positions convert_unitsconvert_pos_from_native_posrK)r!rKr>errmsgr(r)sects r+r zMOL2Reader._read_frames ,K&EE , , ,t99 &//t +  , ++E22&0  D %-d^ T""    HV2:>>>   7  ( ( 6 6 6 ws 0A A66 BBcd|j_dS)Nr)rrKr!s r+_reopenzMOL2Reader._reopens rHN) __name__ __module__ __qualname____doc__r9unitsrrrrLr r] __classcell__)r*s@r+r r s  FZ 0 0E&&&&&@$ $ $ L''''6rHr c>eZdZdZdZdZdddZd dZdZd Z d Z dS) MOL2Writeraqmol2 format writer Write a file in the Tripos_ molecule structure format (MOL2_). Note ---- :class:`MOL2Writer` can only be used to write out previously loaded MOL2 files. If you're trying to convert, for example, a PDB file to MOL you should use other tools, like rdkit_. Here is an example how to use rdkit_ to convert a PDB to MOL:: from rdkit import Chem mol = Chem.MolFromPDBFile("molecule.pdb", removeHs=False) Chem.MolToMolFile(mol, "molecule.mol" ) MOL2 writer is currently not available for rdkit master. It requires SYBYL atomtype generation. See page 7 for list of SYBYL atomtypes (http://tripos.com/tripos_resources/fileroot/pdfs/mol2_format2.pdf). .. _rdkit: http://www.rdkit.org/docs/GettingStartedInPython.html .. versionchanged:: 0.11.0 Frames now 0-based instead of 1-based r TNr r cn||_||_d|_tj|jd|_dS)zCreate a new MOL2Writer Parameters ---------- filename: str name of output file convert_units: bool (optional) units are converted to the MDAnalysis base format; [``True``] rwN)r"rVframes_writtenranyopenfile)r!r"rrVs r+rzMOL2Writer.__init__+s9!   L44 rHc8|jdSr^)rkcloser\s r+rmzMOL2Writer.close>s rHc  |j}n #t$rd}t|dwxYw|jj}|j} |jd}n #t$rd}t|dwxYwdt|jdDt|dr|j }td |D}d g}fd t|dD} | | |d d |}ng}d }dg} | fd|jD| d d | } dg|jdz} n#t$rd } YnwxYw|d} t#t%|jt#t%|c| d<| d<|d} |d}dd| |d<|ddd || z|zd | z}| |d<||d<|S)zS Parameters ---------- obj : AtomGroup or Universe z-Input obj is neither an AtomGroup or UniverseNrNz/MOL2Writer cannot currently write non MOL2 dataci|]\}}|| Srp).0r&rAs r+ z+MOL2Writer.encode_block..XsBBBDAq1aBBBrHr)startbondsc3BK|]}|d|d|jfVdS)rrN)order)rqbs r+ z*MOL2Writer.encode_block.._s3DDQAaD!A$0DDDDDDrHz @BONDcfg|]-\}\}}}d||||.S)z{0:>5} {1:>5} {2:>5} {3:>2})r9)rqbidatom1atom2rvmappings r+ z+MOL2Writer.encode_block..asW/C.%.44rHr.z @ATOMc 3K|]a}d||j|jd|jd|jd|j|j|j|j VbdS)zE{0:>4} {1:>4} {2:>13.4f} {3:>9.4f} {4:>9.4f} {5:>4} {6} {7} {8:>7.4f}rrrN)r9rCpositiontyperesidresnamecharge)rqrAr}s r+rxz*MOL2Writer.encode_block..os   v  1  1  1          rHz@SUBSTRUCTURE rOrz{0}  z@MOLECULE )atomsAttributeError TypeErroruniverse trajectoryrrRrSrJrhasattr intra_bondssortedextendrjoinr4strrr9insert)r!objrYtrajrrN bondgrouprt bond_linesblsr@rO check_sumsmolecule_0_storemolecule_1_store return_valr}s @r+ encode_blockzMOL2Writer.encode_blockAs .)CC . . .DFF## - .|& W 8wz*HH 8 8 8FF%f--4 7 8 CBIciq$A$A$ABBB 3  IDD)DDDDDE)*J3>':':CIs r+_write_next_framezMOL2Writer._write_next_frames3!!#&& U#####rH)NT) r_r`rarbr9 multiframercrrmrrrprHr+rfrf s|:FJZ 0 0E5555&YYYv $ $ $ $ $rHrf) rbnumpyr;rrlibrMDAnalysis.lib.utilr ReaderBaser WriterBaserfrprHr+rs0eeL444444AAAAAAAAH_$_$_$_$_$_$_$_$_$_$rH