B be@sdZddlmZddlmZddlmZddlZddl m Z ddl m Z dd l mZdd lmZdd lmZmZdd lmZmZmZmZdd lmZddlmZddlmZmZddl m!Z!ddl"Z"ddl#Z#eeGddde$Z%ddZ&ddZ'dS)zd Tool for parsing and writing OFF library files to and from dictionaries of ResidueTemplate objects )print_function) OrderedDict)closingN)Atom) RAD_TO_DEG) AmberWarning)FileFormatType)ResidueTemplateResidueTemplateContainer)PROTEINNUCLEICSOLVENTUNKNOWN)periodic_table)genopen) string_types add_metaclass)rangec@seZdZdZedZedZedZedZ edZ edZ edZ ed Z ed Zed Zed Zed ZedZedZedZedZeddZeddZeddZeddZeddZdS)AmberOFFLibraryz_ Class containing static methods responsible for parsing and writing OFF libraries z!!index *array *strz\s*"(\S*?)"\s*$z{!entry\.(\S*?)\.unit\.atoms *table *str *name *str *type *int *typex *int *resx *int *flags *int *seq *int *elmnt *dbl *chgzg!entry\.(\S*?)\.unit\.atomspertinfo *table *str *pname *str *ptype *int *ptypex *int *pelmnt *dbl *pchgz*!entry\.(\S*?)\.unit\.boundbox *array *dblz0!entry\.(\S*?)\.unit\.childsequence *single *intz)!entry\.(\S*?)\.unit\.connect *array *intzO!entry\.(\S*?)\.unit\.connectivity *table *int *atom1x *int *atom2x *int *flagsz`!entry\.(\S*?)\.unit\.hierarchy *table *str *abovetype *int *abovex *str *belowtype *int *belowxz'!entry\.(\S*?)\.unit\.name *single *strz>!entry\.(\S*?)\.unit\.positions *table *dbl *x *dbl *y *dbl *zzg!entry\.(\S*?)\.unit\.residueconnect *table *int *c1x *int *c2x *int *c3x *int *c4x *int *c5x *int *c6xzw!entry\.(\S*?)\.unit\.residues *table *str *name *int *seq *int *childseq *int *startatomx *str *restype *int *imagingxz;!entry\.(\S*?)\.unit\.residuesPdbSequenceNumber *array *intz,!entry\.(\S*?)\.unit\.solventcap *array *dblz?!entry\.(\S*?)\.unit\.velocities *table *dbl *x *dbl *y *dbl *zc Cs2tt|d}tj|r$dSdSQRXdS)a, Sees if an open file is an OFF library file. Parameters ---------- filename : str The name of the file to see if it is an OFF file format Returns ------- is_fmt : bool True if it is recognized as OFF, False otherwise rTFN)rrr _headerrematchreadline)filenamefr2lib/python3.7/site-packages/parmed/amber/offlib.py id_formatAszAmberOFFLibrary.id_formatcCst|trt|d}d}n|}d}|}tj|s>tdt}|}tj |}x4|r|r| d}d||<|}tj |}qZW|st dxV|r| s|}qtj |}|st d| d}t||||<|}qW|r||S) a Parses an Amber OFF library Parameters ---------- filename : str or file-like iterable The file name or file object to parse. If it is an iterable, it will be exhausted Returns ------- residues : OrderedDict {str : :class:`ResidueTemplate`} Dictionary pairing residue names with their :class:`ResidueTemplate` objects Raises ------ ValueError if the first line does not match the file format. This line will be consumed IOError if filename is the name of a file that does not exist RuntimeError if EOF is reached prematurely or other formatting issues found rTFzUnrecognized OFF file formatrNz#Unexpected EOF in Amber OFF libraryzExpected atoms table not found) isinstancerrrrrr ValueErrorr_resregroups RuntimeErrorstrip_sec1re_parse_residueclose)rfileobj own_handlelineZresiduesrematchnamerrrparseVs>         zAmberOFFLibrary.parsec2Cs t|}d}t|}|}x|ddkr|\}}}} } } } } t|}t|}t|}t| } t| } t| } t| } t| } t| ||| d}| |dkr|||d7}t|}| ||}x|r| s|}qWqW|||dkr*g}d}x$|D]}|||t |7}q Wt j |}|sFtdn*|d|krptd|d|f|}x*|ddkr|std|}qzWt j|}|stdn*|d|krtd|d|fyTt| }t| }t| }t| }t| }Wntk r\td Yn0X|dkr|d krz|t9}||||||g|_|}t j|}|std n*|d|krtd|d|ft| }|d|krtd ||d|ftn&t|ts:|t |dkr:td |}t j|}|s^tdn*|d|krtd|d|fy$t| }t| }Wntk rtdYnX|dkr|dkr||d|_n4|dkr$|dkr$|tdd|Dkr$td|dkrH|dkrH||d|_n<|dkr|dkr|tdd|Dkrtd|t|}t |jdkrt j|}|stdn*|d|krtd|d|f|}x|ddkr|\}}}|}|dkrt|d}t|d}x*t |D]\}}||kr<|d8}Pqsz1AmberOFFLibrary._parse_residue..z(HEAD on multi-residue unit not supportedcss|]}t|VqdS)N)r3)r4rrrrr5 sz9TAIL on multi-residue unit not supported (%s). Ignored...z%Expected connectivity table not foundz"Expected hierarchy table not foundz#Expected unit name string not foundz'Expected unit positions table not foundz,Expected unit residueconnect table not foundcss|]}t|VqdS)N)int)r4xrrrr5QsNzHEAD atom is not connect0zTAIL atom is not connect1z&Expected unit residues table not foundz7residue table predicted %d, not %d atoms for residue %spnw?zUnknown residue type "%s"z*Expected residue sequence number not foundz(Expected unit solventcap array not foundcss|]}t|VqdS)N)float)r4r7rrrr5s)7r r rsplit_strip_enveloping_quotesr6r<rappendZadd_atomr$r3r_sec2rerr#r"_sec3rer rbox_sec4rewarningswarnrr_sec5reheadsumtailZatoms_sec6re enumerateZadd_bond_sec7re_sec8re_sec9rexxxyxz_sec10rer connections_sec11rer r1r rr,_sec12re_sec13re_sec14revxvyvz)2r(r,Z containerZnresZtemplr*ZnamtypZtypxZresxflagsseqZelmntZchgatomZ start_atomsZrunsumresr+ZhasboxZangleabcr9rGrIijflagZiiidxZ start_idxr7yzZc1Zc2Zc3Zc4Zc5Zc6ZresnameidnextstartZimgrXrYrZrrrr&s                        "        .  "                     " zAmberOFFLibrary._parse_residuecCs|d}t|dst|d}d}t|}|dx|D]}|d|q8Wx|D]}t|||qTW|rx|dS)a Writes a dictionary of ResidueTemplate units to a file in OFF format Parameters ---------- lib : dict {str : :class:`ResidueTemplate`} Items can be either :class:`ResidueTemplate` or :class:`ResidueTemplateContainer` instances dest : str or file-like Either a file name or a file-like object to write the file to Fwriter:Tz!!index array str z "%s" N)hasattrrsortedkeysrlr_write_residuer')libdestr)namesr,rrrrls       zAmberOFFLibrary.writec Cst|tr"t|j}|||}|d|jxNt|D]B\}}x8|D]0}|d|j|j|d|jd|j |j fqJWq.zE!entry.%s.unit.connectivity table int atom1x int atom2x int flags z %d %d 1 zU!entry.%s.unit.hierarchy table str abovetype int abovex str belowtype int belowx z "U" 0 "R" %d z "R" %d "A" %d z!entry.%s.unit.name single str z "%s" z4!entry.%s.unit.positions table dbl x dbl y dbl z z %.6g %.6g %.6g zZ!entry.%s.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x z %d %d %d %d %d %d zj!entry.%s.unit.residues table str name int seq int childseq int startatomx str restype int imagingx r8r9r:r;zUnrecognized residue type %rz "%s" %d %d %d "%s" %d z3!entry.%s.unit.residuesPdbSequenceNumber array int z$!entry.%s.unit.solventcap array dbl z5!entry.%s.unit.velocities table dbl x dbl y dbl z z %g %g %g z 0.0 0.0 0.0 )%rr r r,r?rlrKr1rfr0r2rBr#r3rGrIanyZbondsZatom1Zatom2rOrPrQrStupler r rrrDrEr _imaging_atomrXrYrZAttributeError) rrr_Ztmprcrr^baseZbondrbZconnZatr[srrrrps            .           &                zAmberOFFLibrary._write_residueN)__name__ __module__ __qualname____doc__recompilerr!r%r@rArCrFrJrLrMrNrRrTrUrVrW staticmethodrr-r&rlrprrrrrs0                  B  rcCsN|d|dkrdks>n|d|dkr:dkrJnn |ddS|S)z0 Strips the quotation marks enveloping a string r"'r.r)Zinprrrr>Hs> r>c Csddlm}d}d}xryrrrrs0          4